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Commit Graph

3540 Commits

Author SHA1 Message Date
Luca Pizzamiglio
5f69b42070 science/lamprop: Update to 3.4
PR:		221544
Submitted by:	rsmith@xs4all.nl (maintainer)
2017-12-29 14:25:16 +00:00
Ben Woods
df125ec212 science/InsightToolkit: Update to 4.13.0
Changes this release:
  https://discourse.itk.org/t/itk-4-13-has-been-released/549
2017-12-29 08:07:19 +00:00
Sunpoet Po-Chuan Hsieh
c0ede16652 Update to 1.25.0
Changes:	https://software.ecmwf.int/wiki/display/GRIB/Latest+news
2017-12-27 19:51:35 +00:00
Jan Beich
95ad0a601c devel/google{test,mock}: update to 1.8.0.450
Changes:	f1a87d7...5490beb
2017-12-27 19:47:20 +00:00
Yuri Victorovich
3c2c583237 science/libefp: Update to 1.5.0
Reported by:	portscout
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13598
2017-12-23 18:19:11 +00:00
Sunpoet Po-Chuan Hsieh
0ba55b5106 Update to 2.2.26
Changes:	https://github.com/Unidata/UDUNITS-2/blob/master/CHANGE_LOG
2017-12-23 16:49:28 +00:00
Yuri Victorovich
787a848e54 e-added port: science/PETSc: Suite of data structures and routines from Argonne National Laboratory (existed 2004/11/21-2014/09/01, deleted in r366959)
Replacing the identical version committed by me as a new port in r456696.
The old math/petsc port also had a slave port math/petsc-mpich that has also been deleted.

Original differential revision is https://reviews.freebsd.org/D13527

Submitted by:	myself
Reported by:	thierry that math/petsc and math/petsc-mpich existed before
Approved by:	adamw (mentor)
2017-12-21 00:26:58 +00:00
Yuri Victorovich
ac7be60714 Deleting science/PETSc: The previously-deleted port math/petsc exists. It will be resurrected and this version will be committed with it. 2017-12-21 00:20:01 +00:00
Baptiste Daroussin
4ce271099d Remove dependency on swig
I can't find any direct call to the swig binary in the code meaning
having swig as a run time dependency should not be a requirement
2017-12-20 15:25:16 +00:00
Baptiste Daroussin
8c16b50d8d Switch from swig1.3 to swig 3.0 2017-12-20 12:25:18 +00:00
Antoine Brodin
1ea2c6ea62 - Canonicalize LIB_DEPENDS
- Limit to python 2.7, the dependencies and the plist are not compatible
  with python3
- Cleanup plist

With hat:	portmgr (poudriere bulk -a broken)
2017-12-19 20:06:09 +00:00
Yuri Victorovich
a03c50d808 Re-added port: science/py-pymol: OpenGL based molecular visualization system (existed 2002/08/13-2014/09/01, deleted in r366862)
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D12902
2017-12-19 19:49:17 +00:00
Yuri Victorovich
e51eda6b05 New port: science/MOOSE-neural-simulator: Multiphysics Object Oriented Simulation Environment
Multiphysics Object Oriented Simulation Environment

MOOSE-neural-simulator allows to simulate
- chemical and biochemical reactions
- networks of neurons
- neural networks

This project is commonly referred to as MOOSE, in the capitalized form.
There is another science project called MOOSE, completely unrelated to this one, which will also be ported.
MOOSE-neural-simulator is a candidate for the future 'chemistry' category in case it will be approved.

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13539
2017-12-19 16:04:34 +00:00
Mark Linimon
f1696c0036 Mark more recently failing ports broken on aarch64.
While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)
2017-12-19 14:41:29 +00:00
Yuri Victorovich
97f90d255e New port: science/PETSc: Suite of data structures and routines from Argonne National Laboratory
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13527
2017-12-19 00:03:01 +00:00
David Naylor
e007fca186 science/R-cran-fastICA: FastICA Algorithms to Perform ICA and Projection Pursuit
Generated by:	portcran (0.1.7)
2017-12-18 12:31:46 +00:00
Dmitry Marakasov
b1f2dcda78 - Fix LICENSE
- Update WWW

Approved by:	portmgr blanket
2017-12-18 09:00:35 +00:00
Wen Heping
e71398843e - Update to 1.1.0 2017-12-16 06:11:08 +00:00
Jason W. Bacon
da78f03134 science/paraview: Unbreak build with clang 4.0
PR:		216634
Submitted by:	Jan Beich
Approved by:	jrm (mentor), maintainer timeout (3.5 months)
Differential Revision:	https://reviews.freebsd.org/D13462
2017-12-13 03:34:37 +00:00
Sunpoet Po-Chuan Hsieh
c9e9f17c7d Update to 1.9.2
- Update MASTER_SITES
- Update WWW

Changes:	https://code.mpimet.mpg.de/news/392
		https://code.mpimet.mpg.de/news/387
2017-12-12 13:32:53 +00:00
Antoine Brodin
a8cc35a10e - Those ports fail to build with python3
- Add some explicit FLAVOR to dependencies where needed
2017-12-12 12:40:15 +00:00
Sunpoet Po-Chuan Hsieh
ae23d9c1e8 Update WWW
- Reformat pkg-descr
2017-12-11 10:37:28 +00:00
Sunpoet Po-Chuan Hsieh
e034889c5e Update WWW
- Reformat pkg-descr
2017-12-11 10:37:24 +00:00
Sunpoet Po-Chuan Hsieh
c831858900 Update WWW
- Reformat pkg-descr
2017-12-11 10:37:19 +00:00
Sunpoet Po-Chuan Hsieh
3a18538b9a Update WWW
- Reformat pkg-descr
2017-12-11 10:37:14 +00:00
Antoine Brodin
a021c1b8c0 - Those ports fail to build with python3
- Add some explicit FLAVOR to dependencies where needed
2017-12-10 20:48:45 +00:00
Antoine Brodin
641aab050a mei fails to build with python3 2017-12-09 11:39:45 +00:00
Steve Wills
43e164ab3e science/mcstas: switch back to PORTVERSION
Avoids an issue with verion going backwards.
2017-12-06 16:18:35 +00:00
Dmitry Marakasov
abfa09ec2b - Fix LICENSE
- Add LICENSE_FILE
- Switch to new test framework
- Update WWW

