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4501 commits

Author SHA1 Message Date
Sunpoet Po-Chuan Hsieh
218bf57515 Update to 4.1.1 
Changes:	https://pyteomics.readthedocs.io/en/latest/changelog.html
 2019-05-25 22:03:25 +00:00
Sunpoet Po-Chuan Hsieh
70d0371995 Update to 2.12.5 
Changes:	https://confluence.ecmwf.int/display/ECC/Latest+news
 2019-05-25 22:02:44 +00:00
Sunpoet Po-Chuan Hsieh
b4a96957bc Add py-eccodes-python 0.9.0 
Python 3 interface to encode and decode GRIB and BUFR files via the ECMWF
ecCodes library.

Features:
- reads and writes GRIB 1 and 2 files,
- reads and writes BUFR 3 and 4 files,
- supports all modern versions of Python 3.7, 3.6, 3.5 and PyPy3,
- works on most Linux distributions and MacOS, the ecCodes C-library is the only
  system dependency,
- PyPI package with no install time build (binds with CFFI ABI level, in-line
  mode),
- supports writing the index of a GRIB file to disk, to save a full-file scan on
  open.

WWW: https://github.com/ecmwf/eccodes-python
 2019-05-25 22:02:27 +00:00
Yuri Victorovich
e0b5281b58 science/py-GPy: Fix build by explicitly setting the path to libomp.so in xx_DEPENDS lines 
Reported by:	fallout
 2019-05-23 21:21:49 +00:00
Jason W. Bacon
73eb992926 science/afni: Upgrade to 19.1.10 
Rapid response from upstream on reported issue.  Additional patches to be
upstreamed in next release.
 2019-05-22 12:44:17 +00:00
Piotr Kubaj
9b1f148f09 science/wxmacmolplt: fix build with GCC-based architectures 
Add USES=compiler:c++11-lang to fix linking:
checking for wxWidgets libraries... not found

Approved by:	mentors (implicit approval)
 2019-05-20 20:09:32 +00:00
Jason W. Bacon
ade7919150 science/afni: Upgrade to 19.1.08 
Switch from personal dist snapshots to Github releases
Improve staging procedure to preserve results of build phase
Temporarily use bundled GLw pending fix of libglw port
 2019-05-20 19:35:57 +00:00
Thierry Thomas
b3a0da2461 Switch to Python 3.6 and upgrade to v5.3.3. 
Note: Code_Saturne does not run with Qt5 in combination with Python 2.7.
See <https://github.com/code-saturne/code_saturne/issues/44>.
 2019-05-19 19:22:45 +00:00
Yuri Victorovich
a60337fb4e science/py-phono3py: Fix build on 12/13 (broken due to missing libgomp.so); Add USES=blaslapack:openblas 
libgomp.so was found in gcc8, which this ports doesn't explicitly depend on,
and openmp wasn't installed but the build was failing later on 12 due to the
lack of libgomp.so.

Solution: Move openmp dependency from LIB_DEPENDS to BUILD_DEPENDS/RUN_DEPENDS.

Reported by:	Gleb Popov <6yearold@gmail.com> (USES=blaslapack:openblas)
 2019-05-19 16:48:08 +00:00
Yuri Victorovich
749b46c96b science/abinit: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 
Reported by:	fallout
 2019-05-19 03:01:48 +00:00
Yuri Victorovich
d95813f563 science/dftbplus: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 2019-05-19 02:47:01 +00:00
Yuri Victorovich
771d3b45a5 science/py-phono3py: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:40:34 +00:00
Yuri Victorovich
0a3ad2a5f4 science/gabedit: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:38:14 +00:00
Yuri Victorovich
34c0e7d61e science/py-GPy: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:35:46 +00:00
Yuri Victorovich
1837418d06 science/openmx: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
LIB_DEPENDS=libomp.so:devel/openmp now causes this problem in multiple ports.

