From ce226e9d8d52d2530f057f2000d36c0d55380ade Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20K=C4=85dzio=C5=82ka?= Date: Sat, 14 Mar 2020 13:02:23 +0100 Subject: [PATCH 001/235] gnu: Add superfamiconv * gnu/packages/graphics.scm (superfamiconv): New variable. --- gnu/packages/graphics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 7414edb4fe..f5ebfaacaa 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2019 Pierre Neidhardt ;;; Copyright © 2019, 2020 Marius Bakke ;;; Copyright © 2019 Tanguy Le Carrour +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -1075,3 +1076,37 @@ interaction library, written in C++, which has become the de facto standard graphics library for 3D visualization and visual simulation software in the scientific and engineering community.") (license license:bsd-3)))) + +(define-public superfamiconv + (package + (name "superfamiconv") + (version "0.8.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Optiroc/SuperFamiconv") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0848szv6a2b8wdganh6mw5i8vn8cqvn1kbwzx7mb9wlrf5wzqn37")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((outdir (assoc-ref outputs "out")) + (bindir (string-append outdir "/bin"))) + (install-file "bin/superfamiconv" bindir) + #t)))))) + (home-page "https://github.com/Optiroc/SuperFamiconv") + (synopsis "Tile graphics converter supporting SNES, Game Boy Color +and PC Engine formats") + (description "SuperFamiconv is a converter for tiled graphics, supporting +the graphics formats of the SNES, Game Boy Color and PC Engine game consoles. +Automated palette selection is supported.") + (license license:expat))) From 59d10c31128ca59b458015f652bb8d3325479a28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Mar 2020 17:30:00 +0100 Subject: [PATCH 002/235] gnu: Add guile3.0-sdl2. * gnu/packages/sdl.scm (guile3.0-sdl2): New variable. --- gnu/packages/sdl.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm index 90719f7e5e..25b0bdba2b 100644 --- a/gnu/packages/sdl.scm +++ b/gnu/packages/sdl.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016, 2017 Efraim Flashner ;;; Copyright © 2017, 2018, 2019 Rutger Helling ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice -;;; Copyright © 2018, 2019 Ricardo Wurmus +;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2019 Kei Kebreau ;;; Copyright © 2019, 2020 Nicolas Goaziou ;;; Copyright © 2019 Marius Bakke @@ -659,6 +659,14 @@ The bindings are written in pure Scheme using Guile's foreign function interface.") (license lgpl3+))) +(define-public guile3.0-sdl2 + (package + (inherit guile-sdl2) + (name "guile3.0-sdl2") + (native-inputs + `(("guile" ,guile-3.0) + ("pkg-config" ,pkg-config))))) + (define-public sdl2-cs (let ((commit "1a3556441e1394eb0b5d46aeb514b8d1090b93f8")) (package From ad1edd03adb1f4412cc50563c8b8530031c65ed7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Mar 2020 17:30:19 +0100 Subject: [PATCH 003/235] gnu: Add guile3.0-opengl. * gnu/packages/gl.scm (guile3.0-opengl): New variable. --- gnu/packages/gl.scm | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index b863283606..ea9b2c579e 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2014, 2016 David Thompson ;;; Copyright © 2014, 2015, 2016, 2017 Mark H Weaver ;;; Copyright © 2016 ng0 -;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2018, 2020 Ricardo Wurmus ;;; Copyright © 2016 David Thompson ;;; Copyright © 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2017 Arun Isaac @@ -603,6 +603,26 @@ extension functionality is exposed in a single header file.") OpenGL graphics API.") (license license:lgpl3+))) +(define-public guile3.0-opengl + (package + (inherit guile-opengl) + (name "guile3.0-opengl") + (arguments + (substitute-keyword-arguments (package-arguments guile-opengl) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'build-with-guile-3.0 + (lambda _ + (substitute* "configure" + (("_guile_versions_to_search=\"") + "_guile_versions_to_search=\"3.0 ")) + #t)))))) + (inputs + `(("guile" ,guile-3.0) + ("mesa" ,mesa) + ("glu" ,glu) + ("freeglut" ,freeglut))))) + (define-public libepoxy (package (name "libepoxy") From abb0ff45487a280d3ab171460b5448620de4b358 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 Mar 2020 17:30:33 +0100 Subject: [PATCH 004/235] gnu: Add guile3.0-chickadee. * gnu/packages/game-development.scm (guile3.0-chickadee): New variable. --- gnu/packages/game-development.scm | 36 +++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 7638a545ca..bf3b12ffd3 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1766,6 +1766,42 @@ built on top of SDL2 and OpenGL. Chickadee aims to provide all the features that parenthetically inclined game developers need to make 2D (and eventually 3D) games in Scheme, such as: +@enumerate +@item extensible, fixed-timestep game loop +@item OpenGL-based rendering engine +@item keyboard, mouse, controller input +@item REPL-driven development model +@end enumerate\n") + (license license:gpl3+))) + +(define-public guile3.0-chickadee + (package + (inherit guile-chickadee) + (name "guile-chickadee") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (string-append "https://files.dthompson.us/chickadee/" + "chickadee-" version ".tar.gz")) + (sha256 + (base32 + "1fdicsgls5cp0yffcm5vjmav67gv9bxhz1s3jvdvinspxb485x7l")))) + (build-system gnu-build-system) + (propagated-inputs + `(("guile-opengl" ,guile3.0-opengl) + ("guile-sdl2" ,guile3.0-sdl2))) + (inputs + `(("guile" ,guile-3.0))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("texinfo" ,texinfo))) + (home-page "https://dthompson.us/projects/chickadee.html") + (synopsis "Game development toolkit for Guile Scheme with SDL2 and OpenGL") + (description "Chickadee is a game development toolkit for Guile Scheme +built on top of SDL2 and OpenGL. Chickadee aims to provide all the features +that parenthetically inclined game developers need to make 2D (and eventually +3D) games in Scheme, such as: + @enumerate @item extensible, fixed-timestep game loop @item OpenGL-based rendering engine From 3dade1d59e7b4caa641670a76c0c48b4c90f6b3c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 Mar 2020 18:52:41 +0200 Subject: [PATCH 005/235] gnu: gcc-9: Update to 9.3.0. * gnu/packages/gcc.scm (gcc-9): Update to 9.3.0. --- gnu/packages/gcc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index ead50bb1dc..1f10ae5119 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -523,14 +523,14 @@ It also includes runtime support libraries for these languages."))) (define-public gcc-9 (package (inherit gcc-8) - (version "9.2.0") + (version "9.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gcc/gcc-" version "/gcc-" version ".tar.xz")) (sha256 (base32 - "01mj3yk7z49i49168hg2cg7qs4bsccrrnv7pjmbdlf8j2a7z0vpa")) + "1la2yy27ziasyf0jvzk58y1i5b5bq2h176qil550bxhifs39gqbi")) (patches (search-patches "gcc-9-strmov-store-file-names.patch" "gcc-9-asan-fix-limits-include.patch" "gcc-5.0-libvtv-runpath.patch")))))) From 393dc1cc0bc4677bfa7929db9b83cf94849dcc21 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Fri, 13 Mar 2020 18:30:37 +0100 Subject: [PATCH 006/235] gnu: dune-*: remove openmpi dependency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency. [arguments]: remove code to setup openmpi for tests. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 37 +++++++------------------------------ 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 499fdb06f7..0e2e6b0ac4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4592,13 +4592,10 @@ linear algebra primitives specifically targeting graph analytics.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("gmp" ,gmp) ("metis" ,metis) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("python" ,python) ("superlu" ,superlu))) @@ -4636,7 +4633,6 @@ Differences} (FD).") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("gmp" ,gmp) @@ -4676,8 +4672,7 @@ This package contains the basic DUNE geometry classes.") (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags)))))) (inputs - `(("dune-common" ,dune-common) - ("openmpi" ,openmpi))) + `(("dune-common" ,dune-common))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4710,16 +4705,13 @@ This package contains the DUNE UG grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("gmp" ,gmp) ("metis" ,metis) ("openblas" ,openblas) - ("openmpi" ,openmpi) ("python" ,python))) (propagated-inputs `(("dune-uggrid" ,dune-uggrid))) @@ -4756,12 +4748,9 @@ This package contains the basic DUNE grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("suitesparse" ,suitesparse) @@ -4809,7 +4798,6 @@ aggregation-based algebraic multigrid.") (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("superlu" ,superlu) @@ -4857,14 +4845,11 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4902,14 +4887,11 @@ cubes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4948,7 +4930,6 @@ provides the full grid interface including adaptive mesh refinement.") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("python" ,python) @@ -4991,9 +4972,7 @@ operating on statically typed trees of objects.") #t)) (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) @@ -5001,7 +4980,6 @@ operating on statically typed trees of objects.") ("dune-grid" ,dune-grid) ("dune-geometry" ,dune-geometry) ("dune-typetree" ,dune-typetree) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("metis" ,metis) ("python" ,python) @@ -5042,7 +5020,6 @@ implemented as callable objects, and bases of finite element spaces.") ("dune-grid" ,dune-grid) ("dune-typetree" ,dune-typetree) ("dune-functions" ,dune-functions) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("eigen" ,eigen) From 6ceb771657bdc3516c6c22f43532ff67d75465f6 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Fri, 13 Mar 2020 18:30:38 +0100 Subject: [PATCH 007/235] gnu: define dune-*-openmpi packages MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (dune-common-openmpi, dune-geometry-openmpi, dune-istl-openmpi, dune-typetree-openmpi, dune-uggrid-openmpi, dune-grid-openmpi, dune-alugrid-openmpi, dune-subgrid-openmpi, dune-localfunctions-openmpi, dune-functions-openmpi, dune-pdelab-openmpi): New variables. (add-openmpi-to-dune-package): New function to add openmpi to the inputs of a dune-* package and replace all dune-* packages in its input with the corresponding dune-*-openmpi package. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 53 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0e2e6b0ac4..6d9fd54e75 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5037,6 +5037,59 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") ;; Either GPL version 2 with "runtime exception" or LGPLv3+. (license (list license:lgpl3+ license:gpl2)))) +(define add-openmpi-to-dune-package + (let ((dune-package? + (lambda (p) (string-prefix? "dune-" (package-name p))))) + (package-mapping + (lambda (p) + (if (dune-package? p) + (package (inherit p) + (name (string-append (package-name p) "-openmpi")) + (inputs `(,@(package-inputs p) + ("openmpi" ,openmpi))) + (arguments + (substitute-keyword-arguments (package-arguments p) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis (string-append (package-synopsis p) " (with MPI support)"))) + p)) + (negate dune-package?)))) + +(define-public dune-common-openmpi + (add-openmpi-to-dune-package dune-common)) + +(define-public dune-geometry-openmpi + (add-openmpi-to-dune-package dune-geometry)) + +(define-public dune-istl-openmpi + (add-openmpi-to-dune-package dune-istl)) + +(define-public dune-typetree-openmpi + (add-openmpi-to-dune-package dune-typetree)) + +(define-public dune-uggrid-openmpi + (add-openmpi-to-dune-package dune-uggrid)) + +(define-public dune-grid-openmpi + (add-openmpi-to-dune-package dune-grid)) + +(define-public dune-alugrid-openmpi + (add-openmpi-to-dune-package dune-alugrid)) + +(define-public dune-subgrid-openmpi + (add-openmpi-to-dune-package dune-subgrid)) + +(define-public dune-localfunctions-openmpi + (add-openmpi-to-dune-package dune-localfunctions)) + +(define-public dune-functions-openmpi + (add-openmpi-to-dune-package dune-functions)) + +(define-public dune-pdelab-openmpi + (add-openmpi-to-dune-package dune-pdelab)) + (define-public mlucas (package (name "mlucas") From d3be522036d251729f61c39079d9e1d08667067f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:13:57 +0100 Subject: [PATCH 008/235] gnu: openlibm: Use HTTPS home page. * gnu/packages/maths.scm (openlibm)[home-page]: Use HTTPS. --- gnu/packages/maths.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d9fd54e75..847cc4a14e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3357,7 +3357,7 @@ access to BLIS implementations via traditional BLAS routine calls.") ;; no configure script (modify-phases %standard-phases (delete 'configure)) #:tests? #f)) ;the tests are part of the default target - (home-page "http://openlibm.org/") + (home-page "https://openlibm.org/") (synopsis "Portable C mathematical library (libm)") (description "OpenLibm is an effort to have a high quality, portable, standalone C From edd3a25606db598209599151482df4d96593ceae Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 21:22:15 +0100 Subject: [PATCH 009/235] gnu: hyperrogue: Update to 11.3a. * gnu/packages/games.scm (hyperrogue): Update to 11.3a. --- gnu/packages/games.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 2791b18dca..df1b31d544 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4105,7 +4105,7 @@ throwing people around in pseudo-randomly generated buildings.") (define-public hyperrogue (package (name "hyperrogue") - (version "11.2q") + (version "11.3a") ;; When updating this package, be sure to update the "hyperrogue-data" ;; origin in native-inputs. (source (origin @@ -4116,7 +4116,7 @@ throwing people around in pseudo-randomly generated buildings.") "-src.tgz")) (sha256 (base32 - "1w4khi2limxhgiq7xnz0rc9nzbk86bhbyzrcd5hdghnhsviaiggq")))) + "1yxabbswq02fc5frigvs43f83m5vlxybc7n5mynkwzj2c70lfp2k")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -4194,7 +4194,7 @@ throwing people around in pseudo-randomly generated buildings.") "-win.zip")) (sha256 (base32 - "1k81zrbq5gmrccjac1i5c6v8j2iilfg2vwrnm8snjmmcnh5z1fgj")))) + "11yhbia45f1w9z0j67h9nynwjqmvakr9l6rnrmdrdkzin6lvzzj4")))) ("unzip" ,unzip))) (inputs `(("font-dejavu" ,font-dejavu) From 189c0b33ba47f42d96d68822c5a277cfc47d1e76 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 21:22:32 +0100 Subject: [PATCH 010/235] gnu: talkfilters: Don't use NAME in source URI. * gnu/packages/games.scm (talkfilters)[source]: Hard-code NAME. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index df1b31d544..44f59d7260 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1688,8 +1688,8 @@ level's exit. The game is presented in a 2D side view.") (source (origin (method url-fetch) - (uri (string-append "http://www.hyperrealm.com/" name "/" - name "-" version ".tar.gz")) + (uri (string-append "http://www.hyperrealm.com/talkfilters/" + "talkfilters-" version ".tar.gz")) (sha256 (base32 "19nc5vq4bnkjvhk8srqddzhcs93jyvpm9r6lzjzwc1mgf08yg0a6")))) (build-system gnu-build-system) From 20035fa7d7eb06ee06dbc03ecc215a59ace51ad1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:31:20 +0100 Subject: [PATCH 011/235] gnu: cube: Use HTTPS home page. * gnu/packages/profiling.scm (cube)[home-page]: Use HTTPS. --- gnu/packages/profiling.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm index 5cc9113ffe..4d3c3faca0 100644 --- a/gnu/packages/profiling.scm +++ b/gnu/packages/profiling.scm @@ -311,7 +311,7 @@ with calls to the POMP2 measurement interface.") (("^source .*frontend.*$") "") (((assoc-ref outputs "out")) lib)) #t)))))) - (home-page "http://www.scalasca.org/software/cube-4.x/download.html") + (home-page "https://www.scalasca.org/software/cube-4.x/download.html") (synopsis "Performance report explorer for parallel programs") (description "CUBE (CUBE Uniform Behavioral Encoding) is a tool to display a variety From a489466b95c5ad39db6a045c65056447617a910d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 16:14:48 +0100 Subject: [PATCH 012/235] gnu: fio: Update to 3.19. * gnu/packages/benchmark.scm (fio): Update to 3.19. --- gnu/packages/benchmark.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 9ae30eefc8..4e6c416518 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017 Marius Bakke ;;; Copyright © 2017 Dave Love -;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2019 Ricardo Wurmus ;;; Copyright © 2019 Eric Bavier ;;; Copyright © 2019 Gábor Boskovits @@ -46,14 +46,14 @@ (define-public fio (package (name "fio") - (version "3.18") + (version "3.19") (source (origin (method url-fetch) (uri (string-append "https://brick.kernel.dk/snaps/" "fio-" version ".tar.bz2")) (sha256 (base32 - "12wzi40hn0ylkdiqwjjljdjmiq78nhwsv3qqa0fad7h3x08w6w6b")))) + "01nc7igmcc6hda32d1y8vidd9x9pdlxvf3i1pwrzvmi6xvmbfvab")))) (build-system gnu-build-system) (arguments '(#:test-target "test" From 0b1d71b2187bdb12e5b7f2770edb5a7b81d97625 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:30:21 +0100 Subject: [PATCH 013/235] gnu: ant: Use HTTPS home page. * gnu/packages/java.scm (ant)[home-page]: Use HTTPS. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index da0f3bfa5b..7cd0ab9e2a 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -330,7 +330,7 @@ JNI.") ("jamvm" ,jamvm-1-bootstrap) ("unzip" ,unzip) ("zip" ,zip))) - (home-page "http://ant.apache.org") + (home-page "https://ant.apache.org") (synopsis "Build tool for Java") (description "Ant is a platform-independent build tool for Java. It is similar to From 1a04595498ff2b26048005bca6dcff783149e9ff Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 19:06:08 +0100 Subject: [PATCH 014/235] gnu: giblib: Add mirror URL. * gnu/packages/image.scm (giblib)[source]: Add another URL. --- gnu/packages/image.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 101fe0dc2a..aaa2a6e2d0 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -903,6 +903,10 @@ more modular, simple, and flexible.") (string-append "http://linuxbrit.co.uk/downloads/giblib-" version ".tar.gz") + (string-append + "https://src.fedoraproject.org/repo/pkgs/giblib/giblib-" + version ".tar.gz/c810ef5389baf24882a1caca2954385e/giblib-" + version ".tar.gz") (string-append "https://sourceforge.net/projects/slackbuildsdirectlinks/" "files/giblib/giblib-" version ".tar.gz"))) From 30e8cf5f22ca148f345abcc6bdcf4c550192e891 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:31:00 +0100 Subject: [PATCH 015/235] gnu: giblib: Use archived home page. * gnu/packages/image.scm (giblib)[home-page]: Use Web Archive snapshot. --- gnu/packages/image.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index aaa2a6e2d0..fffc1e0cec 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -917,7 +917,11 @@ more modular, simple, and flexible.") (inputs `(("libx11" ,libx11) ("imlib2" ,imlib2))) - (home-page "http://linuxbrit.co.uk/software/") ; no real home-page + (home-page + ;; This vanished page is universally accepted as giblib's home despite not + ;; mentioning the package once. + (string-append "https://web.archive.org/web/20140907071208" + "https://linuxbrit.co.uk/software/")) (synopsis "Wrapper library for imlib2") (description "Giblib is a simple library which wraps imlib2's context API, avoiding From 5acaec829fc10a2075dba39f0af8e49e93a4edd4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:06:51 +0100 Subject: [PATCH 016/235] gnu: pangomm: Update home page. * gnu/packages/gtk.scm (pangomm)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/gtk.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 670a943a1b..d9bd15824b 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1113,7 +1113,7 @@ library.") ("cairomm" ,cairomm) ("glibmm" ,glibmm) ("pango" ,pango))) - (home-page "http://www.pango.org/") + (home-page "https://pango.gnome.org//") (synopsis "C++ interface to the Pango text rendering library") (description "Pangomm provides a C++ programming interface to the Pango text rendering From 3344bc495d13315f652eabef4549cdf2e08ef1c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sat, 14 Mar 2020 22:51:49 +0100 Subject: [PATCH 017/235] gnu: java-qdox-1.12: Update source and home-page URI. * gnu/packages/java.scm (java-qdox-1.12)[source]: Update URI. [home-page]: Update URI. --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 7cd0ab9e2a..42ea3799a1 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -3301,7 +3301,7 @@ decompression and random access decompression have been fully implemented.") (version "1.12.1") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/" + (uri (string-append "https://repo1.maven.org/maven2/" "com/thoughtworks/qdox/qdox/" version "/qdox-" version "-sources.jar")) (sha256 @@ -3325,7 +3325,7 @@ decompression and random access decompression have been fully implemented.") (lambda _ (delete-file-recursively "src/com/thoughtworks/qdox/junit") #t))))) - (home-page "http://qdox.codehaus.org/") + (home-page "https://github.com/codehaus/qdox") (synopsis "Parse definitions from Java source files") (description "QDox is a high speed, small footprint parser for extracting From 7779ad5038716e504a53eae7b01a2a7ef77e3a09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sat, 14 Mar 2020 23:01:29 +0100 Subject: [PATCH 018/235] gnu: java-osgi-cmpn: Update source URI. * gnu/packages/java.scm (java-osgi-cmpn)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 42ea3799a1..ab9427aa23 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7361,7 +7361,7 @@ used to generate this API.") (version "6.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/" + (uri (string-append "https://repo1.maven.org/maven2/" "org/osgi/osgi.cmpn/" version "/osgi.cmpn-" version "-sources.jar")) (sha256 From 8031a55a23216b9056263aeafeb1839d7e6b9327 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 23:46:37 +0100 Subject: [PATCH 019/235] gnu: sudo: Update to 1.8.31p1. * gnu/packages/admin.scm (sudo): Update to 1.8.31p1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 5ec34864e2..0862000dd2 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1199,7 +1199,7 @@ system administrator.") (define-public sudo (package (name "sudo") - (version "1.8.31") + (version "1.8.31p1") (source (origin (method url-fetch) (uri @@ -1209,7 +1209,7 @@ system administrator.") version ".tar.gz"))) (sha256 (base32 - "0ks5mm9hda5idivncyfpiz4lrd8fv0dpmsl711788k7f7ixdka3y")) + "1n0mdmgcs92af34xxsnsh1arrngymhdmwd9srjgjbk65q7xzsg67")) (modules '((guix build utils))) (snippet '(begin From 416d098a0e496935d851db472a6d891eb6bb2bad Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 14 Mar 2020 23:43:52 +0100 Subject: [PATCH 020/235] gnu: librep: Don't use NAME in source URI. * gnu/packages/sawfish.scm (librep)[source]: Hard-code NAME. --- gnu/packages/sawfish.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm index 98b0cc7044..6df9417c64 100644 --- a/gnu/packages/sawfish.scm +++ b/gnu/packages/sawfish.scm @@ -43,8 +43,8 @@ (version "0.92.7") (source (origin (method url-fetch) - (uri (string-append "http://download.tuxfamily.org/" name "/" - name "_" version ".tar.xz")) + (uri (string-append "http://download.tuxfamily.org/librep/" + "librep_" version ".tar.xz")) (sha256 (base32 "1bmcjl1x1rdh514q9z3hzyjmjmwwwkziipjpjsl301bwmiwrd8a8")))) From 131f0f853e5ea6c4effe18fbd1a4e68a6c78624d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:24:13 +0100 Subject: [PATCH 021/235] gnu: librep: Update home page. * gnu/packages/sawfish.scm (librep)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/sawfish.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm index 6df9417c64..26d8eba3b6 100644 --- a/gnu/packages/sawfish.scm +++ b/gnu/packages/sawfish.scm @@ -65,7 +65,7 @@ (list (search-path-specification (variable "REP_DL_LOAD_PATH") (files '("lib/rep"))))) - (home-page "http://sawfish.wikia.com/wiki/Librep") + (home-page "https://sawfish.fandom.com/wiki/Librep") (synopsis "Lisp system for sawfish") (description "Librep is a dialect of Lisp, designed to be used both as an extension From 77386648da9c6bd0601d389ddb94ddba088d8b87 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:06:36 +0100 Subject: [PATCH 022/235] gnu: gauche: Use HTTPS home page. * gnu/packages/scheme.scm (gauche)[home-page]: Use HTTPS. --- gnu/packages/scheme.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index d8a1a04ba4..e36564f030 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -1008,7 +1008,7 @@ The core is 12 builtin special forms and 33 builtin functions.") (package (name "gauche") (version "0.9.9") - (home-page "http://practical-scheme.net/gauche/index.html") + (home-page "https://practical-scheme.net/gauche/index.html") (source (origin (method url-fetch) From 183f258ea809c7e93a02b87568dcaf62625e8c93 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 14 Mar 2020 14:14:58 -0400 Subject: [PATCH 023/235] Revert "gnu: VIGRA: Try to fix a build failure on the build farm." This doesn't have any effect on our build farm, because Cuirass does not honor the 'timeout' and 'max-silent-time' properties: https://lists.gnu.org/archive/html/guix-devel/2020-03/msg00209.html This reverts commit 9e89b4196605457cff6ca14b21f86c7b25a22671. * gnu/packages/image.scm (vigra)[properties]: Remove field. --- gnu/packages/image.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index fffc1e0cec..38a8b2ed42 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1020,9 +1020,6 @@ graphics image formats like PNG, BMP, JPEG, TIFF and others.") (sha256 (base32 "1bqs8vx5i1bzamvv563i24gx2xxdidqyxh9iaj46mbznhc84wmm5")))) (build-system cmake-build-system) - ;; Otherwise it fails on in the check phase after 3600 - ;; seconds of silence. - (properties '((max-silent-time . 7200))) (inputs `(("boost" ,boost) ("fftw" ,fftw) From 90beb0ed457a1b2a1724ff03371b8a3ddcf59929 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 14 Mar 2020 14:17:21 -0400 Subject: [PATCH 024/235] gnu: LibreOffice: Update to 6.4.1.2. * gnu/packages/libreoffice.scm (libreoffice): Update to 6.4.1.2. --- gnu/packages/libreoffice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index e7878ea014..2ef813907d 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -987,7 +987,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (define-public libreoffice (package (name "libreoffice") - (version "6.4.0.3") + (version "6.4.1.2") (source (origin (method url-fetch) @@ -997,7 +997,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (version-prefix version 3) "/libreoffice-" version ".tar.xz")) (sha256 (base32 - "09ra8a3ylb08xhy8wy233fs0f87klkpsbi9n3zss0c688afxjcf5")))) + "02iz94flpxgkvlipk3psddzw2gdq2j4nv7z01kphs5107sfs0r0d")))) (build-system glib-or-gtk-build-system) (native-inputs `(("bison" ,bison) From b5ffcbe1af01544cac31f056a700f5382f3e6b14 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 4 Mar 2020 20:59:48 +0200 Subject: [PATCH 025/235] gnu: Add bidiv. * gnu/packages/fribidi.scm (bidiv): New variable. * gnu/packages/patches/bidiv-update-fribidi.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/fribidi.scm | 54 ++++++++++++++++++- .../patches/bidiv-update-fribidi.patch | 50 +++++++++++++++++ 3 files changed, 104 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/bidiv-update-fribidi.patch diff --git a/gnu/local.mk b/gnu/local.mk index 610c81ec97..73fc219383 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -759,6 +759,7 @@ dist_patch_DATA = \ %D%/packages/patches/beignet-correct-file-names.patch \ %D%/packages/patches/benchmark-unbundle-googletest.patch \ %D%/packages/patches/biber-fix-encoding-write.patch \ + %D%/packages/patches/bidiv-update-fribidi.patch \ %D%/packages/patches/binutils-boot-2.20.1a.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blender-2.79-newer-ffmpeg.patch \ diff --git a/gnu/packages/fribidi.scm b/gnu/packages/fribidi.scm index 61aa6fd726..345529b73a 100644 --- a/gnu/packages/fribidi.scm +++ b/gnu/packages/fribidi.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Marek Benc -;;; Copyright © 2016, 2019 Efraim Flashner +;;; Copyright © 2016, 2019, 2020 Efraim Flashner ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -54,3 +54,55 @@ or right-to-left ordering as necessary.") (source (origin (inherit (package-source fribidi)) (patches (search-patches "fribidi-CVE-2019-18397.patch")))))) + +(define-public bidiv + (package + (name "bidiv") + (version "1.5") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://debian/pool/main/b/bidiv/bidiv_" + version ".orig.tar.gz")) + (sha256 + (base32 + "05p5m2ihxbmc1qsgs8rjlww08fy9859fhl7xf196p8g5qygqd7cv")) + (patches (search-patches "bidiv-update-fribidi.patch")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) ; no configure + (add-after 'unpack 'misc-fixes + (lambda _ + (substitute* "bidiv.c" + (("FriBidiCharType") "FriBidiParType") + (("&c") "(char *)&c")) + #t)) + ;; We don't want to use the handwritten makefile + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((fribidi (assoc-ref inputs "fribidi"))) + (invoke "gcc" "-o" "bidiv" "bidiv.c" + ;; pkg-config --cflags fribidi + (string-append "-I" fribidi "/include/fribidi") + ;; pkg-config --libs fribidi + (string-append "-L" fribidi "/lib") "-lfribidi")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (install-file "bidiv" bin) + (install-file "bidiv.1" man)) + #t))) + #:tests? #f)) ; no tests + (inputs + `(("fribidi" ,fribidi))) + (home-page "https://tracker.debian.org/pkg/bidiv") + (synopsis "BiDi viewer - command-line tool displaying logical Hebrew/Arabic") + (description "bidiv is a simple utility for converting logical-Hebrew input +to visual-Hebrew output. This is useful for reading Hebrew mail messages, +viewing Hebrew texts, etc. It was written for Hebrew but Arabic (or other BiDi +languages) should work equally well.") + (license gpl2+))) diff --git a/gnu/packages/patches/bidiv-update-fribidi.patch b/gnu/packages/patches/bidiv-update-fribidi.patch new file mode 100644 index 0000000000..d000cfeda4 --- /dev/null +++ b/gnu/packages/patches/bidiv-update-fribidi.patch @@ -0,0 +1,50 @@ +https://sources.debian.org/data/main/b/bidiv/1.5-6/debian/patches/fribidi_019 + +Description: Fix building with fribidi 1.9 +Author: أحمد المحمودي +Bug-Debian: http://bugs.debian.org/568130 + +--- a/bidiv.c ++++ b/bidiv.c +@@ -141,8 +141,9 @@ bidiv(FILE *fp) + */ + if(c1<0x80||c1>0xbf){ + ungetc(c1, fp); +- unicode_in[len]= +- fribidi_iso8859_8_to_unicode_c(c); ++ fribidi_charset_to_unicode( ++ FRIBIDI_CHAR_SET_ISO8859_8, ++ &c, 1, &unicode_in[len]); + } else + unicode_in[len]=((c & 037) << 6) + (c1 & 077); + newline=0; +@@ -153,8 +154,9 @@ bidiv(FILE *fp) + In the future we will have a language + option, which will control this (as well + as the output encoding). */ +- unicode_in[len]= +- fribidi_iso8859_8_to_unicode_c(c); ++ fribidi_charset_to_unicode( ++ FRIBIDI_CHAR_SET_ISO8859_8, ++ &c, 1, &unicode_in[len]); + #else + in[len]=c; + #endif +@@ -206,11 +208,11 @@ bidiv(FILE *fp) + rtl_line=0; + + if(out_utf8) +- fribidi_unicode_to_utf8(unicode_out, len, +- out); ++ fribidi_unicode_to_charset(FRIBIDI_CHAR_SET_UTF8, ++ unicode_out, len, out); + else +- fribidi_unicode_to_iso8859_8(unicode_out, len, +- out); ++ fribidi_unicode_to_charset(FRIBIDI_CHAR_SET_ISO8859_8, ++ unicode_out, len, out); + /* if rtl_line (i.e., base_dir is RL), and we didn't fill the + entire width, we need to pad with spaces. Maybe in the + future this should be an option. +-- + From 3eca7ff9681b68d19016737dacc0d7a0572af3e6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 4 Mar 2020 21:37:21 +0200 Subject: [PATCH 026/235] gnu: Add python-blurhash. * gnu/packages/python-crypto.scm (python-blurhash): New variable. --- gnu/packages/python-crypto.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 9eee75cbfb..23c06267a7 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -788,6 +788,40 @@ key), SSH public key, ASC-encoded OpenPGP key, APK Android application, LDIFF file, and more.") (license license:gpl3))) +(define-public python-blurhash + (package + (name "python-blurhash") + (version "1.1.4") + (source + (origin + ;; Tests not included in pypi release and releases not tagged in git repo. + (method git-fetch) + (uri (git-reference + (url "https://github.com/halcy/blurhash-python") + (commit "22e081ef1c24da1bb5c5eaa2c1d6649724deaef8"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qq6mhydlp7q3na4kmaq3871h43wh3pyfyxr4b79bia73wjdylxf")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (delete-file "setup.cfg") + (invoke "pytest")))))) + (native-inputs + `(("python-numpy" ,python-numpy) + ("python-pillow" ,python-pillow) + ("python-pytest" ,python-pytest))) + (home-page "https://github.com/halcy/blurhash-python") + (synopsis + "Pure-Python implementation of the blurhash algorithm") + (description + "Pure-Python implementation of the blurhash algorithm.") + (license license:expat))) + (define-public python-ecpy (package (name "python-ecpy") From 6e003bd4ccd7470247b1fdbee3a6c6a0ad8054ac Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 4 Mar 2020 21:13:55 +0200 Subject: [PATCH 027/235] gnu: Add python-pytest-vcr. * gnu/packages/python-check.scm (python-pytest-vcr): New variable. --- gnu/packages/python-check.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index a69619b96a..70a5b1e452 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Ricardo Wurmus ;;; Copyright © 2019 Tobias Geerinckx-Rice -;;; Copyright © 2019 Efraim Flashner +;;; Copyright © 2019, 2020 Efraim Flashner ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Hartmut Goebel ;;; Copyright © 2020 Julien Lepiller @@ -30,6 +30,7 @@ #:use-module (guix utils) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix git-download) #:use-module (guix download) #:use-module (guix build-system python)) @@ -109,6 +110,37 @@ detect the absence of a cassette file and once again record all HTTP interactions, which will update them to correspond to the new API.") (license license:expat))) +(define-public python-pytest-vcr + (package + (name "python-pytest-vcr") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ktosiek/pytest-vcr") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i6fin91mklvbi8jzfiswvwf1m91f43smpj36a17xrzk4gisfs6i")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "tests/")))))) + (propagated-inputs + `(("python-pytest" ,python-pytest) + ("python-vcrpy" ,python-vcrpy))) + (home-page "https://github.com/ktosiek/pytest-vcr") + (synopsis "Plugin for managing VCR.py cassettes") + (description + "Plugin for managing VCR.py cassettes.") + (license license:expat))) + (define-public python-pytest-checkdocs (package (name "python-pytest-checkdocs") From 995b391013aa61c6e7d8d6b89d822542e155286b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Mar 2020 12:03:19 +0100 Subject: [PATCH 028/235] services/web: Remove empty events directive from default-nginx-config. * gnu/services/web.scm (default-nginx-config): Remove empty events directive. --- gnu/services/web.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/services/web.scm b/gnu/services/web.scm index d093f60c8d..e2178faeb8 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -657,8 +657,7 @@ of index files." (map emit-nginx-upstream-config upstream-blocks) (map emit-nginx-server-config server-blocks) extra-content - "\n}\n" - "events {}\n")))) + "\n}\n")))) (define %nginx-accounts (list (user-group (name "nginx") (system? #t)) From b420e6deb96e0760f12e3d941b76e690c4235e47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Mar 2020 12:03:57 +0100 Subject: [PATCH 029/235] services/web: nginx-configuration: Add support for global directives. * gnu/services/web.scm ()[global-directives]: Add field. (emit-global-directive): New procedure. (default-nginx-config): Use it. * doc/guix.texi (Web Services): Document it. --- doc/guix.texi | 11 +++++++++++ gnu/services/web.scm | 10 ++++++++++ 2 files changed, 21 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index 4658c6f5eb..28808b0cd5 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -20272,6 +20272,17 @@ names of loadable modules, as in this example: /etc/nginx/modules/ngx_http_accept_language_module.so"))) @end lisp +@item @code{global-directives} (default: @code{'()}) +Association list of global directives for the top level of the nginx +configuration. Values may themselves be association lists. + +@lisp +(global-directives + `((worker_processes . 16) + (pcre_jit . on) + (events . ((worker_connections . 1024))))) +@end lisp + @item @code{extra-content} (default: @code{""}) Extra content for the @code{http} block. Should be string or a string valued G-expression. diff --git a/gnu/services/web.scm b/gnu/services/web.scm index e2178faeb8..3edc751ea2 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -529,6 +529,7 @@ (server-names-hash-bucket-max-size nginx-configuration-server-names-hash-bucket-max-size (default #f)) (modules nginx-configuration-modules (default '())) + (global-directives nginx-configuration-global-directives (default '())) (extra-content nginx-configuration-extra-content (default "")) (file nginx-configuration-file ;#f | string | file-like @@ -552,6 +553,13 @@ of index files." (define (emit-load-module module) (list "load_module " module ";\n")) +(define emit-global-directive + (match-lambda + ((key . (? list? alist)) + (format #f "~a { ~{~a~}}~%" key (map emit-global-directive alist))) + ((key . value) + (format #f "~a ~a;~%" key value)))) + (define emit-nginx-location-config (match-lambda (($ uri body) @@ -626,12 +634,14 @@ of index files." server-names-hash-bucket-size server-names-hash-bucket-max-size modules + global-directives extra-content) (apply mixed-text-file "nginx.conf" (flatten "user nginx nginx;\n" "pid " run-directory "/pid;\n" "error_log " log-directory "/error.log info;\n" + (map emit-global-directive global-directives) (map emit-load-module modules) "http {\n" " client_body_temp_path " run-directory "/client_body_temp;\n" From a431a63537c8103b2a58c9a55d90184fb5c90361 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Mar 2020 14:17:26 +0100 Subject: [PATCH 030/235] gnu: guile-gi: Embed absolute file name of extension library. * gnu/packages/guile-xyz.scm (guile-gi)[arguments]: Add phase patch-references-to-extension. --- gnu/packages/guile-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 9f8173657e..8ada9c50e6 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2504,8 +2504,35 @@ list of components. This module takes care of that for you.") (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-gnu-filesystem-hierarchy") + #:modules ((guix build gnu-build-system) + (guix build utils) + (ice-9 popen) + (ice-9 rdelim)) #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-references-to-extension + (lambda* (#:key outputs #:allow-other-keys) + (let ((effective (read-line + (open-pipe* OPEN_READ + "guile" "-c" + "(display (effective-version))")))) + (substitute* '("module/gi.scm" + "module/gi/oop.scm" + "module/gi/documentation.scm" + "module/gi/types.scm" + "module/gi/repository.scm") + (("\\(load-extension \"libguile-gi\" \"(.*)\"\\)" m arg) + (format #f "~s" + `(load-extension + (format #f "~alibguile-gi" + (if (getenv "GUILE_GI_UNINSTALLED") + "" + ,(format #f "~a/lib/guile/~a/" + (assoc-ref outputs "out") + effective))) + ,arg))))) + (setenv "GUILE_GI_UNINSTALLED" "1") + #t)) (add-before 'check 'start-xorg-server (lambda* (#:key inputs #:allow-other-keys) ;; The init_check test requires a running X server. From 0b6de85a4abc30fe0fedc3acccf67ac8735ae197 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Mar 2020 15:07:14 +0100 Subject: [PATCH 031/235] gnu: zabbix-agentd: Update to 4.4.6. * gnu/packages/monitoring.scm (zabbix-agentd): Update to 4.4.6. --- gnu/packages/monitoring.