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
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
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
chemtool-devel
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
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
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
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
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
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
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
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
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
molscript
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
rubygem-rgeo-proj4
rubygem-rgeo-shapefile
rubygem-ruby-dcl
rubygem-ruby-netcdf
scidavis
siesta
sigrok-cli
sigrok-firmware
sigrok-firmware-fx2lafw
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
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
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
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