Reported by:	fallout
 2019-05-19 02:24:59 +00:00
Yuri Victorovich
c17f9e6a78 science/esys-particle: Broken on 13-CURRENT 
Reported by:	fallout
 2019-05-18 22:58:19 +00:00
Yuri Victorovich
7d0e3eaf2a science/chrono: Broken on i386 
Reported by:	fallout
 2019-05-18 22:28:29 +00:00
Yuri Victorovich
d7cca70b67 science/nest: Broken on i386 
Reported by:	fallout
 2019-05-18 22:12:49 +00:00
Yuri Victorovich
72a5a25bc9 science/py-paramz: Update 0.9.4 -> 0.9.5 
Reported by:	portscout
 2019-05-18 15:56:47 +00:00
Yuri Victorovich
b399938765 New port: science/libvdwxc: Van der Waals density functional (DFT) library 2019-05-18 05:40:31 +00:00
Yuri Victorovich
e9a104fd10 New port: science/simgrid: Simulator of the behavior of large-scale distributed systems 2019-05-16 16:00:15 +00:00
Yuri Victorovich
2c32727d61 science/lammps: Update patch_30Apr2019 -> patch_15May2019 
Reported by:	github notification
 2019-05-15 04:29:09 +00:00
Yuri Victorovich
9307245c42 science/py-qcelemental: Update 0.3.3 -> 0.4.0 
Reported by:	portscout
 2019-05-14 17:25:54 +00:00
Wen Heping
6d5d69c53d - Update to 0.20.3 
PR:		237759
Submitted by:	wenheping2000@hotmail.com(myself)
Approved by:	demon@(maintainer)
 2019-05-14 02:17:08 +00:00
Yuri Victorovich
4b21a54932 science/hypre: Update 2.15.1 -> 2.16.0 
New github repository is pointed to from their website now.
 2019-05-13 07:57:57 +00:00
Yuri Victorovich
a3fee0ff6d science/nest: Update 2.14.0-2100 -> 2.16.0 
Reported by:	portscout
 2019-05-12 08:24:10 +00:00
Mathieu Arnold
5944e9ef33 Cleanup cython dependency. 2019-05-11 21:10:31 +00:00
Yuri Victorovich
81a5212217 science/nest: PYTHON_USE=python=cython instead of PYTHON_BUILD_DEPENDS 
Reported by:	mat
 2019-05-11 21:01:54 +00:00
Yuri Victorovich
85cb72892b science/coot: Fix build with GCC-based architectures 
PR:		237842
Submitted by:	pkubaj
 2019-05-11 20:40:33 +00:00
Piotr Kubaj
1f4241358e science/clipper: add USES=compiler:c++11-lang 
This is needed to build science/coot.

Approved by:	mentors (implicit approval)
 2019-05-11 20:30:19 +00:00
Yuri Victorovich
5e8b580aa9 New port: science/nest: Simulator for spiking neural network models 2019-05-11 20:29:56 +00:00
Yuri Victorovich
e721b925ab science/avogadrolibs: Update 1.92.0 -> 1.92.1 2019-05-11 18:10:31 +00:00
Antoine Brodin
ef73356c19 Those ports link against llvm's libomp.so 2019-05-11 09:36:21 +00:00
Yuri Victorovich
20a2b516de science/opsin: Update 3.0.20190208 -> 3.0.20190223 2019-05-11 06:00:09 +00:00
Yuri Victorovich
25a7016bf4 science/nwchem: Update 6.8.1.20190412 -> 6.8.1.20190509 2019-05-11 03:41:13 +00:00
Yuri Victorovich
3b5fce1f01 science/agrum: Update 0.14.3 -> 0.15.0 
Reported by:	portscout
 2019-05-10 06:15:21 +00:00
Yuri Victorovich
e0083390a0 science/py-gpaw: Update 1.5.1 -> 1.5.2 
Reported by:	portscout
 2019-05-09 20:12:51 +00:00
Piotr Kubaj
3edb29c651 science/luscus: fix build with GCC-based architectures 
Add USES=compiler:c++11-lang to fix linking:
/usr/local/lib/libgraphite2.so.3: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'

Approved by:	mentors (implicit approval)
 2019-05-09 19:59:20 +00:00
Tobias C. Berner
d27fcc13c5 Update KDE Applications to 19.04.1 
Changelog:
	https://kde.org/announcements/fulllog_applications-aether.php?version=19.04.1
 2019-05-09 18:18:04 +00:00
Jan Beich
3b1a1bcee4 devel/openmp: phase out 
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767
 2019-05-08 16:05:53 +00:00
Yuri Victorovich
bab17abceb science/py-phonopy: Update 2.0.0 -> 2.1.3 2019-05-08 06:35:50 +00:00
Yuri Victorovich
2084646704 science/py-phonopy: 1.13.2.107 -> 2.0.0 2019-05-08 06:11:16 +00:00
Yuri Victorovich
68197f1a2f science/py-pymatgen: Update 2019.1.24 -> 2019.2.28 2019-05-08 05:49:01 +00:00
Yuri Victorovich
60e2c08fee science/chrono: Update 2.0.0-9070 -> 4.0.0-89 2019-05-05 01:42:48 +00:00
Tobias Kortkamp
9b8c35db19 science/ALPSCore: Fix OPENMPI2 spelling after r500723 2019-05-04 11:02:15 +00:00
Yuri Victorovich
f6ccdc8eb7 science/harminv: Add -fPIC 
PR:		234105
Submitted by:	devel@stasyan.com (maintainer)
 2019-05-04 02:08:19 +00:00
Mark Linimon
922dee671e These ports now build on aarch64. 
Where necessary, pet portlint.

Approved by:	portmgr
Obtained from:	aarch64 TRYBROKEN run
 2019-05-03 21:06:51 +00:00
Mathieu Arnold
b139bbf73f Fix the a ports that were broken but did not know it. 
Differential Revision:	https://reviews.freebsd.org/D20140
 2019-05-03 13:58:33 +00:00
Adam Weinberger
a388e76374 compiler.mk is unhappy if CC/CXX is defined before bsd.port.pre.mk 
Reported by:	Peter Jeremy
Submitted by:	mat
 2019-05-03 12:30:40 +00:00
Yuri Victorovich
5ee82ae77a science/apbs: Fix license 2019-05-03 06:15:44 +00:00