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5370 commits

Author SHA1 Message Date
Maxim Cournoyer 129b9b16d9
Merge remote-tracking branch 'origin/version-1.2.0' into master
Conflicts:
	gnu/packages/bioinformatics.scm

The python-pysam package fixed in master was kept instead of the update done
in the version-1.2.0 branch.
2020-11-17 18:00:28 -05:00
Maxim Cournoyer 41f27bf870
guix: system: Make disk-image root file system non-volatile by default.
And add a new '--volatile' option to have it volatile otherwise.

* guix/scripts/system.scm (%options)[volatile-root?]: New boolean option.
(%default-options): Set its default value to #f.
(show-help): Add help doc.
* guix/scripts/system.scm (perform-action): Propagate option...
(system-derivation-for-action): ...here.  Use it to set the volatile-root?
field of the image object passed to SYSTEM-IMAGE.
* doc/guix.texi (Invoking guix system): Document it.
2020-11-17 15:20:03 -05:00
Florian Pelz 29ed17d634
pull: Do not suggest running `guix pull --news' on the first run.
* guix/scripts/pull.scm (display-channel-news-headlines): If there
are no news to display, return false instead of <unspecified>.
2020-11-16 13:44:29 +00:00
Ludovic Courtès 98750a9d99
self: Limit the number of threads used when translating manuals.
* guix/self.scm (translate-texi-manuals)[build](parallel-jobs): New
variable.
Use it as first argument to 'n-par-for-each'.
2020-11-16 11:40:53 +01:00
Danny Milosavljevic b720cf90e7
utils: Add 'cxx-for-target'.
* guix/utils.scm (cxx-for-target): New procedure.
2020-11-16 10:26:46 +01:00
Maxim Cournoyer 630602831d
publish: Harmonize buffer size values and configuration.
This change harmonizes the way we configure the buffer sizes and the socket
options, so that we don't forget to change it at one place like it happened in
commit 5e3d169945.

* guix/scripts/publish.scm (%default-buffer-size)
(%default-socket-options): New variables.
* guix/scripts/publish.scm (configure-socket): New procedure.
(compress-nar): Use %default-buffer-size for the buffer size, increased from
128 to 208 KiB.
(nar-response-port): Likewise, increased from 64 to 208 KiB.
(http-write): Use configure-socket to set socket options.
(open-server-socket): Likewise.
2020-11-16 00:04:32 -05:00
Tobias Geerinckx-Rice 5d15733c42
archive: Warn about replacing an ACL symlink.
* guix/scripts/archive.scm (authorize-key): Warn when %ACL-FILE is a
symbolic link and print an additional hint for Guix System users.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2020-11-15 23:05:34 +01:00
Holger Peters 521d33cdc6
guix: hg-download: Add hg-predicate.
`hg-predicate' acts for mercurial repositories as `git-predicate' acts
for git-repositories.

* guix/hg-download.scm (hg-predicate): New procedure.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-11-14 10:27:00 +00:00
John Soo 0cdc13ce43
guix build: Expose log-url for third parties.
* guix/scripts/build.scm (log-url): Expose it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-11-13 18:11:30 +01:00
John Soo e783cd51ba
pack: Expose some bindings for third-party use.
* guix/scripts/pack.scm (compressor-name, compressor-extension,
compressor-command, %compressors, %formats): Export.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-11-13 18:10:11 +01:00
Ludovic Courtès 07914def98
Merge branch 'version-1.2.0' 2020-11-12 10:47:25 +01:00
Ludovic Courtès b73981369e
lint: patch-file-names: Simplify 'search-patch' error handling.
* guix/lint.scm (check-patch-file-names): Remove 'message-condition?'
guard, which is useless since d51bfe242f.
Remove call to 'format' in the 'formatted-message?' case.
2020-11-12 09:29:05 +01:00
Ludovic Courtès 1cbda46d4a
publish: Increase TCP buffer size when sending non-cached nars.
This increases throughput tenfold (!) on localhost when downloading
large nars without '--cache'.  This is a followup to
5e3d169945.

Reported by Maxim Cournoyer.

