cpet/freebsd-ports
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
052cc4f500
freebsd-ports/science
History
Danilo G. Baio 75a5f7f076 Update Sphinx 
- Repocopy textproc/py-sphinx to textproc/py-sphinx18

  Update it to 1.8.5 (latest version from 1.8.X).
  This version supports Python 2 and 3.
  Add test target.

- textproc/py-sphinx: Update to 3.0.2

  Python 3 only (3.5+).
  Add test target.

- Mk/Uses/python.mk: Add PY_SPHINX

  Shared macro to use with flavors and not break
  ports with USES=python (all versions).

  Python >=3.5  --> textproc/py-sphinx (v3.0.2)
  Python < 3.5  --> textproc/py-sphinx18 (v1.8.5)

  All ports that uses sphinx were changed to use the new variable
  ${PY_SPHINX} in the dependency line, exceptions:

    * Ports that fails to build with sphinx 3.0.2 because of code.
      They are pointing to textproc/py-sphinx18 directly.
      There aren't many ports.

    * Ports that doesn't know Python flavors.

- Add several patches to fix Sphinx consumers

  The most common issues are related with pkg-plist, the output
  files from Sphinx changes between versions, keep this dynamically
  is the better approach.

  This will save time in future sphinx updates.

PR:		245629
Exp-run by:	antoine
2020-05-11 23:51:58 +00:00
..
2d-rewriter science/2d-rewriter: 2020-03-29 05:55:51 +00:00
afni science/afni: update to 20.1.06 2020-05-06 08:22:40 +00:00
agrum science/agrum: fix build on GCC architectures 2020-05-01 02:42:36 +00:00
aircraft-datcom audio/festvox-cmu_us_slt_arctic, games/flightgear-terragear, graphics/zathura-cb, graphics/zathura-pdf-poppler, graphics/zathura-ps, math/nfft, net/py-mpi4py, science/aircraft-datcom, x11-themes/gnome-icons-luv: reset MAINTAINER 2020-03-02 17:35:42 +00:00
ALPSCore - Swap back from net/openmpi3 to net/openmpi 2020-04-21 21:26:56 +00:00
antioch
apbs
atompaw atompaw is actually fetchable 2020-01-05 11:52:46 +00:00
avogadro2 science/avogadro2: Update 1.91.0 -> 1.93.0 2020-02-06 07:09:42 +00:00
avogadrolibs science/avogadrolibs: Remove a broken option VTK set to default by mistake 2020-04-27 16:09:56 +00:00
bagel devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
bddsolve devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
berkeleygw Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
bodr
brian Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
buddy
cdcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
cdf
cdk New port: science/cdk: Chemistry Development Kit 2020-01-09 16:48:21 +00:00
cdo Update jasper to 2.0.16 2019-12-27 13:43:00 +00:00
cgnslib Upgrade to v4.1.1. 2020-03-17 11:01:17 +00:00
cgribex Update jasper to 2.0.16 2019-12-27 13:43:00 +00:00
checkmol - Remove compat < 11 dependencies from bootstrap and compiler. It could fix problems 2020-03-06 06:26:05 +00:00
chemical-mime-data print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
chemps2 Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
chemtool Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
chemtool-devel Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
chrono - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated) 2020-04-19 09:49:02 +00:00
clhep
clipper
code_saturne Update Sphinx 2020-05-11 23:51:58 +00:00
colt Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
coordgenlibs science/coordgenlibs: Update 1.4.0 -> 1.4.0-6; Fix the missing file templates.mae problem 2020-05-10 19:36:07 +00:00
cp2k-data
crf++
dalton Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
datawarrior Deprecate java/openjfx8-devel consumers 2020-03-19 09:33:13 +00:00
dcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
devisor Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
dftbplus Deprecate a few ports 2020-02-23 15:25:53 +00:00
dkh
dlib-cpp Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
dlpoly-classic science/dlpoly-classic: Change dependency to openmpi3 2020-04-12 14:31:17 +00:00
drawxtl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
dvc Deprecate a few ports 2020-02-23 15:25:53 +00:00
eccodes Update to 2.17.0 2020-03-28 12:46:34 +00:00
elk
elmerfem Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