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 1eb095ce50..bcb8df24d0 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Ludovic Courtès ;;; Copyright © 2018 Sou Bunnbu -;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019 Oleg Pykhalov @@ -152,7 +152,7 @@ etc. via a Web interface. Features include: (define-public zabbix-agentd (package (name "zabbix-agentd") - (version "4.4.1") + (version "4.4.6") (source (origin (method url-fetch) @@ -161,7 +161,7 @@ etc. via a Web interface. Features include: "/zabbix-" version ".tar.gz")) (sha256 (base32 - "0jjn2przn9s25slrcxmq8iqdgqkgxnqs45zy0n1ma6nlgmclxxqb")))) + "03mf4sklnw1x0ixp41vnibkz0794yi9jhws7ixld8jj2czk2ifr2")))) (build-system gnu-build-system) (arguments `(#:configure-flags From 76e0b5ba2611c626f0591c0f0cef1609a4d32210 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:27:53 +0100 Subject: [PATCH 032/235] gnu: python-pyside: Update to 5.12.6. * gnu/packages/qt.scm (python-shiboken-2): Update to 5.12.6. [source]: Download tarball release instead of git repository. [arguments]: Add phase to make files writable and update timestamps. (python-pyside-2): Inherit version and source from PYTHON-SHIBOKEN-2. [native-inputs]: Remove LIBCXX-6. Rename "python-wrapper" input to "python". Change from CMAKE to CMAKE-MINIMAL. [arguments]: Remove libcxx substitution. Add "-DPYTHON_EXECUTABLE" in #:configure-flags. (python-pyside-2-tools)[native-inputs]: Add PYTHON-WRAPPER. [arguments]: Set "-DPYTHON_EXECUTABLE" in #:configure-flags. Add phase 'go-to-source-dir'. --- gnu/packages/qt.scm | 301 +++++++++++++++++++++----------------------- 1 file changed, 145 insertions(+), 156 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 6642ed6e77..6ca052c31a 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -2515,168 +2515,157 @@ color-related widgets.") (license license:lgpl3+)))) (define-public python-shiboken-2 - (let ((revision "1") - ;; Pinned to branches with support for qt 5.11.3 - (commit "4018787a3cc01d632fdca7891ac8aa9487110c26")) - (package - (name "python-shiboken-2") - (version (git-version "v5.11.3" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - ;; The latest versions of Shiboken live in the pyside repo. - ;; There is another standalone repo only for Shiboken - ;; but it is outdated - (url "https://code.qt.io/pyside/pyside-setup") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0g8jacm2iqd7lw2m7f1dp1nnrsk38bl3m8pihm8zz9gxs8d31sf5")))) - (build-system cmake-build-system) - (inputs - `(("clang-toolchain" ,clang-toolchain-6) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("python-wrapper" ,python-wrapper) - ("qtbase" ,qtbase) - ("qtxmlpatterns" ,qtxmlpatterns))) - (arguments - `(#:tests? #f - ;; FIXME: Building tests fails - #:configure-flags '("-DBUILD_TESTS=off") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-shiboken-dir-only - (lambda _ (chdir "sources/shiboken2") #t)) - (add-before 'configure 'set-build-env - (lambda* (#:key inputs #:allow-other-keys) - (let ((llvm (assoc-ref inputs "clang-toolchain"))) - (setenv "CLANG_INSTALL_DIR" llvm) - #t)))))) - (home-page "https://wiki.qt.io/Qt_for_Python") - (synopsis - "Shiboken generates bindings for C++ libraries using CPython source code") - (description - "Shiboken generates bindings for C++ libraries using CPython source code") - (license - (list - ;; The main code is GPL3 or LGPL3. - ;; Examples are BSD-3. - license:gpl3 - license:lgpl3 - license:bsd-3))))) + (package + (name "python-shiboken-2") + (version "5.12.6") + (source (origin + (method url-fetch) + (uri (string-append "https://download.qt.io/official_releases" + "/QtForPython/pyside2/PySide2-" version + "-src/pyside-setup-everywhere-src-" + version ".tar.xz")) + (sha256 + (base32 + "1n45l6xxyxs6cfp2l4rp8qs1c2fyfwyrdxa4qcpwfsqsi51rydsk")))) + (build-system cmake-build-system) + (inputs + `(("clang-toolchain" ,clang-toolchain-6) + ("libxml2" ,libxml2) + ("libxslt" ,libxslt) + ("python-wrapper" ,python-wrapper) + ("qtbase" ,qtbase) + ("qtxmlpatterns" ,qtxmlpatterns))) + (arguments + `(#:tests? #f + ;; FIXME: Building tests fails + #:configure-flags '("-DBUILD_TESTS=off") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-shiboken-dir-only + (lambda _ (chdir "sources/shiboken2") #t)) + (add-before 'configure 'make-files-writable-and-update-timestamps + (lambda _ + ;; The build scripts need to modify some files in + ;; the read-only source directory, and also attempts + ;; to create Zip files which fails because the Zip + ;; format does not support timestamps before 1980. + (let ((circa-1980 (* 10 366 24 60 60))) + (for-each (lambda (file) + (make-file-writable file) + (utime file circa-1980 circa-1980)) + (find-files "."))) + #t)) + (add-before 'configure 'set-build-env + (lambda* (#:key inputs #:allow-other-keys) + (let ((llvm (assoc-ref inputs "clang-toolchain"))) + (setenv "CLANG_INSTALL_DIR" llvm) + #t)))))) + (home-page "https://wiki.qt.io/Qt_for_Python") + (synopsis + "Shiboken generates bindings for C++ libraries using CPython source code") + (description + "Shiboken generates bindings for C++ libraries using CPython source code") + (license + (list + ;; The main code is GPL3 or LGPL3. + ;; Examples are BSD-3. + license:gpl3 + license:lgpl3 + license:bsd-3)))) (define-public python-pyside-2 - (let ((revision "1") - ;; Pinned to branches with support for qt 5.11.3 - (commit "4018787a3cc01d632fdca7891ac8aa9487110c26")) - (package - (name "python-pyside-2") - (version (git-version "v5.11.3" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://code.qt.io/pyside/pyside-setup") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0g8jacm2iqd7lw2m7f1dp1nnrsk38bl3m8pihm8zz9gxs8d31sf5")))) - (build-system cmake-build-system) - (inputs - `(("libcxx" ,libcxx-6) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("clang-toolchain" ,clang-toolchain-6) - ("qtbase" ,qtbase) - ("qtdatavis3d" ,qtdatavis3d) - ("qtlocation" ,qtlocation) - ("qtmultimedia" ,qtmultimedia) - ("qtquickcontrols" ,qtquickcontrols) - ("qtscript" ,qtscript) - ("qtscxml" ,qtscxml) - ("qtsensors" ,qtsensors) - ("qtspeech" ,qtspeech) - ("qtsvg" ,qtsvg) - ("qtwebchannel" ,qtwebchannel) - ("qtwebsockets" ,qtwebsockets) - ("qtx11extras" ,qtx11extras) - ("qtxmlpatterns" ,qtxmlpatterns))) - (native-inputs - `(("cmake" ,cmake) - ("python-shiboken-2" ,python-shiboken-2) - ("python-wrapper" ,python-wrapper) - ("qttools" ,qttools) - ("which" ,which))) - (arguments - `(#:tests? #f - ;; FIXME: Building tests fail. - #:configure-flags '("-DBUILD_TESTS=FALSE") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside2") #t)) - (add-before 'configure 'set-clang-dir - (lambda* (#:key inputs #:allow-other-keys) - (let ((clang (assoc-ref inputs "clang-toolchain")) - (libcxx (assoc-ref inputs "libcxx"))) - (setenv "CLANG_INSTALL_DIR" clang) - (substitute* "cmake/Macros/PySideModules.cmake" - (("--include-paths=") - (string-append "--include-paths=" libcxx "/include/c++/v1:"))) - #t)))))) - (home-page "https://wiki.qt.io/Qt_for_Python") - (synopsis - "The Qt for Python product enables the use of Qt5 APIs in Python applications") - (description - "The Qt for Python product enables the use of Qt5 APIs in Python + (package + (name "python-pyside-2") + (version (package-version python-shiboken-2)) + (source (package-source python-shiboken-2)) + (build-system cmake-build-system) + (inputs + `(("libxml2" ,libxml2) + ("libxslt" ,libxslt) + ("clang-toolchain" ,clang-toolchain-6) + ("qtbase" ,qtbase) + ("qtdatavis3d" ,qtdatavis3d) + ("qtlocation" ,qtlocation) + ("qtmultimedia" ,qtmultimedia) + ("qtquickcontrols" ,qtquickcontrols) + ("qtscript" ,qtscript) + ("qtscxml" ,qtscxml) + ("qtsensors" ,qtsensors) + ("qtspeech" ,qtspeech) + ("qtsvg" ,qtsvg) + ("qtwebchannel" ,qtwebchannel) + ("qtwebsockets" ,qtwebsockets) + ("qtx11extras" ,qtx11extras) + ("qtxmlpatterns" ,qtxmlpatterns))) + (native-inputs + `(("cmake" ,cmake-minimal) + ("python-shiboken-2" ,python-shiboken-2) + ("python" ,python-wrapper) + ("qttools" ,qttools) + ("which" ,which))) + (arguments + `(#:tests? #f + ;; FIXME: Building tests fail. + #:configure-flags + (list "-DBUILD_TESTS=FALSE" + (string-append "-DPYTHON_EXECUTABLE=" + (assoc-ref %build-inputs "python") + "/bin/python")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'go-to-source-dir + (lambda _ (chdir "sources/pyside2") #t)) + (add-before 'configure 'set-clang-dir + (lambda* (#:key inputs #:allow-other-keys) + (let ((clang (assoc-ref inputs "clang-toolchain"))) + (setenv "CLANG_INSTALL_DIR" clang) + #t)))))) + (home-page "https://wiki.qt.io/Qt_for_Python") + (synopsis + "The Qt for Python product enables the use of Qt5 APIs in Python applications") + (description + "The Qt for Python product enables the use of Qt5 APIs in Python applications. It lets Python developers utilize the full potential of Qt, using the PySide2 module. The PySide2 module provides access to the individual Qt modules such as QtCore, QtGui,and so on. Qt for Python also comes with the Shiboken2 CPython binding code generator, which can be used to generate Python bindings for your C or C++ code.") - (license (list - license:lgpl3 - ;;They state that: - ;; this file may be used under the terms of the GNU General - ;; Public License version 2.0 or (at your option) the GNU - ;; General Public license version 3 or any later version - ;; approved by the KDE Free Qt Foundation. - ;; Thus, it is currently v2 or v3, but no "+". - license:gpl3 - license:gpl2))))) + (license (list + license:lgpl3 + ;;They state that: + ;; this file may be used under the terms of the GNU General + ;; Public License version 2.0 or (at your option) the GNU + ;; General Public license version 3 or any later version + ;; approved by the KDE Free Qt Foundation. + ;; Thus, it is currently v2 or v3, but no "+". + license:gpl3 + license:gpl2)))) (define-public python-pyside-2-tools - (let ((revision "1") - ;; Pinned to branches with support for qt 5.11.3 - (commit "f1b775537e7fbd718516749583b2abf1cb6adbce")) - (package - (name "python-pyside-2-tools") - (version (git-version "v5.11.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://code.qt.io/pyside/pyside-tools") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1w2g5afvww9r89wmdm9jx8sz67x4bzy9difkh72n4c73ya1n91ry")))) - (build-system cmake-build-system) - (inputs - `(("python-pyside-2" ,python-pyside-2) - ("python-shiboken-2" ,python-shiboken-2) - ("qtbase" ,qtbase))) - (arguments - `(#:tests? #f - #:configure-flags '("-DBUILD_TESTS=off"))) - (home-page "https://wiki.qt.io/Qt_for_Python") - (synopsis - "Contains command line tools for PySide2") - (description - "Contains lupdate, rcc and uic tools for PySide2") - (license license:gpl2)))) + (package + (name "python-pyside-2-tools") + (version (package-version python-shiboken-2)) + (source (package-source python-shiboken-2)) + (build-system cmake-build-system) + (inputs + `(("python-pyside-2" ,python-pyside-2) + ("python-shiboken-2" ,python-shiboken-2) + ("qtbase" ,qtbase))) + (native-inputs + `(("python" ,python-wrapper))) + (arguments + `(#:tests? #f + #:configure-flags + (list "-DBUILD_TESTS=off" + (string-append "-DPYTHON_EXECUTABLE=" + (assoc-ref %build-inputs "python") + "/bin/python")) + #:phases (modify-phases %standard-phases + (add-after 'unpack 'go-to-source-dir + (lambda _ (chdir "sources/pyside2-tools") #t))))) + (home-page "https://wiki.qt.io/Qt_for_Python") + (synopsis + "Contains command line tools for PySide2") + (description + "Contains lupdate, rcc and uic tools for PySide2") + (license license:gpl2))) From c085742e07aab494c9c7f7e00fd6ff4e25eb0568 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:28:27 +0100 Subject: [PATCH 033/235] gnu: libarea: Build with cmake-minimal. * gnu/packages/engineering.scm (libarea)[native-inputs]: Change from CMAKE to CMAKE-MINIMAL. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index f3469b1815..361d4d54a6 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -2432,7 +2432,7 @@ interpolation toolkit.") (inputs `(("boost" ,boost) ("python-wrapper" ,python-wrapper))) (native-inputs - `(("cmake" ,cmake))) + `(("cmake" ,cmake-minimal))) (arguments `(#:tests? #f #:phases From 382550f0be8f0023068dbd7005f0a29efeeea455 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:29:17 +0100 Subject: [PATCH 034/235] gnu: python2-scikit-learn: Downgrade to 0.20.4. This is a follow-up to commit 546893c2965c8114e4d7cfe1de46c46664ec4b9e. * gnu/packages/machine-learning.scm (python-scikit-learn)[properties]: New field. (python2-scikit-learn)[version, source]: New fields. --- gnu/packages/machine-learning.scm | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 52e639723b..62ef7b84e4 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2020 Efraim Flashner -;;; Copyright © 2016, 2017 Marius Bakke +;;; Copyright © 2016, 2017, 2020 Marius Bakke ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Kei Kebreau @@ -847,10 +847,25 @@ computing environments.") (description "Scikit-learn provides simple and efficient tools for data mining and data analysis.") + (properties `((python2-variant . ,(delay python2-scikit-learn)))) (license license:bsd-3))) +;; scikit-learn 0.22 and later only supports Python 3, so we stick with +;; an older version here. (define-public python2-scikit-learn - (package-with-python2 python-scikit-learn)) + (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn)))) + (package + (inherit base) + (version "0.20.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/scikit-learn/scikit-learn.git") + (commit version))) + (file-name (git-file-name "python-scikit-learn" version)) + (sha256 + (base32 + "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))))) (define-public python-autograd (let* ((commit "442205dfefe407beffb33550846434baa90c4de7") From 3987715415532aea14c179650bac331ec436882c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:30:11 +0100 Subject: [PATCH 035/235] gnu: python2-pandas: Fix build with Python 2.7.17. While at it, fix the inheritance. * gnu/packages/python-science.scm (python2-pandas): Use INHERIT instead of PACKAGE/INHERIT. [source](modules, snippet): New fields. --- gnu/packages/python-science.scm | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 8dcc6e77e6..4b3db6d5e0 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke +;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Giacomo Leidi @@ -277,12 +277,21 @@ doing practical, real world data analysis in Python.") (define-public python2-pandas (let ((pandas (package-with-python2 (strip-python2-variant python-pandas)))) - (package/inherit - pandas - (version "0.24.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pandas" version)) - (sha256 - (base32 - "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))))) + (package + (inherit pandas) + (version "0.24.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "pandas" version)) + (sha256 + (base32 + "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Adjust for renamed error message in Python 2.7.17. Taken + ;; from . + (substitute* "pandas/io/parsers.py" + (("if 'NULL byte' in msg:") + "if 'NULL byte' in msg or 'line contains NUL' in msg:")) + #t))))))) From c19930dc6bb60fce283ae00ae21d063780922fc2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:31:03 +0100 Subject: [PATCH 036/235] gnu: python-pyrsistent: Update to 0.15.7. * gnu/packages/python-xyz.scm (python-pyrsistent): Update to 0.15.7. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b010f42647..d444e6ed75 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1819,14 +1819,14 @@ from git information. (define-public python-pyrsistent (package (name "python-pyrsistent") - (version "0.14.11") + (version "0.15.7") (home-page "https://github.com/tobgu/pyrsistent") (source (origin (method url-fetch) (uri (pypi-uri "pyrsistent" version)) (sha256 (base32 - "1qkh74bm296mp5g3r11lgsksr6bh4w1bf8pji4nmxdlfj542ga1w")))) + "103j63g6lb5dfspph96zxjdpnq9h991kazd4f09ddgkpxpivbiyd")))) (build-system python-build-system) (native-inputs `(("python-hypothesis" ,python-hypothesis) From 5a9980d55eb1afe5c5bc2561a7cba16b0c16fe7e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:32:12 +0100 Subject: [PATCH 037/235] gnu: python-networkx: Update to 2.4. * gnu/packages/python-xyz.scm (python-networkx): Update to 2.4. [source](uri): Download tarball instead of zipball. [arguments]: New field. [native-inputs]: Remove PYTHON-NOSE and UNZIP. Add PYTHON-PYTEST. [properties]: New field. (python2-networkx): Stick with version 2.2. --- gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d444e6ed75..1942a9505d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6118,29 +6118,52 @@ interfaces in an easy and portable manner.") (define-public python-networkx (package (name "python-networkx") - (version "2.2") + (version "2.4") (source (origin (method url-fetch) - (uri (pypi-uri "networkx" version ".zip")) + (uri (pypi-uri "networkx" version)) (sha256 - (base32 "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5")))) + (base32 "0r2wr7aqay9fwjrgk35fkjzk8lvvb4i4df7ndaqzkr4ndw5zzx7q")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "pytest" "-vv" "--pyargs" "networkx") + (format #t "test suite not run~%")) + #t))))) ;; python-decorator is needed at runtime. (propagated-inputs `(("python-decorator" ,python-decorator))) (native-inputs - `(("python-nose" ,python-nose) - ("unzip" ,unzip))) + `(("python-pytest" ,python-pytest))) (home-page "https://networkx.github.io/") (synopsis "Python module for creating and manipulating graphs and networks") (description "NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.") + (properties `((python2-variant . ,(delay python2-networkx)))) (license license:bsd-3))) +;; NetworkX 2.2 is the last version with support for Python 2. (define-public python2-networkx - (package-with-python2 python-networkx)) + (let ((base (package-with-python2 (strip-python2-variant python-networkx)))) + (package + (inherit base) + (version "2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "networkx" version ".zip")) + (sha256 + (base32 + "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5")))) + (arguments + `(#:python ,python-2)) + (native-inputs + `(("python-nose" ,python2-nose) + ("unzip" ,unzip)))))) (define-public python-datrie (package From 23bc9a35862a5ecfc9f409b61b0d1c6b3818db11 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:32:40 +0100 Subject: [PATCH 038/235] gnu: python-joblib: Update to 0.14.1. * gnu/packages/python-xyz.scm (python-joblib): Update to 0.14.1. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1942a9505d..4d07d5283d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2596,13 +2596,13 @@ logic-free templating system Mustache.") (define-public python-joblib (package (name "python-joblib") - (version "0.13.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (pypi-uri "joblib" version)) (sha256 (base32 - "0612nazad8dxmn3xghfrmjax6456l4xy6hn9cngs7vydi14ds7v5")))) + "1j464w137w6s367gl697j1l63g52akydrxgv4czlck36ynjfwc06")))) (build-system python-build-system) (arguments `(#:phases From 0731f943e354a7a62e0dee7d85f47503cab62a94 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:33:37 +0100 Subject: [PATCH 039/235] gnu: Update python-seaborn to 0.10.0, python2-seaborn to 0.9.1. * gnu/packages/python-xyz.scm (python-seaborn): Update to 0.9.0. [source](patches): Remove. [arguments]: Remove obsolete phase. [properties]: New field. (python2-seaborn): Update to 0.9.1. --- gnu/packages/python-xyz.scm | 35 ++++++++++++++--------------------- 1 file changed, 14 insertions(+), 21 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4d07d5283d..461f574c74 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6260,25 +6260,13 @@ SVG, EPS, PNG and terminal output.") (define-public python-seaborn (package (name "python-seaborn") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (pypi-uri "seaborn" version)) (sha256 - (base32 "0bqysi3fxfjl1866m5jq8z7mynhqbqnikim74dmzn8539iwkzj3n")) - (patches - (list (origin - (method url-fetch) - ;; This has already been merged, but there is no new - ;; release including this patch. It fixes problems - ;; with axis rotation that would lead to test - ;; failures. - (uri "https://patch-diff.githubusercontent.com/raw/mwaskom/seaborn/pull/1716.diff") - (sha256 - (base32 - "1lm870z316n9ivsyr86hpk1gxaraw0mrjvq42lqsm0znhjdp9q9w")) - (file-name "seaborn-0.9.0-axis-rotation.patch")))))) + (base32 "1ffbms4kllihfycf6j57dziq4imgdjw03sqgifh5wzcd2d743zjr")))) (build-system python-build-system) (arguments `(#:phases @@ -6291,12 +6279,6 @@ SVG, EPS, PNG and terminal output.") (system (format #f "~a/bin/Xvfb :1 &" xorg-server)) (setenv "DISPLAY" ":1") #t))) - (add-after 'unpack 'fix-tests - (lambda _ - ;; test_cbar_ticks fails probably because of matplotlib's - ;; expectation of using an older version of FreeType. - (delete-file "seaborn/tests/test_matrix.py") - #t)) (replace 'check (lambda _ (invoke "pytest" "seaborn") #t))))) (propagated-inputs `(("python-pandas" ,python-pandas) @@ -6313,10 +6295,21 @@ SVG, EPS, PNG and terminal output.") graphics in Python. It is built on top of matplotlib and tightly integrated with the PyData stack, including support for numpy and pandas data structures and statistical routines from scipy and statsmodels.") + (properties `((python2-variant . ,(delay python2-seaborn)))) (license license:bsd-3))) +;; 0.9.1 is the last release with support for Python 2. (define-public python2-seaborn - (package-with-python2 python-seaborn)) + (let ((base (package-with-python2 (strip-python2-variant python-seaborn)))) + (package + (inherit base) + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "seaborn" version)) + (sha256 + (base32 + "1bjnshjz4d6z3vrwfwall1a3yh8h3a1h47c3fg7458x9426alcys"))))))) (define-public python-mpmath (package From e3da9b2e554cf283509c9dfbb89dbb9090c44f48 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:34:20 +0100 Subject: [PATCH 040/235] gnu: Update python-natsort to 7.0.1, python2-natsort to 6.2.1. * gnu/packages/python-xyz.scm (python-natsort): Update to 7.0.1. (python2-natsort): Update to 6.2.1. --- gnu/packages/python-xyz.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 461f574c74..da7bbdcf77 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11621,13 +11621,13 @@ Python to manipulate OpenDocument 1.2 files.") (define-public python-natsort (package (name "python-natsort") - (version "5.4.1") + (version "7.0.1") (source (origin (method url-fetch) (uri (pypi-uri "natsort" version)) (sha256 (base32 - "0i732amg6yzkx4g4c9j09jmqq39q377x9cl2nbkm5hax2c2v0wxf")))) + "1ksqfai72dbcfbwx43pxl658j59mx2rvqypjy1fk0ax2qd6lccx6")))) (build-system python-build-system) (arguments `(#:modules ((guix build utils) @@ -11672,9 +11672,17 @@ command @command{natsort} that exposes this functionality in the command line.") (license license:expat) (properties `((python2-variant . ,(delay python2-natsort)))))) +;; Natsort 6.x are the last versions with support for Python 2. (define-public python2-natsort (let ((base (package-with-python2 (strip-python2-variant python-natsort)))) (package (inherit base) + (version "6.2.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "natsort" version)) + (sha256 + (base32 + "1mc9hbh6fv76xyz13frm7dgi05cf74f9j5wvcyjiy5234gylz565")))) (native-inputs `(("python2-pathlib" ,python2-pathlib) ,@(package-native-inputs base)))))) From a4abed71ae629166a91e5e4e2c6a4d4498c55933 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:34:43 +0100 Subject: [PATCH 041/235] gnu: python-parso: Update to 0.6.2. * gnu/packages/python-xyz.scm (python-parso): Update to 0.6.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index da7bbdcf77..d2bf1c57e7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15490,14 +15490,14 @@ time-based (TOTP) passwords.") (define-public python-parso (package (name "python-parso") - (version "0.5.2") + (version "0.6.2") (source (origin (method url-fetch) (uri (pypi-uri "parso" version)) (sha256 (base32 - "1qgvrkpma7vylrk047mxxvqd66nwqk978n3ig2w8iz9m3bgjbksm")))) + "0mr1j4ijqnrihz1yap34g6i8vjldg5lz814sz4v0d8pbqvh5jmhc")))) (native-inputs `(("python-pytest" ,python-pytest))) (build-system python-build-system) From 7d5f0795c194c515056907c48f31b2f22e62b1ad Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:35:13 +0100 Subject: [PATCH 042/235] gnu: python-sqlalchemy: Update to 1.3.15. * gnu/packages/databases.scm (python-sqlalchemy): Update to 1.3.15. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 9681be8b4b..d26f1ef139 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2530,13 +2530,13 @@ Database API 2.0T.") (define-public python-sqlalchemy (package (name "python-sqlalchemy") - (version "1.3.3") + (version "1.3.15") (source (origin (method url-fetch) (uri (pypi-uri "SQLAlchemy" version)) (sha256 - (base32 "06c3lcv7nijsgqsjaaa4djrwlzgh9f910zlqxkmgq22h6jl4rici")))) + (base32 "0iglkvymfp35zm5pxy5kzqvcv96kkas0chqdx7xpla86sspa9k64")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython) ; for C extensions From ab6e4ab8c3412e28cf75f758da757da843ace902 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 13:35:46 +0100 Subject: [PATCH 043/235] gnu: python-psycopg2: Update to 2.8.4. * gnu/packages/databases.scm (python-psycopg2): Update to 2.8.4. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index d26f1ef139..a4854580e8 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2768,13 +2768,13 @@ designed to be easy and intuitive to use.") (define-public python-psycopg2 (package (name "python-psycopg2") - (version "2.7.7") + (version "2.8.4") (source (origin (method url-fetch) (uri (pypi-uri "psycopg2" version)) (sha256 - (base32 "0zjbabb4qjx9dm07imhf8y5a9rpa06d5zah80myiimgdi83nslpl")))) + (base32 "1djvh98pi4hjd8rxbq8qzc63bg8v78k33yg6pl99wak61b6fb67q")))) (build-system python-build-system) (arguments ;; Tests would require a postgresql database "psycopg2_test" From 745041b59ff90195c5d5aad98310f5ad1a34a693 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 14:23:51 +0100 Subject: [PATCH 044/235] gnu: python-jedi: Update to 0.16. * gnu/packages/patches/python-jedi-deleted-variables.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python-xyz.scm (python-jedi): Update to 0.16. [source](patches): New field. --- gnu/local.mk | 1 + .../python-jedi-deleted-variables.patch | 38 +++++++++++++++++++ gnu/packages/python-xyz.scm | 12 ++---- 3 files changed, 42 insertions(+), 9 deletions(-) create mode 100644 gnu/packages/patches/python-jedi-deleted-variables.patch diff --git a/gnu/local.mk b/gnu/local.mk index 73fc219383..29ca54a0ca 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1330,6 +1330,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-pep8-stdlib-tokenize-compat.patch \ %D%/packages/patches/python-pyfakefs-remove-bad-test.patch \ %D%/packages/patches/python-flint-includes.patch \ + %D%/packages/patches/python-jedi-deleted-variables.patch \ %D%/packages/patches/python-libxml2-utf8.patch \ %D%/packages/patches/python-mox3-python3.6-compat.patch \ %D%/packages/patches/python-testtools.patch \ diff --git a/gnu/packages/patches/python-jedi-deleted-variables.patch b/gnu/packages/patches/python-jedi-deleted-variables.patch new file mode 100644 index 0000000000..53bdc05cde --- /dev/null +++ b/gnu/packages/patches/python-jedi-deleted-variables.patch @@ -0,0 +1,38 @@ +Fix test failure in some environments, including Guix. + +Taken from upstream: +https://github.com/davidhalter/jedi/commit/bec87f7ff82b0731713c6520a14c213341b4cecf + +diff --git a/test/completion/basic.py b/test/completion/basic.py +index b40068179..3ff919ca6 100644 +--- a/test/completion/basic.py ++++ b/test/completion/basic.py +@@ -209,11 +209,11 @@ def global_as_import(): + + deleted_var = 3 + del deleted_var +-#? int() ++#? + deleted_var +-#? ['deleted_var'] ++#? [] + deleted_var +-#! ['deleted_var = 3'] ++#! [] + deleted_var + + # ----------------- +diff --git a/test/test_api/test_full_name.py b/test/test_api/test_full_name.py +index 4fdb861b0..6858b6ca8 100644 +--- a/test/test_api/test_full_name.py ++++ b/test/test_api/test_full_name.py +@@ -112,7 +112,8 @@ def test_os_path(Script): + + def test_os_issues(Script): + """Issue #873""" +- assert [c.name for c in Script('import os\nos.nt''').complete()] == ['nt'] ++ # nt is not found, because it's deleted ++ assert [c.name for c in Script('import os\nos.nt''').complete()] == [] + + + def test_param_name(Script): diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d2bf1c57e7..902a197fbb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11217,25 +11217,19 @@ characters, mouse support, and auto suggestions.") (define-public python-jedi (package (name "python-jedi") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (pypi-uri "jedi" version)) + (patches (search-patches "python-jedi-deleted-variables.patch")) (sha256 (base32 - "0bp4pxhsynaarbvzblsn5x32lzp29svy3sxfy8i6m5iwz9s9r1ds")))) + "1mb5kmrk9bkc3kwzx02j62cdan1jqd92q1z7h7wi9d30jg5p3j6m")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'disable-file-completion-test - ;; A single parameterized test currently fail (see: - ;; https://github.com/davidhalter/jedi/issues/1395). Remove it. - (lambda _ - (substitute* "test/test_api/test_completion.py" - ((".*'example.py', 'rb\"' \\+ join\\('\\.\\.'.*") "")) - #t)) (replace 'check (lambda _ (setenv "HOME" "/tmp") From baea210c04fd9e36340379b580331c9aeea6378b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 14:54:01 +0100 Subject: [PATCH 045/235] gnu: python-editor: Update to 1.0.4. * gnu/packages/python-xyz.scm (python-editor): Update to 1.0.4. [arguments]: New field. [home-page, synopsis]: Adjust indentation. --- gnu/packages/python-xyz.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 902a197fbb..1d99832772 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9631,19 +9631,19 @@ ISO 8859, etc.).") (define-public python-editor (package (name "python-editor") - (version "0.5") + (version "1.0.4") (source (origin (method url-fetch) (uri (pypi-uri "python-editor" version)) (sha256 (base32 - "1ypnpgvzpkbwsg4rdvy4sy51j28b5xq9v8pnkwxncn07vqz06p7n")))) + "0yrjh8w72ivqxi4i7xsg5b1vz15x8fg51xra7c3bgfyxqnyadzai")))) (build-system python-build-system) - (home-page - "https://github.com/fmoo/python-editor") - (synopsis - "Programmatically open an editor, capture the result") + (arguments + '(#:tests? #f)) ;XXX: needs a TTY and an editor + (home-page "https://github.com/fmoo/python-editor") + (synopsis "Programmatically open an editor, capture the result") (description "python-editor is a library that provides the editor module for programmatically interfacing with your system's $EDITOR.") From 45ebd90c186558556f2fe28ff2eb0cd424768b55 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 15:03:33 +0100 Subject: [PATCH 046/235] gnu: python-alembic: Update to 1.4.1. * gnu/packages/patches/python-alembic-exceptions-cause.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/databases.scm (python-alembic): Update to 1.4.1. [source](patches): New field. [arguments]: New field, override check phase. --- gnu/local.mk | 1 + gnu/packages/databases.scm | 10 ++- .../python-alembic-exceptions-cause.patch | 69 +++++++++++++++++++ 3 files changed, 78 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/python-alembic-exceptions-cause.patch diff --git a/gnu/local.mk b/gnu/local.mk index 29ca54a0ca..3be54b2627 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1320,6 +1320,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-3.8-search-paths.patch \ %D%/packages/patches/python-3.8-fix-tests.patch \ %D%/packages/patches/python-CVE-2018-14647.patch \ + %D%/packages/patches/python-alembic-exceptions-cause.patch \ %D%/packages/patches/python-axolotl-AES-fix.patch \ %D%/packages/patches/python-cairocffi-dlopen-path.patch \ %D%/packages/patches/python-cffi-x87-stack-clean.patch \ diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a4854580e8..be4db42332 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2613,15 +2613,21 @@ You might also want to install the following optional dependencies: (define-public python-alembic (package (name "python-alembic") - (version "1.0.11") + (version "1.4.1") (source (origin (method url-fetch) (uri (pypi-uri "alembic" version)) + (patches (search-patches "python-alembic-exceptions-cause.patch")) (sha256 (base32 - "1k5hag0vahd5vrf9abx8fdj2whrwaw2iq2yp736mmxnbsn5xkdyd")))) + "0a4hzn76csgbf1px4f5vfm256byvjrqkgi9869nkcjrwjn35c6kr")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "pytest" "-vv")))))) (native-inputs `(("python-mock" ,python-mock) ("python-pytest-cov" ,python-pytest-cov))) diff --git a/gnu/packages/patches/python-alembic-exceptions-cause.patch b/gnu/packages/patches/python-alembic-exceptions-cause.patch new file mode 100644 index 0000000000..b9844e5ad0 --- /dev/null +++ b/gnu/packages/patches/python-alembic-exceptions-cause.patch @@ -0,0 +1,69 @@ +Fix a test failure with newer versions of SQLalchemy due to missing +"causes" for some exceptions. + +diff --git a/alembic/operations/ops.py b/alembic/operations/ops.py +index 5ec2762..7129472 100644 +--- a/alembic/operations/ops.py ++++ b/alembic/operations/ops.py +@@ -108,6 +108,7 @@ def from_constraint(cls, constraint): + "primary_key_constraint": "primary", + "check_constraint": "check", + "column_check_constraint": "check", ++ "table_or_column_check_constraint": "check", + } + + constraint_table = sqla_compat._table_for_constraint(constraint) +@@ -707,6 +708,7 @@ def batch_create_foreign_key( + "create_check_constraint", "batch_create_check_constraint" + ) + @AddConstraintOp.register_add_constraint("check_constraint") ++@AddConstraintOp.register_add_constraint("table_or_column_check_constraint") + @AddConstraintOp.register_add_constraint("column_check_constraint") + class CreateCheckConstraintOp(AddConstraintOp): + """Represent a create check constraint operation.""" +diff --git a/alembic/testing/assertions.py b/alembic/testing/assertions.py +index 3dc08f0..a78e5e8 100644 +--- a/alembic/testing/assertions.py ++++ b/alembic/testing/assertions.py +@@ -2,10 +2,9 @@ + + import re + ++from sqlalchemy import util + from sqlalchemy.engine import default + from sqlalchemy.testing.assertions import _expect_warnings +-from sqlalchemy.testing.assertions import assert_raises # noqa +-from sqlalchemy.testing.assertions import assert_raises_message # noqa + from sqlalchemy.testing.assertions import eq_ # noqa + from sqlalchemy.testing.assertions import is_ # noqa + from sqlalchemy.testing.assertions import is_false # noqa +@@ -17,6 +16,29 @@ + from ..util.compat import py3k + + ++def assert_raises(except_cls, callable_, *args, **kw): ++ try: ++ callable_(*args, **kw) ++ success = False ++ except except_cls: ++ success = True ++ ++ # assert outside the block so it works for AssertionError too ! ++ assert success, "Callable did not raise an exception" ++ ++ ++def assert_raises_message(except_cls, msg, callable_, *args, **kwargs): ++ try: ++ callable_(*args, **kwargs) ++ assert False, "Callable did not raise an exception" ++ except except_cls as e: ++ assert re.search(msg, util.text_type(e), re.UNICODE), "%r !~ %s" % ( ++ msg, ++ e, ++ ) ++ print(util.text_type(e).encode("utf-8")) ++ ++ + def eq_ignore_whitespace(a, b, msg=None): + # sqlalchemy.testing.assertion has this function + # but not with the special "!U" detection part From 4fc26c659297b3ae3b4b00a979b2db1682d1d131 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 15:47:17 +0100 Subject: [PATCH 047/235] gnu: python-tblib: Update to 1.6.0. * gnu/packages/python-xyz.scm (python-tblib): Update to 1.6.0. --- gnu/packages/python-xyz.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1d99832772..c3cf14476c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10254,24 +10254,17 @@ own code, responding to click events and updating clock every second.") (define-public python-tblib (package (name "python-tblib") - (version "1.3.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (pypi-uri "tblib" version)) - (sha256 (base32 - "1rsg8h069kqgncyv8fgzyj6qflk6j10cb78pa5jk34ixwq044vj3")))) + (sha256 + (base32 + "0i136n5pydmd202254wzrdbspkw0br0c9mbxhfs9hpfbahvyx6r2")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'adjust-tests - (lambda _ - (when (which "python3") - ;; Adjust the example output to match that of Python 3.7: - ;; . - (substitute* "README.rst" - (("Exception\\('fail',") "Exception('fail'")) - #t))) (replace 'check (lambda _ ;; Upstream runs tests after installation and the package itself From f5eb13b21126375ef3aab00c514aab204309d147 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 15 Mar 2020 15:49:05 +0100 Subject: [PATCH 048/235] gnu: mesa-opencl: Build with clang@9. This is a follow-up to commit cf4fdbcb0bf8ef4639dc162e09d152666fc6b89e. * gnu/packages/gl.scm (mesa-opencl)[native-inputs]: Change from CLANG-8 to CLANG-9. (mesa)[inputs]: Add reminder. --- gnu/packages/gl.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index ea9b2c579e..c82d33037e 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -268,6 +268,7 @@ also known as DXTn or DXTC) for Mesa.") ("libxvmc" ,libxvmc) ,@(match (%current-system) ((or "x86_64-linux" "i686-linux") + ;; Note: update the 'clang' input of mesa-opencl when bumping this. `(("llvm" ,llvm-9))) (_ `())) @@ -435,7 +436,7 @@ from software emulation to complete hardware acceleration for modern GPUs.") `(("libclc" ,libclc) ,@(package-inputs mesa))) (native-inputs - `(("clang" ,clang-8) + `(("clang" ,clang-9) ,@(package-native-inputs mesa))))) (define-public mesa-opencl-icd From 244a527d445c48bc7a1d7f78abc9ebdccb0d7bed Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:37 +0100 Subject: [PATCH 049/235] gnu: Add python-pymediainfo * gnu/packages/python-xyz.scm (python-pymediainfo): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c3cf14476c..419b2a26fc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -69,6 +69,7 @@ ;;; Copyright © 2019 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil +;;; Copyright © 2020 Sebastian Schott ;;; ;;; This file is part of GNU Guix. ;;; @@ -169,6 +170,51 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-pymediainfo + (package + (name "python-pymediainfo") + (version "4.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pymediainfo" version)) + (sha256 + (base32 + "0mhpxs7vlqx8w75z93dy7nnvx89kwfdjkla03l19an15rlyqyspd")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm) + ("python-pytest" ,python-pytest))) + (inputs + `(("libmediainfo" ,libmediainfo))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-libmediainfo + (lambda _ + (substitute* "pymediainfo/__init__.py" + (("libmediainfo.so.0") + (string-append (assoc-ref %build-inputs "libmediainfo") + "/lib/libmediainfo.so.0"))) + #t)) + (replace 'check + (lambda _ + ;; Extend PYTHONPATH so the built package will be found. + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + ;; Skip the only failing test "test_parse_url" + (invoke "pytest" "-vv" "-k" "not test_parse_url") + #t))))) + (home-page + "https://github.com/sbraz/pymediainfo") + (synopsis + "Python wrapper for the mediainfo library") + (description + "Python wrapper for the mediainfo library to access the technical and tag +data for video and audio files.") + (license license:expat))) + (define-public python-psutil (package (name "python-psutil") From 1b9c1fdb426dc0474482c2970faf219c85d5475a Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:38 +0100 Subject: [PATCH 050/235] gnu: Add python-easygui * gnu/packages/python-xyz.scm (python-easygui): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 419b2a26fc..0a590ab2cf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -170,6 +170,27 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-easygui + (package + (name "python-easygui") + (version "0.98.