* guix/scripts/publish.scm (http-write): In the
'application/x-nix-archive' case, add call to 'setsockopt'.
2020-11-10 22:56:38 +01:00
Julien Lepiller 6ed2741a35
guix: ocaml: Add package-with-ocaml4.09.
* guix/build-system/ocaml.scm (package-with-ocaml4.09)
(strip-ocaml4.09-variant): New variables.
* gnu/packages/ocaml.scm (ocaml4.09-result, ocaml4.09-csexp)
(ocaml4.09-dune-configurator, ocaml4.09-dune): New variables.
2020-11-10 16:02:59 +01:00
Ludovic Courtès 362529963e
ui: Use the right accessor when reporting '&gexp-input-error'.
* guix/ui.scm (call-with-error-handling): In the 'gexp-input-error?'
case, use 'gexp-error-invalid-input' as the accessor.
2020-11-10 14:40:20 +01:00
Ludovic Courtès d754757628
publish: Create files in the cache as #o644.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/publish.scm (compress-nar): Add 'chmod' call to ensure
PORT is #o644, in the uncompressed case.
(bake-narinfo+nar): Likewise for the narinfo file.
* tests/publish.scm ("with cache"): Check permissions on CACHED and NAR.
2020-11-09 23:27:09 +01:00
Ludovic Courtès 464e7437f4
publish: Create files in the cache as #o644.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/scripts/publish.scm (compress-nar): Add 'chmod' call to ensure
PORT is #o644, in the uncompressed case.
(bake-narinfo+nar): Likewise for the narinfo file.
* tests/publish.scm ("with cache"): Check permissions on CACHED and NAR.
2020-11-08 23:39:33 +01:00
Ludovic Courtès db1b18c397
ui: Add missing format argument in 'warn-about-load-error'.
* guix/ui.scm (warn-about-load-error): Add missing argument to 'warning'.
2020-11-06 21:42:39 +01:00
Ludovic Courtès 4db90a6c15
pack: Do not include the host (guix config).
* guix/scripts/pack.scm (store-database)[build]: Import a
synthetic (guix config).
2020-11-05 16:13:50 +01:00
Ludovic Courtès ca465a9c84
gexp: Warn when importing (guix config) or (ice-9 …).
While importing those modules from the host system is valid, it is often
a mistake that introduces non-reproducibility.  This patch prints a
warning when that happens.

* guix/gexp.scm (gexp-attribute): Add #:validate parameter and honor it.
(gexp-modules)[validate-modules]: New procedure.
Pass it to 'gexp-attribute'.
* tests/gexp.scm ("gexp-modules, warning"): New test.
2020-11-05 16:13:50 +01:00
Ludovic Courtès 18fc84bce8
gexp: Store the source code location in <gexp>.
* guix/gexp.scm (<gexp>)[location]: New field.
(gexp-location): New procedure.
(write-gexp): Print the location of GEXP.
(gexp->derivation): Adjust call to 'make-gexp'.
(gexp): Likewise.
2020-11-05 16:13:50 +01:00
Ludovic Courtès 5e7cf66fb3
publish: Do not path the empty string to 'query-path-info'.
Fixes <https://bugs.gnu.org/44442>.
Regression introduced in 2b2ab7796a.

* guix/scripts/publish.scm (render-nar/cached): Do not call
'bypass-cache?' when ITEM is the empty string.
* tests/publish.scm ("with cache, cache bypass, unmapped hash part"):
New test.
2020-11-04 16:02:53 +01:00
Robert Vollmert f0bb2662bb
guix import stackage: Default to LTS version that matches GHC.
In particular, this means that 'guix lint' won't warn to update to
versions that won't necessarily fit our package set well.

* guix/import/stackage.scm (%stackage-url): Change to "https",
avoiding redirect log messages.
(%default-lts-version): New variable.
(stackage-lts-info-fetch, stackage->guix-package,
latest-lts-release): Use it.
(lts-info-ghc-version): Remove unused procedure.

Signed-off-by: Timothy Sample <samplet@ngyro.com>
2020-11-03 15:36:59 -05:00
Mathieu Othacehe a38d861e57
system: reconfigure: Use the disk-installer if provided.
Fixes: <https://issues.guix.gnu.org/44101>.

* gnu/build/bootloader.scm (write-file-on-device): Pass 'no-fail flag instead
of 'no-create. Use a latin-1 transcoder.
* guix/scripts/system/reconfigure.scm (install-bootloader-program): Add a
"disk-installer" argument and use it as a fallback.
(install-bootloader): Adapt accordingly.
* gnu/tests/reconfigure.scm (run-install-bootloader-test): Ditto.
2020-11-03 07:59:59 +01:00
Ludovic Courtès 76ea70bd70
profiles: Add fast path for 'xdg-mime-database' hook.
Partly fixes <https://bugs.gnu.org/44053>.
Reported by Joshua Branson <jbranso@dismail.de>
and Maxim Cournoyer <maxim.cournoyer@gmail.com>.

