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5562 commits

Author SHA1 Message Date
Yuri Victorovich
91891bd266 science/madness: Make TBB dependency optional, OFF by default until the upstream fixes oneTBB support 
PR:		252694
 2021-01-15 18:35:59 +00:00
Thierry Thomas
3f025aa86d Enable abinit for powerpc64 and fix plist. 
Reported by:	pkg-fallout
 2021-01-15 17:34:17 +00:00
Thierry Thomas
55da7590ef Add some headers to unbreak with Gcc 10. 2021-01-15 11:16:10 +00:00
Mark Linimon
7aaa093a13 Add compiler:c++11-lang to USES to fix build on GCC-based systems: 
cc1plus: error: unrecognized command line option "-std=gnu++11"

Approved by:	portmgr (tier-2 blanket)
 2021-01-15 01:05:21 +00:00
Jose Alonso Cardenas Marquez
82ac7a6add - lang/fpc revert way like linker is taken by fpc compiler 
- lang/fpc add binutils to RUN_DEPENDS
- editors/lazarus add binutils to RUN_DEPENDS
- editors/lazarus add gmake to RUN_DEPENDS
- editors/lazarus install fpc units like RUN_DEPENDS too
- Bump PORTREVISiON of fpc/lazarus ports

PR:		251712
Reported by:	amdmi3
 2021-01-14 21:11:15 +00:00
Yuri Victorovich
caad6e42dc New port: science/shelxle: Graphical user interface for small-molecule structure refinement 2021-01-14 19:14:12 +00:00
Danilo G. Baio
b53abbd839 Remove PY_SPHINX from ports using Python 3 
Approved by:	 portmgr blanket
Differential Revision:	https://reviews.freebsd.org/D28093
 2021-01-14 14:34:38 +00:00
Piotr Kubaj
0a27c5adbc science/rdkit: fix packaging on powerpc64 
Also switch not-working with Clang -mpopcntb with -mpopcntd (as a side effect it also raises requirements from POWER5 to POWER7).

MFH:		2021Q1
 2021-01-14 03:04:49 +00:00
Mark Linimon
f86c964117 Update GCC_DEFAULT from 9 to 10. 
A few (mostly Fortran-based) ports need to be patched because GCC 10
is stricter.  A handful of ports need to be restricted to GCC 9 because
they fail with 10.

5 ports still fail with GCC 10.  However, seeing as this work has been
ongoing since 2020-05-24, it is simply time to make the commit and
notify the affected maintainers.

While here, pet portlint (Makevar order).

PR:		246700
Submitted by:	gerald
Approved by:	antoine (after many, many, -exp runs)
 2021-01-13 23:03:31 +00:00
Thierry Thomas
633aff5008 Upgrade to 3.8.0. 
Changelog is available at <https://gitlab.com/l_sim/v_sim/-/blob/staging/ChangeLog.en>.
 2021-01-13 16:30:07 +00:00
Fernando Apesteguía
1c66f4556c science/afni: update to 21.0.02 
Reported by:	portscout
 2021-01-13 14:23:48 +00:00
Tobias C. Berner
67bf19d8e6 science/kalzium: revrse unnecessary patching 
- OpenBabel3 support was added in r561281 via a patch obtained from upstream
- The patching done in r561406 is therefore not necessary

PR:		252309
 2021-01-13 09:13:48 +00:00
Yuri Victorovich
b7f8e34979 science/openbabel: Update 2.4.1 -> 3.1.1 2021-01-13 04:02:26 +00:00
Yuri Victorovich
b474c9ac63 science/xdrawchem: 1.10.2-1 -> 1.11.0-2 2021-01-13 00:52:20 +00:00
Yuri Victorovich
a29d767ef4 science/openbabel: Upgrade 2.4.1 -> 3.1.1 
PR:		252309
Submitted by:	thierry
 2021-01-13 00:31:38 +00:00
Piotr Kubaj
6900e1f992 science/abinit: enable on powerpc64 2021-01-12 22:18:04 +00:00
Yuri Victorovich
7206d5e80d science/octopus: Update 10.1 -> 10.3 2021-01-12 07:49:47 +00:00
Tobias C. Berner
9f4330b9a1 science/kalzium: add support for OpenBable 3.x 
- Add upstream patch