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "easygui" version)) + (sha256 + (base32 + "1zmvmwgxyzvm83818skhn8b4wrci4kmnixaax8q3ia5cn7xrmj6v")))) + (build-system python-build-system) + (propagated-inputs + `(("python-tkinter" ,python "tk"))) + (home-page "https://github.com/robertlugg/easygui") + (synopsis "GUI programming module for Python") + (description "EasyGUI is a module for very simple, very easy GUI +programming in Python. EasyGUI is different from other GUI generators in that +EasyGUI is NOT event-driven. Instead, all GUI interactions are invoked by +simple function calls.") + (license license:bsd-3))) + (define-public python-pymediainfo (package (name "python-pymediainfo") From a5e76112b61be33bf3e3ba697148e2465983eeb0 Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:39 +0100 Subject: [PATCH 051/235] gnu: Add python-rawkit * gnu/packages/python-xyz.scm (python-rawkit): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0a590ab2cf..a4774be53c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -129,6 +129,7 @@ #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) + #:use-module (gnu packages photo) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-check) @@ -170,6 +171,30 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-rawkit + (package + (name "python-rawkit") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "rawkit" version)) + (sha256 + (base32 + "0vrhrpr70i61y5q5ysk341x1539ff1q1k82g59zq69lv16s0f76s")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-mock" ,python-mock))) + (inputs + `(("libraw" ,libraw))) + (home-page "https://rawkit.readthedocs.io") + (synopsis "Ctypes-based LibRaw binding for Python") + (description "The rawkit package provides two modules: rawkit and libraw. +The rawkit module provides a high-level Pythonic interface for developing raw +photos, while the libraw module provides a CTypes based interface for +interacting with the low-level LibRaw C APIs.") + (license license:expat))) + (define-public python-easygui (package (name "python-easygui") From 5164a92eaa290ba801c079796c05220027f4842b Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:40 +0100 Subject: [PATCH 052/235] gnu: Add python-d2to1 * gnu/packages/python-xyz.scm (python-d2to1): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a4774be53c..b11eb18542 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,27 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-d2to1 + (package + (name "python-d2to1") + (version "0.2.12.post1") + (source (origin + (method url-fetch) + (uri (pypi-uri "d2to1" version)) + (sha256 + (base32 + "09fq7pq1z8d006xh5z75rm2lk61v6yn2xhy53z4gsgibhqb2vvs9")))) + (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) + (home-page "https://github.com/embray/d2to1") + (synopsis "Allows for distutils2-like setup.cfg files as package metadata +in python") + (description "The python package d2to1 (the d is for distutils) allows +using distutils2-like setup.cfg files for a package's metadata with a +distribute/setuptools setup.py script.") + (license license:bsd-2))) + (define-public python-rawkit (package (name "python-rawkit") From 2763f0de41c62623622d2eb9d4c17c04d62afcbd Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:41 +0100 Subject: [PATCH 053/235] gnu: Add python-colour * gnu/packages/python-xyz.scm (python-colour): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b11eb18542..4de78fdf27 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,25 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-colour + (package + (name "python-colour") + (version "0.1.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "colour" version)) + (sha256 + (base32 + "1visbisfini5j14bdzgs95yssw6sm4pfzyq1n3lfvbyjxw7i485g")))) + (build-system python-build-system) + (native-inputs + `(("python-d2to1" ,python-d2to1))) + (home-page "https://github.com/vaab/colour") + (synopsis "Convert and manipulate various color representations") + (description "Pythonic way to manipulate color representations (HSL, RVB, +web, X11, ...).") + (license license:expat))) + (define-public python-d2to1 (package (name "python-d2to1") From f3465dee986ffab4bba27839b2d1d5d4a050d835 Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:42 +0100 Subject: [PATCH 054/235] gnu: Add python-gphoto2 * gnu/packages/python-xyz.scm (python-gphoto2): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4de78fdf27..3ff7bc45a5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,28 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-gphoto2 + (package + (name "python-gphoto2") + (version "2.2.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "gphoto2" version)) + (sha256 + (base32 + "118zm25c8mlajfl0pzssnwz4b8lamj9dgymla9rn4nla7l244a0r")))) + (build-system python-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libgphoto2" ,libgphoto2))) + (home-page "https://github.com/jim-easterbrook/python-gphoto2") + (synopsis "Python interface to libgphoto2") + (description "@code{python-gphoto2} is a comprehensive Python interface +(or binding) to @code{libgphoto2}. It is built using @code{SWIG} to +automatically generate the interface code.") + (license license:gpl3+))) + (define-public python-colour (package (name "python-colour") From 23fde56b330c0d27f6cff161ab16d857d8975303 Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:43 +0100 Subject: [PATCH 055/235] gnu: Add python-pyprind * gnu/packages/python-xyz.scm (python-pyprind): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 3ff7bc45a5..26e1927cb9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,26 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-pyprind + (package + (name "python-pyprind") + (version "2.11.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "PyPrind" version)) + (sha256 + (base32 + "0xg6m5hr33h9bdlrr42kc58jm2m87a9zsagy7n2m4n407d2snv64")))) + (build-system python-build-system) + (propagated-inputs + `(("python-psutil" ,python-psutil))) + (home-page "https://github.com/rasbt/pyprind") + (synopsis "Python Progress Bar and Percent Indicator Utility") + (description "The PyPrind (Python Progress Indicator) module provides a +progress bar and a percentage indicator object that let you track the progress +of a loop structure or other iterative computation.") + (license license:bsd-3))) + (define-public python-gphoto2 (package (name "python-gphoto2") From dcf953299505274e542ea8c79141b21f1f18277d Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:44 +0100 Subject: [PATCH 056/235] gnu: Add python-colorlog * gnu/packages/python-xyz.scm (python-colorlog): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 26e1927cb9..2dd3d04706 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,35 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-colorlog + (package + (name "python-colorlog") + (version "4.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "colorlog" version)) + (sha256 + (base32 + "1lpk8zmfv8vz090h5d0hzb4n39wgasxdd3x3bpn3v1x1n9dfzaih")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Extend PYTHONPATH so the built package will be found. + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (invoke "pytest" "-p" "no:logging") + #t))))) + (home-page "https://github.com/borntyping/python-colorlog") + (synopsis "Log formatting with colors for python") + (description "The @code{colorlog.ColoredFormatter} is a formatter for use +with Python's logging module that outputs records using terminal colors.") + (license license:expat))) + (define-public python-pyprind (package (name "python-pyprind") From 2f12e6608b8dd071e37264c63ea86dcdfb8aaa84 Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:45 +0100 Subject: [PATCH 057/235] gnu: Add python-tenacity * gnu/packages/python-xyz.scm (python-tenacity): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2dd3d04706..2718e9b236 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -171,6 +171,36 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) +(define-public python-tenacity + (package + (name "python-tenacity") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "tenacity" version)) + (sha256 + (base32 + "1j36v9fcpmmd4985ix0cwnvcq71rkrn5cjiiv0id9vkl4kpxh0gv")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm) + ("python-sphinx" ,python-sphinx) + ("python-tornado" ,python-tornado) + ("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-six" ,python-six))) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "pytest") + #t))))) + (home-page "https://github.com/jd/tenacity") + (synopsis "Retrying library for python") + (description "Tenacity is a general-purpose python library to simplify the +task of adding retry behavior to just about anything.") + (license license:asl2.0))) + (define-public python-colorlog (package (name "python-colorlog") From 39af91db7943700b723c96ce1fc100f110aa88d1 Mon Sep 17 00:00:00 2001 From: Sebastian Schott Date: Sat, 7 Mar 2020 16:11:46 +0100 Subject: [PATCH 058/235] gnu: Add rapid-photo-downloader * gnu/packages/photo.scm (rapid-photo-downloader): New variable. Signed-off-by: Christopher Baines --- gnu/packages/photo.scm | 94 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 069767e414..585289daf1 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018 Leo Famulari +;;; Copyright © 2020 Sebastian Schott ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +27,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system perl) + #:use-module (guix build-system python) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -37,12 +39,15 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages file) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages glib) #:use-module (gnu packages graphics) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) @@ -56,9 +61,13 @@ #:use-module (gnu packages popt) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages python-web) + #:use-module (gnu packages qt) #:use-module (gnu packages readline) #:use-module (gnu packages sqlite) #:use-module (gnu packages tex) + #:use-module (gnu packages time) + #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xfig) @@ -67,6 +76,91 @@ #:use-module ((srfi srfi-1) #:hide (zip)) #:use-module (srfi srfi-26)) +(define-public rapid-photo-downloader + (package + (name "rapid-photo-downloader") + (version "0.9.18") + (source (origin + (method url-fetch) + (uri (string-append "https://launchpad.net/rapid/pyqt/" + version "/+download/" name "-" + version ".tar.gz")) + (sha256 + (base32 + "15p7sssg6vmqbm5xnc4j5dr89d7gl7y5qyq44a240yl5aqkjnybw")))) + (build-system python-build-system) + (native-inputs + `(("file" ,file) + ("intltool" ,intltool) + ("gobject-introspection" ,gobject-introspection))) + (inputs + `(("gdk-pixbuf" ,gdk-pixbuf) + ("gexiv2" ,gexiv2) + ("gst-libav" ,gst-libav) + ("gst-plugins-base" ,gst-plugins-base) + ("gst-plugins-good" ,gst-plugins-good) + ("gstreamer" ,gstreamer) + ("libgudev" ,libgudev) + ("libnotify" ,libnotify) + ("libmediainfo" ,libmediainfo) + ("usdisks" ,udisks) + ("python-pyqt" ,python-pyqt) + ("python-pygobject" ,python-pygobject) + ("python-gphoto2" ,python-gphoto2) + ("python-pyzmq" ,python-pyzmq) + ("python-tornado" ,python-tornado) + ("python-psutil" ,python-psutil) + ("python-pyxdg" ,python-pyxdg) + ("python-arrow" ,python-arrow) + ("python-dateutil" ,python-dateutil) + ("python-easygui" ,python-easygui) + ("python-colour" ,python-colour) + ("python-pymediainfo" ,python-pymediainfo) + ("python-sortedcontainers" ,python-sortedcontainers) + ("python-rawkit" ,python-rawkit) + ("python-requests" ,python-requests) + ("python-colorlog" ,python-colorlog) + ("python-pyprind" ,python-pyprind) + ("python-tenacity" ,python-tenacity) + ("perl-image-exiftool" ,perl-image-exiftool))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-libmediainfo + (lambda _ + (substitute* "raphodo/metadatavideo.py" + (("pymedia_library_file = 'libmediainfo.so.0'") + (string-append "pymedia_library_file = '" + (assoc-ref %build-inputs "libmediainfo") + "/lib/libmediainfo.so.0'"))) + #t)) + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (path (string-join + (list (string-append + (assoc-ref inputs "perl-image-exiftool") + "/bin")) + ":")) + (gi-typelib-path (getenv "GI_TYPELIB_PATH")) + (python-path (getenv "PYTHONPATH"))) + (for-each + (lambda (program) + (wrap-program program + `("PATH" ":" prefix (,path)) + `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)) + `("PYTHONPATH" ":" prefix (,python-path)))) + (map (lambda (name) + (string-append out "/bin/" name)) + '("analyze-pv-structure" + "rapid-photo-downloader")))) + #t))))) + (home-page "https://www.damonlynch.net/rapid/") + (synopsis "Import photos and videos from cameras, phones and memory cards") + (description "Import photos and videos from cameras, phones and memory +cards and generate meaningful file and folder names.") + (license license:gpl2+))) + (define-public libraw (package (name "libraw") From ed78340438b7ac58187b78216c48abe002873795 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 Mar 2020 17:59:35 +0100 Subject: [PATCH 059/235] gnu: eolie: Update to 0.9.98.1. * gnu/packages/gnome.scm (eolie): Update to 0.9.98.1. --- gnu/packages/gnome.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index a08cd00d72..a80bce9332 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Mathieu Lirzin ;;; Copyright © 2015, 2017 Andy Wingo ;;; Copyright © 2015 David Hashe -;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner @@ -5424,15 +5424,14 @@ almost all of them.") (define-public eolie (package (name "eolie") - (version "0.9.63") + (version "0.9.98.1") (source (origin (method url-fetch) - (uri (string-append "https://gitlab.gnome.org/World/eolie/" - "uploads/d42b466752729a0d3fa828a721e25043/" - "eolie-" version ".tar.xz")) + (uri (string-append "https://adishatz.org/eolie/eolie-" + version ".tar.xz")) (sha256 (base32 - "11pp8g0w22h1q0bbj9517l5838gcymvvp8fp9kh6h2dmgir2ssih")))) + "1d844zva5w4p9pnp9c2g7zyb4vayr2g2drf78spxsdlc5lbd7lqr")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t From cd773f118573aad42c1e10dd77061fd3d1279189 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sun, 15 Mar 2020 17:47:56 +0100 Subject: [PATCH 060/235] gnu: nose2: Update to 0.9.2. * gnu/packages/check.scm (python-nose2): Update to 0.9.2. Signed-off-by: Leo Famulari --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 15ab54dd8a..fa14ac1544 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -706,14 +706,14 @@ have been used.") (define-public python-nose2 (package (name "python-nose2") - (version "0.6.5") + (version "0.9.2") (source (origin (method url-fetch) (uri (pypi-uri "nose2" version)) (sha256 (base32 - "1x4zjq1zlyrh8b9ba0cmafd3w94pxhid408kibyjd3s6h1lap6s7")))) + "0pmbb6nk31yhgh4zkcblzxsznml7f7pf5q1ihgrwvbxv4mwzfql7")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; 'module' object has no attribute 'collector' (propagated-inputs From 323841bda4e5b8f9b30626ab768aaf711ee6aabf Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Thu, 12 Mar 2020 01:51:12 +0100 Subject: [PATCH 061/235] gnu: Add nvme-cli * gnu/packages/linux.scm (nvme-cli): New variable. Signed-off-by: Leo Famulari --- gnu/packages/linux.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 688d9eefaf..f1bc5798ab 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3577,6 +3577,36 @@ IDE driver subsystem. Many external USB drive enclosures with SCSI-ATA Command Translation (@dfn{SAT}) are also supported.") (license (license:non-copyleft "file://LICENSE.TXT")))) +(define-public nvme-cli + (package + (name "nvme-cli") + (version "1.10.1") + (home-page "https://github.com/linux-nvme/nvme-cli") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (sha256 + (base32 "12wp2wxmsw2v8m9bhvwvdbhdgx1md8iilhbl19sfzz2araiwi2x8")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list "CC=gcc") + #:phases (modify-phases %standard-phases + (delete 'configure) ; No ./configure script + (replace 'install + (lambda _ + (invoke "make" "install-spec" "PREFIX=" + (string-append "DESTDIR=" %output))))) + #:tests? #f)) ; The tests require sysfs, which is not accessible from + ; the build environment + (synopsis "NVM-Express user space tooling for Linux") + (description "Nvme-cli is a utility to provide standards compliant tooling +for NVM-Express drives. It was made specifically for Linux as it relies on the +IOCTLs defined by the mainline kernel driver.") + (license license:gpl2+))) + (define-public rfkill (package (name "rfkill") From f24aaa81de8c709adfda2e89271c562a5ca8d959 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sun, 15 Mar 2020 19:07:57 +0100 Subject: [PATCH 062/235] gnu: BlueZ: Update to 5.54. * gnu/packages/linux.scm (bluez): Update to 5.54. [replacement]: Remove field. (bluez/fixed): Remove variable. * gnu/packages/patches/bluez-CVE-2020-0556.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: Leo Famulari --- gnu/local.mk | 1 - gnu/packages/linux.scm | 13 +- .../patches/bluez-CVE-2020-0556.patch | 180 ------------------ 3 files changed, 2 insertions(+), 192 deletions(-) delete mode 100644 gnu/packages/patches/bluez-CVE-2020-0556.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3be54b2627..b628bbee0c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -764,7 +764,6 @@ dist_patch_DATA = \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blender-2.79-newer-ffmpeg.patch \ %D%/packages/patches/blender-2.79-python-3.7-fix.patch \ - %D%/packages/patches/bluez-CVE-2020-0556.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/calibre-no-updates-dialog.patch \ %D%/packages/patches/calibre-remove-test-bs4.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f1bc5798ab..fda7570d89 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4039,8 +4039,7 @@ Bluetooth audio output devices like headphones or loudspeakers.") (define-public bluez (package (name "bluez") - (replacement bluez/fixed) - (version "5.53") + (version "5.54") (source (origin (method url-fetch) (uri (string-append @@ -4048,7 +4047,7 @@ Bluetooth audio output devices like headphones or loudspeakers.") version ".tar.xz")) (sha256 (base32 - "1g1qg6dz6hl3csrmz75ixr12lwv836hq3ckb259svvrg62l2vaiq")))) + "1p2ncvjz6alr9n3l5wvq2arqgc7xjs6dqyar1l9jp0z8cfgapkb8")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -4105,14 +4104,6 @@ Bluetooth audio output devices like headphones or loudspeakers.") is flexible, efficient and uses a modular implementation.") (license license:gpl2+))) -(define bluez/fixed - (package - (inherit bluez) - (source (origin - (inherit (package-source bluez)) - (patches (append (origin-patches (package-source bluez)) - (search-patches "bluez-CVE-2020-0556.patch"))))))) - (define-public fuse-exfat (package (name "fuse-exfat") diff --git a/gnu/packages/patches/bluez-CVE-2020-0556.patch b/gnu/packages/patches/bluez-CVE-2020-0556.patch deleted file mode 100644 index 7c34459a3a..0000000000 --- a/gnu/packages/patches/bluez-CVE-2020-0556.patch +++ /dev/null @@ -1,180 +0,0 @@ -Fix CVE-2020-0556: - -https://lore.kernel.org/linux-bluetooth/20200310023516.209146-1-alainm@chromium.org/ -https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html -http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2020-0556 - -Patches copied from upstream source repository: - -https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=3cccdbab2324086588df4ccf5f892fb3ce1f1787 -https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=8cdbd3b09f29da29374e2f83369df24228da0ad1 - -From 3cccdbab2324086588df4ccf5f892fb3ce1f1787 Mon Sep 17 00:00:00 2001 -From: Alain Michaud -Date: Tue, 10 Mar 2020 02:35:18 +0000 -Subject: [PATCH] HID accepts bonded device connections only. - -This change adds a configuration for platforms to choose a more secure -posture for the HID profile. While some older mice are known to not -support pairing or encryption, some platform may choose a more secure -posture by requiring the device to be bonded and require the -connection to be encrypted when bonding is required. - -Reference: -https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html ---- - profiles/input/device.c | 23 ++++++++++++++++++++++- - profiles/input/device.h | 1 + - profiles/input/input.conf | 8 ++++++++ - profiles/input/manager.c | 13 ++++++++++++- - 4 files changed, 43 insertions(+), 2 deletions(-) - -diff --git a/profiles/input/device.c b/profiles/input/device.c -index 2cb3811c8..d89da2d7c 100644 ---- a/profiles/input/device.c -+++ b/profiles/input/device.c -@@ -92,6 +92,7 @@ struct input_device { - - static int idle_timeout = 0; - static bool uhid_enabled = false; -+static bool classic_bonded_only = false; - - void input_set_idle_timeout(int timeout) - { -@@ -103,6 +104,11 @@ void input_enable_userspace_hid(bool state) - uhid_enabled = state; - } - -+void input_set_classic_bonded_only(bool state) -+{ -+ classic_bonded_only = state; -+} -+ - static void input_device_enter_reconnect_mode(struct input_device *idev); - static int connection_disconnect(struct input_device *idev, uint32_t flags); - -@@ -970,8 +976,18 @@ static int hidp_add_connection(struct input_device *idev) - if (device_name_known(idev->device)) - device_get_name(idev->device, req->name, sizeof(req->name)); - -+ /* Make sure the device is bonded if required */ -+ if (classic_bonded_only && !device_is_bonded(idev->device, -+ btd_device_get_bdaddr_type(idev->device))) { -+ error("Rejected connection from !bonded device %s", dst_addr); -+ goto cleanup; -+ } -+ - /* Encryption is mandatory for keyboards */ -- if (req->subclass & 0x40) { -+ /* Some platforms may choose to require encryption for all devices */ -+ /* Note that this only matters for pre 2.1 devices as otherwise the */ -+ /* device is encrypted by default by the lower layers */ -+ if (classic_bonded_only || req->subclass & 0x40) { - if (!bt_io_set(idev->intr_io, &gerr, - BT_IO_OPT_SEC_LEVEL, BT_IO_SEC_MEDIUM, - BT_IO_OPT_INVALID)) { -@@ -1203,6 +1219,11 @@ static void input_device_enter_reconnect_mode(struct input_device *idev) - DBG("path=%s reconnect_mode=%s", idev->path, - reconnect_mode_to_string(idev->reconnect_mode)); - -+ /* Make sure the device is bonded if required */ -+ if (classic_bonded_only && !device_is_bonded(idev->device, -+ btd_device_get_bdaddr_type(idev->device))) -+ return; -+ - /* Only attempt an auto-reconnect when the device is required to - * accept reconnections from the host. - */ -diff --git a/profiles/input/device.h b/profiles/input/device.h -index 51a9aee18..3044db673 100644 ---- a/profiles/input/device.h -+++ b/profiles/input/device.h -@@ -29,6 +29,7 @@ struct input_conn; - - void input_set_idle_timeout(int timeout); - void input_enable_userspace_hid(bool state); -+void input_set_classic_bonded_only(bool state); - - int input_device_register(struct btd_service *service); - void input_device_unregister(struct btd_service *service); -diff --git a/profiles/input/input.conf b/profiles/input/input.conf -index 3e1d65aae..166aff4a4 100644 ---- a/profiles/input/input.conf -+++ b/profiles/input/input.conf -@@ -11,3 +11,11 @@ - # Enable HID protocol handling in userspace input profile - # Defaults to false (HIDP handled in HIDP kernel module) - #UserspaceHID=true -+ -+# Limit HID connections to bonded devices -+# The HID Profile does not specify that devices must be bonded, however some -+# platforms may want to make sure that input connections only come from bonded -+# device connections. Several older mice have been known for not supporting -+# pairing/encryption. -+# Defaults to false to maximize device compatibility. -+#ClassicBondedOnly=true -diff --git a/profiles/input/manager.c b/profiles/input/manager.c -index 1d31b0652..5cd27b839 100644 ---- a/profiles/input/manager.c -+++ b/profiles/input/manager.c -@@ -96,7 +96,7 @@ static int input_init(void) - config = load_config_file(CONFIGDIR "/input.conf"); - if (config) { - int idle_timeout; -- gboolean uhid_enabled; -+ gboolean uhid_enabled, classic_bonded_only; - - idle_timeout = g_key_file_get_integer(config, "General", - "IdleTimeout", &err); -@@ -114,6 +114,17 @@ static int input_init(void) - input_enable_userspace_hid(uhid_enabled); - } else - g_clear_error(&err); -+ -+ classic_bonded_only = g_key_file_get_boolean(config, "General", -+ "ClassicBondedOnly", &err); -+ -+ if (!err) { -+ DBG("input.conf: ClassicBondedOnly=%s", -+ classic_bonded_only ? "true" : "false"); -+ input_set_classic_bonded_only(classic_bonded_only); -+ } else -+ g_clear_error(&err); -+ - } - - btd_profile_register(&input_profile); --- -2.25.1 - -From 8cdbd3b09f29da29374e2f83369df24228da0ad1 Mon Sep 17 00:00:00 2001 -From: Alain Michaud -Date: Tue, 10 Mar 2020 02:35:16 +0000 -Subject: [PATCH] HOGP must only accept data from bonded devices. - -HOGP 1.0 Section 6.1 establishes that the HOGP must require bonding. - -Reference: -https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.htm ---- - profiles/input/hog.c | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/profiles/input/hog.c b/profiles/input/hog.c -index 83c017dcb..dfac68921 100644 ---- a/profiles/input/hog.c -+++ b/profiles/input/hog.c -@@ -186,6 +186,10 @@ static int hog_accept(struct btd_service *service) - return -EINVAL; - } - -+ /* HOGP 1.0 Section 6.1 requires bonding */ -+ if (!device_is_bonded(device, btd_device_get_bdaddr_type(device))) -+ return -ECONNREFUSED; -+ - /* TODO: Replace GAttrib with bt_gatt_client */ - bt_hog_attach(dev->hog, attrib); - --- -2.25.1 - From e2c7dbbf98bfd1b73fa3067d92f2924a135f287a Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Sun, 15 Mar 2020 18:42:44 +0100 Subject: [PATCH 063/235] gnu: emacs-debbugs: update to 0.22 * gnu/packages/emacs-xyz.scm (emacs-debbugs): Update to 0.22. Signed-off-by: Leo Famulari --- gnu/packages/emacs-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d45814379b..a821bc7776 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -62,6 +62,7 @@ ;;; Copyright © 2020 Evan Straw ;;; Copyright © 2020 Masaya Tojo ;;; Copyright © 2020 Martin Becze +;;; Copyright © 2020 Michael Rohleder ;;; ;;; This file is part of GNU Guix. ;;; @@ -3606,14 +3607,14 @@ source code using IPython.") (define-public emacs-debbugs (package (name "emacs-debbugs") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/debbugs-" version ".tar")) (sha256 (base32 - "1xx1wjfpsnwx2fpydqhwy9k1b5kjk8dqbkzf8lqaj9c4rvjbn50a")))) + "05ik9qv539b5c1nzxkk3lk23bqj4vqgmfmd8x367abhb7c9gix2z")))) (build-system emacs-build-system) (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$"))) (propagated-inputs From eea58169fb519c392ff3ba4a1ad5730e3be9ff39 Mon Sep 17 00:00:00 2001 From: Alexandru-Sergiu Marton Date: Tue, 4 Feb 2020 15:59:03 +0200 Subject: [PATCH 064/235] gnu: Add ghcid. * gnu/packages/haskell-apps.scm (ghcid): New variable. Signed-off-by: Leo Famulari --- gnu/packages/haskell-apps.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index 6005816260..f5b45d0bfb 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2015 John Soo ;;; Copyright © 2019 Efraim Flashner ;;; Copyright © 2019 Alex Griffin +;;; Copyright © 2020 Alexandru-Sergiu Marton ;;; ;;; This file is part of GNU Guix. ;;; @@ -266,6 +267,40 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}. @end enumerate") (license license:gpl2))) +(define-public ghcid + (package + (name "ghcid") + (version "0.8.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/ghcid/" + "ghcid-" version ".tar.gz")) + (sha256 + (base32 + "0wpm4ikrm1krz1ckzwk0srng091yh2skjal4fh95iz1hq3dw6qlw")))) + (build-system haskell-build-system) + (inputs + `(("ghc-extra" ,ghc-extra) + ("ghc-ansi-terminal" ,ghc-ansi-terminal) + ("ghc-cmdargs" ,ghc-cmdargs) + ("ghc-fsnotify" ,ghc-fsnotify) + ("ghc-terminal-size" ,ghc-terminal-size))) + (native-inputs + `(("ghc-tasty" ,ghc-tasty) + ("ghc-tasty-hunit" ,ghc-tasty-hunit))) + (home-page + "https://github.com/ndmitchell/ghcid#readme") + (synopsis "GHCi based bare bones IDE") + (description + "Either \"GHCi as a daemon\" or \"GHC + a bit of an IDE\". A very simple Haskell +development tool which shows you the errors in your project and updates them whenever +you save. Run @code{ghcid --topmost --command=ghci}, where @code{--topmost} makes the +window on top of all others (Windows only) and @code{--command} is the command to start +GHCi on your project (defaults to @code{ghci} if you have a @file{.ghci} file, or else +to @code{cabal repl}).") + (license license:bsd-3))) + (define-public git-annex (package (name "git-annex") From 70d9ef51392e9f8b33af4a7dea459eedd2ca738b Mon Sep 17 00:00:00 2001 From: Alexandros Theodotou Date: Tue, 25 Feb 2020 15:11:29 +0000 Subject: [PATCH 065/235] gnu: Add lv2lint. * gnu/packages/audio.scm (lv2lint): New variable. Signed-off-by: Leo Famulari --- gnu/packages/audio.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 758c87cb2c..b429aeb107 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -58,6 +58,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) + #:use-module (gnu packages elf) #:use-module (gnu packages emacs) #:use-module (gnu packages file) #:use-module (gnu packages flex) @@ -4051,3 +4052,35 @@ libsamplerate for reading and resampling audio files, based on Robin Gareus' @code{audio_decoder} code.") (home-page "https://git.zrythm.org/cgit/libaudec") (license license:agpl3+))) + +(define-public lv2lint + (package + (name "lv2lint") + (version "0.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.open-music-kontrollers.ch/lv2/lv2lint") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1pspwqpzl2dw1hd9ra9yr53arqbbqjn7d7j0f7p9g3iqa76vblpi")))) + (build-system meson-build-system) + (arguments + `(#:configure-flags + `("-Delf-tests=true" ; for checking symbol visibility + "-Donline-tests=true"))) ; for checking URI existence + (inputs + `(("curl", curl) + ("libelf", libelf) + ("lilv", lilv))) + (native-inputs + `(("pkg-config", pkg-config))) + (synopsis "LV2 plugin lint tool") + (description "lv2lint is an LV2 lint-like tool that checks whether a +given plugin and its UI(s) match up with the provided metadata and adhere +to well-known best practices.") + (home-page "https://open-music-kontrollers.ch/lv2/lv2lint/") + (license license:artistic2.0))) From fa315559a651469c4e29eb88d22c5dbd1cd29794 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:51:47 +0100 Subject: [PATCH 066/235] gnu: java-osgi-service-component-annotations: Update source URI. * gnu/packages/java.scm (java-osgi-service-component-annotations)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index ab9427aa23..e8b8cb1610 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7392,7 +7392,7 @@ in compiling bundles.") (version "1.3.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.component.annotations/" version "/org.osgi.service.component.annotations-" version "-sources.jar")) From fc1c5dbde514b34dcfcbc4e7c59b6b07d85c8f80 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:53:34 +0100 Subject: [PATCH 067/235] gnu: java-osgi-dto: Update source URI. * gnu/packages/java.scm (java-osgi-dto)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e8b8cb1610..411c9b268a 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7419,7 +7419,7 @@ the support annotations for osgi-service-component.") (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.dto/" version "/org.osgi.dto-" version "-sources.jar")) (sha256 From 1f2643faa3a3c5199532192565f00b8a151900ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:54:59 +0100 Subject: [PATCH 068/235] gnu: java-osgi-resource: Update source URI. * gnu/packages/java.scm (java-osgi-resource)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 411c9b268a..8656beb195 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7448,7 +7448,7 @@ objects of the listed types or aggregates.") (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.resource/" version "/org.osgi.resource-" version "-sources.jar")) From fccce6616b9824679ab9dedaf1a702da2700d6af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:56:17 +0100 Subject: [PATCH 069/235] gnu: java-osgi-namespace-extender: Update source URI. * gnu/packages/java.scm (java-osgi-namespace-extender)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 8656beb195..48f6754aeb 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7504,7 +7504,7 @@ the names for the attributes and directives for a namespace with contracts.") (version "1.0.1") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.namespace.extender/" version "/org.osgi.namespace.extender-" version "-sources.jar")) From ec4ba4178b198b10e606480794de0cdcba78ec6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:57:43 +0100 Subject: [PATCH 070/235] gnu: java-osgi-namespace-service: Update source URI. * gnu/packages/java.scm (java-osgi-namespace-service)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 48f6754aeb..b682061755 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7532,7 +7532,7 @@ the names for the attributes and directives for an extender namespace.") (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.namespace.service/" version "/org.osgi.namespace.service-" version "-sources.jar")) From 43be029996192dd3d8819234b803a2988e3490fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 00:59:09 +0100 Subject: [PATCH 071/235] gnu: java-osgi-util-function: Update source URI. * gnu/packages/java.scm (java-osgi-util-function)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index b682061755..4c9a27c758 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7560,7 +7560,7 @@ the names for the attributes and directives for a service namespace.") (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.util.function/" version "/org.osgi.util.function-" version "-sources.jar")) From c962e6c414ed97996431b5f3f62c5243bc89e8ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:00:50 +0100 Subject: [PATCH 072/235] gnu: java-osgi-util-promise: Update source URI. * gnu/packages/java.scm (java-osgi-util-promise)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 4c9a27c758..f01a10f1db 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7587,7 +7587,7 @@ an interface for a function that accepts a single argument and produces a result (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.util.promise/" version "/org.osgi.util.promise-" version "-sources.jar")) From 98b1985fdc1489e4329d097affc376ea27541e0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:03:10 +0100 Subject: [PATCH 073/235] gnu: java-osgi-service-metatype-annotations: Update source URI. * gnu/packages/java.scm (java-osgi-service-metatype-annotations)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index f01a10f1db..f762ea8e52 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7616,7 +7616,7 @@ value. It handles the interactions for asynchronous processing.") (version "1.3.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.metatype.annotations/" version "/org.osgi.service.metatype.annotations-" version "-sources.jar")) From 7a5c5017d3ad362feedad0d058242492f9c61c4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:05:16 +0100 Subject: [PATCH 074/235] gnu: java-osgi-service-repository: Update source URI. * gnu/packages/java.scm (java-osgi-service-repository)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index f762ea8e52..c8de7ec305 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7643,7 +7643,7 @@ the support annotations for metatype.") (version "1.1.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.repository/" version "/org.osgi.service.repository-" version "-sources.jar")) From 05662561f4f0362a1c174bb56052588fce0b8933 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:06:55 +0100 Subject: [PATCH 075/235] gnu: java-osgi-framework: Update source URI. * gnu/packages/java.scm (java-osgi-framework)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index c8de7ec305..9246f63550 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7672,7 +7672,7 @@ a repository service that contains resources.") (version "1.8.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.framework/" version "/org.osgi.framework-" version "-sources.jar")) (sha256 From 9b0bf25c578fa3fef466d82a4ba71c8a34048355 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:08:04 +0100 Subject: [PATCH 076/235] gnu: java-osgi-service-log: Update source URI. * gnu/packages/java.scm (java-osgi-service-log)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 9246f63550..91da54c04c 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7699,7 +7699,7 @@ and service platform for the Java programming language.") (version "1.3.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.log/" version "/org.osgi.service.log-" version "-sources.jar")) From 4a6a7b2d0c0cbbe160c2dbf524cac897a7c04368 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:09:22 +0100 Subject: [PATCH 077/235] gnu: java-osgi-service-jdbc: Update source URI. * gnu/packages/java.scm (java-osgi-service-jdbc)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 91da54c04c..15473a28c2 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7726,7 +7726,7 @@ the log service.") (version "1.0.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.jdbc/" version "/org.osgi.service.jdbc-" version "-sources.jar")) From b787534b7bdb304e084383f8bf4a845578c74c97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 01:10:42 +0100 Subject: [PATCH 078/235] gnu: java-osgi-service-resolver: Update source URI. * gnu/packages/java.scm (java-osgi-service-resolver)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 15473a28c2..a644ee889a 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7758,7 +7758,7 @@ factories for getting JDBC connections: (version "1.0.1") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.resolver/" version "/org.osgi.service.resolver-" version "-sources.jar")) From e0695da9168d3b522712b4ae789e9ce4ac2f465c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 19:45:56 +0100 Subject: [PATCH 079/235] gnu: java-osgi-util-tracker: Update source URI. * gnu/packages/java.scm (java-osgi-util-tracker)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index a644ee889a..2f20e17b5e 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7787,7 +7787,7 @@ by the caller.") (version "1.5.1") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.util.tracker/" version "/org.osgi.util.tracker-" version "-sources.jar")) From f8f2fefbac7ed5247d5c84dd253996d2b784e3d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 19:54:06 +0100 Subject: [PATCH 080/235] gnu: java-osgi-service-cm: Update source URI. * gnu/packages/java.scm (java-osgi-service-cm)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 2f20e17b5e..5dffd394b5 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7815,7 +7815,7 @@ bundle tracking utility classes.") (version "1.5.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.cm/" version "/org.osgi.service.cm-" version "-sources.jar")) From 839e3e89deb0da1d477ff236204526724f64b5c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 19:55:49 +0100 Subject: [PATCH 081/235] gnu: java-osgi-service-packageadmin: Update source URI. * gnu/packages/java.scm (java-osgi-service-packageadmin)[source]: Update URI. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 5dffd394b5..c7dd87cb6e 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -7843,7 +7843,7 @@ utility classes for the configuration of services.") (version "1.2.0") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/org/osgi/" + (uri (string-append "https://repo1.maven.org/maven2/org/osgi/" "org.osgi.service.packageadmin/" version "/org.osgi.service.packageadmin-" version "-sources.jar")) From 3e550fc8357f5fe3ecafcc712ddfdc02deb41a8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 20:07:05 +0100 Subject: [PATCH 082/235] gnu: java-qdox: Update source and home-page URI. * gnu/packages/java.scm (java-qdox)[source]: Update URI. [home-page]: Update URI. --- gnu/packages/java.