epte
erd
erkale - Update math/armadillo to 9.870.2 2020-05-06 21:19:22 +00:00
erkale-pseudopotentials science/erkale-pseudopotentials: Update g20190114 -> g20200426 2020-05-07 00:32:03 +00:00
fastcap
fasthenry
fisicalab Return theraven's ports to the pool after safekeeping his commit bit. 2020-03-05 20:49:05 +00:00
fleur Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
fsom
fvcom
fvcom-mpi - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated) 2020-04-19 09:49:02 +00:00
gabedit Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
gamess-us Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
gchemutils Remove textproc/gnome-doc-utils. 2020-01-27 19:40:17 +00:00
gdma
getdp - Update to 3.3.0. 2019-12-22 02:28:57 +00:00
ghemical science/ghemical: Not compatible with the upcoming OpenBabel-3 => disable this internal option 2020-05-10 21:40:08 +00:00
ghmm print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
gnudatalanguage There is a bug with GraphicsMagick: see 2019-11-23 18:05:22 +00:00
gpaw-setups
gramps Convert the tree to use PY_PILLOW 2020-03-24 19:54:57 +00:00
grib_api
gromacs science/gromacs: Fix plist when MPI=on 2020-05-05 01:20:18 +00:00
gsmc print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
gtamsanalyzer
h5utils
h5z-zfp
harminv Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
hdf
hdf5 Revert r529778, ports depending on it were not tested 2020-03-29 20:41:45 +00:00
hdf5-18
healpix
highfive science/highfiv: Update 2.2 -> 2.2.1 2020-04-29 07:05:09 +00:00
hypre - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated) 2020-04-19 09:49:02 +00:00
iboview Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
InsightToolkit - Update devel/gdcm to 3.0.5. 2020-02-22 23:28:41 +00:00
isaac-cfd
jdftx
jmol science/jmol: Update 14.30.1 -> 14.30.2 and unbreak 2020-02-01 03:32:16 +00:00
jstrack
kalzium Update KDE Applications (release-service) to 20.04 2020-04-23 17:00:52 +00:00
kim-api
kst2
lammps Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
lamprop
latte science/latte: Update 1.2.1 -> 1.2.2 2020-05-07 01:02:37 +00:00
libaec
libccp4
libcint Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
libctl
libefp
libgeodecomp devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
libghemical Pet portlint (trailing whitespace). 2019-11-08 03:23:25 +00:00
libgridxc
libint
libint2 science/libint2: Update 2.5.0-beta.2-20 -> 2.6.0 2020-01-13 02:54:47 +00:00
libkml Convert REINPLACE_CMD to patch files 2020-05-08 20:50:41 +00:00
liblinear
libmsym
liboglappth Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
libquantum
libssm
libsvm
libsvm-python
libvdwxc
libxc science/libxc: remove patch 2020-05-02 20:20:28 +00:00
liggghts science/liggghts: Remove the unnecessary VTK_DIR 2020-04-27 16:26:42 +00:00
lm Bump PORTREVISION for devel/protobuf shlib change 2020-01-22 05:53:20 +00:00
luscus Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
madness Update devel/tbb to 2020.2 and bump dependent port's revisions 2020-04-01 14:14:51 +00:00
maeparser science/maeparser: Update 1.2.2 -> 1.2.3 2020-03-17 07:19:57 +00:00
massxpert Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
mbdyn science/mbdyn: use math/metis instead of expired math/metis4 for METIS option 2020-02-22 18:53:40 +00:00
mcstas
mcstas-comps
mcxtrace
mcxtrace-comps
mdynamix
medit Unbreak medit. 2019-11-20 20:40:53 +00:00
metaphysicl
minc2
mmdb2 science/mmdb2: Update 2.0.19 -> 2.0.20 2020-01-13 03:30:45 +00:00
mmtf-cpp
mol2ps - Remove compat < 11 dependencies from bootstrap and compiler. It could fix problems 2020-03-06 06:26:05 +00:00
molgif Bump PORTREVISION after r517743 to force relinking. 2019-11-16 12:52:39 +00:00
molscript Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
molsketch
mpb
mpqc Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
msms
multiwfn Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
namd
nest Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
netcdf Update to 4.7.3 2019-12-08 16:52:27 +00:00
netcdf-cxx
netcdf-fortran
nifticlib
nwchem science/nwchem: Update to 7.0.0-release 2020-05-07 07:58:36 +00:00