PR:		252309
Reported by:	thierry
Obtained from:	https://invent.kde.org/education/kalzium/commit/2b9ebd85
 2021-01-11 21:46:47 +00:00
Piotr Kubaj
afaf37b033 science/dlib-cpp: fix build on powerpc64le 
clang doesn't implement vec_rsqrt.
 2021-01-11 14:07:58 +00:00
Sunpoet Po-Chuan Hsieh
97462ed900 Remove py-pytest-runner from BUILD_DEPENDS 2021-01-10 23:14:16 +00:00
Sunpoet Po-Chuan Hsieh
f8366a1fc7 Remove py-pytest-runner from BUILD_DEPENDS 2021-01-10 23:14:12 +00:00
Sunpoet Po-Chuan Hsieh
57a53c376f Remove py-pytest-runner from BUILD_DEPENDS 2021-01-10 23:14:07 +00:00
Rene Ladan
878b93dbd9 Remove empty PY_TYPING from ports using Python 3.6+ 
Leave out textproc/py-sphinx[18] for now.
 2021-01-10 19:32:23 +00:00
Fernando Apesteguía
a6e755d84a science/afni: update to 21.0.00 
Reported by:	portscout
 2021-01-10 08:34:20 +00:00
Sunpoet Po-Chuan Hsieh
cc84a37957 Update to 2.3.5 
Changes:	https://github.com/pysal/esda/releases
 2021-01-10 08:22:13 +00:00
Rene Ladan
9eae9f798c science/py-dlib: remove unused py27 flavor code. 2021-01-09 20:51:19 +00:00
Yuri Victorovich
7aac519091 science/gromacs: Update 2020.4 -> 2020.5 
Reported by:	portscout
 2021-01-09 10:33:49 +00:00
Jason W. Bacon
858d1dcc69 science/gromacs: Upgrade hwloc dep to hwloc2 
hwloc2 conflicts with hwloc, so updating all dependents ASAP.

PR:             252526
Submitted by:   jwb
Approved by:    yuri
 2021-01-08 20:44:02 +00:00
Tobias C. Berner
4fb2cd10f1 Update KDE Release Service ports to 20.12.1 
Full changelog:
	https://kde.org/announcements/fulllog_releases-20.12.1/
 2021-01-08 19:15:30 +00:00
Dima Panov
2ec10e7dd9 devel/doxygen: Update to 1.9.0 
- regen patches by 'make makepatch'
- adjust consumers which affected by new doxygen styles
- take maintainersip

Changelog: https://www.doxygen.nl/manual/changelog.html#log_1_9_0

PR:		242347
Submitted by:	fluffy
Reported by:	Naram Qashat (ex-maintainer)
Exp-run by:	antoine
 2021-01-08 07:47:02 +00:00
Yuri Victorovich
8113767fac science/agrum: Add Python dependencies 2021-01-07 23:00:29 +00:00
Sunpoet Po-Chuan Hsieh
8e64be3c6b Update to 1.5.0 
Changes:	https://github.com/pysal/segregation/releases
 2021-01-06 20:32:27 +00:00
Sunpoet Po-Chuan Hsieh
7261c6d965 Update to 2.3.2 
Changes:	https://github.com/pysal/esda/releases
 2021-01-06 20:32:23 +00:00
Max Brazhnikov
be837bca6f science/lamprop: 
- Update to 2020.12.28
- The port does not install Python modules, therefore remove PKGNAMEPREFIX

PR:		252287
Submitted by:	(maintainer)
 2021-01-06 16:06:28 +00:00
Yuri Victorovich
f6856b7401 science/agrum: Update 0.18.2 -> 0.19.0 2021-01-06 01:29:56 +00:00
Rene Ladan
89b454230d Follow up on graphics/py-pillow6 port removal in r559976 
The graphics/py-pillow6 port was removed in r559976 as it was for
Python 2.7 only and no longer referenced in the default cases.
However it was still defined in Mk/Uses/python.mk in PY_PILLOW,
leaving a dangling reference.

