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4629 commits

Author SHA1 Message Date
Kai Knoblich
88d3223f6c science/py-ruffus: Update to 2.8.2 
Changelog:

* Implement retry behaviour for input file check.
 2019-08-10 19:21:57 +00:00
Sunpoet Po-Chuan Hsieh
4d0396a4c8 Update to 2.1.0 
Changes:	https://github.com/rgeo/rgeo/blob/master/History.md
 2019-08-09 20:01:46 +00:00
Sunpoet Po-Chuan Hsieh
34c8ee34fc Revert r508450 
r508454 has fixed the problem (bulk -a with BUILD_ALL_PYTHON_FLAVORS).
 2019-08-09 18:34:46 +00:00
Mathieu Arnold
cdbddd4583 Fix bulk -a with BUILD_ALL_PYTHON_FLAVORS. 
devel/py-typing-extensions does not support Python 3.7+, so ports
requiring it can't either.
 2019-08-09 12:54:26 +00:00
Yuri Victorovich
dc59472dd9 science/jmol: Update 14.29.49 -> 14.29.50 
Reported by:	portscout
 2019-08-09 06:42:26 +00:00
Yuri Victorovich
3baf2e986b New port: science/py-chainer-chemistry: Library for deep learning in biology and chemistry 2019-08-08 21:05:43 +00:00
Sunpoet Po-Chuan Hsieh
43fd453bca Fix typo: add missing quotation marks 2019-08-08 20:47:19 +00:00
Yuri Victorovich
87a548fc56 science/py-chainer: Remove the irrelevant category 2019-08-08 20:08:09 +00:00
Yuri Victorovich
48bb80d29b New port: science/py-chainer: Deep learning framework 2019-08-08 20:07:04 +00:00
Sunpoet Po-Chuan Hsieh
d3f552d9f1 Fix RUN_DEPENDS: typing is used for Python 3.4 and below 
- Bump PORTREVISION for dependency change

With hat:	python
 2019-08-08 19:22:20 +00:00
Yuri Victorovich
f1d0b3247f New port: science/py-onnx: Open Neural Network eXchange 2019-08-08 17:53:24 +00:00
Yuri Victorovich
82029411ed science/simbody: Backport the pull request that fixed the pathname handling on BSDs, and one failing testcase. 2019-08-08 04:53:25 +00:00
Yuri Victorovich
482064760e science/simbody: Add the option EXAMPLE_PROGRAMS that builds and installs example programs 2019-08-08 04:06:03 +00:00
Yuri Victorovich
2afd1823b8 science/simbody: Add VISUALIZER_DESC for the VISUALIZER option 2019-08-08 01:42:05 +00:00
Yuri Victorovich
64a3190a05 science/lammps: patch_6Aug2019 -> stable_7Aug2019 
Reported by:	portscout
 2019-08-08 01:37:14 +00:00
Yuri Victorovich
069ecdaf12 Re-add science/py-tensorflow: Computation using data flow graphs for scalable machine learning 
Many thanks to Anthony who was highly persistent and skillful in getting the Tensorflow build on FreeBSD!