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index c7dd87cb6e..79bf20dd1d 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -11395,7 +11395,7 @@ such as log4j or @code{java.util.logging} (JUL)."))) ;; Older releases at https://github.com/codehaus/qdox/ ;; Note: The release at maven is pre-generated. The release at ;; github requires jflex. - (uri (string-append "http://central.maven.org/maven2/" + (uri (string-append "https://repo1.maven.org/maven2/" "com/thoughtworks/qdox/qdox/" version "/qdox-" version "-sources.jar")) (sha256 @@ -11405,7 +11405,7 @@ such as log4j or @code{java.util.logging} (JUL)."))) (arguments `(#:jar-name "qdox.jar" #:tests? #f)); no tests - (home-page "http://qdox.codehaus.org/") + (home-page "https://github.com/codehaus/qdox") (synopsis "Parse definitions from Java source files") (description "QDox is a high speed, small footprint parser for extracting class/interface/method definitions from source files complete with JavaDoc From 5281ba175b4deb33971d8bfc33b8d5f17d1f61de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 20:09:29 +0100 Subject: [PATCH 083/235] gnu: java-qdox: Move version 2.0-M2 side by side with version 1.12.1. * gnu/packages/java.scm (java-qdox): Move package definition up, such that it is side by side with version 1.12.1. --- gnu/packages/java.scm | 58 +++++++++++++++++++++---------------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 79bf20dd1d..03ed0c6534 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -3334,6 +3334,35 @@ class/interface/method definitions from source files complete with JavaDoc documentation tools.") (license license:asl2.0))) +(define-public java-qdox + (package + (name "java-qdox") + ; Newer version exists, but this version is required by java-plexus-component-metadata + (version "2.0-M2") + (source (origin + (method url-fetch) + ;; 2.0-M4, -M5 at https://github.com/paul-hammant/qdox + ;; Older releases at https://github.com/codehaus/qdox/ + ;; Note: The release at maven is pre-generated. The release at + ;; github requires jflex. + (uri (string-append "https://repo1.maven.org/maven2/" + "com/thoughtworks/qdox/qdox/" version + "/qdox-" version "-sources.jar")) + (sha256 + (base32 + "10xxrcaicq6axszcr2jpygisa4ch4sinyx5q7kqqxv4lknrmxp5x")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "qdox.jar" + #:tests? #f)); no tests + (home-page "https://github.com/codehaus/qdox") + (synopsis "Parse definitions from Java source files") + (description "QDox is a high speed, small footprint parser for extracting +class/interface/method definitions from source files complete with JavaDoc +@code{@@tags}. It is designed to be used by active code generators or +documentation tools.") + (license license:asl2.0))) + (define-public java-jarjar (package (name "java-jarjar") @@ -11384,35 +11413,6 @@ Moreover, @code{logback-classic} natively implements the slf4j API so that you can readily switch back and forth between logback and other logging frameworks such as log4j or @code{java.util.logging} (JUL)."))) -(define-public java-qdox - (package - (name "java-qdox") - ; Newer version exists, but this version is required by java-plexus-component-metadata - (version "2.0-M2") - (source (origin - (method url-fetch) - ;; 2.0-M4, -M5 at https://github.com/paul-hammant/qdox - ;; Older releases at https://github.com/codehaus/qdox/ - ;; Note: The release at maven is pre-generated. The release at - ;; github requires jflex. - (uri (string-append "https://repo1.maven.org/maven2/" - "com/thoughtworks/qdox/qdox/" version - "/qdox-" version "-sources.jar")) - (sha256 - (base32 - "10xxrcaicq6axszcr2jpygisa4ch4sinyx5q7kqqxv4lknrmxp5x")))) - (build-system ant-build-system) - (arguments - `(#:jar-name "qdox.jar" - #:tests? #f)); no tests - (home-page "https://github.com/codehaus/qdox") - (synopsis "Parse definitions from Java source files") - (description "QDox is a high speed, small footprint parser for extracting -class/interface/method definitions from source files complete with JavaDoc -@code{@@tags}. It is designed to be used by active code generators or -documentation tools.") - (license license:asl2.0))) - (define-public java-jgit (package (name "java-jgit") From c3d56df50b96e884be57d95e20717e440b8bcfe4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 22:18:16 +0100 Subject: [PATCH 084/235] gnu: java-xsdlib: Use archived home page URI, update source URI. * gnu/packages/xml.scm (java-xsdlib)[home-page]: Use archived URI. [source]: Update URI. --- gnu/packages/xml.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 76fb3ea072..32696e30ee 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1683,7 +1683,7 @@ that strives for correctness and simplicity.") (version "2013.2") (source (origin (method url-fetch) - (uri (string-append "http://central.maven.org/maven2/com/sun/msv/" + (uri (string-append "https://repo1.maven.org/maven2/com/sun/msv/" "datatype/xsd/xsdlib/" version "/xsdlib-" version "-sources.jar")) (sha256 @@ -1696,7 +1696,8 @@ that strives for correctness and simplicity.") #:jdk ,icedtea-8)) (inputs `(("java-xerces" ,java-xerces))) - (home-page "http://central.maven.org/maven2/com/sun/msv/datatype/xsd/xsdlib/") + (home-page (string-append "https://web.archive.org/web/20161127144537/" + "https://msv.java.net//")) (synopsis "Sun Multi-Schema Validator") (description "Xsdlib contains an implementation of sun.com.msv, an XML validator.") From b19f155cf842b5ed6f7ae9c94ef7389e20c10e0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?= Date: Sun, 15 Mar 2020 22:23:42 +0100 Subject: [PATCH 085/235] gnu: java-snakeyaml: Update hash. Compared to the the old tarfile available on ci.guix.gnu.org, only the file '.hg_archival.txt' was removed. * gnu/packages/java.scm (java-snakeyaml)[source]: Update hash. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 03ed0c6534..76a0c6234c 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -8532,7 +8532,7 @@ of deserialization.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0rf5ha6w0waz50jz2479jsrbgmd0dnx0gs337m126j5z7zlmg7mg")))) + "0474cqcv46zgv9bhms2vgawakq1vyj0hp3h3f1bfys46msia90bh")))) (build-system ant-build-system) (arguments `(#:jar-name "java-snakeyaml.jar" From 8bbbbb39350eb559951972abae2622195393b51e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 15 Mar 2020 21:03:39 -0400 Subject: [PATCH 086/235] Revert "gnu: BlueZ: Update to 5.54." This reverts commit f24aaa81de8c709adfda2e89271c562a5ca8d959. This change caused too many rebuilds for the master branch. --- gnu/local.mk | 1 + gnu/packages/linux.scm | 13 +- .../patches/bluez-CVE-2020-0556.patch | 180 ++++++++++++++++++ 3 files changed, 192 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/bluez-CVE-2020-0556.patch diff --git a/gnu/local.mk b/gnu/local.mk index b628bbee0c..3be54b2627 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -764,6 +764,7 @@ dist_patch_DATA = \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blender-2.79-newer-ffmpeg.patch \ %D%/packages/patches/blender-2.79-python-3.7-fix.patch \ + %D%/packages/patches/bluez-CVE-2020-0556.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/calibre-no-updates-dialog.patch \ %D%/packages/patches/calibre-remove-test-bs4.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index fda7570d89..f1bc5798ab 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4039,7 +4039,8 @@ Bluetooth audio output devices like headphones or loudspeakers.") (define-public bluez (package (name "bluez") - (version "5.54") + (replacement bluez/fixed) + (version "5.53") (source (origin (method url-fetch) (uri (string-append @@ -4047,7 +4048,7 @@ Bluetooth audio output devices like headphones or loudspeakers.") version ".tar.xz")) (sha256 (base32 - "1p2ncvjz6alr9n3l5wvq2arqgc7xjs6dqyar1l9jp0z8cfgapkb8")))) + "1g1qg6dz6hl3csrmz75ixr12lwv836hq3ckb259svvrg62l2vaiq")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -4104,6 +4105,14 @@ Bluetooth audio output devices like headphones or loudspeakers.") is flexible, efficient and uses a modular implementation.") (license license:gpl2+))) +(define bluez/fixed + (package + (inherit bluez) + (source (origin + (inherit (package-source bluez)) + (patches (append (origin-patches (package-source bluez)) + (search-patches "bluez-CVE-2020-0556.patch"))))))) + (define-public fuse-exfat (package (name "fuse-exfat") diff --git a/gnu/packages/patches/bluez-CVE-2020-0556.patch b/gnu/packages/patches/bluez-CVE-2020-0556.patch new file mode 100644 index 0000000000..7c34459a3a --- /dev/null +++ b/gnu/packages/patches/bluez-CVE-2020-0556.patch @@ -0,0 +1,180 @@ +Fix CVE-2020-0556: + +https://lore.kernel.org/linux-bluetooth/20200310023516.209146-1-alainm@chromium.org/ +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html +http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2020-0556 + +Patches copied from upstream source repository: + +https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=3cccdbab2324086588df4ccf5f892fb3ce1f1787 +https://git.kernel.org/pub/scm/bluetooth/bluez.git/commit/?id=8cdbd3b09f29da29374e2f83369df24228da0ad1 + +From 3cccdbab2324086588df4ccf5f892fb3ce1f1787 Mon Sep 17 00:00:00 2001 +From: Alain Michaud +Date: Tue, 10 Mar 2020 02:35:18 +0000 +Subject: [PATCH] HID accepts bonded device connections only. + +This change adds a configuration for platforms to choose a more secure +posture for the HID profile. While some older mice are known to not +support pairing or encryption, some platform may choose a more secure +posture by requiring the device to be bonded and require the +connection to be encrypted when bonding is required. + +Reference: +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.html +--- + profiles/input/device.c | 23 ++++++++++++++++++++++- + profiles/input/device.h | 1 + + profiles/input/input.conf | 8 ++++++++ + profiles/input/manager.c | 13 ++++++++++++- + 4 files changed, 43 insertions(+), 2 deletions(-) + +diff --git a/profiles/input/device.c b/profiles/input/device.c +index 2cb3811c8..d89da2d7c 100644 +--- a/profiles/input/device.c ++++ b/profiles/input/device.c +@@ -92,6 +92,7 @@ struct input_device { + + static int idle_timeout = 0; + static bool uhid_enabled = false; ++static bool classic_bonded_only = false; + + void input_set_idle_timeout(int timeout) + { +@@ -103,6 +104,11 @@ void input_enable_userspace_hid(bool state) + uhid_enabled = state; + } + ++void input_set_classic_bonded_only(bool state) ++{ ++ classic_bonded_only = state; ++} ++ + static void input_device_enter_reconnect_mode(struct input_device *idev); + static int connection_disconnect(struct input_device *idev, uint32_t flags); + +@@ -970,8 +976,18 @@ static int hidp_add_connection(struct input_device *idev) + if (device_name_known(idev->device)) + device_get_name(idev->device, req->name, sizeof(req->name)); + ++ /* Make sure the device is bonded if required */ ++ if (classic_bonded_only && !device_is_bonded(idev->device, ++ btd_device_get_bdaddr_type(idev->device))) { ++ error("Rejected connection from !bonded device %s", dst_addr); ++ goto cleanup; ++ } ++ + /* Encryption is mandatory for keyboards */ +- if (req->subclass & 0x40) { ++ /* Some platforms may choose to require encryption for all devices */ ++ /* Note that this only matters for pre 2.1 devices as otherwise the */ ++ /* device is encrypted by default by the lower layers */ ++ if (classic_bonded_only || req->subclass & 0x40) { + if (!bt_io_set(idev->intr_io, &gerr, + BT_IO_OPT_SEC_LEVEL, BT_IO_SEC_MEDIUM, + BT_IO_OPT_INVALID)) { +@@ -1203,6 +1219,11 @@ static void input_device_enter_reconnect_mode(struct input_device *idev) + DBG("path=%s reconnect_mode=%s", idev->path, + reconnect_mode_to_string(idev->reconnect_mode)); + ++ /* Make sure the device is bonded if required */ ++ if (classic_bonded_only && !device_is_bonded(idev->device, ++ btd_device_get_bdaddr_type(idev->device))) ++ return; ++ + /* Only attempt an auto-reconnect when the device is required to + * accept reconnections from the host. + */ +diff --git a/profiles/input/device.h b/profiles/input/device.h +index 51a9aee18..3044db673 100644 +--- a/profiles/input/device.h ++++ b/profiles/input/device.h +@@ -29,6 +29,7 @@ struct input_conn; + + void input_set_idle_timeout(int timeout); + void input_enable_userspace_hid(bool state); ++void input_set_classic_bonded_only(bool state); + + int input_device_register(struct btd_service *service); + void input_device_unregister(struct btd_service *service); +diff --git a/profiles/input/input.conf b/profiles/input/input.conf +index 3e1d65aae..166aff4a4 100644 +--- a/profiles/input/input.conf ++++ b/profiles/input/input.conf +@@ -11,3 +11,11 @@ + # Enable HID protocol handling in userspace input profile + # Defaults to false (HIDP handled in HIDP kernel module) + #UserspaceHID=true ++ ++# Limit HID connections to bonded devices ++# The HID Profile does not specify that devices must be bonded, however some ++# platforms may want to make sure that input connections only come from bonded ++# device connections. Several older mice have been known for not supporting ++# pairing/encryption. ++# Defaults to false to maximize device compatibility. ++#ClassicBondedOnly=true +diff --git a/profiles/input/manager.c b/profiles/input/manager.c +index 1d31b0652..5cd27b839 100644 +--- a/profiles/input/manager.c ++++ b/profiles/input/manager.c +@@ -96,7 +96,7 @@ static int input_init(void) + config = load_config_file(CONFIGDIR "/input.conf"); + if (config) { + int idle_timeout; +- gboolean uhid_enabled; ++ gboolean uhid_enabled, classic_bonded_only; + + idle_timeout = g_key_file_get_integer(config, "General", + "IdleTimeout", &err); +@@ -114,6 +114,17 @@ static int input_init(void) + input_enable_userspace_hid(uhid_enabled); + } else + g_clear_error(&err); ++ ++ classic_bonded_only = g_key_file_get_boolean(config, "General", ++ "ClassicBondedOnly", &err); ++ ++ if (!err) { ++ DBG("input.conf: ClassicBondedOnly=%s", ++ classic_bonded_only ? "true" : "false"); ++ input_set_classic_bonded_only(classic_bonded_only); ++ } else ++ g_clear_error(&err); ++ + } + + btd_profile_register(&input_profile); +-- +2.25.1 + +From 8cdbd3b09f29da29374e2f83369df24228da0ad1 Mon Sep 17 00:00:00 2001 +From: Alain Michaud +Date: Tue, 10 Mar 2020 02:35:16 +0000 +Subject: [PATCH] HOGP must only accept data from bonded devices. + +HOGP 1.0 Section 6.1 establishes that the HOGP must require bonding. + +Reference: +https://www.intel.com/content/www/us/en/security-center/advisory/intel-sa-00352.htm +--- + profiles/input/hog.c | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/profiles/input/hog.c b/profiles/input/hog.c +index 83c017dcb..dfac68921 100644 +--- a/profiles/input/hog.c ++++ b/profiles/input/hog.c +@@ -186,6 +186,10 @@ static int hog_accept(struct btd_service *service) + return -EINVAL; + } + ++ /* HOGP 1.0 Section 6.1 requires bonding */ ++ if (!device_is_bonded(device, btd_device_get_bdaddr_type(device))) ++ return -ECONNREFUSED; ++ + /* TODO: Replace GAttrib with bt_gatt_client */ + bt_hog_attach(dev->hog, attrib); + +-- +2.25.1 + From 2ec46078630a09b326822a7565fc7764fd9957a7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 16 Mar 2020 02:16:38 +0100 Subject: [PATCH 087/235] services: nginx: Fix broken default configuration. * gnu/services/web.scm (nginx-configuration): Emit an empty events{} block by default. * doc/guix.texi (Web Services): Document it. --- doc/guix.texi | 2 +- gnu/services/web.scm | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 28808b0cd5..202d1347f7 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -20272,7 +20272,7 @@ names of loadable modules, as in this example: /etc/nginx/modules/ngx_http_accept_language_module.so"))) @end lisp -@item @code{global-directives} (default: @code{'()}) +@item @code{global-directives} (default: @code{'((events . ()))}) Association list of global directives for the top level of the nginx configuration. Values may themselves be association lists. diff --git a/gnu/services/web.scm b/gnu/services/web.scm index 3edc751ea2..ac247ec39a 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2018 Marius Bakke ;;; Copyright © 2019 Florian Pelz ;;; Copyright © 2020 Ricardo Wurmus +;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -529,7 +530,8 @@ (server-names-hash-bucket-max-size nginx-configuration-server-names-hash-bucket-max-size (default #f)) (modules nginx-configuration-modules (default '())) - (global-directives nginx-configuration-global-directives (default '())) + (global-directives nginx-configuration-global-directives + (default '((events . ())))) (extra-content nginx-configuration-extra-content (default "")) (file nginx-configuration-file ;#f | string | file-like From 85f0958693588191852b3f3c04c413fc089b0c81 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Mar 2020 09:58:56 +0100 Subject: [PATCH 088/235] services/web: Export nginx-configuration-global-directives. This is a follow-up to commit b420e6deb96e0760f12e3d941b76e690c4235e47. * gnu/services/web.scm (nginx-configuration-global-directives): Export procedure. --- gnu/services/web.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/services/web.scm b/gnu/services/web.scm index ac247ec39a..fa5c34d5af 100644 --- a/gnu/services/web.scm +++ b/gnu/services/web.scm @@ -100,6 +100,7 @@ nginx-configuration-server-names-hash-bucket-size nginx-configuration-server-names-hash-bucket-max-size nginx-configuration-modules + nginx-configuration-global-directives nginx-configuration-extra-content nginx-configuration-file From bc6bf142d333f05cfb214295db0756d7e3ad0d67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 Mar 2020 13:59:20 +0100 Subject: [PATCH 089/235] gnu: star: Update to 2.7.3a. * gnu/packages/bioinformatics.scm (star): Update to 2.7.3a. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dedee6223..9044ebca8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6322,16 +6322,16 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.7.1a") + (version "2.7.3a") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/alexdobin/STAR.git") (commit version))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "0n6g4s4hgw7qygs1z97j7a2dgz8gfaa4cv5pjvvvmarvk0x07hyg")) + "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq")) (modules '((guix build utils))) (snippet '(begin From 4df02ab675b262bc2d43f83ad33785eb434ea6cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 10:33:29 +0100 Subject: [PATCH 090/235] tests: rsync: Set PATH. This is a followup to 8b9cad01e9619f53dc5a65892ca6a09ca5de3447, which would leave PATH unset. * gnu/tests/rsync.scm (run-rsync-test)[test]("service running"): Add call to 'setenv' for PATH. --- gnu/tests/rsync.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/tests/rsync.scm b/gnu/tests/rsync.scm index 096580022f..24e60d9d9d 100644 --- a/gnu/tests/rsync.scm +++ b/gnu/tests/rsync.scm @@ -64,6 +64,10 @@ PORT." (marionette-eval '(begin (use-modules (gnu services herd)) + + ;; Make sure the 'rsync' command is found. + (setenv "PATH" "/run/current-system/profile/bin") + (start-service 'rsync)) marionette)) From ef0f5ff2a74e5e4dc49dfdd0ba6509a91281ddd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 11:17:15 +0100 Subject: [PATCH 091/235] tests: dhcpd: Adjust network interface name. This is a followup to 8e53fe2b91d2776bc1529e7b34967c8f1d9edc32. * gnu/tests/networking.scm (dhcpd-v4-configuration) (%dhcpd-os): Use "ens3" instead of "eth0". --- gnu/tests/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/tests/networking.scm b/gnu/tests/networking.scm index d1234442bb..e90b247883 100644 --- a/gnu/tests/networking.scm +++ b/gnu/tests/networking.scm @@ -270,11 +270,11 @@ subnet 192.168.1.0 netmask 255.255.255.0 { (dhcpd-configuration (config-file minimal-dhcpd-v4-config-file) (version "4") - (interfaces '("eth0")))) + (interfaces '("ens3")))) (define %dhcpd-os (simple-operating-system - (static-networking-service "eth0" "192.168.1.4" + (static-networking-service "ens3" "192.168.1.4" #:netmask "255.255.255.0" #:gateway "192.168.1.1" #:name-servers '("192.168.1.2" "192.168.1.3")) From 0f13dd2b7f7675310e4a9bbfd37ee946b9f0dea3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 11:25:57 +0100 Subject: [PATCH 092/235] services: dhcpd: Use 'invoke/quiet' when validating the config file. This avoids the lengthy copyright/config message from dhcpd. * gnu/services/networking.scm (dhcpd-activation): Use 'invoke/quiet' instead of 'invoke'. --- gnu/services/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 59b895d60b..618dd95969 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2016 John Darrington @@ -313,7 +313,7 @@ Protocol (DHCP) client, on all the non-loopback network interfaces." (with-output-to-file #$lease-file (lambda _ (display "")))) ;; Validate the config. - (invoke + (invoke/quiet #$(file-append package "/sbin/dhcpd") "-t" "-cf" #$config-file)))))) From c215d9ec1ce108844b14c0c2952199a0da5f4176 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 12:18:59 +0100 Subject: [PATCH 093/235] tests: opensmtpd: Gracefully handle test failure. Previously the 'wait' loop would run for ~1024 seconds, at which point we'd reach the file descriptor limit due to the leak in 'queue-empty?'. * gnu/tests/mail.scm (run-opensmtpd-test)[test]("mail arrived"): In 'queue-empty?', close PIPE to avoid file descriptor leak. In 'wait' loop, arrange to run at most 20 times. --- gnu/tests/mail.scm | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/gnu/tests/mail.scm b/gnu/tests/mail.scm index 298918b3a7..58172cd1d6 100644 --- a/gnu/tests/mail.scm +++ b/gnu/tests/mail.scm @@ -140,16 +140,21 @@ match from any for local action inbound (ice-9 rdelim)) (define (queue-empty?) - (eof-object? - (read-line - (open-input-pipe - (string-append #$(file-append opensmtpd "/sbin/smtpctl") - " show queue"))))) + (let* ((pipe (open-pipe* OPEN_READ + #$(file-append opensmtpd + "/sbin/smtpctl") + "show" "queue")) + (line (read-line pipe))) + (close-pipe pipe) + (eof-object? line))) - (let wait () - (if (queue-empty?) - (file-exists? "/var/mail/root") - (begin (sleep 1) (wait))))) + (let wait ((n 20)) + (cond ((queue-empty?) + (file-exists? "/var/mail/root")) + ((zero? n) + (error "root mailbox didn't show up")) + (else + (sleep 1) (wait (- n 1)))))) marionette)) (test-end) From a37e03d60e18dfcf119d0b92d9008e54fc350bf1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 12:21:05 +0100 Subject: [PATCH 094/235] tests: opensmtpd: Check /var/spool/mail instead of /var/mail. The test had been failing since the upgrade to 6.6.3p1 in commit 2dbfd8eec43b602d23cee3fdd2842cc333e36c24. * gnu/services/mail.scm (opensmtpd-activation): Create /var/spool/mail. * gnu/tests/mail.scm (run-opensmtpd-test): Check /var/spool/mail instead of /var/mail. --- gnu/services/mail.scm | 4 +++- gnu/tests/mail.scm | 6 +++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm index d97316512f..7791780dfc 100644 --- a/gnu/services/mail.scm +++ b/gnu/services/mail.scm @@ -1670,7 +1670,9 @@ match from local for any action outbound ;; Create mbox and spool directories. (mkdir-p "/var/mail") (mkdir-p "/var/spool/smtpd") - (chmod "/var/spool/smtpd" #o711)))))) + (chmod "/var/spool/smtpd" #o711) + (mkdir-p "/var/spool/mail") + (chmod "/var/spool/mail" #o711)))))) (define %opensmtpd-pam-services (list (unix-pam-service "smtpd"))) diff --git a/gnu/tests/mail.scm b/gnu/tests/mail.scm index 58172cd1d6..a50fb1dbca 100644 --- a/gnu/tests/mail.scm +++ b/gnu/tests/mail.scm @@ -99,8 +99,8 @@ match from any for local action inbound (test-assert "mbox is empty" (marionette-eval - '(and (file-exists? "/var/mail") - (not (file-exists? "/var/mail/root"))) + '(and (file-exists? "/var/spool/mail") + (not (file-exists? "/var/spool/mail/root"))) marionette)) (test-eq "accept an email" @@ -150,7 +150,7 @@ match from any for local action inbound (let wait ((n 20)) (cond ((queue-empty?) - (file-exists? "/var/mail/root")) + (file-exists? "/var/spool/mail/root")) ((zero? n) (error "root mailbox didn't show up")) (else From e8cec7cc120fc95b2e869a1834a01e257e0f63c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 12:34:13 +0100 Subject: [PATCH 095/235] tests: nfs: Ensure 'rpcinfo' can be found. The test was failing since 8b9cad01e9619f53dc5a65892ca6a09ca5de3447. * gnu/tests/nfs.scm (run-nfs-test)[test]("RPC service running"): Add 'setenv' call for PATH. --- gnu/tests/nfs.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/tests/nfs.scm b/gnu/tests/nfs.scm index 014d049ab5..635c4a7322 100644 --- a/gnu/tests/nfs.scm +++ b/gnu/tests/nfs.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2020 Ludovic Courtès ;;; Copyright © 2016 John Darrington ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2017 Tobias Geerinckx-Rice @@ -101,6 +101,10 @@ (marionette-eval '(begin (use-modules (gnu services herd)) + + ;; Ensure 'rpcinfo' can be found below. + (setenv "PATH" "/run/current-system/profile/bin") + (start-service 'rpcbind-daemon)) marionette)) From 76d2b9a2e8893dc566d954c3e5be457fbfab5e17 Mon Sep 17 00:00:00 2001 From: Joseph LaFreniere Date: Wed, 11 Mar 2020 21:48:59 -0500 Subject: [PATCH 096/235] gnu: Add libgccjit. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gcc.scm (libgccjit): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gcc.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 1f10ae5119..08afd80358 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2016 Carlos Sánchez de La Lama ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Marius Bakke +;;; Copyright © 2020 Joseph LaFreniere ;;; ;;; This file is part of GNU Guix. ;;; @@ -690,6 +691,34 @@ as the 'native-search-paths' field." ;; report two gfortran@5 that are in fact identical. gfortran-7) +(define-public libgccjit + (package + (inherit gcc-9) + (name "libgccjit") + (outputs (delete "lib" (package-outputs gcc))) + (properties (alist-delete 'hidden? (package-properties gcc))) + (arguments + (substitute-keyword-arguments `(#:modules ((guix build gnu-build-system) + (guix build utils) + (ice-9 regex) + (srfi srfi-1) + (srfi srfi-26)) + ,@(package-arguments gcc)) + ((#:configure-flags flags) + `(append `("--enable-host-shared" + ,(string-append "--enable-languages=jit")) + (remove (cut string-match "--enable-languages.*" <>) + ,flags))) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'install 'remove-broken-or-conflicting-files + (lambda* (#:key outputs #:allow-other-keys) + (for-each delete-file + (find-files (string-append (assoc-ref outputs "out") "/bin") + ".*(c\\+\\+|cpp|g\\+\\+|gcov|gcc|gcc-.*)")) + #t)))))))) + + (define-public gccgo-4.9 (custom-gcc gcc-4.9 "gccgo" '("go") %generic-search-paths From a1dc5898fbae4c97a37364e91ae49a55d5641f16 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:14:19 +0100 Subject: [PATCH 097/235] gnu: python-stem: Update to 1.8.0. * gnu/packages/python-xyz.scm (python-stem): Update to 1.8.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2718e9b236..f673b5ec15 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11516,14 +11516,14 @@ etc.") (define-public python-stem (package (name "python-stem") - (version "1.7.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (pypi-uri "stem" version)) (sha256 (base32 - "18lc95pmc7i089nlsb06dsxyjl5wbhxfqgdxbjcia35ndh8z7sn9")))) + "1hk8alc0r4m669ggngdfvryndd0fbx0w62sclcmg55af4ak8xd50")))) (build-system python-build-system) (arguments `(#:phases From 44b885656aa1eb1d2dff9ecda35149c71d51b1fe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:10:51 +0100 Subject: [PATCH 098/235] gnu: python-werkzeug: Update to 1.0.0. * gnu/packages/python-web.scm (python-werkzeug): Update to 1.0.0. [source](uri): Capitalize PyPI project name. [native-inputs]: Add PYTHON-PYTEST-TIMEOUT. --- gnu/packages/python-web.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 07c1ceb2db..d1e09fc727 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2783,14 +2783,14 @@ List. Forked from and using the same API as the publicsuffix package.") (define-public python-werkzeug (package (name "python-werkzeug") - (version "0.14.1") + (version "1.0.0") (source (origin (method url-fetch) - (uri (pypi-uri "werkzeug" version)) + (uri (pypi-uri "Werkzeug" version)) (sha256 (base32 - "0z2m4snn1vc9518r2vzgdj1nc90kcgi60wijvd29yvcp85ypmzf3")))) + "15kh0z61klp62mrc1prka13xsshxn0rsp1j1s2964iw86yisi6qn")))) (build-system python-build-system) (arguments '(#:phases @@ -2803,7 +2803,8 @@ List. Forked from and using the same API as the publicsuffix package.") (propagated-inputs `(("python-requests" ,python-requests))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-pytest" ,python-pytest) + ("python-pytest-timeout" ,python-pytest-timeout))) (home-page "https://www.palletsprojects.org/p/werkzeug/") (synopsis "Utilities for WSGI applications") (description "One of the most advanced WSGI utility modules. It includes a From 15af040cc35895e779397ab42f53561666d9301a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:27:50 +0100 Subject: [PATCH 099/235] gnu: python-flask: Update to 1.1.1. * gnu/packages/python-web.scm (python-flask): Update to 1.1.1. --- gnu/packages/python-web.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d1e09fc727..985d03f8d1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1728,20 +1728,22 @@ minimum of WSGI.") (define-public python-flask (package (name "python-flask") - (version "1.0.3") + (version "1.1.1") (source (origin (method url-fetch) (uri (pypi-uri "Flask" version)) (sha256 (base32 - "1wxnhjlxwwjhjxmghykjhllpahv5pkdc5hln4ab6nab43s26sz5d")))) + "0ljdjgyjn7vh8ic1n1dc2l1cl421i6pr3kx5sz2w5irhyfbg3y8k")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda _ - (invoke "python" "-m" "pytest")))))) + (setenv "PYTHONPATH" (string-append "./build/lib:" + (getenv "PYTHONPATH"))) + (invoke "pytest" "-vv" "tests")))))) (native-inputs `(("python-pytest" ,python-pytest))) (propagated-inputs From 4393dafd320ad5d10d8c87d4ae46ce21fdd4ffb6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:33:57 +0100 Subject: [PATCH 100/235] gnu: python-flask-login: Update to 0.5.0. * gnu/packages/python-web.scm (python-flask-login): Update to 0.5.0. [arguments]: Remove. [native-inputs]: Remove PYTHON-NOSE and PYTHON-PEP8. Add PYTHON-COVERAGE, PYTHON-PYCODESTYLE. and PYTHON-PYTEST. --- gnu/packages/python-web.scm | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 985d03f8d1..b17de9953f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2394,7 +2394,7 @@ on the command line.") (define-public python-flask-login (package (name "python-flask-login") - (version "0.4.1") + (version "0.5.0") (source (origin (method git-fetch) @@ -2403,25 +2403,18 @@ on the command line.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1rj0qwyxapxnp84fi4lhmvh3d91fdiwz7hibw77x3d5i72knqaa9")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'avoid-yanc - ;; Work around '.nosetests-real: error: no such option: --with-yanc'. - (lambda _ - (setenv "NOCOLOR" "set") - #t))))) + (base32 "11ac924w0y4m0kf3mxnxdlidy88jfa7njw5yyrq16dvnx4iwd8gg")))) (build-system python-build-system) (propagated-inputs `(("python-flask" ,python-flask))) (native-inputs ;; For tests. `(("python-blinker" ,python-blinker) + ("python-coverage" ,python-coverage) ("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-pep8" ,python-pep8) + ("python-pycodestyle" ,python-pycodestyle) ("python-pyflakes" ,python-pyflakes) + ("python-pytest" ,python-pytest) ("python-semantic-version" ,python-semantic-version) ("python-werkzeug" ,python-werkzeug))) (home-page "https://github.com/maxcountryman/flask-login") From 33901ed8c0a85e9b0badbc7ea042d310bdfac970 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:41:51 +0100 Subject: [PATCH 101/235] gnu: python-flask-babel: Update to 1.0.0. * gnu/packages/python-web.scm (python-flask-babel): Update to 1.0.0. [arguments]: New field. --- gnu/packages/python-web.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b17de9953f..b87764b907 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -440,15 +440,21 @@ between a web browser and web server.") (define-public python-flask-babel (package (name "python-flask-babel") - (version "0.11.2") + (version "1.0.0") (source (origin (method url-fetch) (uri (pypi-uri "Flask-Babel" version)) (sha256 (base32 - "0ff9n165vhf1nhv6807ckhpp224jw7k7sd7jz5kfh3sbpl85gmy0")))) + "0gmb165vkwv5v7dxsxa2i3zhafns0fh938m2zdcrv4d8z5l099yn")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (with-directory-excursion "tests" + (invoke "python" "tests.py"))))))) (propagated-inputs `(("python-flask" ,python-flask) ("python-babel" ,python-babel) From 8f29817ed523dd4e5dbd459ecb94dbd1cab6a4fc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:43:25 +0100 Subject: [PATCH 102/235] gnu: python-flask-wtf: Update to 0.14.3. * gnu/packages/python-web.scm (python-flask-wtf): Update to 0.14.3. [arguments]: Remove obsolete phase. Override check phase. [native-inputs]: Remove PYTHON-NOSE. Add PYTHON-PYTEST. --- gnu/packages/python-web.scm | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b87764b907..6d4204bad0 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1770,31 +1770,29 @@ presume or force a developer to use a particular tool or library.") (define-public python-flask-wtf (package (name "python-flask-wtf") - (version "0.13.1") + (version "0.14.3") (source (origin (method url-fetch) (uri (pypi-uri "Flask-WTF" version)) (sha256 (base32 - "04l5743j2dici46038sqlzvf0xzpg8rf7s9ld2x24xv7f4idg990")))) + "086pvg2x69n0nczcq7frknfjd8am1zdy8qqpva1sanwb02hf65yl")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases - (add-before 'check 'drop-failing-test + (replace 'check (lambda _ - ;; FIXME: This file tries resolving an external server, which - ;; fails. Try to patch out the offending section instead of - ;; deleting the whole thing. - (delete-file "tests/test_recaptcha.py") - #t))))) + (setenv "PYTHONPATH" (string-append "./build/lib:" + (getenv "PYTHONPATH"))) + (invoke "pytest" "-vv")))))) (propagated-inputs `(("python-flask-babel" ,python-flask-babel) ("python-babel" ,python-babel) ("python-wtforms" ,python-wtforms))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/lepture/flask-wtf") (synopsis "Simple integration of Flask and WTForms") (description "Flask-WTF integrates Flask and WTForms, including CSRF, file From 0a044f75b54d92417debf600fe7c4c4f86af344d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 03:55:16 +0100 Subject: [PATCH 103/235] gnu: python-flask-restful: Update to 0.3.8. * gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.8. [source](patches): New field. [native-inputs]: Remove PYTHON-SPHINX. --- gnu/local.mk | 1 + ...python-flask-restful-werkzeug-compat.patch | 36 +++++++++++++++++++ gnu/packages/python-web.scm | 8 ++--- 3 files changed, 41 insertions(+), 4 deletions(-) create mode 100644 gnu/packages/patches/python-flask-restful-werkzeug-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3be54b2627..1dd7e0a6a8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1327,6 +1327,7 @@ dist_patch_DATA = \ %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ %D%/packages/patches/python-faker-fix-build-32bit.patch \ + %D%/packages/patches/python-flask-restful-werkzeug-compat.patch \ %D%/packages/patches/python-keras-integration-test.patch \ %D%/packages/patches/python-pep8-stdlib-tokenize-compat.patch \ %D%/packages/patches/python-pyfakefs-remove-bad-test.patch \ diff --git a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch new file mode 100644 index 0000000000..0e928ef455 --- /dev/null +++ b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch @@ -0,0 +1,36 @@ +We need one patch on top of 0.3.8 for compatibility with Werkzeug 1.0. + +Taken from upstream: +https://github.com/flask-restful/flask-restful/commit/73376a488907af3042b52678ac4c23f8a8911e5b + +diff --git a/tests/test_api.py b/tests/test_api.py +index f7f8e661..6795d362 100644 +--- a/tests/test_api.py ++++ b/tests/test_api.py +@@ -445,7 +445,9 @@ def test_handle_non_api_error(self): + + resp = app.get("/foo") + self.assertEquals(resp.status_code, 404) +- self.assertEquals('text/html', resp.headers['Content-Type']) ++ # in newer versions of werkzeug this is `text/html; charset=utf8` ++ content_type, _, _ = resp.headers['Content-Type'].partition(';') ++ self.assertEquals('text/html', content_type) + + def test_non_api_error_404_catchall(self): + app = Flask(__name__) +diff --git a/tests/test_reqparse.py b/tests/test_reqparse.py +index 2f1fbedf..9776f17c 100644 +--- a/tests/test_reqparse.py ++++ b/tests/test_reqparse.py +@@ -2,9 +2,9 @@ + import unittest + from mock import Mock, patch + from flask import Flask +-from werkzeug import exceptions, MultiDict ++from werkzeug import exceptions + from werkzeug.wrappers import Request +-from werkzeug.datastructures import FileStorage ++from werkzeug.datastructures import FileStorage, MultiDict + from flask_restful.reqparse import Argument, RequestParser, Namespace + import six + import decimal diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 6d4204bad0..ae01f83611 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2173,14 +2173,15 @@ pretty printer and a tree visitor.") (define-public python-flask-restful (package (name "python-flask-restful") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (pypi-uri "Flask-RESTful" version)) + (patches (search-patches "python-flask-restful-werkzeug-compat.patch")) (sha256 (base32 - "1a9cbwkr6krryyzq4sd3f415nkkc6dyfls5i3pgyibs94g0hw97q")))) + "05b9lzx5yc3wgml2bcq50lq35h66m8zpj6dc9advcb5z3acsbaay")))) (build-system python-build-system) (propagated-inputs `(("python-aniso8601" ,python-aniso8601) @@ -2191,8 +2192,7 @@ pretty printer and a tree visitor.") `(;; Optional dependency of Flask. Tests need it. ("python-blinker" ,python-blinker) ("python-mock" ,python-mock) ; For tests - ("python-nose" ,python-nose) ; For tests - ("python-sphinx" ,python-sphinx))) + ("python-nose" ,python-nose))) ;for tests (home-page "https://www.github.com/flask-restful/flask-restful/") (synopsis From 200acbc34b9fe24f6c204e419d357da3197ea891 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:05:16 +0100 Subject: [PATCH 104/235] gnu: python-stdnum: Update to 1.13. * gnu/packages/finance.scm (python-stdnum): Update to 1.13. [arguments]: New field. [native-inputs]: Add PYTHON-NOSE. --- gnu/packages/finance.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 89a7ffe956..0e44802fe1 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -982,15 +982,22 @@ agent.") (define-public python-stdnum (package (name "python-stdnum") - (version "1.8.1") + (version "1.13") (source (origin (method url-fetch) (uri (pypi-uri "python-stdnum" version)) (sha256 (base32 - "0hvr47q32xbyiznpmbg4r8rcvxhnf0lwf33hcpnynyik57djy5np")))) + "0q4128rjdgavywhzlm2gz2n5ybc9b9sxs81g50dvxf5q7z9q63qj")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "nosetests")))))) + (native-inputs + `(("python-nose" ,python-nose))) (home-page "https://arthurdejong.org/python-stdnum/") (synopsis From e5b4b8028ae59eab96b12df5e1e615cb63fca8ca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:08:26 +0100 Subject: [PATCH 105/235] gnu: python-flask-restful-swagger: Update to 0.20.1. * gnu/packages/python-web.scm (python-flask-restful-swagger): Update to 0.20.1. [arguments]: New field. Explicitly disable tests. --- gnu/packages/python-web.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index ae01f83611..19d3255d79 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2309,15 +2309,16 @@ documentation builder.") (define-public python-flask-restful-swagger (package (name "python-flask-restful-swagger") - (version "0.19") + (version "0.20.1") (source (origin (method url-fetch) (uri (pypi-uri "flask-restful-swagger" version)) (sha256 (base32 - "16msl8hd5xjmj833bpy264v98cpl5hkw5bgl5gf5vgndxbv3rm6v")))) + "1p66f98b5zpypnnz56pxpbirchqj6aniw6qyrp8h572l0dn9xlvq")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ;no tests (propagated-inputs `(("python-flask-restful" ,python-flask-restful))) (home-page "https://github.com/rantav/flask-restful-swagger") From b85822eaf9b8c85d0a579e37df813d35c3e5d314 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:14:48 +0100 Subject: [PATCH 106/235] gnu: python-flask-migrate: Update to 2.5.3. * gnu/packages/python-web.scm (python-flask-migrate): Update to 2.5.3. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 19d3255d79..1000784d6d 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2606,14 +2606,14 @@ itself.") (define-public python-flask-migrate (package (name "python-flask-migrate") - (version "2.0.3") + (version "2.5.3") (source (origin (method url-fetch) (uri (pypi-uri "Flask-Migrate" version)) (sha256 (base32 - "107x78lkqsnbg92dld3dkagg07jvchp3ib3y0sivc4ipz6n1y7rk")))) + "1vip9ww6l18dxffjsggm83k71zkvihxpnhaswpv8klh95s6517d6")))) (build-system python-build-system) (propagated-inputs `(("python-flask" ,python-flask) From f8205d9a7838678f9c633ad5c429029f280f254e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:15:07 +0100 Subject: [PATCH 107/235] gnu: python2-flake8: Add missing propagated dependency. * gnu/packages/python-xyz.scm (python2-flake8)[propagated-inputs]: Add PYTHON-FUNCTOOLS32. --- gnu/packages/python-xyz.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f673b5ec15..2aea2be56e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7037,6 +7037,7 @@ complexity of Python source code.") (propagated-inputs `(("python2-configparser" ,python2-configparser) ("python2-enum34" ,python2-enum34) + ("python2-functools32" ,python2-functools32) ("python2-typing" ,python2-typing) ,@(package-propagated-inputs base)))))) From 066c21cda4a9893a0cc8398d1a4d3f9f1ac1dfbb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:32:31 +0100 Subject: [PATCH 108/235] gnu: Remove python2-flask-migrate. Upstream no longer supports Python 2 and there are no dependencies on it in Guix. * gnu/packages/python-web.scm (python2-flask-migrate): Remove variable. --- gnu/packages/python-web.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 1000784d6d..e431a072d1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2628,9 +2628,6 @@ Alembic") for Flask programs that are using @code{python-alembic}.") (license license:expat))) -(define-public python2-flask-migrate - (package-with-python2 python-flask-migrate)) - (define-public python-genshi (package (name "python-genshi") From e76cbdcd90e603d98f9d074aa2ee0788c65d97df Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 04:39:17 +0100 Subject: [PATCH 109/235] gnu: beets: Fix build with newer Werkzeug. * gnu/packages/patches/beets-werkzeug-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/music.scm (beets)[source](patches): New field. --- gnu/local.mk | 1 + gnu/packages/music.scm | 1 + .../patches/beets-werkzeug-compat.patch | 18 ++++++++++++++++++ 3 files changed, 20 insertions(+) create mode 100644 gnu/packages/patches/beets-werkzeug-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1dd7e0a6a8..5cde920c8c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -756,6 +756,7 @@ dist_patch_DATA = \ %D%/packages/patches/bash-completion-directories.patch \ %D%/packages/patches/bastet-change-source-of-unordered_set.patch \ %D%/packages/patches/bazaar-CVE-2017-14176.patch \ + %D%/packages/patches/beets-werkzeug-compat.patch \ %D%/packages/patches/beignet-correct-file-names.patch \ %D%/packages/patches/benchmark-unbundle-googletest.patch \ %D%/packages/patches/biber-fix-encoding-write.patch \ diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index f6585f60d4..fd9cd6c30f 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2941,6 +2941,7 @@ Songs can be searched by artist, name or even by a part of the song text.") (source (origin (method url-fetch) (uri (pypi-uri "beets" version)) + (patches (search-patches "beets-werkzeug-compat.patch")) (sha256 (base32 "0m40rjimvfgy1dv04p8f8d5dvi2855v4ix99a9xr900cmcn476yj")))) diff --git a/gnu/packages/patches/beets-werkzeug-compat.patch b/gnu/packages/patches/beets-werkzeug-compat.patch new file mode 100644 index 0000000000..1a91c3a3f9 --- /dev/null +++ b/gnu/packages/patches/beets-werkzeug-compat.patch @@ -0,0 +1,18 @@ +Be compatible with python-werkzeug 1.0.0. + +Taken from upstream: +https://github.com/beetbox/beets/commit/d43d54e21cde97f57f19486925ab56b419254cc8 + +diff --git a/beetsplug/web/__init__.py b/beetsplug/web/__init__.py +index f53fb3a954..21ff5d94ed 100644 +--- a/beetsplug/web/__init__.py ++++ b/beetsplug/web/__init__.py +@@ -169,7 +169,7 @@ def to_python(self, value): + return ids + + def to_url(self, value): +- return ','.join(value) ++ return ','.join(str(v) for v in value) + + + class QueryConverter(PathConverter): From 2680a3d83e3115f0337c43e3ac3e0d0996d66210 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 12:59:55 +0100 Subject: [PATCH 110/235] gnu: Remove git-annex-remote-hubic. This package does not build and is officially unmaintained since 2017. * gnu/packages/version-control.scm (git-annex-remote-hubic): Remove variable. --- gnu/packages/version-control.scm | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5d0fa267a9..599fb2839e 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2069,36 +2069,6 @@ supports a large number of version control systems: Git, Subversion, Mercurial, Bazaar, Darcs, CVS, Fossil, and Veracity.") (license license:gpl2+))) -(define-public git-annex-remote-hubic - (package - (name "git-annex-remote-hubic") - (version "0.3.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/Schnouki/git-annex-remote-hubic.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "16y9sk67hfi17h9n2kkffyabfccksh5rab40hhk69v6cxmbpn2sx")))) - (build-system python-build-system) - (arguments `(#:python ,python-2)) - (native-inputs - `(;; for the tests - ("python2-six" ,python2-six))) - (propagated-inputs - `(("python2-dateutil" ,python2-dateutil) - ("python2-futures" ,python2-futures) - ("python2-rauth" ,python2-rauth) - ("python2-swiftclient" ,python2-swiftclient))) - (home-page "https://github.com/Schnouki/git-annex-remote-hubic/") - (synopsis "Use hubic as a git-annex remote") - (description - "This package allows you to use your hubic account as a \"special -repository\" with git-annex.") - (license license:gpl3+))) - (define-public git-annex-remote-rclone (package (name "git-annex-remote-rclone") From d440e020943c133b8d6e214b116cfac32c9a1f59 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:03:01 +0100 Subject: [PATCH 111/235] gnu: Remove python2-keystoneclient. This package fails to build and has no reverse dependencies. * gnu/packages/openstack.scm (python2-keystoneclient): Remove variable. --- gnu/packages/openstack.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 3b6ec6b44f..c3ab3fe953 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -786,21 +786,6 @@ SQLite for its identity store database, with the option to connect to external LDAP.") (license asl2.0))) -(define-public python2-keystoneclient - (let ((keystoneclient (package-with-python2 python-keystoneclient))) - (package (inherit keystoneclient) - (propagated-inputs - `(("python2-requests" ,python2-requests) - ,@(alist-delete "python-requests" - (package-propagated-inputs keystoneclient)))) - (native-inputs - `(("python2-oauthlib" ,python2-oauthlib) - ("python2-oslosphinx" ,python2-oslosphinx) - ("python2-requests-mock" ,python2-requests-mock) - ("python2-tempest-lib" ,python2-tempest-lib) - ,@(fold alist-delete (package-native-inputs keystoneclient) - '("python-oauthlib" "python-oslosphinx" "python-requests-mock" "python-tempest-lib"))))))) - (define-public python-swiftclient (package (name "python-swiftclient") From 3b9610b559d162c3f894a700a0118186a5e7a483 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:04:23 +0100 Subject: [PATCH 112/235] gnu: Remove python2-swiftclient. This package fails to build and has no reverse dependencies. * gnu/packages/openstack.scm (python2-swiftclient): Remove variable. (python-swiftclient)[properties]: Remove. --- gnu/packages/openstack.scm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index c3ab3fe953..07c443b3da 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -825,17 +825,8 @@ data that best fit this type of storage model are virtual machine images, photo storage, email storage and backup archiving. Having no central \"brain\" or master point of control provides greater scalability, redundancy and permanence.") - (properties `((python2-variant . ,(delay python2-swiftclient)))) (license asl2.0))) -(define-public python2-swiftclient - (let ((swiftclient (package-with-python2 - (strip-python2-variant python-swiftclient)))) - (package (inherit swiftclient) - (propagated-inputs - `(("python2-futures" ,python2-futures) - ,@(package-propagated-inputs swiftclient)))))) - (define-public python-git-review (package (name "python-git-review") From dc99be08ef148776f536c04a55cc81bcb76a1b9c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:06:07 +0100 Subject: [PATCH 113/235] gnu: Remove python2-tempest-lib. This package fails to build and has no users in Guix. * gnu/packages/openstack.scm (python2-tempest-lib): Remove variable. --- gnu/packages/openstack.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 07c443b3da..07c2dbe169 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -376,9 +376,6 @@ extensions.") common features used in Tempest.") (license asl2.0))) -(define-public python2-tempest-lib - (package-with-python2 python-tempest-lib)) - ;; Packages from the Oslo library (define-public python-oslo.config (package From e778c457a5e3f1dd63aa3947dcf9f41c5bb350ca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:07:09 +0100 Subject: [PATCH 114/235] gnu: Remove python2-oslo.log. This package fails to build and has no users in Guix. * gnu/packages/openstack.scm (python2-oslo.log): Remove variable. --- gnu/packages/openstack.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 07c2dbe169..f7e806b218 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -520,9 +520,6 @@ configuration for all OpenStack projects. It also provides custom formatters, handlers and support for context specific logging (like resource id’s etc).") (license asl2.0))) -(define-public python2-oslo.log - (package-with-python2 python-oslo.log)) - (define-public python-oslo.serialization (package (name "python-oslo.serialization") From 710f7b57422bbbd171dac823de91d4c279f6ddef Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:08:01 +0100 Subject: [PATCH 115/235] gnu: Remove python2-oslo.serialization. * gnu/packages/openstack.scm (python2-oslo.serialization): Remove variable. (python-oslo.serialization)[properties]: Remove. --- gnu/packages/openstack.scm | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index f7e806b218..cfec338bb1 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -549,18 +549,8 @@ handlers and support for context specific logging (like resource id’s etc).") (description "The oslo.serialization library provides support for representing objects in transmittable and storable formats, such as JSON and MessagePack.") - (properties `((python2-variant . ,(delay python2-oslo.serialization)))) (license asl2.0))) -(define-public python2-oslo.serialization - (let ((base (package-with-python2 (strip-python2-variant - python-oslo.serialization)))) - (package - (inherit base) - (native-inputs - `(("python2-ipaddress" ,python2-ipaddress) - ,@(package-native-inputs base)))))) - (define-public python-reno (package (name "python-reno") From 538f44de9ba74ebce637ab437b245bc546c6318b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:08:48 +0100 Subject: [PATCH 116/235] gnu: Remove python2-oslo.utils. This package fails to build and has no users in Guix. * gnu/packages/openstack.scm (python2-oslo.utils): Remove variable. --- gnu/packages/openstack.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index cfec338bb1..4593b397a0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -706,9 +706,6 @@ functions, such as encoding, exception handling, string manipulation, and time handling.") (license asl2.0))) -(define-public python2-oslo.utils - (package-with-python2 python-oslo.utils)) - (define-public python-keystoneclient (package (name "python-keystoneclient") From 9ff7c73ba51e6c577afa88c899827075d1227c39 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:09:33 +0100 Subject: [PATCH 117/235] gnu: Remove python2-oslo.config. This package fails to build and has no users in Guix. * gnu/packages/openstack.scm (python2-oslo.config): Remove variable. --- gnu/packages/openstack.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 4593b397a0..734af38737 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -416,9 +416,6 @@ common features used in Tempest.") .ini style configuration files.") (license asl2.0))) -(define-public python2-oslo.config - (package-with-python2 python-oslo.config)) - (define-public python-oslo.context (package (name "python-oslo.context") From da44dcb87e713dcb6e75a465ed41eb64f5ffad0c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:10:13 +0100 Subject: [PATCH 118/235] gnu: Remove python2-bandit. This package fails to build and has no users in Guix. * gnu/packages/openstack.scm (python2-bandit): Remove variable. --- gnu/packages/openstack.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 734af38737..8dd8c1907c 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -87,9 +87,6 @@ appropriate plugins against the AST nodes. Once Bandit has finished scanning all the files it generates a report.") (license asl2.0))) -(define-public python2-bandit - (package-with-python2 python-bandit)) - (define-public python-debtcollector (package (name "python-debtcollector") From 751c1b5960508645d1257eb584ff3d5c1627e6c3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:11:01 +0100 Subject: [PATCH 119/235] gnu: Remove python2-gitpython. This package fails to build and has no users in Guix. * gnu/packages/version-control.scm (python2-gitpython): Remove variable. --- gnu/packages/version-control.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 599fb2839e..4249d4edcf 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1061,9 +1061,6 @@ either a pure Python implementation, or the faster, but more resource intensive @command{git} command implementation.") (license license:bsd-3))) -(define-public python2-gitpython - (package-with-python2 python-gitpython)) - (define-public shflags (package (name "shflags") From 24464edd31256ac81d02b2d9f0a00a72aee8d8d8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:11:45 +0100 Subject: [PATCH 120/235] gnu: Remove python2-gitdb. Upstream no longer supports Python 2 and there are no users in Guix. * gnu/packages/version-control.scm (python2-gitdb): Remove variable. --- gnu/packages/version-control.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 4249d4edcf..bf97f89cd6 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1017,9 +1017,6 @@ with performance and scalability in mind. It operates exclusively on streams, allowing to handle large objects with a small memory footprint.") (license license:bsd-3))) -(define-public python2-gitdb - (package-with-python2 python-gitdb)) - (define-public python-gitpython (package (name "python-gitpython") From aa0e4413b70819beea554b8071694b296642d842 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:24:14 +0100 Subject: [PATCH 121/235] gnu: python-kivy: Remove unused input. * gnu/packages/python-xyz.scm (python-kivy)[native-inputs]: Remove GIT. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2aea2be56e..f467e28064 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11603,8 +11603,7 @@ and/or Xon/Xoff. The port is accessed in RAW mode.") "/include/SDL2")) #t))))) (native-inputs - `(("git" ,git) - ("pkg-config" ,pkg-config) + `(("pkg-config" ,pkg-config) ("python-cython" ,python-cython))) (inputs `(("gstreamer" ,gstreamer) From f11b55563723164886939f5dd01598197ddcc8d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:33:06 +0100 Subject: [PATCH 122/235] gnu: python-gevent: Update to 1.4.0. * gnu/packages/python-xyz.scm (python-gevent): Update to 1.4.0. [arguments]: Adjust unbundling variables. Future-proof the C_INCLUDE_PATH override. Add phases "pretend-to-be-CI" and "adjust-tests". Run the tests with "python -m gevent.tests", and respect PARALLEL-JOB-COUNT. [native-inputs]: Add PYTHON-DNSPYTHON, PYTHON-PSUTIL, PYTHON-ZOPE-EVENT and PYTHON-ZOPE-INTERFACE. (python2-gevent)[native-inputs]: Fix input inheritance. --- gnu/packages/python-xyz.scm | 97 ++++++++++++++++++++++++++++--------- 1 file changed, 73 insertions(+), 24 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f467e28064..be02b03639 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10581,13 +10581,13 @@ graphviz.") (define-public python-gevent (package (name "python-gevent") - (version "1.3.7") + (version "1.4.0") (source (origin (method url-fetch) (uri (pypi-uri "gevent" version)) (sha256 (base32 - "0b0fr04qdk1p4sniv87fh8z5psac60x01pv054kpgi94520g81iz")) + "1lchr4akw2jkm5v4kz7bdm4wv3knkfhbfn9vkkz4s5yrkcxzmdqy")) (modules '((guix build utils))) (snippet '(begin @@ -10614,10 +10614,7 @@ graphviz.") #t)) (add-before 'build 'do-not-use-bundled-sources (lambda* (#:key inputs #:allow-other-keys) - (setenv "CONFIG_SHELL" (which "bash")) - (setenv "LIBEV_EMBED" "false") - (setenv "CARES_EMBED" "false") - (setenv "EMBED" "false") + (setenv "GEVENTSETUP_EMBED" "0") ;; Prevent building bundled libev. (substitute* "setup.py" @@ -10632,15 +10629,65 @@ graphviz.") (string-prefix? "python" item))) ((python) (setenv "C_INCLUDE_PATH" - (string-append greenlet "/" python))))) + (string-append greenlet "/" python ":" + (or (getenv "C_INCLUDE_PATH") + "")))))) #t)) - (add-before 'check 'skip-timer-test + (add-before 'check 'pretend-to-be-CI (lambda _ - ;; XXX: Skip 'TestTimerResolution', which appears to be - ;; unreliable. - (substitute* "src/greentest/test__core_timer.py" - (("not greentest.RUNNING_ON_CI") "False")) + ;; A few tests are skipped due to network constraints or + ;; get longer timeouts when running in a CI environment. + ;; Piggy-back on that, as we need the same adjustments. + (setenv "TRAVIS" "1") + (setenv "APPVEYOR" "1") #t)) + (add-before 'check 'adjust-tests + (lambda _ + (let ((disabled-tests + '(;; These tests rely on networking which is not + ;; available in the build container. + "test_urllib2net.py" + "test__server.py" + "test__server_pywsgi.py" + "test_socket.py" + "test__socket.py" + "test__socket_ssl.py" + "test__socket_dns.py" + "test__socket_dns6.py" + "test___example_servers.py" + "test__getaddrinfo_import.py" + "test__examples.py" + "test_httplib.py" + "test_https.py" + "test_urllib2_localnet.py" + "test_ssl.py" + "test__ssl.py" + ;; XXX: These tests borrow functionality from the + ;; Python builtin 'test' module, but it is not + ;; installed with the Guix Python distribution. + "test_smtpd.py" + "test_wsgiref.py" + "test_urllib2.py" + "test_thread.py" + "test_threading.py" + "test__threading_2.py" + ;; FIXME: test_patch_twice_warning_events fails for + ;; no apparent reason. Needs more investigation! + "test__monkey.py" + ;; These tests rely on KeyboardInterrupts which do not + ;; work inside the build container for some reason + ;; (lack of controlling terminal?). + "test_subprocess.py" + "test__issues461_471.py" + ;; TODO: Patch out the tests that use getprotobyname, etc + ;; instead of disabling all the tests from these files. + "test__all__.py" + "test___config.py" + "test__execmodules.py"))) + (call-with-output-file "skipped_tests.txt" + (lambda (port) + (display (string-join disabled-tests "\n") port))) + #t))) (replace 'check (lambda _ ;; Make sure the build directory is on PYTHONPATH. @@ -10649,21 +10696,23 @@ graphviz.") (getenv "PYTHONPATH") ":" (getcwd) "/build/" (car (scandir "build" (cut string-prefix? "lib." <>))))) - (with-directory-excursion "src/greentest" - ;; XXX: Many tests require network access. Instead we only - ;; run known-good tests. Unfortunately we cannot use - ;; recursion here since this directory also contains - ;; Python-version-specific subfolders. - (apply invoke "python" "testrunner.py" "--config" - "known_failures.py" - (scandir "." (cut regexp-exec - (make-regexp "test_+(subprocess|core)") - <>))))))))) + + ;; Use the build daemons configured number of workers. + (setenv "NWORKERS" (number->string (parallel-job-count))) + + (invoke "python" "-m" "gevent.tests" "--config" + "known_failures.py" "--ignore" "skipped_tests.txt")))))) (propagated-inputs `(("python-greenlet" ,python-greenlet) ("python-objgraph" ,python-objgraph))) (native-inputs - `(("python-six" ,python-six))) + `(("python-six" ,python-six) + + ;; For tests. + ("python-dnspython" ,python-dnspython) + ("python-psutil" ,python-psutil) + ("python-zope.event" ,python-zope-event) + ("python-zope.interface" ,python-zope-interface))) (inputs `(("c-ares" ,c-ares) ("libev" ,libev))) @@ -10680,7 +10729,7 @@ to provide a high-level synchronous API on top of the libev event loop.") (strip-python2-variant python-gevent)))) (package (inherit base) - (native-inputs `(,@(package-native-inputs python-gevent) + (native-inputs `(,@(package-native-inputs base) ("python-mock" ,python2-mock)))))) (define-public python-fastimport From 5af516544856373e07fb8d57f14b7eef369623a8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:34:09 +0100 Subject: [PATCH 123/235] gnu: python-zope-interface: Update to 4.7.2. * gnu/packages/python-web.scm (python-zope-interface): Update to 4.7.2. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e431a072d1..775c87f194 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -992,14 +992,14 @@ dispatching systems can be built.") (define-public python-zope-interface (package (name "python-zope-interface") - (version "4.6.0") + (version "4.7.2") (source (origin (method url-fetch) (uri (pypi-uri "zope.interface" version)) (sha256 (base32 - "1rgh2x3rcl9r0v0499kf78xy86rnmanajf4ywmqb943wpk50sg8v")))) + "0r9kvb1q3lxrdhxabliv9nwhjsdmn1n0vcjv93rlqkyb7yyh24gx")))) (build-system python-build-system) (native-inputs `(("python-zope-event" ,python-zope-event))) From 9a1dfda6fa3f2efcb1125f51e854cf788c936387 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:35:03 +0100 Subject: [PATCH 124/235] gnu: python-zope-exceptions: Update to 4.3. * gnu/packages/python-web.scm (python-zope-exceptions): Update to 4.3. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 775c87f194..72377f11e6 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1017,14 +1017,14 @@ conforming to a given API or contract.") (define-public python-zope-exceptions (package (name "python-zope-exceptions") - (version "4.0.8") + (version "4.3") (source (origin (method url-fetch) (uri (pypi-uri "zope.exceptions" version)) (sha256 (base32 - "0zwxaaa66sqxg5k7zcrvs0fbg9ym1njnxnr28dfmchzhwjvwnfzl")))) + "04bjskwas17yscl8bs3l44maxspw1gdji0zcmr499fs420y9r9az")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; circular dependency with zope.testrunner From 16839ec340414a7cf7cff6427e8cf1756efaef8e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:36:42 +0100 Subject: [PATCH 125/235] gnu: python-zope-testing: Update to 4.7. * gnu/packages/python-web.scm (python-zope-testing): Update to 4.7. [source](modules, snippet): Remove. --- gnu/packages/python-web.scm | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 72377f11e6..51e246f513 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1042,20 +1042,14 @@ that have uses outside of the Zope framework.") (define-public python-zope-testing (package (name "python-zope-testing") - (version "4.6.2") + (version "4.7") (source (origin (method url-fetch) (uri (pypi-uri "zope.testing" version)) (sha256 (base32 - "0iiq54hjhkk2gpvzfjac70vyn4r0kw0ngvicshxbdwrkgf2gjq3g")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Remove pre-compiled .pyc files backup files from source. - (for-each delete-file (find-files "." "(\\.pyc|~)$")) - #t)))) + "1sh3c3i0m8n8fnhqiry0bk3rr356i56ry7calmn57s1pvv8yhsyn")))) (build-system python-build-system) (home-page "https://pypi.org/project/zope.testing/") (synopsis "Zope testing helpers") From ddacd13d564b38ac2cb3fee7aa6372790d033b2c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:42:45 +0100 Subject: [PATCH 126/235] gnu: python-zope-testrunner: Update to 5.1. * gnu/packages/python-web.scm (python-zope-testrunner): Update to 5.1. [source](uri): Download tarball instead of zipball. [native-inputs]: Remove UNZIP. Move PYTHON-ZOPE-INTERFACE and PYTHON-ZOPE-EXCEPTIONS ... [propagated-inputs]: ... here. --- gnu/packages/python-web.scm | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 51e246f513..176e54a6ac 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1063,25 +1063,23 @@ forms, HTTP servers, regular expressions, and more.") (define-public python-zope-testrunner (package (name "python-zope-testrunner") - (version "4.4.9") + (version "5.1") (source (origin (method url-fetch) - (uri (pypi-uri "zope.testrunner" version ".zip")) + (uri (pypi-uri "zope.testrunner" version)) (sha256 (base32 - "1r7iqknhh55y45f64mz5hghgvzx34h1i11k350s0avx6q8gznja1")))) + "0w3q66cy4crpj7c0hw0vvvvwf3g931rnvw7wwa20av7yqvv6ajim")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. (native-inputs - `(("python-six" ,python-six) - ;("python-zope-interface" ,python-zope-interface) - ("python-zope-exceptions" ,python-zope-exceptions) - ("python-zope-testing" ,python-zope-testing) - ("unzip" ,unzip))) + `(("python-zope-testing" ,python-zope-testing))) (propagated-inputs - `(("python-zope-interface" ,python-zope-interface))) + `(("python-six" ,python-six) + ("python-zope-exceptions" ,python-zope-exceptions) + ("python-zope-interface" ,python-zope-interface))) (home-page "https://pypi.org/project/zope.testrunner/") (synopsis "Zope testrunner script") (description "Zope.testrunner provides a script for running Python @@ -1089,13 +1087,7 @@ tests.") (license license:zpl2.1))) (define-public python2-zope-testrunner - (let ((base (package-with-python2 python-zope-testrunner))) - (package - (inherit base) - (native-inputs - (append (package-native-inputs base) - `(("python2-subunit" ,python2-subunit) - ("python2-mimeparse" ,python2-mimeparse))))))) + (package-with-python2 python-zope-testrunner)) (define-public python-zope-i18nmessageid (package From ce4b7a44366b0d40699c082fbfa8d985681187c7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 13:55:29 +0100 Subject: [PATCH 127/235] gnu: python-zope-i18nmessageid: Update to 5.0.1. * gnu/packages/python-web.scm (python-zope-i18nmessageid): Update to 5.0.1. [native-inputs]: Add PYTHON-COVERAGE and PYTHON-ZOPE-TESTRUNNER. [propagated-inputs]: Add PYTHON-SIX. --- gnu/packages/python-web.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 176e54a6ac..848d5856b5 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1092,15 +1092,20 @@ tests.") (define-public python-zope-i18nmessageid (package (name "python-zope-i18nmessageid") - (version "4.0.3") + (version "5.0.1") (source (origin (method url-fetch) (uri (pypi-uri "zope.i18nmessageid" version)) (sha256 (base32 - "1rslyph0klk58dmjjy4j0jxy21k03azksixc3x2xhqbkv97cmzml")))) + "0ndhn4w1qgwkfbwf9vm2bgq418z5g0wmfsgl0d9nz62cd0mi8d4m")))) (build-system python-build-system) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-zope-testrunner" ,python-zope-testrunner))) + (propagated-inputs + `(("python-six" ,python-six))) (home-page "https://pypi.org/project/zope.i18nmessageid/") (synopsis "Message identifiers for internationalization") (description "Zope.i18nmessageid provides facilities for declaring From a1e9c929fa7e0b8b79f86c32830dad8ca3263b85 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:11:59 +0100 Subject: [PATCH 128/235] gnu: python-zope-schema: Update to 5.0.1. * gnu/packages/python-web.scm (python-zope-schema): Update to 5.0.1. [propagated-inputs]: Remove PYTHON-ZOPE-EXCEPTIONS. [native-inputs]: Remove PYTHON-NOSE and PYTHON-COVERAGE. Add PYTHON-ZOPE-TESTRUNNER and PYTHON-ZOPE-I18NMESSAGEID. --- gnu/packages/python-web.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 848d5856b5..82185cd81f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1118,25 +1118,24 @@ internationalized messages within program source text.") (define-public python-zope-schema (package (name "python-zope-schema") - (version "4.4.2") + (version "5.0.1") (source (origin (method url-fetch) (uri (pypi-uri "zope.schema" version)) (sha256 (base32 - "1p943jdxb587dh7php4vx04qvn7b2877hr4qs5zyckvp5afhhank")))) + "0q93j0x52a42khw12al90jw2bk0wly3jwghql3a25zpwwxvn24ya")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.event. (propagated-inputs `(("python-zope-event" ,python-zope-event) - ("python-zope-exceptions" ,python-zope-exceptions) ("python-zope-interface" ,python-zope-interface))) (native-inputs - `(("python-zope-testing" ,python-zope-testing) - ("python-coverage" ,python-coverage) - ("python-nose" ,python-nose))) + `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) + ("python-zope-testing" ,python-zope-testing) + ("python-zope-testrunner" ,python-zope-testrunner))) (home-page "https://pypi.org/project/zope.schema/") (synopsis "Zope data schemas") (description "Zope.scheme provides extensions to zope.interface for From 2585304c6ea7293b71f8db4dd00cd11cb3e07cb5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:15:28 +0100 Subject: [PATCH 129/235] gnu: python-zope-configuration: Update to 4.3.1. * gnu/packages/python-web.scm (python-zope-configuration): Update to 4.3.1. [native-inputs]: Add PYTHON-ZOPE-TESTING and PYTHON-ZOPE-TESTRUNNER. [propagated-inputs]: Add PYTHON-ZOPE-INTERFACE. --- gnu/packages/python-web.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 82185cd81f..b1e60bc2a1 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1148,18 +1148,22 @@ defining data schemas.") (define-public python-zope-configuration (package (name "python-zope-configuration") - (version "4.0.3") + (version "4.3.1") (source (origin (method url-fetch) (uri (pypi-uri "zope.configuration" version)) (sha256 (base32 - "1x9dfqypgympnlm25p9m43xh4qv3p7d75vksv9pzqibrb4cggw5n")))) + "1qb88764fd7nkkmqv7fl9bxd1jirynkg5vbqkpqdiffnkxzp85kf")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. + (native-inputs + `(("python-zope-testing" ,python-zope-testing) + ("python-zope-testrunner" ,python-zope-testrunner))) (propagated-inputs `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) + ("python-zope-interface" ,python-zope-interface) ("python-zope-schema" ,python-zope-schema))) (home-page "https://pypi.org/project/zope.configuration/") (synopsis "Zope Configuration Markup Language") From a3a7a0331282a4d39f0f7c71ab551fc3038e835b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:18:04 +0100 Subject: [PATCH 130/235] gnu: python-zope-proxy: Update to 4.3.4. * gnu/packages/python-web.scm (python-zope-proxy): Update to 4.3.4. [native-inputs]: Add PYTHON-ZOPE-TESTRUNNER. --- gnu/packages/python-web.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index b1e60bc2a1..43f62883a8 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1177,17 +1177,19 @@ Markup Language.") (define-public python-zope-proxy (package (name "python-zope-proxy") - (version "4.1.6") + (version "4.3.4") (source (origin (method url-fetch) (uri (pypi-uri "zope.proxy" version)) (sha256 (base32 - "0pqwwmvm1prhwv1ziv9lp8iirz7xkwb6n2kyj36p2h0ppyyhjnm4")))) + "1g0rcfnbchpvqhm76aixqlz544dawrgmy8gw9zwmijhk6wfl9f26")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. + (native-inputs + `(("python-zope-testrunner" ,python-zope-testrunner))) (propagated-inputs `(("python-zope-interface" ,python-zope-interface))) (home-page "https://pypi.org/project/zope.proxy/") From 386d2fd130dd557a81620e8409e05e6be7c7507a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:20:16 +0100 Subject: [PATCH 131/235] gnu: python-zope-location: Update to 4.2. * gnu/packages/python-web.scm (python-zope-location): Update to 4.2. [native-inputs]: Add PYTHON-ZOPE-TESTRUNNER. [propagated-inputs]: Add PYTHON-ZOPE-INTERFACE. --- gnu/packages/python-web.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 43f62883a8..6ff5482612 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1207,19 +1207,22 @@ brokering, etc.) for which the proxy is responsible.") (define-public python-zope-location (package (name "python-zope-location") - (version "4.0.3") + (version "4.2") (source (origin (method url-fetch) (uri (pypi-uri "zope.location" version)) (sha256 (base32 - "1nj9da4ksiyv3h8n2vpzwd0pb03mdsh7zy87hfpx72b6p2zcwg74")))) + "1b40pzl8v00d583d3gsxv1qjdw2dhghlgkbgxl3m07d5r3izj857")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.interface. + (native-inputs + `(("python-zope-testrunner" ,python-zope-testrunner))) (propagated-inputs - `(("python-zope-proxy" ,python-zope-proxy) + `(("python-zope-interface" ,python-zope-interface) + ("python-zope-proxy" ,python-zope-proxy) ("python-zope-schema" ,python-zope-schema))) (home-page "https://pypi.org/project/zope.location/") (synopsis "Zope location library") From e26e084fbb33608379d124030d8f9413fcb00a16 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:23:24 +0100 Subject: [PATCH 132/235] gnu: python-zope-security: Update to 5.1.0. * gnu/packages/python-web.scm (python-zope-security): Update to 5.1.0. [native-inputs]: Remove PYTHON-SIX. Move PYTHON-ZOPE-COMPONENT and PYTHON-ZOPE-LOCATION ... [propagated-inputs]: ... here. Add PYTHON-ZOPE-INTERFACE. (python2-zope-security)[propagated-inputs]: Remove. --- gnu/packages/python-web.scm | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 6ff5482612..b02ffd5f58 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1236,26 +1236,26 @@ Zope3, which are are special objects that have a structural location.") (define-public python-zope-security (package (name "python-zope-security") - (version "4.0.3") + (version "5.1.0") (source (origin (method url-fetch) (uri (pypi-uri "zope.security" version)) (sha256 (base32 - "14zmf684amc0x32kq05yxnhfqd1cmyhafkw05gn81rn90zjv6ssy")))) + "1npfrgnm202v48wavpwn3450dsn7az12lfww95vbhxyjl11f14yb")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; FIXME: Tests can't find zope.testrunner. (propagated-inputs - `(("python-zope-i18nmessageid" ,python-zope-i18nmessageid) + `(("python-zope-component" ,python-zope-component) + ("python-zope-i18nmessageid" ,python-zope-i18nmessageid) + ("python-zope-interface" ,python-zope-interface) + ("python-zope-location" ,python-zope-location) ("python-zope-proxy" ,python-zope-proxy) ("python-zope-schema" ,python-zope-schema))) (native-inputs - `(("python-six" ,python-six) - ("python-zope-component" ,python-zope-component) - ("python-zope-configuration" ,python-zope-configuration) - ("python-zope-location" ,python-zope-location) + `(("python-zope-configuration" ,python-zope-configuration) ("python-zope-testrunner" ,python-zope-testrunner) ("python-zope-testing" ,python-zope-testing))) (home-page "https://pypi.org/project/zope.security/") @@ -1265,13 +1265,7 @@ security policies on Python objects.") (license license:zpl2.1))) (define-public python2-zope-security - (let ((zope-security (package-with-python2 python-zope-security))) - (package (inherit zope-security) - (propagated-inputs - `(("python2-zope-testrunner" ,python2-zope-testrunner) - ,@(alist-delete - "python-zope-testrunner" - (package-propagated-inputs zope-security))))))) + (package-with-python2 python-zope-security)) (define-public python-zope-component (package From 8317c89aa3573f4a597fc0b2eaf08769239c5e37 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 16 Mar 2020 14:51:20 +0100 Subject: [PATCH 133/235] gnu: python-tqdm: Update to 4.43.0. * gnu/packages/python-xyz.scm (python-tqdm): Update to 4.43.0. [arguments]: New field. [native-inputs]: Remove PYTHON-FLAKE8 and PYTHON-COVERAGE. [properties]: Remove. (python2-tqdm): Use PACKAGE-WITH-PYTHON2. --- gnu/packages/python-xyz.scm | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index be02b03639..c6d3e2ce19 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14496,34 +14496,35 @@ ignoring formatting changes.") (define-public python-tqdm (package (name "python-tqdm") - (version "4.19.6") + (version "4.43.0") (source (origin (method url-fetch) (uri (pypi-uri "tqdm" version)) (sha256 (base32 - "1pw0ngm0zn9papdmkwipi3yih5c3di6d0w849bdmrraq4d2d9h2y")))) + "093v4c2x5hpigv47zvyxl8wh10y2yd2gvz3l9vchn0zsp8hv2pzk")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + ;; This invokation is taken from tox.ini. + (invoke "nosetests" "--ignore-files=\"test_perf.py\"" + "-d" "-v" "tqdm/")))))) (native-inputs - `(("python-flake8" ,python-flake8) - ("python-nose" ,python-nose) - ("python-coverage" ,python-coverage))) + `(("python-nose" ,python-nose))) (home-page "https://github.com/tqdm/tqdm") (synopsis "Fast, extensible progress meter") (description "Make loops show a progress bar on the console by just wrapping any iterable with @code{|tqdm(iterable)|}. Offers many options to define design and layout.") - (license (list license:mpl2.0 license:expat)) - (properties `((python2-variant . ,(delay python2-tqdm)))))) + (license (list license:mpl2.0 license:expat)))) (define-public python2-tqdm - (let ((tqdm (package-with-python2 - (strip-python2-variant python-tqdm)))) - (package (inherit tqdm) - (native-inputs `(("python2-functools32" ,python2-functools32) - ,@(package-native-inputs tqdm)))))) + (package-with-python2 python-tqdm)) (define-public python-pkginfo (package From 948200832108311f4f6876b1ab60b098bbcb742d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 16 Mar 2020 15:25:58 +0100 Subject: [PATCH 134/235] gnu: wxwidgets: Refer to xdg-open. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Add xdg-utils. [arguments]: Add ‘refer-to-inputs’ phase to patch xdg-open calls. --- gnu/packages/wxwidgets.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm index 5a2ea1c88e..49b190b9df 100644 --- a/gnu/packages/wxwidgets.scm +++ b/gnu/packages/wxwidgets.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2017 Rene Saavedra ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017 Thomas Danckaert -;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019 Arun Isaac ;;; ;;; This file is part of GNU Guix. @@ -35,6 +35,7 @@ #:use-module (gnu packages) #:use-module (gnu packages compression) #:use-module (gnu packages databases) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gl) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) @@ -73,7 +74,8 @@ ("libtiff" ,libtiff) ("mesa" ,mesa) ("webkitgtk" ,webkitgtk) - ("sdl" ,sdl))) + ("sdl" ,sdl) + ("xdg-utils" ,xdg-utils))) (native-inputs `(("pkg-config" ,pkg-config))) (arguments @@ -91,7 +93,15 @@ (list (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib")) ;; No 'check' target. - #:tests? #f)) + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'refer-to-inputs + (lambda _ + (substitute* "src/unix/utilsx11.cpp" + (("wxExecute\\(xdg_open \\+") + (string-append "wxExecute(\"" (which "xdg-open") "\""))) + #t))))) (home-page "https://www.wxwidgets.org/") (synopsis "Widget toolkit for creating graphical user interfaces") (description From 5adc59e6fe8abb701df8fc97d56a6e60258318a4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:51:12 +0100 Subject: [PATCH 135/235] gnu: cook: Use archived home page. * gnu/packages/cook.scm (cook)[home-page]: Use a Web Archived copy. --- gnu/packages/cook.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cook.scm b/gnu/packages/cook.scm index 17e090d725..fb0f9104ec 100644 --- a/gnu/packages/cook.scm +++ b/gnu/packages/cook.scm @@ -73,7 +73,8 @@ ;; This test is therefore just skipped. ;; ("inetutils" ,inetutils) ("ed" ,ed))) - (home-page "http://miller.emu.id.au/pmiller/software/cook") + (home-page "https://web.archive.org/web/20140727122520/" + "http://miller.emu.id.au/pmiller/software/cook/") (synopsis "Tool for constructing files") (description "Cook is a tool for constructing files. It is given a set of files to create, and recipes of how to create them. In any non-trivial program From 0d2753ccc138877aea367512c8e6e3babb0ed474 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:51:22 +0100 Subject: [PATCH 136/235] gnu: agda: Use HTTPS home page. * gnu/packages/agda.scm (agda)[home-page]: Use HTTPS. --- gnu/packages/agda.