Remove it from Mk/Uses/python.mk, leaving only the Python 3
version of that port, graphics/py-pillow, defined and bump the
minimal verion of Python to 3.6 for affected ports.
 2021-01-05 20:53:59 +00:00
Yuri Victorovich
1701f4c2f0 science/elk: Not broken any more. 2021-01-05 07:42:49 +00:00
Yuri Victorovich
fbe4bdc450 science/simgrid: Update 3.25 -> 3.26 2021-01-04 22:59:09 +00:00
Yuri Victorovich
efa676cd8d science/jmol: Update 14.31.21 -> 14.31.23 2021-01-04 22:06:58 +00:00
Piotr Kubaj
b9fbf136a4 science/py-scipy: fix build on GCC architectures 
/usr/local/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:65:6: error: #error pybind11 requires gcc 4.8 or newer

MFH:		2021Q1
 2021-01-04 21:33:16 +00:00
Rene Ladan
75121688f1 science/afni: use math/qhull instead of expired math/qhull5 2021-01-04 15:33:02 +00:00
Yuri Victorovich
73f6ad871f science/jmol: Update 14.31.20 -> 14.31.21 
Reported by:	portscout
 2021-01-04 01:45:26 +00:00
Sunpoet Po-Chuan Hsieh
758cb28eaf Update to 2.2.0 
Changes:	https://github.com/pysal/pysal/releases
 2021-01-03 20:16:04 +00:00
Sunpoet Po-Chuan Hsieh
424da78664 Update to 2.2.28 
Changes:	https://github.com/Unidata/UDUNITS-2/blob/master/CHANGE_LOG
 2021-01-03 20:05:21 +00:00
Sunpoet Po-Chuan Hsieh
9c6b482b20 Add py-tobler 0.5.4 
tobler is a library for areal interpolation and dasymetric mapping. The name is
an homage to the legendary geographer Waldo Tobler.

WWW: https://pysal.org/tobler/
WWW: https://github.com/pysal/tobler
 2021-01-03 19:58:24 +00:00
Sunpoet Po-Chuan Hsieh
07febaa62b Add py-spaghetti 1.4.2 
SPAtial GrapHs: nETworks, Topology, & Inference

Spaghetti is an open-source Python library for the analysis of network-based
spatial data. Originating from the network module in PySAL (Python Spatial
Analysis Library), it is under active development for the inclusion of newly
proposed methods for building graph-theoretic networks and the analysis of
network events.

WWW: https://pysal.org/spaghetti/
WWW: https://github.com/pysal/spaghetti
 2021-01-03 19:58:19 +00:00
Sunpoet Po-Chuan Hsieh
f013c58dda Add py-segregation 1.4.0 
Segregation Analysis, Inference, and Decomposition with PySAL

The PySAL segregation package is a tool for analyzing patterns of urban
segregation. With only a few lines of code, segregation users can calculate over
40 segregation measures from simple to state-of-the art.

WWW: https://pysal.org/segregation/
WWW: https://github.com/pysal/segregation
 2021-01-03 19:58:14 +00:00
Sunpoet Po-Chuan Hsieh
c917dfab31 Add py-libpysal 4.3.0 
Python Spatial Analysis Library Core

libpysal offers four modules that form the building blocks in many upstream
packages in the PySAL family:
- Spatial Weights: libpysal.weights
- Input-and output: libpysal.io
- Computational geometry: libpysal.cg
- Built-in example datasets libpysal.examples

WWW: https://pysal.org/libpysal/
WWW: https://github.com/pysal/libpysal
 2021-01-03 19:58:09 +00:00
Sunpoet Po-Chuan Hsieh
d691c243fb Add py-inequality 1.0.0 
inequality implements measures for the analysis of inequality over space and
time and is part of the PySAL family.

WWW: https://inequality.readthedocs.io/en/latest/
WWW: https://github.com/pysal/inequality
 2021-01-03 19:58:04 +00:00
Sunpoet Po-Chuan Hsieh
0989228194 Add py-esda 2.3.1 
ESDA: Exploratory Spatial Data Analysis

ESDA is an open-source Python library for the exploratory analysis of spatial
data. A subpackage of PySAL (Python Spatial Analysis Library), it is under
active development and includes methods for global and local spatial
autocorrelation analysis.

WWW: https://pysal.org/esda/
WWW: https://github.com/pysal/esda
 2021-01-03 19:57:58 +00:00