nwchem-data science/nwchem-data: Update 6.8.1.20190125 -> 7.0.0 2020-05-07 02:54:17 +00:00
octopus - update libgd to 2.3.0 2020-05-04 21:31:39 +00:00
openbabel
openkim
openkim-models
opensim-core Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
opensph
opsin
p5-Algorithm-SVMLight
p5-Chemistry-3DBuilder
p5-Chemistry-Bond-Find
p5-Chemistry-Canonicalize
p5-Chemistry-Elements
p5-Chemistry-File-MDLMol
p5-Chemistry-File-Mopac
p5-Chemistry-File-PDB
p5-Chemistry-File-SLN
p5-Chemistry-File-SMARTS
p5-Chemistry-File-SMILES
p5-Chemistry-File-VRML
p5-Chemistry-File-XYZ
p5-Chemistry-FormulaPattern
p5-Chemistry-InternalCoords
p5-Chemistry-Isotope
p5-Chemistry-MacroMol
p5-Chemistry-MidasPattern
p5-Chemistry-Mok
p5-Chemistry-Mol
p5-Chemistry-Pattern
p5-Chemistry-Reaction
p5-Chemistry-Ring
p5-Geo-BUFR
p5-Geo-Coordinates-Converter Add NO_ARCH 2020-04-21 19:47:40 +00:00
p5-Geo-Coordinates-Converter-iArea Cosmetic change 2020-04-21 19:37:40 +00:00
p5-Geo-WebService-Elevation-USGS - Update to 0.117 2020-04-18 08:35:03 +00:00
p5-Mcstas-Tools
p5-PerlMol
p5-Physics-Unit
packmol
pagmo2 Update devel/tbb to 2020.2 and bump dependent port's revisions 2020-04-01 14:14:51 +00:00
paje
paraview Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
pcmsolver
PETSc Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
plumed Add compiler:c++11-lang to USES to fix build on GCC-based systems: 2020-05-06 12:00:53 +00:00
pnetcdf - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated) 2020-04-19 09:49:02 +00:00
pulseview science/pulseview: Use buildtools, linguisttools as build dependencies. 2020-05-10 12:13:52 +00:00
py-abipy science/py-abipy: Unbreak 2020-03-31 05:50:30 +00:00
py-asdf Update to 2.6.0 2020-04-24 18:03:39 +00:00
py-ase science/py-ase: Update 3.19.0 -> 3.19.1 2020-04-04 07:30:04 +00:00
py-avogadrolibs science/py-avogadrolib: Update 1.91.0-107 -> 1.93.0 2020-02-06 07:17:20 +00:00
py-cdo
py-chainer science/py-chainer: Update 7.1.0 -> 7.2.0 2020-02-15 03:59:09 +00:00
py-chainer-chemistry science/py-chainer-chemistry: Update 0.6.0 -> 0.7.0 2019-12-22 03:10:17 +00:00
py-chempy science/py-chempy: Update 0.7.9 -> 0.7.10 2020-03-07 20:47:22 +00:00
py-coards
py-DendroPy
py-dlib science/dlib-cpp and science/py-dlib: Update to 19.19. 2020-02-12 17:28:11 +00:00
py-eccodes-python Update to 0.9.5 2020-01-17 16:40:13 +00:00
py-geolinks Add py-geolinks 0.2.0 2020-01-18 18:23:32 +00:00
py-geomet Add py-geomet 0.2.1 2019-12-29 12:46:17 +00:00
py-geometer Update to 0.2.2 2020-02-17 19:43:41 +00:00
py-gpaw Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
py-GPy science/py-GPy: Change to USES=python because it builds fine with python-3.7 2020-04-08 06:35:03 +00:00
py-GPyOpt science/py-GPyOpt: Update 1.2.5 -> 1.2.6 2020-04-08 06:39:07 +00:00
py-gsd science/py-gsd: Update 1.9.3 -> 1.10.0 2020-01-03 03:58:46 +00:00
py-h5json New port: science/py-h5json: Tools and library for representing HDF5 in JSON 2020-01-26 10:07:36 +00:00
py-h5py
py-kim-query New port: science/py-kim-query: Helper routines for querying the OpenKIM repository 2020-05-03 19:38:33 +00:00
py-kinematics
py-kliff New port: science/py-kliff: KIM-based Learning-Integrated Fitting Framework 2020-05-03 20:58:00 +00:00
py-lifelines
py-MDAnalysis
py-MDAnalysisTests
py-mdp
py-mlpy Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-mmtf-python
py-molmod
py-netCDF4
py-obspy - Update to 1.2.1 2020-03-12 03:58:15 +00:00
py-oddt science/py-oddt: Update 0.6 -> 0.7 2019-12-27 05:12:21 +00:00
py-OpenFermion science/py-OpenFermion: Update 0.10.0 -> 0.11.0 2020-04-07 21:49:28 +00:00
py-openpiv
py-paida
py-paramz
py-phono3py Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
py-phonopy
py-pupynere
py-pyaixi
py-pycsw Add py-pycsw 2.4.2 2020-01-18 18:23:39 +00:00
py-pydicom - Update to 1.4.2 2020-04-22 08:01:18 +00:00
py-PyFR Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-pygeodesy
py-pygeometa Add py-pygeometa 0.5.0 2020-01-18 18:23:44 +00:00
py-pymatgen science/py-pymatgen: fix build on GCC architectures 2020-01-23 10:44:41 +00:00
py-pymol Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-pyosf
py-PyQuante Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-pysal
