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6103 Commits

Author SHA1 Message Date
Mateusz Piotrowski
6a66372473 science/linux-zotero: Add new port 
Zotero is a reference management software to manage bibliographic data and
related research materials.

WWW: https://www.zotero.org/

MFH:		2021Q4
(cherry picked from commit 8c6cd1e918)
 2021-11-03 19:22:16 +01:00
Yuri Victorovich
6014fe2a2f science/opensph: 0.3.8 release was moved to include the OpebVDB fix 2021-10-03 01:53:36 -07:00
Yuri Victorovich
b635bf0d5b science/opensph: Update 0.3.7 -> 0.3.8 
oneTBB is now supported.
 2021-10-02 16:00:02 -07:00
Yuri Victorovich
373f51362e science/tinker: Update 8.9.4 -> 8.9.5 
Reported by:	portscout
 2021-10-02 16:00:01 -07:00
Piotr Kubaj
421f92a120 science/openems: fix build on powerpc64* 
Add FreeBSD names for 64-bit POWER to the check.
 2021-10-01 14:39:19 +00:00
Fernando Apesteguía
292ec73c27 science/afni: update to 21.2.09 2021-10-01 07:41:12 +02:00
Rene Ladan
620968a43a cleanup: drop support for EOL FreeBSD 11.X 
Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index
 2021-09-30 23:23:30 +02:00
Yuri Victorovich
fc03b499c6 science/lammps: Update patch_2Jul2021 -> stable_29Sep2021 
Reported by:	upstream notification
 2021-09-30 10:30:10 -07:00
Yuri Victorovich
8eac9dc021 science/votca: Update 2021.2 -> 2021.2-18560 
This fixed 6 failing testcases. The patch fixing these testcases
doesn't apply to 2021.2, so the port is updated to the latest
commit.
 2021-09-28 17:49:03 -07:00
Po-Chuan Hsieh
fa1a81e87e
science/libaec: Update to 1.0.6 
Changes:	https://gitlab.dkrz.de/k202009/libaec/-/blob/master/CHANGELOG.md
 2021-09-28 03:48:08 +08:00
Po-Chuan Hsieh
9b778e94c8
science/py-spaghetti: Update to 1.6.4 
Changes:	https://github.com/pysal/spaghetti/releases
 2021-09-27 23:56:01 +08:00
Po-Chuan Hsieh
931b97d41f
science/py-h5py: Update version requirement of BUILD_DEPENDS 2021-09-27 23:56:01 +08:00
Yuri Victorovich
c0f1282a1c science/libghemical: Remove LD_PRELOAD vecause it configured now without it 
PR:		258733
Reported by:	mikael
 2021-09-26 10:43:55 -07:00
Mikael Urankar
76a14ebdfd science/nwchem: Mark as broken on aarch64. 2021-09-26 10:25:25 +02:00
Yuri Victorovich
cbc50017fa science/shelxle: Update 1.0.1320 -> 1.0.1322 
Reported by:	portscout
 2021-09-25 22:45:23 -07:00
Yuri Victorovich
6f6a8a2af1 science/siconos: Update 4.4.0.rc4 -> 4.4.0 
PYTHON option is broken.