PR:		226400
Submitted by:	Anthony <amzo1337@gmail.com>
 2019-08-06 15:28:01 +00:00
Yuri Victorovich
a7b0878922 science/lammps: Update 2Aug2019 -> 6Aug2019 
Reported by:	portscout
 2019-08-05 23:30:37 +00:00
Jan Beich
325aed58cb multimedia/ffmpeg: update to 4.2 
Changes:	https://git.ffmpeg.org/gitweb/ffmpeg.git/blob/n4.2:/Changelog
ABI:		https://abi-laboratory.pro/tracker/timeline/ffmpeg/
 2019-08-05 23:06:50 +00:00
Antoine Brodin
df4aac35f0 Mark BROKEN: unfetchable 2019-08-05 06:37:30 +00:00
Yuri Victorovich
bff2487d86 science/dalton: Update 2018.0 -> 2018.2 
Reported by:	repology
 2019-08-04 04:22:31 +00:00
Yuri Victorovich
3b466c657d science/wannier90: Update 2.1.0 -> 3.0.0 
The project moved to GitHub.
 2019-08-04 04:09:32 +00:00
Ben Woods
d12a1a88b8 science/InsightToolkit: Update to 5.0.1 
Changes this release:
  https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.0.0
  https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.0.1
 2019-08-04 03:07:31 +00:00
Yuri Victorovich
ce446974c2 science/maeparser: Update 1.1 -> 1.2 
Reported by:	portgscout
 2019-08-04 00:47:28 +00:00
Sunpoet Po-Chuan Hsieh
f6058bac37 Use PYNUMPY 2019-08-03 20:56:13 +00:00
Sunpoet Po-Chuan Hsieh
c43180ab93 Use PYNUMPY 2019-08-03 20:56:09 +00:00
Sunpoet Po-Chuan Hsieh
759510d76d Use PYNUMPY 2019-08-03 20:56:04 +00:00
Yuri Victorovich
171da8331f science/jdftx: 1.4.2-74 -> 1.5.0 
Reported by:	portscout
 2019-08-03 20:12:32 +00:00
Yuri Victorovich
eeba775c30 science/dftbplus: Update 18.2 -> 19.1 
Reported by:	portscout
 2019-08-03 19:59:34 +00:00
Yuri Victorovich
f293cc2064 science/lammps: Update 19Jul2019 -> 2Aug2019 
Reported by:	portscout
 2019-08-03 08:21:25 +00:00
Yuri Victorovich
716c95b18a science/py-phonopy: Update 2.1.4 -> 2.2.0 
Reported by:	portscout
 2019-08-02 20:59:34 +00:00
Yuri Victorovich
59ad9d5e06 science/py-qcengine: Update 0.7.1 -> 0.8.2 
Reported by:	portscout
 2019-08-02 20:45:01 +00:00
Yuri Victorovich
69d6541bb1 science/metaphysicl: Update 0.5.0 -> 0.5.2 
Reported by:	portscout
 2019-08-02 20:20:29 +00:00
Sunpoet Po-Chuan Hsieh
d41dd4068c Cosmetic change 2019-08-02 19:28:57 +00:00
Yuri Victorovich
a921e1d567 Hook up science/openkim-models to build. 2019-08-02 18:44:20 +00:00
Yuri Victorovich
143237e61c New port: science/openkim-models: Open Knowledgebase of Interatomic Models 
Requested by:	Ryan S. Elliott <relliott@umn.edu>
 2019-08-02 17:26:27 +00:00
Yuri Victorovich
1a8b8e1d5c science/jmol: Update 14.29.46 -> 14.29.49 
Reported by:	portscout
 2019-08-02 06:29:26 +00:00
Piotr Kubaj
4af00fce4c science/libkml: fix build with GCC architectures 
Typedef redefinitions were introduced in C11.

Approved by:	mentors (implicit approval)
 2019-08-01 21:24:41 +00:00
Yuri Victorovich
e0dd0c0068 science/wwplot: Update 0.0.4 -> 0.0.6 
Reported by:	portscout
 2019-08-01 02:27:28 +00:00
Sunpoet Po-Chuan Hsieh
4f3e0d828f Bump PORTREVISION for devel/protobuf shlib change 2019-07-31 16:38:52 +00:00
Yuri Victorovich
4f537b340b science/py-qcelemental: Update 0.4.2 -> 0.5.0 
Reported by:	portscout
 2019-07-31 06:26:37 +00:00
Yuri Victorovich
1d2be50ce1 science/smoldyn: Update 2.60 -> 2.61 
Reported by:	portscout
 2019-07-31 06:15:12 +00:00
Yuri Victorovich
7db2ddef5b science/qmcpack: Update 3.7.0 -> 3.8.0 
Reported by:	portscout
 2019-07-31 06:09:39 +00:00
Yuri Victorovich
82c32da496 science/simgrid: Update 3.22.2.20190515 -> 3.23.2 
Reported by:	repology
 2019-07-30 03:31:30 +00:00
Yuri Victorovich
d834026e4d science/kim-api: Update 2.1.1 -> 2.1.2 2019-07-30 02:54:41 +00:00
Antoine Brodin
8d0c8c5c44 Unbreak bulk 2019-07-28 18:52:00 +00:00
Yuri Victorovich
6c0577c732 science/py-ase: It is python 3.5+ now. 
Reported by:	fallout
 2019-07-28 18:17:27 +00:00
Tobias C. Berner
a430427055 science/libgeodecomp: fix build with cmake 3.15 2019-07-28 15:29:33 +00:00
Yuri Victorovich
da9df2a409 science/py-gsd: Update 1.6.1 -> 1.7.0 
Reported by:	repology
 2019-07-28 03:24:30 +00:00
Yuri Victorovich
a194765fbd science/py-GPy: Update 1.9.6 -> 1.9.8 
Reported by:	repology
 2019-07-28 03:22:14 +00:00
Piotr Kubaj
f87e4c2ecb science/ncnn: fix build with GCC-based architectures 
This adds USES=compiler:c11 because of:
/usr/local/poudriere/ports/default/science/ncnn/work/ncnn-20190611-40-gd3be711/src/layer/convolutiondepthwise.cpp:450: error: expected '#pragma omp' clause before 'collapse'

It's detected that our base compiler supports OpenMP and new OpenMP features are then used.

That's why we need new GCC. USES=compiler:openmp would work but it uses a base compiler. Since this port builds also without OpenMP, no further modifications are needed.

Approved by:	mentors (implicit approval)
 2019-07-27 22:08:21 +00:00