* guix/profiles.scm (xdg-mime-database): When PKGDIRS contains only one
element, symlink directly to it.  Invoke 'update-mime-database' only
when PKGDIRS contains two or more elements, which is less frequent.
2020-11-02 14:59:34 +01:00
Miguel Ángel Arruga Vivas 582cf9257c
system: Add store-directory-prefix to boot-parameters.
Fixes <http://issues.guix.gnu.org/44196>

* gnu/machine/ssh.scm (roll-back-managed-host): Use
boot-parameters-store-directory-prefix.
* gnu/system.scm (define-module): Export
boot-parameters-store-directory-prefix.
(<boot-parameters>)[store-directory-prefix]: New field. It is used to
generate the correct paths when /gnu/store is installed on a btrfs
subvolume whose name doesn't match the final runtime path, as the
bootloader doesn't have knowledge about the final mounting points.
[boot-parameters-store-directory-prefix]: New accessor.
(read-boot-parameters): Read directory-prefix from store field.
(operating-system-boot-parameters-file): Add directory-prefix to
store field.
* guix/scripts/system.scm (reinstall-bootloader): Use
boot-parameters-store-directory-prefix.
* test/boot-parameters.scm (%default-btrfs-subvolume,
%default-store-directory-prefix): New variables.
(%grub-boot-parameters): Use %default-store-directory-prefix.
(%default-operating-system): Use %default-btrfs-subvolume.
(test-boot-parameters): Add directory-prefix.
(test optional fields): Add test for directory-prefix.
(test os store-directory-prefix): New test.
2020-11-01 02:28:38 +01:00
Ludovic Courtès 31726f32ac
transformations: Raise '&formatted-message' exceptions instead of 'leave'.
* guix/transformations.scm (evaluate-replacement-specs)
(package-git-url, evaluate-git-replacement-specs)
(transform-package-source-git-url)
(transform-package-toolchain): Use 'raise' and 'formatted-message'
instead of 'leave'.
2020-10-31 23:16:43 +01:00
Ludovic Courtès f68b3ba12d
guix build: Move transformation options to (guix transformations).
* guix/transformations.scm: New file.
* tests/scripts-build.scm: Rename to...
* tests/transformations.scm: ... this.
* Makefile.am (MODULES): Add 'guix/transformations.scm'.
(SCM_TESTS): Adjust to rename.
* guix/scripts/build.scm (numeric-extension?)
(tarball-base-name, <downloaded-file>, download-to-store*)
(compile-downloaded-file, package-with-source)
(transform-package-source, evaluate-replacement-specs)
(transform-package-inputs, transform-package-inputs/graft)
(%not-equal, package-git-url, evaluate-git-replacement-specs)
(transform-package-source-branch, transform-package-source-commit)
(transform-package-source-git-url, package-dependents/spec)
(package-toolchain-rewriting, transform-package-toolchain)
(transform-package-with-debug-info, transform-package-tests)
(%transformations, transformation-procedure, %transformation-options)
(show-transformation-options-help, options->transformation)
(package-transformations): Move to (guix transformations).
* guix/scripts/environment.scm: Adjust accordingly.
* guix/scripts/graph.scm: Likewise.
* guix/scripts/install.scm: Likewise.
* guix/scripts/pack.scm: Likewise.
* guix/scripts/package.scm: Likewise.
* guix/scripts/upgrade.scm: Likewise.
* po/guix/POTFILES.in: Add 'guix/transformations.scm'.
2020-10-31 23:16:43 +01:00
Ludovic Courtès 1ae33664a6
guix build: 'options->transformation' no longer takes a 'store' parameter.
* guix/scripts/build.scm (transform-package-source)
(transform-package-inputs, transform-package-inputs/graft)
(transform-package-source-branch, transform-package-source-commit)
(transform-package-source-git-url, transform-package-toolchain)
(transform-package-with-debug-info, transform-package-tests): Remove
'store' parameter.
(options->transformation, options->derivations): Adjust accordingly.
* guix/scripts/environment.scm (options/resolve-packages): Likewise.
* guix/scripts/graph.scm (guix-graph): Likewise.
* guix/scripts/pack.scm (guix-pack): Likewise.
* guix/scripts/package.scm (transaction-upgrade-entry): Likewise.
(process-actions): Likewise.
* tests/scripts-build.scm ("options->transformation, no transformations")
("options->transformation, with-source, replacement"):
Adjust tests.
("options->transformation, with-source")
("options->transformation, with-source, with version")
("options->transformation, with-source, PKG=URI"): Use 'lower-object' to
compute the store file name of the source.
("options->transformation, with-source, no matches"): Remove
'with-store' and adjust accordingly.
("options->transformation, with-input"): Likewise.
("options->transformation, with-graft"): Likewise.
("options->transformation, with-branch"): Likewise.
("options->transformation, with-commit"): Likewise.
("options->transformation, with-git-url"): Likewise.
("options->transformation, with-git-url + with-branch"): Likewise.
("options->transformation, with-c-toolchain"): Likewise.
("options->transformation, with-c-toolchain twice"): Likewise.
("options->transformation, with-c-toolchain, no effect"): Likewise.
("options->transformation, with-debug-info"): Likewise.
("options->transformation, without-tests"): Likewise.
2020-10-31 23:16:43 +01:00
Ludovic Courtès e72cc79263
guix build: Remove unnecessary (replacement #f).
* guix/scripts/build.scm (package-with-source): Remove 'replacement'
field, which is innate since d5ec5ed719.
2020-10-31 23:16:43 +01:00
Ludovic Courtès 139c4ac199
guix build: 'package-with-source' no longer takes a 'store' parameter.
* guix/scripts/build.scm (<downloaded-file>): New record type.
(download-to-store*): New variable.
(compile-downloaded-file): New procedure.
(package-with-source): Remove 'store' parameter.  Use 'downloaded-file'
instead of 'download-to-store'.
(transform-package-source): Adjust accordingly.
2020-10-31 23:16:42 +01:00
Eric Bavier 4184998c70
guix: pack: Only wrap executable files.
* guix/scripts/pack.scm (wrapped-package)<build>: Build wrappers for
executable files and symlink others.
* tests/guix-pack-relocatable.sh: Test relocatable example of mixed
executable and non-executable files.
2020-10-30 10:00:35 -05:00
Eric Bavier a73896425e
guix: pack: Fix offset calculation for store directory mount point.
Fixes wrapping of non-package things, where the target store directory may
differ in length from the original.