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 60944ddb04..98768c668a 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -126,7 +126,7 @@ (for-each (cut invoke agda-compiler <>) (find-files (string-append out "/share") "\\.agda$")) #t)))))) - (home-page "http://wiki.portal.chalmers.se/agda/") + (home-page "https://wiki.portal.chalmers.se/agda/") (synopsis "Dependently typed functional programming language and proof assistant") (description From 89b49245ef1230aba62abac8263b39d04e144fb1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:51:38 +0100 Subject: [PATCH 137/235] gnu: cogl: Use HTTPS home page. * gnu/packages/gnome.scm (cogl)[home-page]: Use HTTPS. --- gnu/packages/gnome.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index a80bce9332..1a213bebf0 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4586,7 +4586,7 @@ throughout GNOME for API documentation).") (assoc-ref inputs "xorg-server"))) (setenv "DISPLAY" ":1") #t))))) - (home-page "http://www.cogl3d.org") + (home-page "https://www.cogl3d.org") (synopsis "Object oriented GL/GLES Abstraction/Utility Layer") (description "Cogl is a small library for using 3D graphics hardware to draw pretty From 1fddf8ef1702f96340d7bede8ecbd90b64c2019f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 16 Mar 2020 16:48:18 +0100 Subject: [PATCH 138/235] gnu: cook: Fix. This follows up on commit 5adc59e6fe8abb701df8fc97d56a6e60258318a4. * gnu/packages/cook.scm (cook)[home-page]: Better. Reported-by: Marius Bakke --- gnu/packages/cook.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cook.scm b/gnu/packages/cook.scm index fb0f9104ec..16c288cc82 100644 --- a/gnu/packages/cook.scm +++ b/gnu/packages/cook.scm @@ -73,8 +73,8 @@ ;; This test is therefore just skipped. ;; ("inetutils" ,inetutils) ("ed" ,ed))) - (home-page "https://web.archive.org/web/20140727122520/" - "http://miller.emu.id.au/pmiller/software/cook/") + (home-page (string-append "https://web.archive.org/web/20140727122520/" + "http://miller.emu.id.au/pmiller/software/cook/")) (synopsis "Tool for constructing files") (description "Cook is a tool for constructing files. It is given a set of files to create, and recipes of how to create them. In any non-trivial program From 057b34478fd8ec7fa1de8c66b125b197d02b3ee5 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 16 Mar 2020 13:54:51 -0400 Subject: [PATCH 139/235] gnu: linux-libre@4.19: Update to 4.19.110. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.110. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f1bc5798ab..8dd5061b6c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -370,10 +370,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.109") +(define-public linux-libre-4.19-version "4.19.110") (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "0kwnlv5336vqdf38dzn077ic17zkb4rl5khxmc47syzd9zm4fhnh"))) + (hash (base32 "15kbgj13vsr74c61vzs96a72k86x205jjq5bz9pbn70698n3s4fa"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) From f86dd71cbdc4de5c4a38a7c598c99e630f360757 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:27:51 +0200 Subject: [PATCH 140/235] gnu: rust-cargon-0.0: Don't skip build. * gnu/pacakges/crates-io.scm (rust-cargon-0.0)[arguments]: Don't skip build. Move rust-gcc-0.3 from cargo-development-inputs to cargo-inputs. --- gnu/packages/crates-io.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 87493cff05..57b192c4b3 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -1745,8 +1745,7 @@ capabilities") "1cszlab7jk736p0lb50ag4l9nv72m7j41bwrmygl0lr4iz0350w2")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-development-inputs + `(#:cargo-inputs (("rust-gcc" ,rust-gcc-0.3)))) (home-page "https://github.com/bryant/argon2rs") (synopsis "Thin wrapper around the Argon2 C library") From 182f2a471d85c4936126de84aaa494896a9d940a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:28:51 +0200 Subject: [PATCH 141/235] gnu: rust-argon2rs-0.2: Don't skip build. * gnu/packages/crates-io.scm (rust-argon2rs-0.2)[arguments]: Don't skip build. Add phase to find all rust dependencies. --- gnu/packages/crates-io.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 57b192c4b3..45b941d189 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -476,12 +476,18 @@ text or blue underlined text, on ANSI terminals.") "14mkgkrjd4b4zy92pflz6yb4j1wn2chbd8jczxknxbkdm2vb0rrz")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-inputs + `(#:cargo-inputs (("rust-blake2-rfc" ,rust-blake2-rfc-0.2) ("rust-scoped-threadpool" ,rust-scoped-threadpool-0.1)) #:cargo-development-inputs - (("rust-cargon" ,rust-cargon-0.0)))) + (("rust-cargon" ,rust-cargon-0.0)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-cargo-toml + (lambda _ + (substitute* "Cargo.toml" + (("\\{ path =.*,") "{")) + #t))))) (home-page "https://github.com/bryant/argon2rs") (synopsis "Rust password hashing library that runs on Argon2") (description "This package provides a pure Rust password hashing library From c11eea603e8829daf7397c270b60ea96bfea8a29 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:34:19 +0200 Subject: [PATCH 142/235] gnu: rust-rawpointer-0.1: Don't skip build. * gnu/packages/crates-io.scm (rust-rawpointer-0.1)[arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 45b941d189..da82ecbeba 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13618,7 +13618,6 @@ random number generators.") (base32 "06ghpm9y7gacks78s3maakha07kbnwrxif5q37r2l7z1sali3b7b")))) (build-system cargo-build-system) - (arguments '(#:skip-build? #t)) (home-page "https://github.com/bluss/rawpointer/") (synopsis "Extra methods for raw pointers") (description "Extra methods for raw pointers. For example From fde752baa7a71f96c293c3d6ee68348fd35c41f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:36:47 +0200 Subject: [PATCH 143/235] gnu: rust-rand-xorshift-0.2: Don't skip build. * gnu/packages/crates-io.scm (rust-rand-xorshift-0.2)[arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index da82ecbeba..9fbcadf3bc 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13474,8 +13474,7 @@ generator based on timing jitter.") "1a6wy76lc5fimm1n9n8fzhp4cfjwfwxh4hx63bg3vlh1d2w1dm3p")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-inputs + `(#:cargo-inputs (("rust-rand-core" ,rust-rand-core-0.5) ("rust-serde" ,rust-serde-1.0)) #:cargo-development-inputs From 723c5d577212a740acca580dcf90f732f08bee08 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:39:32 +0200 Subject: [PATCH 144/235] gnu: rust-rand-0.3: Don't skip build. * gnu/packages/crates-io.scm (rust-rand-0.3)[arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 9fbcadf3bc..a7c4198d5e 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13121,8 +13121,7 @@ useful types and distributions, and some randomness-related algorithms.") (base32 "0v679h38pjjqj5h4md7v2slsvj6686qgcn7p9fbw3h43iwnk1b34")))) (arguments - `(#:skip-build? #t - #:cargo-inputs + `(#:cargo-inputs (("rust-libc" ,rust-libc-0.2) ("rust-rand" ,rust-rand-0.4)))))) From 8a65ca6f8c1270e63d3581ca11b6b86e22a5e9e7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 Mar 2020 21:41:34 +0200 Subject: [PATCH 145/235] gnu: rust-rand-0.4: Don't skip build. * gnu/packages/crates-io.scm (rust-rand-0.4)[arguments]: Don't skip build. --- gnu/packages/crates-io.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a7c4198d5e..1e1e9bf5db 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -13099,8 +13099,7 @@ useful types and distributions, and some randomness-related algorithms.") (base32 "14qjfv3gggzhnma20k0sc1jf8y6pplsaq7n1j9ls5c8kf2wl0a2m")))) (arguments - `(#:skip-build? #t - #:cargo-inputs + `(#:cargo-inputs (("rust-fuchsia-cprng" ,rust-fuchsia-cprng-0.1) ("rust-rand-core" ,rust-rand-core-0.3) ("rust-rdrand" ,rust-rdrand-0.4) From a55472955d7dbe7385fb25a5c31b26f8ebfa6e93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 17:39:08 +0100 Subject: [PATCH 146/235] tests: nfs-server: Use marionette helper procedures. * gnu/tests/nfs.scm (run-nfs-server-test)[test](wait-for-file): Remove. ("nscd is listening on its socket"): Use 'wait-for-unix-socket'. --- gnu/tests/nfs.scm | 30 ++---------------------------- 1 file changed, 2 insertions(+), 28 deletions(-) diff --git a/gnu/tests/nfs.scm b/gnu/tests/nfs.scm index 635c4a7322..00109b752e 100644 --- a/gnu/tests/nfs.scm +++ b/gnu/tests/nfs.scm @@ -196,18 +196,6 @@ (define marionette (make-marionette (list #$(virtual-machine os)))) - (define (wait-for-file file) - ;; Wait until FILE exists in the guest - (marionette-eval - `(let loop ((i 10)) - (cond ((file-exists? ,file) - #t) - ((> i 0) - (sleep 1) - (loop (- i 1))) - (else - (error "File didn't show up: " ,file)))) - marionette)) (mkdir #$output) (chdir #$output) @@ -231,22 +219,8 @@ marionette)) (test-assert "nscd is listening on its socket" - (marionette-eval - ;; XXX: Work around a race condition in nscd: nscd creates its - ;; PID file before it is listening on its socket. - '(let ((sock (socket PF_UNIX SOCK_STREAM 0))) - (let try () - (catch 'system-error - (lambda () - (connect sock AF_UNIX "/var/run/nscd/socket") - (close-port sock) - (format #t "nscd is ready~%") - #t) - (lambda args - (format #t "waiting for nscd...~%") - (usleep 500000) - (try))))) - marionette)) + (wait-for-unix-socket "/var/run/nscd/socket" + marionette)) (test-assert "network is up" (marionette-eval From e28770df718b733959a4cae933e9c2e8d32715be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 17:45:32 +0100 Subject: [PATCH 147/235] services: nfs: Move activation snippet out of line. * gnu/services/nfs.scm (%nfs-activation): New variable. (nfs-service-type)[extensions]: Refer to %NFS-ACTIVATION. --- gnu/services/nfs.scm | 42 +++++++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 19 deletions(-) diff --git a/gnu/services/nfs.scm b/gnu/services/nfs.scm index 140a11856a..3b7dd78eca 100644 --- a/gnu/services/nfs.scm +++ b/gnu/services/nfs.scm @@ -360,31 +360,35 @@ #t)) (respawn? #f))))) +(define %nfs-activation + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (system* "mount" "-t" "nfsd" + "nfsd" "/proc/fs/nfsd") + + (mkdir-p "/var/lib/nfs") + ;; directory containing monitor list + (mkdir-p "/var/lib/nfs/sm") + ;; Needed for client recovery tracking + (mkdir-p "/var/lib/nfs/v4recovery") + (let ((user (getpw "nobody"))) + (chown "/var/lib/nfs" + (passwd:uid user) + (passwd:gid user)) + (chown "/var/lib/nfs/v4recovery" + (passwd:uid user) + (passwd:gid user))) + #t))) + (define nfs-service-type (service-type (name 'nfs) (extensions (list (service-extension shepherd-root-service-type nfs-shepherd-services) - (service-extension activation-service-type - (const #~(begin - (use-modules (guix build utils)) - (system* "mount" "-t" "nfsd" - "nfsd" "/proc/fs/nfsd") - - (mkdir-p "/var/lib/nfs") - ;; directory containing monitor list - (mkdir-p "/var/lib/nfs/sm") - ;; Needed for client recovery tracking - (mkdir-p "/var/lib/nfs/v4recovery") - (let ((user (getpw "nobody"))) - (chown "/var/lib/nfs" - (passwd:uid user) - (passwd:gid user)) - (chown "/var/lib/nfs/v4recovery" - (passwd:uid user) - (passwd:gid user))) - #t))) + (service-extension activation-service-type (const %nfs-activation)) (service-extension etc-service-type (lambda (config) `(("exports" From 70526bdbe0221ed9077df31cb24374100685725b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 18:31:09 +0100 Subject: [PATCH 148/235] services: nfs: Remove unnecessary "mount" invocation. * gnu/services/nfs.scm (%nfs-activation): Remove unnecessary "mount" invocation (/proc/fs/nfsd is automatically mounted, somehow). Remove unnecessary 'mkdir-p' call. --- gnu/services/nfs.scm | 4 ---- 1 file changed, 4 deletions(-) diff --git a/gnu/services/nfs.scm b/gnu/services/nfs.scm index 3b7dd78eca..c90984387e 100644 --- a/gnu/services/nfs.scm +++ b/gnu/services/nfs.scm @@ -365,10 +365,6 @@ #~(begin (use-modules (guix build utils)) - (system* "mount" "-t" "nfsd" - "nfsd" "/proc/fs/nfsd") - - (mkdir-p "/var/lib/nfs") ;; directory containing monitor list (mkdir-p "/var/lib/nfs/sm") ;; Needed for client recovery tracking From d3fecbab82f17ef6736300cf2e18981d04ffc25f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 Mar 2020 22:18:15 +0100 Subject: [PATCH 149/235] gnu: Add tla. * gnu/packages/version-control.scm (tla): New variable. --- gnu/packages/version-control.scm | 59 +++++++++++++++++++++++++++++++- 1 file changed, 58 insertions(+), 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index bf97f89cd6..86b1d58654 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2013 Cyril Roelandt -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès ;;; Copyright © 2013, 2014 Andreas Enge ;;; Copyright © 2015, 2016 Mathieu Lirzin ;;; Copyright © 2014, 2015, 2016 Mark H Weaver @@ -2407,3 +2407,60 @@ interrupted, published, and collaborated on while in progress.") videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server.") (license license:expat))) + +(define-public tla + (package + (name "gnu-arch") + (version "1.3.5") + (source (origin + (method url-fetch) + (uri (string-append "https://ftp.gnu.org/old-gnu/gnu-arch/" + "tla-" version ".tar.gz")) + (sha256 + (base32 + "01mfzj1i6p4s8191cgd5850hds1zls88hkf9rb6qx1vqjv585aj0")) + (modules '((guix build utils))) + (snippet + '(begin + ;; In tar 1.32, '--preserve' is ambiguous and leads to an + ;; error, so address that. + (substitute* "src/tla/libarch/archive.c" + (("\"--preserve\"") + "\"--preserve-permissions\"")) + #t)))) + (build-system gnu-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (chdir "src") + + (mkdir "=build") + (chdir "=build") + + ;; For libneon's 'configure' script. + ;; XXX: There's a bundled copy of neon. + (setenv "CONFIG_SHELL" (which "sh")) + + (invoke "../configure" "--prefix" out + "--config-shell" (which "sh") + "--with-posix-shell" (which "sh") + "--with-cc" "gcc"))))) + + + ;; There are build failures when building in parallel. + #:parallel-build? #f + #:parallel-tests? #f + + #:test-target "test")) + (native-inputs + `(("which" ,which))) + (synopsis "Historical distributed version-control system") + (description + "GNU Arch, aka. @code{tla}, was one of the first free distributed +version-control systems (DVCS). It saw its last release in 2006. This +package is provided for users who need to recover @code{tla} repositories and +for historians.") + (home-page "https://www.gnu.org/software/gnu-arch/") + (license license:gpl2))) ;version 2 only From 19b7d41d3407d2e3c64edffa37042551e06c4b07 Mon Sep 17 00:00:00 2001 From: Ekaitz Zarraga Date: Mon, 16 Mar 2020 21:12:22 +0100 Subject: [PATCH 150/235] gnu: gnome-shell-extension-appindicator: Update to 33. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome-xyz.scm (gnome-shell-extension-appindicator): Update to 33. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index b8cd32db08..aeeced42bd 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -123,7 +123,7 @@ the Obsidian icon theme.") (define-public gnome-shell-extension-appindicator (package (name "gnome-shell-extension-appindicator") - (version "30") + (version "33") (source (origin (method git-fetch) (uri (git-reference @@ -132,7 +132,7 @@ the Obsidian icon theme.") (commit (string-append "v" version)))) (sha256 (base32 - "1fjhx23jqwv3d0smwhnjvc35gqhwk9p5f96ic22pfax653cn5vh8")) + "0qm77s080nbf4gqnfzpwp8a7jf7lliz6fxbsd3lasvrr11pgsk87")) (file-name (git-file-name name version)))) (build-system copy-build-system) (arguments From 06f0453ad27c92633d3630dbe49a16dcb0281d04 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 17 Mar 2020 00:05:32 +0100 Subject: [PATCH 151/235] guix: import: opam: Use a default repository. * guix/import/opam.scm (opam->guix-package): Use a default value for `repository`. --- guix/import/opam.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/import/opam.scm b/guix/import/opam.scm index 394415fdd4..ae7df8a8b5 100644 --- a/guix/import/opam.scm +++ b/guix/import/opam.scm @@ -250,7 +250,7 @@ path to the repository." (substring version 1) version))))) -(define* (opam->guix-package name #:key repository) +(define* (opam->guix-package name #:key (repository (get-opam-repository))) "Import OPAM package NAME from REPOSITORY (a directory name) or, if REPOSITORY is #f, from the official OPAM repository. Return a 'package' sexp or #f on failure." From 70c910eb98f1abc9a4a9bd31d08c629f2f5e8f0c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 16 Mar 2020 18:45:08 +0100 Subject: [PATCH 152/235] gnu: reaver: Update to 1.6.6. * gnu/packages/networking.scm (reaver): Update to 1.6.6. [source]: Hard-code NAME. --- gnu/packages/networking.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 4fa5008149..48b2570d9d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -990,15 +990,15 @@ non-existing entropy of some access points.") (define-public reaver (package (name "reaver") - (version "1.6.5") + (version "1.6.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/t6x/reaver-wps-fork-t6x/releases/" - "download/v" version "/" name "-" version ".tar.xz")) + "download/v" version "/reaver-" version ".tar.xz")) (sha256 (base32 - "0sva3g0kwgv143n9l3lg4qp5iiqz7nk76nr0hwivsnglbhk9sbil")))) + "00k7mc81ifv0wma7k4v18mj498badbw5yls6c28qin3d1gda0ag3")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -1021,7 +1021,7 @@ non-existing entropy of some access points.") (find-files "." "README.*")) (install-file "reaver.1" man1) #t)))) - #:tests? #f)) ; there are no tests + #:tests? #f)) ; there are no tests (inputs `(("libpcap" ,libpcap))) (propagated-inputs From aa0bcb6c5326c96d0a730bbb27af1e496914a5c9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 16 Mar 2020 20:46:27 +0100 Subject: [PATCH 153/235] gnu: doctest: Update to 2.3.7. * gnu/packages/check.scm (doctest): Update to 2.3.7. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index fa14ac1544..1b60b99ce1 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -392,7 +392,7 @@ and it supports a very flexible form of test discovery.") (define-public doctest (package (name "doctest") - (version "2.3.6") + (version "2.3.7") (home-page "https://github.com/onqtam/doctest") (source (origin (method git-fetch) @@ -400,7 +400,7 @@ and it supports a very flexible form of test discovery.") (file-name (git-file-name name version)) (sha256 (base32 - "070gkwffi73i2p0azga9yxj8km32bp8bw4jvkvz1vzlpavyii5kn")))) + "134lx7pjnglrl4wdmyr9dz3rjb6d4ir6rvapg00gp52n44dbhnrq")))) (build-system cmake-build-system) (synopsis "C++ test framework") (description From 5144e314925d6014b496bcc6090f46e97318b5fa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 00:19:01 +0100 Subject: [PATCH 154/235] gnu: eigen: Update to 3.3.7. * gnu/packages/algebra.scm (eigen): Update to 3.3.7. [source]: Add a patch to fix a test failure. * gnu/packages/patches/eigen-stabilise-sparseqr-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/algebra.scm | 7 +- .../eigen-stabilise-sparseqr-test.patch | 74 +++++++++++++++++++ 3 files changed, 79 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/eigen-stabilise-sparseqr-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5cde920c8c..caa73d44d4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -826,6 +826,7 @@ dist_patch_DATA = \ %D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \ %D%/packages/patches/dstat-skip-devices-without-io.patch \ %D%/packages/patches/dvd+rw-tools-add-include.patch \ + %D%/packages/patches/eigen-stabilise-sparseqr-test.patch \ %D%/packages/patches/einstein-build.patch \ %D%/packages/patches/elfutils-tests-ptrace.patch \ %D%/packages/patches/elixir-path-length.patch \ diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 50cb3001cb..8682ecd8d0 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014, 2018 Mark H Weaver ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017, 2019 Eric Bavier ;;; Copyright © 2020 Björn Höfling @@ -910,15 +910,16 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).") (define-public eigen (package (name "eigen") - (version "3.3.5") + (version "3.3.7") (source (origin (method url-fetch) (uri (string-append "https://bitbucket.org/eigen/eigen/get/" version ".tar.bz2")) (sha256 (base32 - "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk")) + "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz")) (file-name (string-append name "-" version ".tar.bz2")) + (patches (search-patches "eigen-stabilise-sparseqr-test.patch")) (modules '((guix build utils))) (snippet ;; There are 3 test failures in the "unsupported" directory, diff --git a/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch b/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch new file mode 100644 index 0000000000..b95b46077a --- /dev/null +++ b/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch @@ -0,0 +1,74 @@ +From: Tobias Geerinckx-Rice +Date: Mon, 16 Mar 2020 22:51:37 +0000 +Subject: gnu: eigen: Stabilise sparseqr test. + +Taken verbatim from this[0] upstream commit. + +[0]: https://gitlab.com/libeigen/eigen/-/commit/3b5deeb546d4017b24846f5b0dc3296a50a039fe + +From 3b5deeb546d4017b24846f5b0dc3296a50a039fe Mon Sep 17 00:00:00 2001 +From: Gael Guennebaud +Date: Tue, 19 Feb 2019 22:57:51 +0100 +Subject: [PATCH] bug #899: make sparseqr unit test more stable by 1) trying + with larger threshold and 2) relax rank computation for rank-deficient + problems. + +--- + test/sparseqr.cpp | 31 ++++++++++++++++++++++++++----- + 1 file changed, 26 insertions(+), 5 deletions(-) + +diff --git a/test/sparseqr.cpp b/test/sparseqr.cpp +index 3ffe62314..3576cc626 100644 +--- a/test/sparseqr.cpp ++++ b/test/sparseqr.cpp +@@ -43,6 +43,7 @@ int generate_sparse_rectangular_problem(MatrixType& A, DenseMat& dA, int maxRows + + template void test_sparseqr_scalar() + { ++ typedef typename NumTraits::Real RealScalar; + typedef SparseMatrix MatrixType; + typedef Matrix DenseMat; + typedef Matrix DenseVector; +@@ -91,14 +92,34 @@ template void test_sparseqr_scalar() + exit(0); + return; + } +- +- VERIFY_IS_APPROX(A * x, b); +- +- //Compare with a dense QR solver ++ ++ // Compare with a dense QR solver + ColPivHouseholderQR dqr(dA); + refX = dqr.solve(b); + +- VERIFY_IS_EQUAL(dqr.rank(), solver.rank()); ++ bool rank_deficient = A.cols()>A.rows() || dqr.rank() we might have to increase the threshold ++ // to get a correct solution. ++ RealScalar th = RealScalar(20)*dA.colwise().norm().maxCoeff()*(A.rows()+A.cols()) * NumTraits::epsilon(); ++ for(Index k=0; (k<16) && !test_isApprox(A*x,b); ++k) ++ { ++ th *= RealScalar(10); ++ solver.setPivotThreshold(th); ++ solver.compute(A); ++ x = solver.solve(b); ++ } ++ } ++ ++ VERIFY_IS_APPROX(A * x, b); ++ ++ // For rank deficient problem, the estimated rank might ++ // be slightly off, so let's only raise a warning in such cases. ++ if(rank_deficient) ++g_test_level; ++ VERIFY_IS_EQUAL(solver.rank(), dqr.rank()); ++ if(rank_deficient) --g_test_level; ++ + if(solver.rank()==A.cols()) // full rank + VERIFY_IS_APPROX(x, refX); + // else +-- +2.24.1 + From bf782bfc3f960a65298af2fffa205b41ab7f71e1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 00:19:30 +0100 Subject: [PATCH 155/235] gnu: five-or-more: Update to 3.32.1. * gnu/packages/gnome.scm (five-or-more): Update to 3.32.1. [source]: Hard-code NAME. --- gnu/packages/gnome.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 1a213bebf0..77a888b3b9 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -3872,16 +3872,15 @@ and other secrets. It communicates with the \"Secret Service\" using DBus.") (define-public five-or-more (package (name "five-or-more") - (version "3.32.0") + (version "3.32.1") (source (origin (method url-fetch) - (uri (string-append "mirror://gnome/sources/" name "/" + (uri (string-append "mirror://gnome/sources/five-or-more/" (version-major+minor version) "/" - name "-" version ".tar.xz")) + "five-or-more-" version ".tar.xz")) (sha256 - (base32 - "0v52i22ygv6y4zqs8nyb1qmacmj9whhqrw7qss6vn7by4nsikhrn")))) + (base32 "0xw05dd2dwi9vsph9h158b4n89s5k07xrh6bjz1icm0pdmjwhpgk")))) (build-system meson-build-system) (arguments '(#:glib-or-gtk? #t From 97845067b12764ea8d4d7f207213144f7ccb8881 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 02:31:23 +0100 Subject: [PATCH 156/235] gnu: perl-test-simple: Update to 1.302172. * gnu/packages/perl-check.scm (perl-test-simple): Update to 1.302172. --- gnu/packages/perl-check.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 67bdfd81c4..6af240a40a 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -10,7 +10,7 @@ ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017 Christopher Baines ;;; Copyright © 2017 Petter -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Pierre Neidhardt ;;; Copyright © 2018 Kei Kebreau @@ -1237,14 +1237,14 @@ makes fork(2) safe to use in test cases.") (define-public perl-test-simple (package (name "perl-test-simple") - (version "1.302171") + (version "1.302172") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/E/EX/EXODIST/" "Test-Simple-" version ".tar.gz")) (sha256 (base32 - "12in730hr51h42dwd3c5k7ysyp0xyk17583mfvx6zg56nb990zz2")))) + "1z1l8dgssf0mqbgik33sc5j48iiapppkwmacwah990hj0j7pd23k")))) (build-system perl-build-system) (synopsis "Basic utilities for writing tests") (description From df10a64efc9fd9cd725dfc67347fdbfa1e1075c2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:20:45 +0100 Subject: [PATCH 157/235] gnu: shogun: Use HTTPS home page. * gnu/packages/machine-learning.scm (shogun)[home-page]: Use HTTPS. --- gnu/packages/machine-learning.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 62ef7b84e4..7deb6ee29a 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -566,7 +566,7 @@ optimizing, and searching weighted finite-state transducers (FSTs).") ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) - (home-page "http://shogun-toolbox.org/") + (home-page "https://shogun-toolbox.org/") (synopsis "Machine learning toolbox") (description "The Shogun Machine learning toolbox provides a wide range of unified and From 831d64cc174ec0607503006b243824df6e086f03 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:23:05 +0100 Subject: [PATCH 158/235] gnu: openimageio: Use HTTPS home page. * gnu/packages/graphics.scm (openimageio)[home-page]: Use HTTPS. --- gnu/packages/graphics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index f5ebfaacaa..1a1038eca2 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -420,7 +420,7 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.") related classes, utilities, and applications. There is a particular emphasis on formats and functionality used in professional, large-scale animation and visual effects work for film.") - (home-page "http://www.openimageio.org") + (home-page "https://www.openimageio.org") (license license:bsd-3))) ;; This older version of OpenImageIO is required for Blender 2.79. From fe5ed0bbe3acc58a71954adc836687d3c96cbb68 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:46:10 +0100 Subject: [PATCH 159/235] gnu: wireless-tools: Use HTTPS home page. * gnu/packages/linux.scm (wireless-tools)[home-page]: Use HTTPS. --- gnu/packages/linux.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8dd5061b6c..3ac7e616c8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3065,7 +3065,7 @@ Linux Wireless Extensions; consider using @code{iw} instead. The Wireless Extension was an interface allowing you to set Wireless LAN specific parameters and get the specific stats. It is deprecated in favor the nl80211 interface.") - (home-page "http://www.hpl.hp.com/personal/Jean_Tourrilhes/Linux/Tools.html") + (home-page "https://www.hpl.hp.com/personal/Jean_Tourrilhes/Linux/Tools.html") ;; wireless.21.h and wireless.22.h are distributed under lgpl2.1+, the ;; other files are distributed under gpl2. (license (list license:gpl2 license:lgpl2.1+)))) From c9938fa84f17b267e769fa1fbaa80dc9ad821ebe Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:50:20 +0100 Subject: [PATCH 160/235] gnu: glfw: Use HTTPS home page. * gnu/packages/gl.scm (glfw)[home-page]: Use HTTPS. --- gnu/packages/gl.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index c82d33037e..01241cd88e 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -733,7 +733,7 @@ OpenGL.") ("libxinerama" ,libxinerama) ("libxcursor" ,libxcursor) ("libxxf86vm" ,libxxf86vm))) - (home-page "http://www.glfw.org") + (home-page "https://www.glfw.org") (synopsis "OpenGL application development library") (description "GLFW is a library for OpenGL, OpenGL ES and Vulkan development for From cfff0b386d1d1b52bedad6977ef7e0ce1546ecb1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:51:06 +0100 Subject: [PATCH 161/235] gnu: fritzing: Use HTTPS home page. * gnu/packages/engineering.scm (fritzing)[home-page]: Use HTTPS. --- gnu/packages/engineering.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 361d4d54a6..6adb142ffb 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -648,7 +648,7 @@ multipole-accelerated algorithm.") (sha256 (base32 "1d2v8k7p176j0lczx4vx9n9gbg3vw09n2c4b6w0wj5wqmifywhc1")))))) - (home-page "http://fritzing.org") + (home-page "https://fritzing.org") (synopsis "Electronic circuit design") (description "The Fritzing application is @dfn{Electronic Design Automation} (EDA) From d74647b04a41e1b84092fb7d461e169e714e2aca Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:01:45 +0100 Subject: [PATCH 162/235] gnu: qdbm: Use HTTPS home page. * gnu/packages/databases.scm (qdbm)[home-page]: Use HTTPS. --- gnu/packages/databases.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index be4db42332..8491f7ac11 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1070,7 +1070,7 @@ Most public APIs are compatible with @command{mysqlclient} and MySQLdb.") (assoc-ref %outputs "out") "/lib")) #:make-flags (list "CFLAGS=-fPIC"))) - (home-page "http://fallabs.com/qdbm") + (home-page "https://fallabs.com/qdbm/") (synopsis "Key-value database") (description "QDBM is a library of routines for managing a database. The database is a simple data file containing key-value From f4766a181018c84327d840f0a7e6c9d4e38c04d4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:15:41 +0100 Subject: [PATCH 163/235] gnu: libjaylink: Use HTTPS home page. * gnu/packages/embedded.scm (libjaylink)[home-page]: Use HTTPS. --- gnu/packages/embedded.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm index 46c7a03104..131a928d80 100644 --- a/gnu/packages/embedded.scm +++ b/gnu/packages/embedded.scm @@ -450,7 +450,7 @@ languages are C and C++.") ("pkg-config" ,pkg-config))) (inputs `(("libusb" ,libusb))) - (home-page "http://repo.or.cz/w/libjaylink.git") + (home-page "https://repo.or.cz/w/libjaylink.git") (synopsis "Library to interface Segger J-Link devices") (description "libjaylink is a shared library written in C to access SEGGER J-Link and compatible devices.") From ce91eeacad28153c9517aef4c3eefc428c9ff470 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:16:23 +0100 Subject: [PATCH 164/235] gnu: libmng: Use HTTPS home page. * gnu/packages/image.scm (libmng)[home-page]: Use HTTPS. --- gnu/packages/image.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 38a8b2ed42..ad288b87ec 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1171,7 +1171,7 @@ channels.") `(("lcms" ,lcms) ("libjpeg" ,libjpeg) ("zlib" ,zlib))) - (home-page "http://www.libmng.com/") + (home-page "https://www.libmng.com/") (synopsis "Library for handling MNG files") (description "Libmng is the MNG (Multiple-image Network Graphics) reference library.") From 10b52f4695b337f399eb936d5fa68131ae3452bf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:17:00 +0100 Subject: [PATCH 165/235] gnu: simplescreenrecorder: Use HTTPS home page. * gnu/packages/video.scm (simplescreenrecorder)[home-page]: Use HTTPS. --- gnu/packages/video.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index c9d9cd5b91..cc1a011d9a 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2546,7 +2546,7 @@ making @dfn{screencasts}.") (list "-DWITH_QT5=TRUE") #:tests? #f)) ; no test suite ;; Using HTTPS causes part of the page to be displayed improperly. - (home-page "http://www.maartenbaert.be/simplescreenrecorder/") + (home-page "https://www.maartenbaert.be/simplescreenrecorder/") (synopsis "Screen recorder") (description "SimpleScreenRecorder is an easy to use screen recorder with a graphical user interface. It supports recording the entire screen, or a From 8fc83d98ddd887dab7e5ddce1e210076776e24cb Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 17 Mar 2020 11:10:45 +0100 Subject: [PATCH 166/235] gnu: httrack: Fix Texinfo markup in description. * gnu/packages/web.scm (httrack): Fix Texinfo markup in description. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index ac156b2b99..bde8c2bbb5 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -7207,7 +7207,7 @@ the Internet to a local directory, building recursively all directories, getting HTML, images, and other files from the server to your computer. HTTrack arranges the original site's relative link-structure. Simply open -a page of the @code{mirrored} website in your browser, and you can browse the +a page of the @emph{mirrored} website in your browser, and you can browse the site from link to link, as if you were viewing it online. HTTrack can also update an existing mirrored site, and resume interrupted downloads. From 0f8ae2ea08a8bb74885a3c9e9c5d714d03a69a0c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 17 Mar 2020 11:20:42 +0100 Subject: [PATCH 167/235] gnu: scintilla: Update to 4.3.2. * gnu/packages/text-editors.scm (scintilla): Update to 4.3.2. --- gnu/packages/text-editors.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 9a35e7edce..b7758f106d 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -661,14 +661,14 @@ and Octave. TeXmacs is completely extensible via Guile.") (define-public scintilla (package (name "scintilla") - (version "4.3.0") + (version "4.3.2") (source (origin (method url-fetch) (uri (let ((v (apply string-append (string-split version #\.)))) (string-append "https://www.scintilla.org/scintilla" v ".tgz"))) (sha256 - (base32 "0c52b2wg0y55kv3w7rnzp0nbd1yn2kksy0w8bjdp3gkl0v28wwx5")))) + (base32 "0d8ssl0d8r6bslbzd507l9c5g8mwn1zriak3fnf85936pdmkhq9h")))) (build-system gnu-build-system) (arguments `(#:make-flags (list "GTK3=1" "CC=gcc" "-Cgtk") From db9b6161104f7faeab62af7c01b8c141f7742856 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 Mar 2020 10:48:24 +0200 Subject: [PATCH 168/235] doc: Fix typo in prosody configuration. * doc/guix.texi (Messaging Services)[Prosody Service]: Switch 'cons' to 'cons*' in example prosody-service-type. --- doc/guix.texi | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 202d1347f7..a0920adc1c 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -32,7 +32,7 @@ Copyright @copyright{} 2015, 2016, 2017, 2019, 2020 Leo Famulari@* Copyright @copyright{} 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus@* Copyright @copyright{} 2016 Ben Woodcroft@* Copyright @copyright{} 2016, 2017, 2018 Chris Marusich@* -Copyright @copyright{} 2016, 2017, 2018, 2019 Efraim Flashner@* +Copyright @copyright{} 2016, 2017, 2018, 2019, 2020 Efraim Flashner@* Copyright @copyright{} 2016 John Darrington@* Copyright @copyright{} 2016, 2017 ng0@* Copyright @copyright{} 2016, 2017, 2018, 2019 Jan Nieuwenhuizen@* @@ -18152,7 +18152,7 @@ record as in this example: @lisp (service prosody-service-type (prosody-configuration - (modules-enabled (cons "groups" "mam" %default-modules-enabled)) + (modules-enabled (cons* "groups" "mam" %default-modules-enabled)) (int-components (list (int-component-configuration From 3c0456c6b556b438d4bfc4753d2fe4bc2b96868a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Mar 2020 13:22:01 +0100 Subject: [PATCH 169/235] gnu: Add guile-irc. * gnu/packages/guile-xyz.scm (guile-irc): New variable. --- gnu/packages/guile-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 8ada9c50e6..124373bf8c 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3201,3 +3201,35 @@ models and also supports a rich set of boolean query operators.") @code{.torrent} or metainfo files. Implements a bencode reader and writer according to Bitorrent BEP003.") (license license:gpl3+))) + +(define-public guile-irc + (let ((commit "375d3bde9c6ae7ccc9d7cc65817966b6fda8f26a") + (revision "0")) + (package + (name "guile-irc") + (version (git-version "0.3.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rekado/guile-irc.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "113lcckcywrz9060w1c3fnvr8d7crdsjgsv4h47hgmr1slgadl4y")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--enable-gnutls=yes"))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("texinfo" ,texinfo))) + (inputs + `(("gnutls" ,gnutls) + ("guile" ,guile-2.2))) + (home-page "https://github.com/rekado/guile-irc") + (synopsis "IRC library for Guile") + (description "This package provides a Guile library for @dfn{Internet +Relay Chat} (IRC).") + ;; Some file headers incorrectly say LGPLv2+. + (license license:lgpl2.1+)))) From 8ee8eb2698f495cebb6df01ddd56aab883d72915 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Tue, 17 Mar 2020 13:27:56 +0100 Subject: [PATCH 170/235] gnu: gpsd: Install python modules and scripts. * gnu/packages/gps.scm (gpsd)[native-inputs]: Remove python and add bc. [inputs]: Add python, python-pycairo, python-pygobject, python-pyserial, python-wrapper and qtbase. [arguments]: Update scons-flags, remove fix-paths phase, improve fix-build phase and add wrap-python-scripts phase. --- gnu/packages/gps.scm | 94 +++++++++++++++++++++----------------------- 1 file changed, 45 insertions(+), 49 deletions(-) diff --git a/gnu/packages/gps.scm b/gnu/packages/gps.scm index 936c3aeda0..cd2e09e966 100644 --- a/gnu/packages/gps.scm +++ b/gnu/packages/gps.scm @@ -27,7 +27,9 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system scons) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix utils) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages docbook) @@ -39,6 +41,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages sqlite) #:use-module (gnu packages xml)) @@ -227,64 +230,57 @@ such as elevation, speed, heart rate, power, temperature, and gear shifts.") (base32 "0faz2mvk82hi7ispxxih07lhpyz5dazs4gcknym9piiabga29p97")))) (build-system scons-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python))) + `(("bc" ,bc) + ("pkg-config" ,pkg-config))) (inputs `(("bluez" ,bluez) ("dbus" ,dbus) ("libcap" ,libcap) ("libusb" ,libusb) - ("ncurses" ,ncurses))) + ("ncurses" ,ncurses) + ("python" ,python) + ("python-pycairo" ,python-pycairo) + ("python-pygobject" ,python-pygobject) + ("python-pyserial" ,python-pyserial) + ("python-wrapper" ,python-wrapper) + ("qtbase" ,qtbase))) (arguments - `(#:scons-flags (list (string-append "prefix=" %output) - ;; TODO: Install python bindings. - "python=no") + `(#:scons-flags + (list (string-append "prefix=" %output) + (let ((version ,(version-major+minor (package-version python)))) + (string-append "python_libdir=" %output + "/lib/python" version + "/site-packages")) + "qt_versioned=5") #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((python3 (string-append (assoc-ref inputs "python") - "/bin/python3"))) - (substitute* '("contrib/gpsData.py" - "contrib/ntpshmviz" - "contrib/skyview2svg" - "contrib/webgps.py" - "devtools/ais.py" - "devtools/aivdmtable" - "devtools/cycle_analyzer" - "devtools/flocktest" - "devtools/identify_failing_build_options.py" - "devtools/regress-builder" - "devtools/regressdiff" - "devtools/sizes" - "devtools/striplog" - "devtools/tablegen.py" - "devtools/test_json_validity.py" - "devtools/uninstall_cleanup.py" - "gegps" - "gps/gps.py" - "gpscat" - "gpsfake" - "gpsprof" - "jsongen.py" - "leapsecond.py" - "maskaudit.py" - "test_maidenhead.py" - "test_misc.py" - "test_xgps_deps.py" - "ubxtool" - "valgrind-audit.py" - "xgps" - "xgpsspeed" - "zerk") - (("/usr/bin/python") python3) - (("/usr/bin/env python") python3))) - #t)) - (add-after 'fix-paths 'fix-build - (lambda _ + (add-after 'unpack 'fix-build + (lambda* (#:key outputs #:allow-other-keys) (substitute* "SConstruct" - (("'PATH'") - "'PATH','CPATH','LIBRARY_PATH'")) + (("envs = \\{\\}") + "envs = os.environ")) + #t)) + (add-after 'install 'wrap-python-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (pycairo (assoc-ref inputs "python-pycairo")) + (pygobject (assoc-ref inputs "python-pygobject")) + (pyserial (assoc-ref inputs "python-pyserial")) + (sitedir (lambda (package) + (string-append package + "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages"))) + (pythonpath (string-join (map sitedir + (list out pycairo pygobject + pyserial)) + ":"))) + (for-each (lambda (script) + (wrap-program (string-append out "/bin/" script) + `("PYTHONPATH" ":" prefix (,pythonpath)))) + '("gegps" "gpscat" "gpsfake" "gpsprof" + "ubxtool" "xgps" "xgpsspeed" "zerk"))) #t))))) (synopsis "GPS service daemon") (description From 8d003ca34499705d8dbccfcae4b7dd9bfe30c93c Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 17 Mar 2020 16:51:14 +0100 Subject: [PATCH 171/235] build-system: linux-module: Break some long lines. * gnu/build/linux-modules.scm (make-linux-module-builder, lower): Break some long commentary lines. --- guix/build-system/linux-module.