py-pyteomics Update to 4.2 2020-03-01 06:49:00 +00:00
py-qcelemental science/py-qcelemental: Update 0.11.0 -> 0.12.0 2020-01-12 21:07:37 +00:00
py-qcengine
py-qspin
py-quantities science/py-quantities: Update 0.12.3 -> 0.12.4 2020-01-12 07:24:33 +00:00
py-rmf
py-rmsd
py-ruffus
py-scikit-fuzzy Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-scikit-learn Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-scikit-optimize Add PLOTS option 2020-04-22 21:28:17 +00:00
py-scikit-sparse
py-scimath
py-scipy Revert r524969 and unbreak bulk -a 2020-02-02 16:40:43 +00:00
py-scoria science/py-scoria: Update 1.0.4 -> 1.0.5 2020-03-28 04:04:51 +00:00
py-SimpleSpectral
py-spglib
py-tensorflow devel/icu: update to 67.1 2020-04-23 20:14:49 +00:00
py-veusz Update py-sip to 4.19.21 and qscintilla2 to 2.11.4 2020-04-11 05:04:40 +00:00
py-ws2300 Deprecate a few ports 2020-02-23 15:25:53 +00:00
pybrain
pynn - Update to 0.9.5 2020-02-22 15:05:40 +00:00
qbox science: Update 1.69.1 -> 1.71.0 2020-05-09 07:33:58 +00:00
qcl
qiskit-aer devel/libfmt: Update to 6.2.1 2020-05-10 07:43:44 +00:00
qmcpack Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
quantum-espresso science/quantum-espresso: Update 6.4.1 -> 6.5 2019-12-31 19:32:59 +00:00
quantum-espresso-pseudopotentials
qwalk
R-cran-AMORE math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-bayesm math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-cmprsk math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-DCluster math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-e1071 math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-eco math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-Epi math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-epicalc math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-etm math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-FAdist math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-fastICA math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-kernlab math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-snow math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-som math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
R-cran-udunits2 math/R: Update to version 4.0.0 2020-05-05 16:07:53 +00:00
rdkit Convert the tree to use PY_PILLOW 2020-03-24 19:54:57 +00:00
rmf Fix build with hdf5 1.10.6 2020-01-01 16:31:57 +00:00
rubygem-ai4r
rubygem-cdo
rubygem-rgeo
rubygem-rgeo-geojson Cosmetic change 2019-11-03 17:23:27 +00:00
rubygem-rgeo-proj4
rubygem-rgeo-shapefile
rubygem-ruby-dcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
rubygem-ruby-netcdf
scidavis
siesta
sigrok-cli
sigrok-firmware
sigrok-firmware-fx2lafw science/sigrok-firmware-fx2lafw: Update to version 0.1.7 2019-11-15 20:39:58 +00:00
sigrok-firmware-utils
silo
simbody Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
simgrid devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
simint
simlib
simsmith Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
smoldyn Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
sparta - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated) 2020-04-19 09:49:02 +00:00
spglib
step Update KDE Applications (release-service) to 20.04 2020-04-23 17:00:52 +00:00
svmlight
szip
teem
tfel science/tfel: update to version 3.3 2019-12-21 19:53:14 +00:00
tinker science/tinker: Update 8.7.1 -> 8.7.2 2019-11-29 07:44:51 +00:00
udunits
v_sim Make fetchable again. 2019-11-19 21:38:47 +00:00
vipster science/vipster: Update 1.18b-75 -> 1.18b-174 2020-05-07 16:08:27 +00:00
vmd Return dbn's ports to the pool after safekeeping his commit bit. 2020-02-03 20:21:08 +00:00
voro++
votca Add compiler:c++14-lang to USES to fix build on GCC-based systems: 2020-05-06 12:04:05 +00:00
wannier90 science/wannier90: Update 3.0.0 -> 3.1.0 2020-03-08 02:34:49 +00:00
wwplot science/wwplot: Update 0.0.7 -> 0.0.8 2020-01-25 17:53:30 +00:00
wxmacmolplt
xcrysden Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
xdrawchem
xfce4-equake-plugin
yoda science/yoda: Update 1.7.7 -> 1.8.0 2020-01-19 09:06:26 +00:00
Makefile Remove expired ports: 2020-05-05 15:38:11 +00:00