* guix/scripts/pack.scm (wrapped-package)<build-wrapper>: Define
WRAPPER_PROGRAM macro with wrapper's file name.
* gnu/packages/aux-files/run-in-namespace.c (main): Offset index by len of
that file name.
2020-10-30 10:00:29 -05:00
zimoun 58db2e6877
scripts: lint: Add '--exclude' option.
* guix/scripts/lint.scm (%options, parse-options): Add '--exclude' option.
(option-checker): New helper function.
* doc/guix.texi (Invoking guix lint): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-10-30 01:14:20 +01:00
zimoun 80c7f02468
scripts: lint: Fix '--no-network' option.
* guix/scripts/lint.scm: (show-help): Add '--no-network' option message.
(%options, parse-options): Fix argument order.
* doc/guix.texi (Invoking guix lint): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-10-30 01:14:20 +01:00
Vagrant Cascadian 159c5943e4
build/maven: Fix typo.
* guix/build/maven/pom: Fix spelling of "with".
2020-10-28 21:11:11 -07:00
Vagrant Cascadian 28680722b2
build/maven: fix-pom-dependencies: Fix typo.
* guix/build/maven/pom (fix-pom-dependencies): Fix spelling of "overrides".
2020-10-28 21:11:06 -07:00
Vagrant Cascadian 05ee7ef8b7
build/maven: fix-pom-dependencies: Fix typo.
* guix/build/maven/pom (fix-pom-dependencies): Fix spelling of "overridden".
2020-10-28 21:11:01 -07:00
Miguel Ángel Arruga Vivas 504fd36a85
substitute: Do not discard ttl info when the response code is 202.
* guix/scripts/substitute.scm (fetch-narinfos)
[handle-narinfo-response]: Add code 202 to the condition.  This will
allow in the future the use of 404 for nar requests which cannot be
built in the present, leaving for the 202 to indicate that a request has
triggered a nar generation that might be completed later, as specified
in <https://www.ietf.org/rfc/rfc2616.txt>.
2020-10-28 19:29:11 +01:00
Ludovic Courtès ecaa102a58
publish: Add '--cache-bypass-threshold'.
* guix/scripts/publish.scm (show-help, %options): Add
'--cache-bypass-threshold'.
(low-compression): New procedure.
(cache-bypass-threshold): New parameter.
(bypass-cache?): New procedure.
(render-narinfo/cached): Call 'render-narinfo' when 'bypass-cache?'
returns true.
(render-nar/cached): Call 'render-nar' when 'bypass-cache?' returns
true.
(guix-publish): Parameterize 'cache-bypass-threshold'.
* tests/publish.scm ("with cache", "with cache, lzip + gzip")
("with cache, uncompressed"): Pass '--cache-bypass-threshold=0'.
("with cache, vanishing item"): Expect 200 for RESPONSE.
("with cache, cache bypass"): New test.
2020-10-28 16:24:47 +01:00
Amar Singh 6955cff962
publish: Provide server's signing key.
* guix/scripts/publish.scm (render-signing-key): New procedure.
(render-home-page): Add link to it.
(make-request-handler): Handle it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-10-27 00:40:24 +01:00
Björn Höfling f503cfc9c5
build/maven-build-system: Return #t in fix-pom-files phase.
* guix/build/maven-build-system.scm (fix-pom-files): Return #t.
2020-10-26 21:36:09 +01:00
Ludovic Courtès c9278dc9c1
offload: Adjust default 'max-silent-time' value of 'open-ssh-session'.
* guix/scripts/offload.scm (open-ssh-session): Have 'max-silent-time'
default to #f rather than -1, which is not a valid timeout value.
Adjust body accordingly.
2020-10-25 01:06:09 +02:00
Ludovic Courtès d3f02752b5
offload: Export <build-machine> accessors.
* guix/scripts/offload.scm: Export 'build-machine' accessors.
2020-10-25 01:06:08 +02:00
Ludovic Courtès 8425a9b60a
git: Support HTTP and HTTPS proxies.
This allows 'guix pull' and similar to fetch code over a proxy.