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/guix/build-system/linux-module.scm b/guix/build-system/linux-module.scm index ba76ab85c3..1e1a07d0a2 100644 --- a/guix/build-system/linux-module.scm +++ b/guix/build-system/linux-module.scm @@ -78,7 +78,8 @@ (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (out-lib-build (string-append out "/lib/modules/build"))) - ; TODO: Only preserve the minimum, i.e. [Kbuild], Kconfig, scripts, include, ".config". + ;; TODO: Only preserve the minimum, i.e. [Kbuild], Kconfig, + ;; scripts, include, ".config". (copy-recursively "." out-lib-build) (let* ((linux (assoc-ref inputs "linux"))) (install-file (string-append linux "/System.map") @@ -111,7 +112,11 @@ ("linux-module-builder" ,(make-linux-module-builder linux)) ,@native-inputs - ;; TODO: Remove "gmp", "mpfr", "mpc" since they are only needed to compile the gcc plugins. Maybe remove "flex", "bison", "elfutils", "perl", "openssl". That leaves very little ("bc", "gcc", "kmod"). + ;; TODO: Remove "gmp", "mpfr", "mpc" since they are + ;; only needed to compile the gcc plugins. Maybe + ;; remove "flex", "bison", "elfutils", "perl", + ;; "openssl". That leaves very little ("bc", "gcc", + ;; "kmod"). ,@(package-native-inputs linux))) (outputs outputs) (build linux-module-build) From eecf72433fef8dee6bc3e1c69ea4f3f90410e096 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Mar 2020 16:59:17 +0100 Subject: [PATCH 172/235] gnu: agi-bio: Fix unqualified file reference. * gnu/packages/opencog.scm (agi-bio)[arguments]: Add phase 'fix-unqualified-load. --- gnu/packages/opencog.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/opencog.scm b/gnu/packages/opencog.scm index ea6858507e..c3b89d41dc 100644 --- a/gnu/packages/opencog.scm +++ b/gnu/packages/opencog.scm @@ -276,7 +276,17 @@ combination.") "/include/guile/2.2/") (string-append "-DGUILE_SITE_DIR=" (assoc-ref %outputs "out") - "/share/guile/site/2.2/")))) + "/share/guile/site/2.2/")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-unqualified-load + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "bioscience/bioscience.scm" + (("\\(load \"bioscience/types/bioscience_types.scm\"\\)") + (format #f "(load \"~a/bioscience/types/bioscience_types.scm\")" + (string-append (assoc-ref outputs "out") + "/share/guile/site/2.2/opencog")))) + #t))))) (inputs `(("atomspace" ,atomspace) ("cogutil" ,cogutil) From 5331dcd6fc8073ae7147e3c081247722270b490c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:30:12 +0100 Subject: [PATCH 173/235] gnu: opensubdiv: Use HTTPS home page. * gnu/packages/graphics.scm (opensubdiv)[home-page]: Use HTTPS. --- gnu/packages/graphics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 1a1038eca2..2d50a5f539 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -979,7 +979,7 @@ requirements.") ("libxi" ,libxi) ("zlib" ,zlib) ("glfw" ,glfw))) - (home-page "http://graphics.pixar.com/opensubdiv/") + (home-page "https://graphics.pixar.com/opensubdiv/") (synopsis "High performance subdivision surface evaluation") (description "OpenSubdiv is a set of libraries that implement high performance subdivision surface (subdiv) evaluation on massively parallel CPU From 096ed4f935168e4e02eb947d016a83397dad13c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:42:12 +0100 Subject: [PATCH 174/235] gnu: guitarix: Use HTTPS home page. * gnu/packages/audio.scm (guitarix)[home-page]: Use HTTPS. --- gnu/packages/audio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index b429aeb107..56eac50526 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1443,7 +1443,7 @@ patches that can be used with softsynths such as Timidity and WildMidi.") (list (search-path-specification (variable "LV2_PATH") (files '("lib/lv2"))))) - (home-page "http://guitarix.org/") + (home-page "https://guitarix.org/") (synopsis "Virtual guitar amplifier") (description "Guitarix is a virtual guitar amplifier running JACK. Guitarix takes the signal from your guitar as a mono-signal from your sound From 359b137cd62bbe9a3854bab692600acd8d487154 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:26:21 +0100 Subject: [PATCH 175/235] gnu: liboop: Use HTTPS home page. * gnu/packages/ssh.scm (liboop)[home-page]: Use HTTPS. --- gnu/packages/ssh.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index fdb3450e01..e3af517997 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -478,7 +478,7 @@ particularly useful for embedded systems, such as wireless routers.") (base32 "1q0p1l72pq9k3bi7a366j2rishv7dzzkg3i6r2npsfg7cnnidbsn")))) (build-system gnu-build-system) - (home-page "http://www.lysator.liu.se/liboop/") + (home-page "https://www.lysator.liu.se/liboop/") (synopsis "Event loop library") (description "Liboop is a low-level event loop management library for POSIX-based operating systems. It supports the development of modular, From 9bd0f41509ae405ed62f90af28769761fbe58a98 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:36:52 +0100 Subject: [PATCH 176/235] gnu: tftp-hpa: Use HTTPS home page. * gnu/packages/networking.scm (tftp-hpa)[home-page]: Use HTTPS. --- gnu/packages/networking.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 48b2570d9d..607416fe41 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1724,7 +1724,7 @@ speedtest.net.") "This is a tftp client derived from OpenBSD tftp with some extra options added and bugs fixed. The source includes readline support but it is not enabled due to license conflicts between the BSD advertising clause and the GPL.") - (home-page "http://git.kernel.org/cgit/network/tftp/tftp-hpa.git/about/") + (home-page "https://git.kernel.org/cgit/network/tftp/tftp-hpa.git/about/") ;; Some source files are distributed under a 3-clause BSD license, and ;; others under a 4-clause BSD license. Refer to the files in the source ;; distribution for clarification. From 6c71d56d7757b5f35bdd0d6fc623ba133c9c3e2e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 19:40:55 +0100 Subject: [PATCH 177/235] gnu: Add straw-viewer. * gnu/packages/video.scm (straw-viewer): New public variable. --- gnu/packages/video.scm | 85 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index cc1a011d9a..62b19e2dfb 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -123,6 +123,7 @@ #:use-module (gnu packages networking) #:use-module (gnu packages ocr) #:use-module (gnu packages perl) + #:use-module (gnu packages perl-check) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) #:use-module (gnu packages pretty-print) @@ -511,6 +512,90 @@ H.264 (MPEG-4 AVC) video streams.") (@command{mkvmerge}).") (license license:gpl2))) +(define-public straw-viewer + (package + (name "straw-viewer") + (version "0.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/trizen/straw-viewer") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "067j8wdfy29bi5ahky10xzzs8cr3mn95wl4kyqqjvjzri77a25j3")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build) + ("perl-test-pod" ,perl-test-pod))) + (inputs + `(("perl-data-dump" ,perl-data-dump) + ("perl-json" ,perl-json) + ("perl-libwww" ,perl-libwww) + ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) + ("perl-lwp-useragent-cached" ,perl-lwp-useragent-cached) + ("perl-mozilla-ca" ,perl-mozilla-ca) + ("perl-term-readline-gnu" ,perl-term-readline-gnu) + ("perl-unicode-linebreak" ,perl-unicode-linebreak) + ("xdg-utils" ,xdg-utils) + + ;; Some videos play without youtube-dl, but others silently fail to. + ("youtube-dl" ,youtube-dl))) + + ;; Required only when building the graphical interface (--gtk). + ;;("perl-file-sharedir" ,perl-file-sharedir) + (arguments + `(#:modules ((guix build perl-build-system) + (guix build utils) + (srfi srfi-26)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'refer-to-inputs + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/WWW/StrawViewer.pm" + (("'youtube-dl'") + (format #f "'~a/bin/youtube-dl'" + (assoc-ref inputs "youtube-dl")))) + (substitute* "bin/gtk-straw-viewer" + (("'xdg-open'") + (format #f "'~a/bin/xdg-open'" + (assoc-ref inputs "xdg-utils")))) + #t)) + (add-after 'install 'install-desktop + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (sharedir (string-append out "/share"))) + (install-file "share/gtk-straw-viewer.desktop" + (string-append sharedir "/applications")) + (install-file "share/icons/gtk-straw-viewer.png" + (string-append sharedir "/pixmaps")) + #t))) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin-dir (string-append out "/bin/")) + (site-dir (string-append out "/lib/perl5/site_perl/")) + (lib-path (getenv "PERL5LIB"))) + (for-each (cut wrap-program <> + `("PERL5LIB" ":" prefix (,lib-path ,site-dir))) + (find-files bin-dir)) + #t)))))) + (synopsis + "Light-weight application for searching and streaming videos from YouTube") + (description + "Straw-viewer searches for YouTube videos using @uref{https://invidio.us/, +invidio.us} and plays them locally in a native media player like @command{vlc} +or @command{mpv}. + +You can search for videos, playlists, and/or channels. The videos are streamed +directly to the player at the best chosen resolution and with closed captions if +available.") + ;; XXX Add #:module-build-flags '("--gtk") dependencies and this sentence. + ;; Both a command-line and a graphical interface are available. + (home-page "https://github.com/trizen/youtube-viewer") + (license license:perl-license))) + (define-public x265 (package (name "x265") From e496ee679d2c9548f5e3541a2a6486df179194d5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:56:38 +0100 Subject: [PATCH 178/235] gnu: bridge-utils: Update home page. * gnu/packages/linux.scm (bridge-utils)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/linux.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3ac7e616c8..6a29565aad 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2099,8 +2099,7 @@ Linux-based operating systems.") #t))) #:tests? #f)) ; no 'check' target - (home-page - "http://www.linuxfoundation.org/collaborate/workgroups/networking/bridge") + (home-page "https://wiki.linuxfoundation.org/networking/bridge") (synopsis "Manipulate Ethernet bridges") (description "Utilities for Linux's Ethernet bridging facilities. A bridge is a way From 720aa97782084d7c70bfae324b14f2f062ac1848 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:44:10 +0100 Subject: [PATCH 179/235] gnu: sipcalc: Use HTTPS home page. * gnu/packages/admin.scm (sipcalc)[home-page]: Use HTTPS. --- gnu/packages/admin.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 0862000dd2..9b1844f36d 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -709,7 +709,7 @@ IPv6, proxies, and Unix sockets.") (base32 "0mv3wndj4z2bsshh2k8d5sy3j8wxzgf8mzmmkvj1k8gpcz37dm6g")))) (build-system gnu-build-system) - (home-page "http://www.routemeister.net/projects/sipcalc/") + (home-page "https://www.routemeister.net/projects/sipcalc/") (synopsis "Command-line IP subnet calculator") (description "Sipcalc is an advanced command-line IP subnet calculator. It can take From 5a3cbfceb16da07c4b828dfa6add342f1afc1679 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:39:00 +0100 Subject: [PATCH 180/235] gnu: redis: Use HTTPS home page. * gnu/packages/databases.scm (redis)[home-page]: Use HTTPS. --- gnu/packages/databases.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 8491f7ac11..5727905beb 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1892,7 +1892,7 @@ similar to BerkeleyDB, LevelDB, etc.") (description "Redis is an advanced key-value cache and store. Redis supports many data structures including strings, hashes, lists, sets, sorted sets, bitmaps and hyperloglogs.") - (home-page "http://redis.io/") + (home-page "https://redis.io/") (license license:bsd-3))) (define-public kyotocabinet From 57f6ac8d902ca0103dd61cd2526aeb7284b171fc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 17 Mar 2020 20:28:33 +0100 Subject: [PATCH 181/235] gnu: pigx-scrnaseq: Update to 1.1.4. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9044ebca8d..6dfc23c1dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12815,7 +12815,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12823,7 +12823,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi")))) + "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) From 98c873181aa0005aa07e23566a37b3ede5523687 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 2 Mar 2020 14:47:20 -0500 Subject: [PATCH 182/235] gnu: go-github-com-pkg-errors: Update to 0.9.1. * gnu/packages/golang.scm (go-github-com-pkg-errors): Update to 0.9.1. --- gnu/packages/golang.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 0d92139311..184233b522 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3067,7 +3067,7 @@ network protocol.") (define-public go-github-com-pkg-errors (package (name "go-github-com-pkg-errors") - (version "0.9.0") + (version "0.9.1") (source (origin (method git-fetch) (uri (git-reference @@ -3076,7 +3076,7 @@ network protocol.") (file-name (git-file-name name version)) (sha256 (base32 - "1hlivqlcnm9wrj0v7h43gamw7mvg6svz9sm31fx28zn4ll25ablh")))) + "1761pybhc2kqr6v5fm8faj08x9bql8427yqg6vnfv6nhrasx1mwq")))) (build-system go-build-system) (arguments `(#:import-path "github.com/pkg/errors")) From cb78846c130c74c7c136c7b54584c94e2c672d1b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 2 Mar 2020 15:11:53 -0500 Subject: [PATCH 183/235] gnu: go-github-com-spaolacci-murmur3: Update to 1.1.0 * gnu/packages/golang.scm (go-github-com-spaolacci-murmur3): Update to 1.1.0. --- gnu/packages/golang.scm | 44 ++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 23 deletions(-) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 184233b522..bf6209d8ea 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2131,32 +2131,30 @@ increase approaching hashing speeds of 1GB/sec on a single core.") (license license:asl2.0)))) (define-public go-github-com-spaolacci-murmur3 - (let ((commit "f09979ecbc725b9e6d41a297405f65e7e8804acc") - (revision "0")) - (package - (name "go-github-com-spaolacci-murmur3") - (version (git-version "1.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/spaolacci/murmur3.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1lv3zyz3jy2d76bhvvs8svygx66606iygdvwy5cwc0p5z8yghq25")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/spaolacci/murmur3")) - (home-page "https://github.com/spaolacci/murmur3") - (synopsis "Native MurmurHash3 Go implementation") - (description "Native Go implementation of Austin Appleby's third -MurmurHash revision (aka MurmurHash3). + (package + (name "go-github-com-spaolacci-murmur3") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spaolacci/murmur3.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lv3zyz3jy2d76bhvvs8svygx66606iygdvwy5cwc0p5z8yghq25")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/spaolacci/murmur3")) + (home-page "https://github.com/spaolacci/murmur3") + (synopsis "Native MurmurHash3 Go implementation") + (description "Native Go implementation of Austin Appleby's third MurmurHash +revision (aka MurmurHash3). Reference algorithm has been slightly hacked as to support the streaming mode required by Go's standard Hash interface.") - (license license:bsd-3)))) + (license license:bsd-3))) (define-public go-github-com-multiformats-go-multihash (let ((commit "97cdb562a04c6ef66d8ed40cd62f8fbcddd396d6") From 88841a3ead043f032d60e994bceeb20889d66262 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 2 Mar 2020 15:12:38 -0500 Subject: [PATCH 184/235] gnu: Add go-github-com-willf-bitset. * gnu/packages/golang.scm (go-github-com-willf-bitset): New variable. --- gnu/packages/golang.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index bf6209d8ea..b0dd5ffe12 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3394,3 +3394,26 @@ data serialization format.") (description " A glob library that implements descending into other directories. It is optimized for filewalking. ") (license license:expat))) + +(define-public go-github-com-willf-bitset + (package + (name "go-github-com-willf-bitset") + (version "1.1.10") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/willf/bitset") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0wpaxg6va3qwd0hq0b8rpb1hswvzzbfm2h8sjmcsdpbkydjjx9zg")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/willf/bitset")) + (synopsis "Bitsets in Go") + (description "This package provides a Go implementation of bitsets, which +are a mapping between non-negative integers and boolean values focused on +efficient space usage.") + (home-page "https://github.com/willf/bitset") + (license license:bsd-3))) From 79405c030f802df3631a6b3617b4a9ea284b638d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 2 Mar 2020 15:13:16 -0500 Subject: [PATCH 185/235] gnu: Add go-github-com-willf-bloom. * gnu/packages/golang.scm (go-github-com-willf-bloom): New variable. --- gnu/packages/golang.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index b0dd5ffe12..f684470419 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3417,3 +3417,28 @@ are a mapping between non-negative integers and boolean values focused on efficient space usage.") (home-page "https://github.com/willf/bitset") (license license:bsd-3))) + +(define-public go-github-com-willf-bloom + (package + (name "go-github-com-willf-bloom") + (version "2.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/willf/bloom") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ygan8pgcay7wx3cs3ja8rdqj7nly7v3and97ddcc66020jxchzg")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/willf/bloom")) + (propagated-inputs + `(("go-github-com-spaolacci-murmur3" ,go-github-com-spaolacci-murmur3) + ("go-github-com-willf-bitset" ,go-github-com-willf-bitset))) + (synopsis "Bloom filters in Go") + (description "This package provides a Go implementation of bloom filters, +based on murmurhash.") + (home-page "https://github.com/willf/bloom") + (license license:bsd-2))) From 6838611252d027a1ef8324cd6dae049040374067 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 2 Mar 2020 15:13:37 -0500 Subject: [PATCH 186/235] gnu: Syncthing: Update to 1.4.0. * gnu/packages/syncthing.scm (syncthing): Update to 1.4.0. [inputs]: Add go-github-com-willf-bloom. --- gnu/packages/syncthing.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index afa32e99b4..77f0aa326d 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -30,7 +30,7 @@ (define-public syncthing (package (name "syncthing") - (version "1.3.4") + (version "1.4.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/syncthing/syncthing" @@ -38,7 +38,7 @@ "/syncthing-source-v" version ".tar.gz")) (sha256 (base32 - "025fhfqzcl5qd38zak8485pd67iqkzsf6frm02cl25s3ggv2f0p4")) + "1p9y943kd09pxmsaahbdml2mn2qlwbx23hvbsm1sqbbm8ma9ai8c")) (modules '((guix build utils))) ;; Delete bundled ("vendored") free software source code. (snippet '(begin @@ -95,6 +95,7 @@ ("go-github-com-ccding-go-stun" ,go-github-com-ccding-go-stun) ("go-github-com-audriusbutkevicius-pfilter" ,go-github-com-audriusbutkevicius-pfilter) ("go-github-com-lucas-clemente-quic-go" ,go-github-com-lucas-clemente-quic-go) + ("go-github-com-willf-bloom" ,go-github-com-willf-bloom) ;; For tests ("go-github-com-d4l3k-messagediff" ,go-github-com-d4l3k-messagediff))) From 317b13f30e1e23e8fb2f18fcff50b8ee2e448321 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 23:00:42 +0100 Subject: [PATCH 187/235] gnu: american-fuzzy-lop: Fix documentation directory. * gnu/packages/debug.scm (american-fuzzy-lop)[arguments]: Install documentation into its conventional location. --- gnu/packages/debug.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 34cc479589..3e3c308dae 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -230,6 +230,8 @@ tools that process C/C++ code.") #t)))))))))))) (arguments `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "DOC_PATH=$(PREFIX)/share/doc/" + ,name "-" ,version) "CC=gcc") #:phases (modify-phases %standard-phases (delete 'configure) From 3ba980b188ec52bdbd447e6385e4d1d5e93706aa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 23:02:56 +0100 Subject: [PATCH 188/235] gnu: american-fuzzy-lop: Update to 2.56b. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/debug.scm (american-fuzzy-lop): Update to 2.56b. [source]: Use GIT-FETCH from the new upstream, and GIT-FILE-NAME. [inputs]: Adjust custom-qemu's ‘apply-afl-patches’ phase to this new reality. Don't apply upstreamed Qemu patches. [arguments]: Make the git check-out writable. --- gnu/packages/debug.scm | 50 +++++++++++++++++++++++++++--------------- 1 file changed, 32 insertions(+), 18 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 3e3c308dae..83c9f6ae03 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -171,15 +171,16 @@ tools that process C/C++ code.") (_ "UNSUPPORTED")))) (package (name "american-fuzzy-lop") - (version "2.52b") ;It seems all releases have the 'b' suffix + (version "2.56b") ;It seems all releases have the 'b' suffix (source (origin - (method url-fetch) - (uri (string-append "http://lcamtuf.coredump.cx/afl/releases/" - "afl-" version ".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/google/AFL") + (commit (string-append "v" version)))) (sha256 - (base32 - "0ig0ij4n1pwry5dw1hk4q88801jzzy2cric6y2gd6560j55lnqa3")))) + (base32 "1q1g59gkm48aa4cg9h70jx4i2gapmypgp5rzs156b2avd95vwkn1")) + (file-name (git-file-name name version)))) (build-system gnu-build-system) (inputs `(("custom-qemu" @@ -204,24 +205,33 @@ tools that process C/C++ code.") (add-after 'unpack 'apply-afl-patches (lambda* (#:key inputs #:allow-other-keys) - (let* ((afl-dir (string-append "afl-" ,version)) - (patch-dir - (string-append afl-dir - "/qemu_mode/patches"))) - (invoke "tar" "xf" - (assoc-ref inputs "afl-src")) - (install-file (string-append patch-dir - "/afl-qemu-cpu-inl.h") - ".") - (copy-file (string-append afl-dir "/config.h") + (let* ((afl-src (assoc-ref inputs "afl-src")) + (patch-dir "qemu_mode/patches")) + (copy-recursively (string-append afl-src "/" + patch-dir) + patch-dir) + (install-file + (string-append patch-dir + "/afl-qemu-cpu-inl.h") + ".") + (copy-file (string-append afl-src "/config.h") "./afl-config.h") - (install-file (string-append afl-dir "/types.h") + (install-file (string-append afl-src "/types.h") ".") (substitute* "afl-qemu-cpu-inl.h" (("\\.\\./\\.\\./config.h") "afl-config.h")) (substitute* (string-append patch-dir "/cpu-exec.diff") (("\\.\\./patches/") "")) + + ;; These were already applied to qemu-minimal-2.10. + (for-each (lambda (obsolete-patch) + (delete-file (string-append + patch-dir "/" + obsolete-patch))) + (list "configure.diff" + "memfd.diff")) + (for-each (lambda (patch-file) (invoke "patch" "--force" "-p1" "--input" patch-file)) @@ -234,6 +244,10 @@ tools that process C/C++ code.") ,name "-" ,version) "CC=gcc") #:phases (modify-phases %standard-phases + (add-after 'unpack 'make-git-checkout-writable + (lambda _ + (for-each make-file-writable (find-files ".")) + #t)) (delete 'configure) ,@(if (string=? (%current-system) (or "x86_64-linux" "i686-linux")) @@ -258,7 +272,7 @@ tools that process C/C++ code.") (symlink (string-append qemu "/bin/qemu-" ,machine) (string-append out "/bin/afl-qemu-trace")) #t))) - (delete 'check)))) ; Tests are run during 'install phase. + (delete 'check)))) ; tests are run during 'install phase (home-page "http://lcamtuf.coredump.cx/afl") (synopsis "Security-oriented fuzzer") (description From 38e1b9efc8f18e3b2f6c28fc69e636357dc712db Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 17 Mar 2020 23:08:48 +0100 Subject: [PATCH 189/235] gnu: american-fuzzy-lop: Use HTTPS home page. * gnu/packages/debug.scm (american-fuzzy-lop)[home-page]: Use HTTPS. --- gnu/packages/debug.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 83c9f6ae03..718a76310d 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -273,7 +273,7 @@ tools that process C/C++ code.") (string-append out "/bin/afl-qemu-trace")) #t))) (delete 'check)))) ; tests are run during 'install phase - (home-page "http://lcamtuf.coredump.cx/afl") + (home-page "https://lcamtuf.coredump.cx/afl/") (synopsis "Security-oriented fuzzer") (description "American fuzzy lop is a security-oriented fuzzer that employs a novel From ac5bd7f0f07ca1ff57db00d4cf54fa3cbf42b2e8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:11:23 +0100 Subject: [PATCH 190/235] gnu: Use HTTPS for www.rforge.net home pages. * gnu/packages/cran.scm (r-rjava, r-tiff, r-uuid, r-fastmatch, r-jpeg) [home-page]: Use HTTPS. * gnu/packages/statistics.scm (r-base64enc)[home-page]: Likewise --- gnu/packages/cran.scm | 10 +++++----- gnu/packages/statistics.scm | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 406ccc644b..a34f91642e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1351,7 +1351,7 @@ applications. That is, compute distances and related measures for angular "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x")))) (build-system r-build-system) (inputs `(("libjpeg" ,libjpeg))) - (home-page "http://www.rforge.net/jpeg/") + (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both @@ -1979,7 +1979,7 @@ use in R. It also provides a simple way for variable interpolation in R.") (base32 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) (build-system r-build-system) - (home-page "http://www.rforge.net/fastmatch") + (home-page "https://www.rforge.net/fastmatch") (synopsis "Fast match function") (description "This package provides a fast @code{match} replacement for cases that @@ -4141,7 +4141,7 @@ terminals.") (base32 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q")))) (build-system r-build-system) - (home-page "http://www.rforge.net/uuid") + (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") (description "This package provides tools for generating and handling of @@ -9698,7 +9698,7 @@ redundant complex conjugate when the input is real data.") `(("libtiff" ,libtiff) ("libjpeg" ,libjpeg) ("zlib" ,zlib))) - (home-page "http://www.rforge.net/tiff/") + (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description "This package provides an easy and simple way to read, write and display @@ -13848,7 +13848,7 @@ the corresponding outputs (tables and graphs).") ("jdk" ,icedtea-8 "jdk") ("pcre" ,pcre) ("zlib" ,zlib))) - (home-page "http://www.rforge.net/rJava/") + (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") (description "This package provides a low-level interface to the Java VM very much diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6616780081..1270b644d5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3179,7 +3179,7 @@ Shiny). The @code{DataTables} library has been included in this R package.") (base32 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) (build-system r-build-system) - (home-page "http://www.rforge.net/base64enc") + (home-page "https://www.rforge.net/base64enc") (synopsis "Tools for Base64 encoding") (description "This package provides tools for handling Base64 encoding. It is more From 1c131432bdb6cb10514b80fd3f2e8081f5605774 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:43:10 +0100 Subject: [PATCH 191/235] gnu: r-tsa: Use HTTPS home page. * gnu/packages/cran.scm (r-tsa)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a34f91642e..ee447d3dd7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018 Roel Janssen -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; Copyright © 2018 Sahithi Yarlagadda @@ -4513,7 +4513,7 @@ University Press, 2000.") `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) ("r-mgcv" ,r-mgcv))) - (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") + (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description "This package contains R functions and datasets detailed in the book From 6068cbe1e12f460ce4ed9be2c14000b75924d656 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:36:06 +0100 Subject: [PATCH 192/235] gnu: r-acs: Update home page. * gnu/packages/cran.scm (r-acs)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ee447d3dd7..12ed6ffd41 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17768,7 +17768,7 @@ errors.") ("r-rcpp" ,r-rcpp) ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) - (home-page "http://dusp.mit.edu/faculty/ezra-glenn") + (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description "This package provides a general toolkit for downloading, managing, From 3ee2070241448908115d9f951dce3666b23c9f15 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:40:10 +0100 Subject: [PATCH 193/235] gnu: r-beeswarm: Use HTTPS home page. * gnu/packages/statistics.scm (r-beeswarm)[home-page]: Use HTTPS. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1270b644d5..758909edd5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4328,7 +4328,7 @@ within a category based on their density using quasirandom noise.") (base32 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581")))) (build-system r-build-system) - (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/") + (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/") (synopsis "Implementation of bee swarm plots") (description "This package provides an implementation of bee swarm plots. The bee From 486a08004850f30d8d860640c41378b130288f21 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:22:43 +0100 Subject: [PATCH 194/235] gnu: r-htqpcr: Update home page. * gnu/packages/bioconductor.scm (r-htqpcr)[home-page]: Use HTTPS link to PDF paper. --- gnu/packages/bioconductor.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4320bc0bb5..bc7623eac3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6630,7 +6630,8 @@ measures.") ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "http://www.ebi.ac.uk/bertone/software") + (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" + "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time From f8c3d903e921ceb7e216192579d8f615db2547a9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:35:49 +0100 Subject: [PATCH 195/235] gnu: r-hapassoc: Use HTTPS home page. * gnu/packages/cran.scm (r-hapassoc)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 12ed6ffd41..659660225e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13752,7 +13752,7 @@ variance components, using the likelihood-ratio statistics G.") (base32 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) (build-system r-build-system) - (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html") + (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html") (synopsis "Inference of trait associations with SNP haplotypes") (description "Hapassoc performs likelihood inference of trait associations with From 0e36f3e488f6435a7fec71dfdd84ce4e0fbfc744 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:40:03 +0100 Subject: [PATCH 196/235] gnu: r-emplik: Use HTTPS home page. * gnu/packages/cran.scm (r-emplik)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 659660225e..bf2719c3a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19044,7 +19044,7 @@ OpenMP.") (build-system r-build-system) (propagated-inputs `(("r-quantreg" ,r-quantreg))) - (home-page "http://www.ms.uky.edu/~mai/EmpLik.html") + (home-page "https://www.ms.uky.edu/~mai/EmpLik.html") (synopsis "Empirical likelihood ratio for censored/truncated data") (description "This package provides empirical likelihood ratio tests for From 39c57484ea604c7d9d742e4f14e84ae0548fecdc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:42:56 +0100 Subject: [PATCH 197/235] gnu: r-rcppparallel: Use HTTPS home page. * gnu/packages/cran.scm (r-rcppparallel)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bf2719c3a5..b727534a03 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9253,7 +9253,7 @@ package provides a minimal R interface by relying on the Rcpp package.") "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) - (home-page "http://rcppcore.github.io/RcppParallel") + (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description "This package provides high level functions for parallel programming with From 4ce61a90801c9f6efa9869b50cce31dc064c5639 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:54:44 +0100 Subject: [PATCH 198/235] gnu: r-forcats: Use HTTPS home page. * gnu/packages/statistics.scm (r-forcats)[home-page]: Use HTTPS. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 758909edd5..17fde68f41 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5499,7 +5499,7 @@ and the corresponding decision threshold.") ("r-magrittr" ,r-magrittr) ("r-tibble" ,r-tibble) ("r-rlang" ,r-rlang))) - (home-page "http://forcats.tidyverse.org") + (home-page "https://forcats.tidyverse.org") (synopsis "Tools for working with factors") (description "This package provides helpers for reordering factor levels (including moving specified levels to front, ordering by first From b8930fd86b199d5df2714be759343eee83fe5f1b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 17 Mar 2020 17:45:09 -0400 Subject: [PATCH 199/235] gnu: libfdk: Update to 2.0.1. * gnu/packages/audio.scm (libfdk): Update to 2.0.1. --- gnu/packages/audio.scm | 51 ++++++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 27 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 56eac50526..6880e74cce 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3699,38 +3699,35 @@ using ALSA, MPD, PulseAudio, or a FIFO buffer as its input.") (license license:expat)))) (define-public libfdk - (let ((commit "2326faaf8f2cdf2c3a9108ccdaf1d7551aec543e") - (revision "0")) - (package - (name "libfdk") - ;; The latest upstream revision, with many bug fixes. - (version (git-version "0.1.6" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mstorsjo/fdk-aac") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0yy6ndd9d61bwl283vl1r5kva2a4acc0f4r9g0sza156f2abr9ws")))) - (build-system gnu-build-system) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - (home-page "https://github.com/mstorsjo/fdk-aac") - (synopsis "Fraunhofer FDK AAC library") - (description "FDK is a library for encoding and decoding Advanced Audio + (package + (name "libfdk") + (version "2.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mstorsjo/fdk-aac") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fkrnzs78fmj11n9z3l0w53i2fl16jcfiyavwidck9bzmkmsf486")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (home-page "https://github.com/mstorsjo/fdk-aac") + (synopsis "Fraunhofer FDK AAC library") + (description "FDK is a library for encoding and decoding Advanced Audio Coding (AAC) format audio, developed by Fraunhofer IIS, and included as part of Android. It supports several Audio Object Types including MPEG-2 and MPEG-4 AAC LC, HE-AAC (AAC LC + SBR), HE-AACv2 (LC + SBR + PS) as well AAC-LD (low delay) and AAC-ELD (enhanced low delay) for real-time communication. The encoding library supports sample rates up to 96 kHz and up to eight channels (7.1 -surround).") - (license (license:fsf-free "https://github.com/mstorsjo/fdk-aac/blob/master/NOTICE" - "https://www.gnu.org/licenses/license-list.html#fdk"))))) + surround).") + (license (license:fsf-free "https://github.com/mstorsjo/fdk-aac/blob/master/NOTICE" + "https://www.gnu.org/licenses/license-list.html#fdk")))) (define-public libopenshot-audio (package From caaefa40072115ef3ba131d0875a87c521a9b3f4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 00:36:38 +0100 Subject: [PATCH 200/235] gnu: tracker: Update to 2.3.4. * gnu/packages/gnome.scm (tracker): Update to 2.3.4. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 77a888b3b9..895bf4ffd8 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -7453,7 +7453,7 @@ easy, safe, and automatic.") (define-public tracker (package (name "tracker") - (version "2.3.2") + (version "2.3.4") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/tracker/" @@ -7461,7 +7461,7 @@ easy, safe, and automatic.") "tracker-" version ".tar.xz")) (sha256 (base32 - "1nzbnvwwsk6kv6kqbxwlz8vk70l9ai6b4r9qypw51vp4qy72ny54")))) + "0vai0qz9jn3z5dlzysynwhbbmslp84ygdql81f5wfxxr98j54yap")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t From de60ac2ff2cadcd000248bc11c458cf6c69ce837 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 00:36:55 +0100 Subject: [PATCH 201/235] gnu: tracker-miners: Update to 2.3.3. * gnu/packages/gnome.scm (tracker-miners): Update to 2.3.3. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 895bf4ffd8..0f9241edfc 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -7523,7 +7523,7 @@ endpoint and it understands SPARQL. ") (define-public tracker-miners (package (name "tracker-miners") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/tracker-miners/" @@ -7531,7 +7531,7 @@ endpoint and it understands SPARQL. ") "/tracker-miners-" version ".tar.xz")) (sha256 (base32 - "1kizavw9gbdjkw4wykgv0fcl2y6fj788nycx9p4byn6ylb1277h6")))) + "06abxrnrz7xayykrabn135rpsm6z0fqw7gibrb9j09l6swlalwkl")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t From 2c674796d4dc535186a8f820141229047fb02099 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 01:31:32 +0100 Subject: [PATCH 202/235] gnu: tintin++: Update to 2.02.02. * gnu/packages/games.scm (tintin++): Update to 2.02.02. --- gnu/packages/games.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 44f59d7260..30045c9f96 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3916,7 +3916,7 @@ a style similar to the original Super Mario games.") (define-public tintin++ (package (name "tintin++") - (version "2.02.00") + (version "2.02.02") (source (origin (method url-fetch) @@ -3924,8 +3924,7 @@ a style similar to the original Super Mario games.") (string-drop-right version 1) "/tintin-" version ".tar.gz")) (sha256 - (base32 - "02qmbhzhh2sdy5b37v54gihs9k4bxmlz3j96gyx7icvx2grkbg5i")))) + (base32 "11ylbp8ip7dwmh4gzb53z147pcfxkl3lwhyy8ngyn2zc634vdn65")))) (inputs `(("gnutls" ,gnutls) ("pcre" ,pcre) From dbe0e0db40a235ceae4e432d82a22432e70805a8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 02:07:16 +0100 Subject: [PATCH 203/235] gnu: godot: Update to 3.2.1. * gnu/packages/game-development.scm (godot): Update to 3.2.1. --- gnu/packages/game-development.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index bf3b12ffd3..2a66f4a40c 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1536,7 +1536,7 @@ games.") (define-public godot (package (name "godot") - (version "3.2") + (version "3.