Approved by:	portmgr blanket
2017-12-06 09:00:23 +00:00
Yuri Victorovich
9e8cc175a0 New port: science/mcxtrace: Monte Carlo X-ray tracing package
PR:		206505
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13216
2017-12-05 19:15:49 +00:00
Steve Wills
ef7b06f26c science/mcstas: simplify Makefile
While here, remove unecessary pkg-install/deinstall

PR:		223905
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk> (maintainer)
2017-12-05 17:32:37 +00:00
Rodrigo Osorio
1b363765bd Add new port science/aircraft-datcom
aircraft-datcom is a modified version of USAF Aircraft DATCOM
The goal of the project is to update the code and make it more usable by the end users

PR:		207928
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
2017-12-03 21:26:18 +00:00
Yuri Victorovich
0026e03cbb New port: science/ALPSCore: Generic algorithms and utilities for condensed matter physics
PR:		223850
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13237
2017-12-03 19:29:13 +00:00
Thierry Thomas
77bcb2723e Forgot to bump revision of FORTRAN libs in the previous commit. 2017-12-03 15:30:23 +00:00
Thierry Thomas
c25c56bf29 Upgrade HDF5 to 1.8.20.
Release notes at
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20-RELEASE.txt
2017-12-03 15:14:06 +00:00
David Chisnall
f9197640d9 Fix configure options for gnustep-make
We were not setting the flag to select the GNUstep ABI, so were defaulting to
using the GCC-compatible version, which was likely to trigger a lot of subtle
bugs.  This was noticed when C++ exceptions thrown through Objective-C stack
frames caused segfaults.
2017-12-03 12:23:53 +00:00
Antoine Brodin
07faea058d Cleanup LIB_DEPENDS on libpng 2017-12-01 07:19:53 +00:00
Matthias Andree
1fb0ae7cf9 Security update OpenEXR and ilmbase to 2.2.1.
While here, fix libIlmImfUtil_la_LDFLAGp so that when linking libIlmImfUtil,
the locally built libIlmImf gets precedence over the one in /usr/local,
to permit upgrades in a running system with the older version installed.

This changes the library's SONAME, so bump PORTREVISION of all dependees.

Unfortunately, this looks a bit too intrusive for an MFH to 2017Q4.

Security:	CVE-2017-9110
Security:	CVE-2017-9111
Security:	CVE-2017-9112
Security:	CVE-2017-9113
Security:	CVE-2017-9114
Security:	CVE-2017-9115
Security:	CVE-2017-9116
Security:	803879e9-4195-11e7-9b08-080027ef73ec
2017-12-01 01:58:23 +00:00
Mathieu Arnold
551be3c723 Convert Python ports to FLAVORS.
Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
  current python flavor.  It can be used in dependency lines when the
  port itself is not python flavored.  For example, deskutils/calibre.

  By default, all the flavors are generated.  To only generate flavors
  for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
  BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.

  In all the ports with Python dependencies, the *_DEPENDS entries MUST
  end with the flavor so that the framework knows which to build/use.
  This is done by appending '@${PY_FLAVOR}' after the origin (or
  @${FLAVOR} if in a Python module with Python flavors, as the content
  will be the same).  For example:

    RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}

PR:		223071
Reviewed by:	portmgr, python
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D12464
2017-11-30 15:50:30 +00:00
Mark Linimon
b9fc4cbf35 Also not for armv7. Missed in previous sweep. 2017-11-30 06:43:49 +00:00
Mark Linimon
bf43557044 For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
2017-11-30 06:13:34 +00:00
Mark Linimon
14295721d4 For ports that are marked NOT_FOR/ONLY_FOR armv6, also mark them so
on armv7.

This is part one of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
2017-11-30 05:55:17 +00:00
Thierry Thomas
111d6e8555 Upgrade to 3.0.2.
The new version brings important support for Abaqus(TM) and will be supported
in a future release of CalculiX.

PR:		216315
Submitted by:	Pedro F. Giffuni
2017-11-25 10:43:57 +00:00
Yuri Victorovich
4fb7bfbe5a New port: science/chemps2: Spin-adapted implementation of DMRG for ab initio quantum chemistry
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13100
2017-11-23 05:58:51 +00:00
Yuri Victorovich
fbacb4ad48 New port: science/gdma: Anthony Stone's Gaussian Distributed Multipole Analysis
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13110
2017-11-18 05:12:35 +00:00
Thierry Thomas
ee38c2d348 Chase metis-edf's upgrade. 2017-11-16 20:55:27 +00:00
Yuri Victorovich
54eb14a119 New port: science/py-scoria: Lightweight molecule manipulation codebase
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13119
2017-11-16 18:27:47 +00:00
Yuri Victorovich
3d96790bcd New port: science/erd: AcesIII electron repulsion integrals
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13080
2017-11-14 18:44:05 +00:00
Yuri Victorovich
1d9170fe49 New port: science/pcmsolver: API for the Polarizable Continuum Model
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13069
2017-11-14 18:05:42 +00:00
Yuri Victorovich
b666bfd0cf New port: science/libefp: Effective fragment potential method in quantum chemistry
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13072
2017-11-14 04:31:58 +00:00