* guix/git.scm (make-default-fetch-options): Pass #:proxy-url.
2020-10-22 17:10:25 +02:00
Ludovic Courtès 298f9d29d6
git: Display a progress bar while fetching a repo.
Fixes <https://bugs.gnu.org/39260>.

This uses the API of the yet-to-be-released Guile-Git 0.4.0.  Using an
older version is still possible, but progress report is disabled.

* guix/git.scm (show-progress, make-default-fetch-options): New
procedures.
(clone*, update-cached-checkout): Use it instead of
'make-fetch-options'.
2020-10-22 17:10:25 +02:00
Ludovic Courtès 59bb1ae3a9
git: Require Guile-Git 0.3.0 or later.
* guix/git.scm (auth-supported?): Remove.
(clone*): Inline code that was dependent on AUTH-SUPPORTED?.
(update-cached-checkout): Likewise.
(resolve-reference): Remove check for 'object-lookup-prefix' and use it
unconditionally.
(load-git-submodules): Remove.
(update-submodules): Use 'repository-submodules', 'submodule-lookup',
etc. unconditionally.
(update-cached-checkout): Use 'repository-close!' unconditionally.
* m4/guix.m4 (GUIX_CHECK_GUILE_GIT): New macro.
* configure.ac: Use it and error out when it fails.
* doc/guix.texi (Requirements): Bump to Guile-Git 0.3.0.
2020-10-22 17:10:25 +02:00
Ludovic Courtès 16155bbeb8
graph: Don't insist on "Helvetica" in the Graphviz backend.
Suggested by Fulbert <fulbert@bluewin.ch>.

* guix/graph.scm (emit-node): Use "sans" instead of "Helvetica".
2020-10-22 17:10:21 +02:00
Ludovic Courtès 6701f64f73
guix build: Move package transformation options behind '--help-transform'.
This change declutters the '--help' output.

* guix/scripts/build.scm (show-build-options-help)
(%standard-build-options): Add '--help-transform'.
(show-transformation-options-help): Make private.
(show-help): Remove call to 'show-transformation-options-help'.
* guix/scripts/build.scm (show-help): Likewise.
* guix/scripts/environment.scm (show-help): Likewise.
* guix/scripts/graph.scm (show-help): Likewise.
* guix/scripts/install.scm (show-help): Likewise.
* guix/scripts/pack.scm (show-help): Likewise.
* guix/scripts/package.scm (show-help): Likewise.
* guix/scripts/upgrade.scm (show-help): Likewise.
* doc/guix.texi (Package Transformation Options): Mention '--help-transform'.
2020-10-20 16:30:16 +02:00
Ludovic Courtès 6aeda81602
guix build: Add '--with-debug-info'.
* guix/scripts/build.scm (transform-package-with-debug-info): New
procedure.
(%transformations): Add 'with-debug-info'.
(%transformation-options, show-transformation-options-help): Add
'--with-debug-info'.
* tests/scripts-build.scm ("options->transformation, with-debug-info"):
New test.
* doc/guix.texi (Package Transformation Options): Document
'--with-debug-info'.
(Installing Debugging Files): Introduce sections.  Remove bit about
eventual "opt-out" since this is not happening.  Document
'--with-debug-info' under "Rebuilding with Debugging Info".
2020-10-20 16:30:16 +02:00