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -1545,7 +1545,7 @@ games.") (file-name (git-file-name name version)) (sha256 (base32 - "0f15izjl4i2xlz1xj5pcslzl9gm3rmr3c21gh256ynpi2zhhkcdd")) + "1kndls0rklha7kz9l4i2ivjxab4jpk3b2j7dcgcg2qc3s81yd0r6")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) From f764111bfb56045385ede43a7bc18969037780a6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:45:19 +0100 Subject: [PATCH 204/235] gnu: r-iso: Use HTTPS home page. * gnu/packages/cran.scm (r-iso)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b727534a03..86ef002548 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10440,7 +10440,7 @@ the combination of non-negative and non-positive constraints.") (properties `((upstream-name . "Iso"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://www.stat.auckland.ac.nz/~rolf/") + (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description "This package provides support for linear order and unimodal From 1994e638e53ff60e074ad3bfdf59fd908f0965ea Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:48:32 +0100 Subject: [PATCH 205/235] gnu: r-elasticnet: Update home page. * gnu/packages/cran.scm (r-elasticnet)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 86ef002548..64291d41e0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16880,7 +16880,7 @@ data.") (build-system r-build-system) (propagated-inputs `(("r-lars" ,r-lars))) - (home-page "http://www.stat.umn.edu/~hzou") + (home-page "http://users.stat.umn.edu/~zouxx019/") (synopsis "Elastic-Net for sparse estimation and sparse PCA") (description "This package provides functions for fitting the entire solution path of From ddf69c4afeebdeb088214969b9a263fdad50d344 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:53:36 +0100 Subject: [PATCH 206/235] gnu: r-epi: Use HTTPS home page. * gnu/packages/cran.scm (r-epi)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64291d41e0..c477bc2688 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11492,7 +11492,7 @@ model with finite state space using the Aalen-Johansen estimator.") ("r-plyr" ,r-plyr) ("r-survival" ,r-survival) ("r-zoo" ,r-zoo))) - (home-page "http://BendixCarstensen.com/Epi/") + (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description "This package provides functions for demographic and epidemiological From 72ac69941468b855e2fd0be1931b94ff5f94c0bc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:04:38 +0100 Subject: [PATCH 207/235] gnu: r-pls: Use HTTPS home page. * gnu/packages/cran.scm (r-pls)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c477bc2688..b95c981935 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1592,7 +1592,7 @@ error stream.") (sha256 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7")))) (build-system r-build-system) - (home-page "http://mevik.net/work/software/pls.html") + (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") (description "The pls package implements multivariate regression methods: Partial Least From e661c96f84bf985a50d71d5c3dc5dc80566ff2fd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:15:27 +0100 Subject: [PATCH 208/235] gnu: r-mclust: Use HTTPS home page. * gnu/packages/statistics.scm (r-mclust)[home-page]: Use HTTPS. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 17fde68f41..3855e1c65d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4698,7 +4698,7 @@ models, generalized linear models and model-based clustering.") (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://www.stat.washington.edu/mclust/") + (home-page "https://www.stat.washington.edu/mclust/") (synopsis "Gaussian mixture modelling for model-based clustering etc.") (description "This package provides Gaussian finite mixture models fitted via EM From d07b513a30a6728a4cda65a3ff3cb5164b4550c2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:17:56 +0100 Subject: [PATCH 209/235] gnu: r-tractor-base: Use HTTPS home page. * gnu/packages/cran.scm (r-tractor-base)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b95c981935..4ed6927d54 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10317,7 +10317,7 @@ conditional reporting based on the current \"output level\".") ("r-reportr" ,r-reportr) ("r-rnifti" ,r-rnifti) ("r-shades" ,r-shades))) - (home-page "http://www.tractor-mri.org.uk") + (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description "This package provides functions for working with magnetic resonance From f9d9a7e4a62282d26ea1404f2c09c703bb8d2beb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:13:03 +0100 Subject: [PATCH 210/235] gnu: r-lars: Update home page. * gnu/packages/statistics.scm (r-lars)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3855e1c65d..fa2b8d6ed5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4563,7 +4563,7 @@ mixture models.") (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) - (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS") + (home-page "https://web.stanford.edu/~hastie/Papers/LARS/") (synopsis "Least angle regression software") (description "Least Angle Regression (\"LAR\") is a model selection algorithm; a From 3c1a10e3417db2dd1c78acf648eb3abe062ac1c1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:23:49 +0100 Subject: [PATCH 211/235] gnu: r-gsubfn: Update home page. * gnu/packages/cran.scm (r-gsubfn)[home-page]: Update and use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4ed6927d54..951904785e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5077,7 +5077,7 @@ It also includes interpolation functions.") "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs `(("r-proto" ,r-proto))) - (home-page "http://gsubfn.googlecode.com") + (home-page "https://code.google.com/archive/p/gsubfn/") (synopsis "Utilities for strings and function arguments.") (description "This package provides @code{gsubfn} which is like @code{gsub} but can From ce9fc7e8ab821d12977bdf4ca9bff3e20eb16c07 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:27:33 +0100 Subject: [PATCH 212/235] gnu: r-imager: Use HTTPS home page. * gnu/packages/cran.scm (r-imager)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 951904785e..b9b3367691 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18345,7 +18345,7 @@ number embedded in the file rather than the file extension.") ("r-readbitmap" ,r-readbitmap) ("r-stringr" ,r-stringr))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://dahtah.github.io/imager") + (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description "This is a package for fast image processing for images in up to 4 From f6b950319cb41822e2b3f1b55357037da433e1df Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 17 Mar 2020 22:10:40 -0400 Subject: [PATCH 213/235] gnu: system: Export %sudoers-specification. Exporting this variable allows reusing the default value of the `sudoers-file' field when configuring it. * gnu/system.scm (gnu): Export %sudoers-specification. * doc/guix.texi (Invoking guix deploy): Document an example, to use with 'guix deploy'. --- doc/guix.texi | 24 ++++++++++++++++++++++-- gnu/system.scm | 1 + 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index a0920adc1c..086b1d9751 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -26996,8 +26996,28 @@ login over SSH may be forbidden in some cases. To work around this, @command{guix deploy} can log in as an unprivileged user and employ @code{sudo} to escalate privileges. This will only work if @code{sudo} is currently installed on the remote and can be invoked non-interactively as -@code{user}. That is: the line in @code{sudoers} granting @code{user} the -ability to use @code{sudo} must contain the @code{NOPASSWD} tag. +@code{user}. That is, the line in @code{sudoers} granting @code{user} the +ability to use @code{sudo} must contain the @code{NOPASSWD} tag. This can +be accomplished with the following operating system configuration snippet: + +@lisp +(use-modules ... + (gnu system) ;for %sudoers-specification)) + +(define %user "username") + +(operating-system + ... + (sudoers-file + (plain-file "sudoers" + (string-append (plain-file-content %sudoers-specification) + (format #f "~a ALL = NOPASSWD: ALL~%" + %username))))) + +@end lisp + +For more information regarding the format of the @file{sudoers} file, +consult @command{man sudoers}. @deftp {Data Type} machine This is the data type representing a single machine in a heterogeneous Guix diff --git a/gnu/system.scm b/gnu/system.scm index cfc730a41c..06c58c27ba 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -138,6 +138,7 @@ local-host-aliases %root-account %setuid-programs + %sudoers-specification %base-packages %base-firmware)) From aaffde38b54c978e2425fa88eea733dc80f87444 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 19 Feb 2020 15:35:46 -0500 Subject: [PATCH 214/235] bootloader: grub: Use the all_video module in graphic mode. * gnu/bootloader/grub.scm (eye-candy): Load the module 'all_video' which automatically loads all the available and relevant video modules. --- gnu/bootloader/grub.scm | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/gnu/bootloader/grub.scm b/gnu/bootloader/grub.scm index b99f5fa4f4..36a964e8f5 100644 --- a/gnu/bootloader/grub.scm +++ b/gnu/bootloader/grub.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen +;;; Copyright © 2020 Maxim Cournoyer ;;; ;;; This file is part of GNU Guix. ;;; @@ -162,21 +163,8 @@ system string---e.g., \"x86_64-linux\"." (string-append "set gfxmode=" (string-join gfxmode ";")) "# Leave 'gfxmode' to 'auto'.")) " - insmod video_bochs - insmod video_cirrus + insmod all_video insmod gfxterm - - if [ \"${grub_platform}\" == efi ]; then - # This is for (U)EFI systems (these modules are unavailable in the - # non-EFI GRUB.) If we don't load them, GRUB boots in \"blind mode\", - # which isn't convenient. - insmod efi_gop - insmod efi_uga - else - # These are specific to non-EFI Intel machines. - insmod vbe - insmod vga - fi ") "")) From 6794653e1b0fce8981eb179b9d4cab4a0c5f926f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 19 Feb 2020 15:59:06 -0500 Subject: [PATCH 215/235] bootloader: grub: Refactor eye-candy a bit. * gnu/bootloader/grub.scm (eye-candy)[setup-gfxterm-body]: Define the GFXMODE binding using AND-LET* instead of chained AND=>. Add a comment about supporting graphical mode on other systems than x86. Generate configuration string using FORMAT rather than STRING-APPEND. --- gnu/bootloader/grub.scm | 37 ++++++++++++++++++++----------------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/gnu/bootloader/grub.scm b/gnu/bootloader/grub.scm index 36a964e8f5..28e6cb1f5f 100644 --- a/gnu/bootloader/grub.scm +++ b/gnu/bootloader/grub.scm @@ -36,6 +36,7 @@ #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-2) #:export (grub-image grub-image? grub-image-aspect-ratio @@ -149,24 +150,26 @@ STORE-MOUNT-POINT is its mount point; these are used to determine where the background image and fonts must be searched for. SYSTEM must be the target system string---e.g., \"x86_64-linux\"." (define setup-gfxterm-body - ;; Intel and EFI systems need to be switched into graphics mode, whereas - ;; most other modern architectures have no other mode and therefore don't - ;; need to be switched. - (if (string-match "^(x86_64|i[3-6]86)-" system) - (string-append - " -" - (let ((gfxmode (and=> - (and=> config bootloader-configuration-theme) - grub-gfxmode))) - (if gfxmode - (string-append "set gfxmode=" (string-join gfxmode ";")) - "# Leave 'gfxmode' to 'auto'.")) - " + (let ((gfxmode + (or (and-let* ((theme (bootloader-configuration-theme config)) + (gfxmode (grub-gfxmode theme))) + (string-join gfxmode ";")) + "auto"))) + + ;; Intel and EFI systems need to be switched into graphics mode, whereas + ;; most other modern architectures have no other mode and therefore + ;; don't need to be switched. + + ;; XXX: Do we really need to restrict to x86 systems? We could imitate + ;; what the GRUB default configuration does and decide based on whether + ;; a user provided 'gfxterm' in the terminal-outputs field of their + ;; bootloader-configuration record. + (if (string-match "^(x86_64|i[3-6]86)-" system) + (format #f " + set gfxmode=~a insmod all_video - insmod gfxterm -") - "")) + insmod gfxterm~%" gfxmode) + ""))) (define (setup-gfxterm config font-file) (if (memq 'gfxterm (bootloader-configuration-terminal-outputs config)) From 771c5e155d7862ed91a5d503eecc00c1db1150ad Mon Sep 17 00:00:00 2001 From: Florian Pelz Date: Thu, 12 Mar 2020 11:08:16 +0100 Subject: [PATCH 216/235] store: Fix many guix commands failing on some locales. Partly fixes . At least 'guix environment', 'guix install' and 'guix pull' on 'az_AZ.utf8' and 'tr_TR.utf8' were affected. * guix/store.scm (store-path-hash-part): Move base path detection to ... (store-path-base): ... this new exported procedure. (store-path-package-name): Use it instead of locale-dependent regexps. (store-regexp*): Remove. --- guix/store.scm | 32 +++++++++++++++----------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/guix/store.scm b/guix/store.scm index 5768a2ba7a..2c3675dca6 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2018 Jan Nieuwenhuizen ;;; Copyright © 2019, 2020 Mathieu Othacehe +;;; Copyright © 2020 Florian Pelz ;;; ;;; This file is part of GNU Guix. ;;; @@ -43,7 +44,6 @@ #:use-module (srfi srfi-35) #:use-module (srfi srfi-39) #:use-module (ice-9 match) - #:use-module (ice-9 regex) #:use-module (ice-9 vlist) #:use-module (ice-9 popen) #:use-module (ice-9 threads) @@ -173,6 +173,7 @@ store-path? direct-store-path? derivation-path? + store-path-base store-path-package-name store-path-hash-part direct-store-path @@ -1949,29 +1950,26 @@ valid inputs." "Return #t if PATH is a derivation path." (and (store-path? path) (string-suffix? ".drv" path))) -(define store-regexp* - ;; The substituter makes repeated calls to 'store-path-hash-part', hence - ;; this optimization. - (mlambda (store) - "Return a regexp matching a file in STORE." - (make-regexp (string-append "^" (regexp-quote store) - "/([0-9a-df-np-sv-z]{32})-([^/]+)$")))) +(define (store-path-base path) + "Return the base path of a path in the store." + (and (string-prefix? (%store-prefix) path) + (let ((base (string-drop path (+ 1 (string-length (%store-prefix)))))) + (and (> (string-length base) 33) + (not (string-index base #\/)) + base)))) (define (store-path-package-name path) "Return the package name part of PATH, a file name in the store." - (let ((path-rx (store-regexp* (%store-prefix)))) - (and=> (regexp-exec path-rx path) - (cut match:substring <> 2)))) + (let ((base (store-path-base path))) + (string-drop base (+ 32 1)))) ;32 hash part + 1 hyphen (define (store-path-hash-part path) "Return the hash part of PATH as a base32 string, or #f if PATH is not a syntactically valid store path." - (and (string-prefix? (%store-prefix) path) - (let ((base (string-drop path (+ 1 (string-length (%store-prefix)))))) - (and (> (string-length base) 33) - (let ((hash (string-take base 32))) - (and (string-every %nix-base32-charset hash) - hash)))))) + (let* ((base (store-path-base path)) + (hash (string-take base 32))) + (and (string-every %nix-base32-charset hash) + hash))) (define (derivation-log-file drv) "Return the build log file for DRV, a derivation file name, or #f if it From e002332b8a136638c2a4fc1a2f2a26541ce0211d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 18 Mar 2020 10:42:38 +0100 Subject: [PATCH 217/235] gnu: mcron: Depend on Guile 2.2.7. Fixes . * gnu/packages/guile-xyz.scm (mcron)[inputs]: Replace GUILE-2.2 with GUILE-2.2.7. --- gnu/packages/guile-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 124373bf8c..dbf3c8ee57 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -2174,7 +2174,7 @@ is no support for parsing block and inline level HTML.") #t))))) (native-inputs `(("pkg-config" ,pkg-config) ("tzdata" ,tzdata-for-tests))) - (inputs `(("guile" ,guile-2.2))) + (inputs `(("guile" ,guile-2.2.7))) ;fix (home-page "https://www.gnu.org/software/mcron/") (synopsis "Run jobs at scheduled times") (description From aaa7d17dce91f00b7313ca93795cc84ec216a86a Mon Sep 17 00:00:00 2001 From: Tanguy Le Carrour Date: Wed, 19 Feb 2020 11:18:53 +0100 Subject: [PATCH 218/235] gnu: gnunet: Update to 0.12.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnunet.scm (gnunet): Update to 0.12.2. [inputs]: Add libjpeg. [arguments]: Deactivate more tests, set LANG env variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gnunet.scm | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index f9b71a2f3a..1bcff1bf66 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018 Alex Vong ;;; Copyright © 2019 Brett Gilio +;;; Copyright © 2020 Tanguy Le Carrour ;;; ;;; This file is part of GNU Guix. ;;; @@ -249,7 +250,7 @@ supports HTTP, HTTPS and GnuTLS.") (define-public gnunet (package (name "gnunet") - (version "0.11.8") + (version "0.12.2") (source (origin (method url-fetch) @@ -257,7 +258,7 @@ supports HTTP, HTTPS and GnuTLS.") ".tar.gz")) (sha256 (base32 - "1zkmcq75sfr3iyg8rgxp9dbl7fwsvc1a71rc0vgisghcbrx1n7yj")))) + "1mwcy7fj1rpd39w7j7k3jdwlil5s889b2qlhfdggqmhigl28na5c")))) (build-system gnu-build-system) (inputs `(("bluez" ,bluez) @@ -269,6 +270,7 @@ supports HTTP, HTTPS and GnuTLS.") ("libextractor" ,libextractor) ("libidn" ,libidn2) ("libgcrypt" ,libgcrypt) + ("libjpeg" ,libjpeg) ("libltdl" ,libltdl) ("libmicrohttpd" ,libmicrohttpd) ("libogg" ,libogg) @@ -289,11 +291,30 @@ supports HTTP, HTTPS and GnuTLS.") #:phases (modify-phases %standard-phases (add-after 'configure 'remove-failing-tests - ;; These tests fail in Guix's building envrionment. + ;; These tests fail in Guix's building environment. (lambda _ + (substitute* "src/cadet/Makefile" + (("test_cadet_2_reopen\\$\\(EXEEXT\\) \\\\\n") "test_cadet_2_reopen$(EXEEXT)") + (("test_cadet_5_forward\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_signal\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_keepalive\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_speed\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_speed_ack\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_speed_reliable\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_speed_reliable_backwards\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_speed_backwards\\$\\(EXEEXT\\) \\\\\n") "") + (("test_cadet_5_reopen\\$\\(EXEEXT\\)") "")) (substitute* "src/transport/Makefile" + (("\\$\\(am__EXEEXT_15\\)") "") ; test_transport_api_https + (("test_transport_api_manipulation_cfg\\$\\(EXEEXT\\) \\\\\n") "") (("test_transport_api_udp_nat\\$\\(EXEEXT\\) \\\\\n") "") - (("test_transport_api_manipulation_cfg\\$\\(EXEEXT\\) \\\\\n") "")) + (("test_transport_blacklisting_multiple_plugins\\$\\(EXEEXT\\) \\\\\n") "")) + (substitute* "src/testbed/Makefile" + (("test_testbed_api_2peers_1controller\\$\\(EXEEXT\\) \\\\\n") "") + (("test_testbed_api_test\\$\\(EXEEXT\\) \\\\\n") "") + (("test_testbed_api_statistics\\$\\(EXEEXT\\) \\\\\n") "") + (("test_testbed_api_topology\\$\\(EXEEXT\\) \\\\\n") "") + (("test_testbed_api_topology_clique\\$\\(EXEEXT\\) \\\\\n") "")) (substitute* "src/topology/Makefile" (("^check_PROGRAMS.*") "\n") (("test_gnunet_daemon_topology\\$\\(EXEEXT\\)\n") "")) @@ -308,6 +329,9 @@ supports HTTP, HTTPS and GnuTLS.") "src/transport/gnunet-transport-certificate-creation.in") (("gnutls-certtool") "certtool")) #t)) + (add-before 'check 'set-env-var-for-tests + (lambda _ + (setenv "LANG" "en_US.UTF-8"))) ;; Swap 'check and 'install phases and add installed binaries to $PATH. (add-before 'check 'set-path-for-check (lambda* (#:key outputs #:allow-other-keys) From 370cb2e0a493ca7efcac02a43606d8f69f73c2c7 Mon Sep 17 00:00:00 2001 From: Tanguy Le Carrour Date: Wed, 19 Feb 2020 11:29:32 +0100 Subject: [PATCH 219/235] gnu: gnunet-gtk: Update to 0.12.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnunet.scm (gnunet-gtk): Update to 0.12.0. Signed-off-by: Ludovic Courtès --- gnu/packages/gnunet.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 1bcff1bf66..8ad2576bd2 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -388,14 +388,14 @@ services.") (define-public gnunet-gtk (package (inherit gnunet) (name "gnunet-gtk") - (version "0.11.7") + (version "0.12.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gnunet/gnunet-gtk-" version ".tar.gz")) (sha256 (base32 - "061ifhqk6q9kx71z5404fm4d60yj2dihlwwmdqmhkn5nn4bvcwb5")))) + "08a43ayv1rhajdklfcv78w2h76jfaz64kgp5krqgj1w1sq8xm6fb")))) (arguments `(#:configure-flags (list "--with-libunique" From d0f501647587154c4763b6c42e3c17adb83f01d0 Mon Sep 17 00:00:00 2001 From: raingloom Date: Sun, 16 Feb 2020 00:00:35 +0100 Subject: [PATCH 220/235] gnu: gspell: --enable-vala for VAPI (for geary) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (gspell)[arguments]: Add #:configure-flags. [native-inputs]: Add VALA. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 0f9241edfc..8e77b5f76e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -8946,7 +8946,8 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).") (patches (search-patches "gspell-dash-test.patch")))) (build-system glib-or-gtk-build-system) (arguments - '(#:phases + '(#:configure-flags (list "--enable-vala") + #:phases (modify-phases %standard-phases (add-before 'check 'pre-check (lambda* (#:key inputs #:allow-other-keys) @@ -8971,6 +8972,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).") `(("glib" ,glib "bin") ("gobject-introspection" ,gobject-introspection) ("pkg-config" ,pkg-config) + ("vala" ,vala) ;for VAPI, needed by Geary ("xmllint" ,libxml2) ;; For tests. From 0e26c3cfcf0e7fe74f942c5278a8fe6110a7ab38 Mon Sep 17 00:00:00 2001 From: raingloom Date: Sun, 9 Feb 2020 04:18:04 +0100 Subject: [PATCH 221/235] gnu: Add Geary. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (geary): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 92 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 92 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 8e77b5f76e..da3241ad6e 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -47,6 +47,7 @@ ;;; Copyright © 2019 Leo Prikler ;;; Copyright © 2020 Oleg Pykhalov ;;; Copyright © 2020 Pierre Neidhardt +;;; Copyright © 2020 raingloom ;;; ;;; This file is part of GNU Guix. ;;; @@ -118,6 +119,7 @@ #:use-module (gnu packages kerberos) #:use-module (gnu packages libcanberra) #:use-module (gnu packages libunistring) + #:use-module (gnu packages libunwind) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages lirc) @@ -9956,3 +9958,93 @@ manage remote and virtual systems.") license:cc-by2.0 ;; For all others. license:lgpl2.0+)))) + +(define-public geary + (package + (name "geary") + (version "3.34.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.gnome.org/GNOME/geary") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01cc921kyh3zxz07biqbdzkjgmdcc36kwjyajm4y382a75cl5zg7")))) + (build-system meson-build-system) + (arguments + `(#:glib-or-gtk? #t + #:phases (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + (lambda _ + (substitute* "test/meson.build" + (("test\\('client-tests', geary_test_client_bin\\)") + "")) + #t)) + (add-after 'unpack 'disable-postinstall-script + (lambda _ + (substitute* "meson.build" + (("meson.add_install_script\\(\ +join_paths\\('build-aux', 'post_install.py'\\)\\)") + "")) + #t)) + (add-before 'check 'setup-xvfb + (lambda _ + (system "Xvfb :1 &") + (setenv "DISPLAY" ":1") + #t))))) + (inputs + `(("enchant" ,enchant) + ("folks" ,folks) + ("gcr" ,gcr) + ("glib" ,glib) + ("gmime" ,gmime-2.6) + ("gnome-online-accounts:lib" + ,gnome-online-accounts "lib") + ("gspell" ,gspell) + ("gtk+" ,gtk+) + ("iso-codes" ,iso-codes) + ("json-glib" ,json-glib) + ("libcanberra" ,libcanberra) + ("libgee" ,libgee) + ("libhandy" ,libhandy) + ("libpeas" ,libpeas) + ("libsecret" ,libsecret) + ("libunwind" ,libunwind) + ("sqlite" ,sqlite) + ("webkitgtk" ,webkitgtk) + ("ytnef" ,ytnef))) + (native-inputs + `(("appstream-glib" ,appstream-glib) + ("cmake-minimal" ,cmake-minimal) + ("desktop-file-utils" ,desktop-file-utils) + ("gettext" ,gnu-gettext) + ("glib:bin" ,glib "bin") + ("gobject-introspection" ,gobject-introspection) + ("itstool" ,itstool) + ("libarchive" ,libarchive) + ("libxml2" ,libxml2) + ("pkg-config" ,pkg-config) + ("vala" ,vala) + ("xvfb" ,xorg-server-for-tests))) + (synopsis "GNOME email application built around conversations") + (description + "Geary collects related messages together into conversations, +making it easy to find and follow your discussions. Full-text and keyword +search makes it easy to find the email you are looking for. Geary's +full-featured composer lets you send rich, styled text with images, links, and +lists, but also send lightweight, easy to read text messages. Geary +automatically picks up your existing GNOME Online Accounts, and adding more is +easy. Geary has a clean, fast, modern interface that works like you want it +to.") + (home-page "https://wiki.gnome.org/Apps/Geary") + (license (list + ;; geary + license:lgpl2.1+ + ;; icons + license:cc-by3.0 + license:cc-by-sa3.0 + license:public-domain + ;; snowball + license:bsd-2)))) From 382ba7bad59ec7205cd883bb93b5e6cf33329d66 Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Wed, 18 Mar 2020 12:26:28 +0100 Subject: [PATCH 222/235] gnu: Add emacs-org-static-blog. * gnu/packages/emacs-xyz.scm (emacs-org-static-blog): New variable. --- gnu/packages/emacs-xyz.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a821bc7776..932170f136 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -63,6 +63,7 @@ ;;; Copyright © 2020 Masaya Tojo ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2020 Michael Rohleder +;;; Copyright © 2020 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -21762,6 +21763,34 @@ records can be browsed and searched from the Emacs Calendar for convenience. All entries in a specified TODO state will be carried over to the next day.") (license license:bsd-3))) +(define-public emacs-org-static-blog + ;; Use the latest commit as the last release only contains half of the + ;; current total commits. New release requested at + ;; . + (package + (name "emacs-org-static-blog") + (version "20200117") + (home-page "https://github.com/bastibe/org-static-blog") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit "5c19300d7634e94ae813b1b66abc716fbb1e5fc9"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1m7vmibjc6yk2npfrnnqd3g2099300r0q8mr8cvyivmk5ailbfrh")))) + (build-system emacs-build-system) + (synopsis + "Simple Org mode based static blog generator") + (description + "@code{emacs-org-static-blog} is one more static blog generator, it +focuses on being simple. All file are simple Org files in a directory. The +only requirement is that every Org file must have a @samp{title} and +a @samp{date} keywords, and optionally, a @samp{filetags} keyword.") + (license license:bsd-3))) + (define-public emacs-ddskk ;; XXX: Upstream adds code names to their release tags, so version and code ;; name below need to be updated together. From 202c674ca794649070a13a5aa87ba034f15566bd Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Tue, 17 Mar 2020 19:10:10 +0100 Subject: [PATCH 223/235] gnu: emacs-which-key: update to 3.4.0 [[PGP Signed Part:No public key for 7C7AFFBEFEF2CB25 created at 2020-03-17T19:10:10+0100 using RSA]] * gnu/packages/emacs-xyz.scm (emacs-which-key): Update to 3.4.0 From f36fee740bab3d74b526358be421a1527af9b69d Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Tue, 17 Mar 2020 19:03:45 +0100 Subject: [PATCH] gnu: emacs-which-key: update to 3.4.0 * gnu/packages/emacs-xyz.scm (emacs-which-key): Update to 3.4.0 --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 932170f136..22f8f149f9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -10404,7 +10404,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") (define-public emacs-which-key (package (name "emacs-which-key") - (version "3.3.1") + (version "3.4.0") (source (origin (method git-fetch) @@ -10413,7 +10413,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1dh6kr00wmql46whjkvnl953zngiv5j99ypvr1b3cb2174623afb")))) + (base32 "1ahgb7dqdc75farkl0fg0a6hvx2067gdvjq99cd3z2dz56km0p05")))) (build-system emacs-build-system) (arguments `(#:tests? #t From c1ec7149ed9950e8e285941ecfe96d9bcf980eed Mon Sep 17 00:00:00 2001 From: Dimakakos Dimos Date: Tue, 17 Mar 2020 23:42:04 +0200 Subject: [PATCH 224/235] gnu: emacs-lsp-ui: Update to 6.2. * gnu/packages/emacs-xyz.scm (emacs-lsp-ui): Update to 6.2. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 22f8f149f9..723a1b2444 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -42,7 +42,7 @@ ;;; Copyright © 2018 Thorsten Wilms ;;; Copyright © 2018, 2019 Pierre Langlois ;;; Copyright © 2018, 2019, 2020 Brett Gilio -;;; Copyright © 2019 Dimakakos Dimos +;;; Copyright © 2019, 2020 Dimakakos Dimos ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 mikadoZero ;;; Copyright © 2019 Gabriel Hondet @@ -18175,7 +18175,7 @@ processes for Emacs") (define-public emacs-lsp-ui (package (name "emacs-lsp-ui") - (version "6.0") + (version "6.2") (source (origin (method git-fetch) (uri (git-reference @@ -18184,7 +18184,7 @@ processes for Emacs") (file-name (git-file-name name version)) (sha256 (base32 - "1r4327fd8cvjxfwkddp5c4bdskyncbs4sx9m3z2w4d773y2jrakc")))) + "024753bi0p1jyjhw7wk8k6s16kbwab5ar4cfasvbn8g08acf293b")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash) From 97dba3876d90c1f988c3c962520a8b368f071bef Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 18 Mar 2020 14:42:10 +0100 Subject: [PATCH 225/235] gnu: emacs-org-static-blog: Update to 1.3.0. * gnu/packages/emacs-xyz.scm (emacs-org-static-blog): Update to 1.3.0. --- gnu/packages/emacs-xyz.scm | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 723a1b2444..298cfb23b0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21764,24 +21764,20 @@ All entries in a specified TODO state will be carried over to the next day.") (license license:bsd-3))) (define-public emacs-org-static-blog - ;; Use the latest commit as the last release only contains half of the - ;; current total commits. New release requested at - ;; . (package (name "emacs-org-static-blog") - (version "20200117") - (home-page "https://github.com/bastibe/org-static-blog") + (version "1.3.0") (source (origin (method git-fetch) (uri (git-reference - (url home-page) - (commit "5c19300d7634e94ae813b1b66abc716fbb1e5fc9"))) + (url "https://github.com/bastibe/org-static-blog") + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 - "1m7vmibjc6yk2npfrnnqd3g2099300r0q8mr8cvyivmk5ailbfrh")))) + (base32 "15iy3z8rglaqbx1fz14inh18ksgjsmq30b8hyv3lgjvcc9ssaiw0")))) (build-system emacs-build-system) + (home-page "https://github.com/bastibe/org-static-blog") (synopsis "Simple Org mode based static blog generator") (description From 7b1fb40dff774d04f80f4a6f8d2961c22d21c741 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 18 Mar 2020 14:57:27 +0100 Subject: [PATCH 226/235] gnu: Add opencpn. * gnu/packages/geo.scm (opencpn): New variable. --- gnu/packages/geo.scm | 76 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 0e5afdae30..590da69934 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -47,15 +47,21 @@ #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages astronomy) + #:use-module (gnu packages audio) #:use-module (gnu packages autotools) + #:use-module (gnu packages backup) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages documentation) + #:use-module (gnu packages elf) #:use-module (gnu packages fonts) #:use-module (gnu packages fontutils) + #:use-module (gnu packages gettext) + #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) @@ -66,8 +72,10 @@ #:use-module (gnu packages maths) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) + #:use-module (gnu packages photo) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) @@ -1549,3 +1557,71 @@ exchanged form one Spatial DBMS and the other.") (license (list license:gpl2+ license:lgpl2.1+ license:mpl1.1)))) + +(define-public opencpn + (package + (name "opencpn") + (version "5.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenCPN/OpenCPN.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xv3h6svw9aay5ixpql231md3pf00qxvhg62z88daraf18hlkfja")))) + (build-system cmake-build-system) + (native-inputs + `(("gettext" ,gettext-minimal) + ("pkg-config" ,pkg-config))) + (inputs + `(("bzip2" ,bzip2) + ("cairo" ,cairo) + ("curl" ,curl) + ("glu" ,glu) + ("gtk+" ,gtk+) + ("libarchive" ,libarchive) + ("libelf" ,libelf) + ("libexif" ,libexif) + ("libsndfile" ,libsndfile) + ("lz4" ,lz4) + ("mesa" ,mesa) + ("pango" ,pango) + ("portaudio" ,portaudio) + ("sqlite" ,sqlite) + ("tinyxml" ,tinyxml) + ("wxsvg" ,wxsvg) + ("wxwidgets" ,wxwidgets) + ("xz" ,xz) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags '("-DENABLE_PORTAUDIO=ON" + "-DENABLE_SNDFILE=ON" + "-DBUNDLE_TCDATA=ON" + "-DBUNDLE_GSHHS=CRUDE") + #:tests? #f ; No tests defined + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-build + (lambda _ + (substitute* "CMakeLists.txt" + (("set\\(wxWidgets_CONFIG_OPTIONS.*--toolkit=gtk3" all) + (string-append all " --libs all"))) + #t))))) + (synopsis "Chart plotter and marine GPS navigation software") + (description + "OpenCPN is a chart plotter and marine navigation software designed to be +used at the helm station of your boat while underway. Chart a course and +track your position right from your laptop.") + (home-page "https://opencpn.org/") + (license (list license:asl2.0 + license:cc0 + license:bsd-2 + license:bsd-3 + license:expat + license:gpl3+ + license:lgpl2.1+ + license:lgpl3+ + license:sgifreeb2.0 + license:zlib)))) From 6c3881078afb1f98236da1020e5eef4f9061ae43 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 18 Mar 2020 11:16:57 -0400 Subject: [PATCH 227/235] doc: Follow-up commit to f6b950319c. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Invoking guix deploy): Fix typo in example. Reported-by: Ludovic Courtès --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 086b1d9751..d1fa8d033a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -27002,7 +27002,7 @@ be accomplished with the following operating system configuration snippet: @lisp (use-modules ... - (gnu system) ;for %sudoers-specification)) + (gnu system)) ;for %sudoers-specification (define %user "username") From 083a95b7e0af07beedaac1923ab559425fc294f4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:47:33 +0100 Subject: [PATCH 228/235] gnu: r-shinyace: Use HTTPS home page. * gnu/packages/cran.scm (r-shinyace)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b9b3367691..5cd7955f1a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4926,7 +4926,7 @@ files.") (propagated-inputs `(("r-shiny" ,r-shiny) ("r-jsonlite" ,r-jsonlite))) - (home-page "http://cran.r-project.org/web/packages/shinyAce") + (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description "This package provides Ace editor bindings to enable a rich text editing From b89993fbd44684b86f8756af2abf79f61f082ff9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:55:19 +0100 Subject: [PATCH 229/235] gnu: r-ldheatmap: Use HTTPS home page. * gnu/packages/cran.scm (r-ldheatmap)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5cd7955f1a..df177b9e86 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13535,7 +13535,7 @@ inbred lines, F2 intercrosses, and association mapping populations.") `(("r-genetics" ,r-genetics) ("r-rcpp" ,r-rcpp) ("r-snpstats" ,r-snpstats))) - (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") + (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description "This package provides tools to produce a graphical display, as a heat From 917edde5802065e7fe62b3b38a1c00e1c2eda293 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:58:48 +0100 Subject: [PATCH 230/235] gnu: r-stepwise: Use HTTPS home page. * gnu/packages/cran.scm (r-stepwise)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index df177b9e86..d7f64a5ec5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12929,7 +12929,7 @@ Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") (base32 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) (build-system r-build-system) - (home-page "http://stat.sfu.ca/statgen/research/stepwise.html") + (home-page "https://stat.sfu.ca/statgen/research/stepwise.html") (synopsis "Stepwise detection of recombination breakpoints") (description "This package provides a stepwise approach to identifying recombination From 8a02807a127b424419fd4f8c5eb13579a0e46b7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:07:18 +0100 Subject: [PATCH 231/235] gnu: r-proc: Update home page. * gnu/packages/cran.scm (r-proc)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d7f64a5ec5..d1d5774a52 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6878,7 +6878,7 @@ containing one or more SNPs that evolved under directional selection.") (propagated-inputs `(("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp))) - (home-page "http://expasy.org/tools/pROC/") + (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description "This package provides tools for visualizing, smoothing and comparing From e309b7206f61274e654588f915e4bcb563274014 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 00:21:20 +0100 Subject: [PATCH 232/235] gnu: r-stabledist: Use HTTPS home page. * gnu/packages/cran.scm (r-stabledist)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d1d5774a52..565fef8628 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9579,7 +9579,7 @@ related functions.") (base32 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) (build-system r-build-system) - (home-page "http://www.rmetrics.org") + (home-page "https://www.rmetrics.org") (synopsis "Stable distribution functions") (description "This package provides density, probability and quantile functions, and From 2bc3ec3b44ffb7d2da0b0dabcc3135dcf8f2057d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 05:49:06 +0100 Subject: [PATCH 233/235] gnu: dovecot: Support LZ4 compression. * gnu/packages/mail.scm (dovecot)[inputs]: Add lz4. --- gnu/packages/mail.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index fb5446107c..f3499b28d2 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1393,11 +1393,12 @@ facilities for checking incoming mail.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("openssl" ,openssl) - ("zlib" ,zlib) - ("bzip2" ,bzip2) + `(("bzip2" ,bzip2) + ("linux-pam" ,linux-pam) + ("lz4" ,lz4) + ("openssl" ,openssl) ("sqlite" ,sqlite) - ("linux-pam" ,linux-pam))) + ("zlib" ,zlib))) (arguments `(#:configure-flags '("--sysconfdir=/etc" "--localstatedir=/var") From 61d399c5fb2c50c7a0f34b8000c03ad1f0f44082 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:57:39 +0100 Subject: [PATCH 234/235] gnu: pioneer: Use HTTPS home page. * gnu/packages/games.scm (pioneer)[home-page]: Use HTTPS. --- gnu/packages/games.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 30045c9f96..59639a0138 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5662,7 +5662,7 @@ elements to achieve a simple goal in the most complex way possible.") #:configure-flags (list "-DUSE_SYSTEM_LIBLUA:BOOL=YES" (string-append "-DPIONEER_DATA_DIR=" %output "/share/games/pioneer")))) - (home-page "http://pioneerspacesim.net") + (home-page "https://pioneerspacesim.net") (synopsis "Game of lonely space adventure") (description "Pioneer is a space adventure game set in our galaxy at the turn of the From 4de63cf3fc0a831d75cb507456821104f24800c2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 18 Mar 2020 17:48:43 +0100 Subject: [PATCH 235/235] gnu: tor: Update to 0.4.2.7. * gnu/packages/tor.scm (tor): Update to 0.4.2.7. --- gnu/packages/tor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index d0b8dd6af4..61e52ba22c 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner ;;; Copyright © 2016, 2017 ng0 -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017, 2018, 2019 Eric Bavier ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2018 Ricardo Wurmus @@ -50,14 +50,14 @@ (define-public tor (package (name "tor") - (version "0.4.2.6") + (version "0.4.2.7") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "1i766s211nrbjvwvkd2375mjsbbc28yrg46564rbx6w46cj10005")))) + "0v82ngwwmmcb7i9563bgsmrjy6xp83xyhqhaljygd0pkvlsxi886")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config)