Reported by:	portscout
 2021-09-25 22:45:19 -07:00
Guangyuan Yang
a7d1c2da92 science/R-cran-fastICA: Update to 1.2-3 2021-09-25 18:13:13 -04:00
Stephen Montgomery-Smith
a841ed9388 science/getdp: Update to 3.4.0. 2021-09-24 12:35:11 -05:00
Yuri Victorovich
fae27f575d science/votca: Update 2021.1 -> 2021.2 
Reported by:	portscout
 2021-09-23 19:04:20 -07:00
Po-Chuan Hsieh
15592565d3
science/py-pyteomics: Update to 4.5 
Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html
 2021-09-22 06:23:38 +08:00
Po-Chuan Hsieh
8b699cb1f1
science/py-pygeodesy: Update to 21.9.16 
Changes:	https://github.com/mrJean1/PyGeodesy/commits/master
 2021-09-22 06:23:38 +08:00
Po-Chuan Hsieh
39163999ba
science/eccodes: Update to 2.23.0 
Changes:	https://confluence.ecmwf.int/display/ECC/Latest+news
 2021-09-22 06:23:22 +08:00
Yuri Victorovich
3b0c178aab science/py-chempy: Update 0.8.1 -> 0.8.2 
Reported by:	portscout
 2021-09-21 10:47:02 -07:00
Danilo Egea Gondolfo
170cb07fe4 math/armadillo: Update to 10.6.2 
Drop maintainership.
 2021-09-21 10:25:15 +01:00
Po-Chuan Hsieh
43198643e0
science/py-segregation: Update to 2.1.0 
Changes:	https://github.com/pysal/segregation/releases
 2021-09-21 11:44:55 +08:00
Po-Chuan Hsieh
0cbc87f551
science/py-pygeometa: Update to 0.8.0 
Changes:	https://github.com/geopython/pygeometa/releases
		https://github.com/geopython/pygeometa/blob/master/debian/changelog
 2021-09-21 11:44:55 +08:00
Po-Chuan Hsieh
6f119b46fa
science/py-h5py: Update to 3.4.0 
Changes:	https://github.com/h5py/h5py/releases
		https://github.com/h5py/h5py/blob/master/docs/whatsnew/3.4.rst
		https://docs.h5py.org/en/stable/whatsnew/index.html
 2021-09-21 11:44:54 +08:00
Po-Chuan Hsieh
233ad9c646
science/py-esda: Add SHAPE option 2021-09-21 11:44:54 +08:00
Wen Heping
20438ba77d science/py-pydicom: Update to 2.2.1 2021-09-21 08:57:04 +08:00
Yuri Victorovich
1dcd34af41 science/cantera: Fix handling of Python versions 2021-09-19 20:08:25 -07:00
Yuri Victorovich
f628a6e453 science/cantera: Update 2.5.1-552 -> 2.5.1-611 
The PYTHON option is now fixed and is enabled.
 2021-09-19 19:53:43 -07:00
Po-Chuan Hsieh
509e356160
science/py-pysal: Update to 2.5.0 
Changes:	https://github.com/pysal/pysal/releases
 2021-09-19 14:00:21 +08:00
Yuri Victorovich
79be00646b science/axom: Add dependencies 2021-09-18 12:37:10 -07:00
Yuri Victorovich
f0257531e9 science/py-nilearn: Update 0.8.0 -> 0.8.1 
Reported by:	portscout
 2021-09-18 10:48:28 -07:00
TAKATSU Tomonari
34e9235dee science/R-cran-e1071: Update to 1.7-9 2021-09-18 13:18:14 +00:00
Yuri Victorovich
009e0a233d science/shelxle: Update 1.0.1306 -> 1.0.1320 2021-09-17 01:48:02 -07:00
Yuri Victorovich
7f4490149b science/conduit: Add dependencies 2021-09-16 12:48:34 -07:00
Yuri Victorovich
91e83b602b science/ascent: New port: Visualization and analysis runtime for multi-physics HPC simulations 2021-09-16 09:46:15 -07:00
Yuri Victorovich
c4942f9114 science/conduit: Add fortran interface; Turn on MPI. 
Both because consumers (like ascent) need it.
 2021-09-16 01:35:52 -07:00
Yuri Victorovich
4b586534a9 science/py-qcelemental: Update 0.21.0 -> 0.22.0 2021-09-14 02:21:06 -07:00
Yuri Victorovich
6eb990f406 science/agrum: Update 0.22.0 -> 0.22.1 2021-09-13 15:28:57 -07:00
Yuri Victorovich
ec95bfb566 science/py-scikit-sparse: Update 0.4.5 -> 0.4.6 
Reported by:	portscout
 2021-09-13 15:28:57 -07:00
Yuri Victorovich
fe77478798 science/yoda: Update 1.9.0 -> 1.9.1 
Now the python binding builds fine.
The project also installs the completion file by itself.
 2021-09-12 10:27:25 -07:00
Yuri Victorovich
66f0d417dc science/helfem: Update g20210807 -> g20210912 
Shared libraries now work.
 2021-09-12 10:27:23 -07:00
Fernando Apesteguía
71ac81015e science/afni: update to 21.2.06 
* Remove openmp support. We don't seem to need it.
 * Adjust patch
 * Add -fcommon to make it build in 13 and 14-current
 * Add patch to include -DPIC -fPIC in i386. Otherwise we get:

ld: error: can't create dynamic relocation R_386_32 against symbol: .L.str.13 in
readonly segment
 2021-09-12 15:58:20 +02:00
Yuri Victorovich
c9f9c0d71b science/cantera: Add missing boost dependency 
Reported by:	fallout
 2021-09-11 20:10:09 -07:00
Yuri Victorovich
94d91d8361 science/helfem: New port: Finite element methods for electronic structure calculations 2021-09-11 02:24:45 -07:00
Yuri Victorovich
dfc0238640 science/py-pyked: New port: Package for manipulating Chemical Kinetics Experimental Data files 2021-09-11 00:13:16 -07:00
Yuri Victorovich
c43e8a0f4b science/cantera: Small corrections 2021-09-10 12:03:36 -07:00
Yuri Victorovich
af1b8fdf83 science/cantera: New port: Chemical kinetics, thermodynamics, and transport tool suite 2021-09-10 11:50:08 -07:00