diff options
Diffstat (limited to 'science')
112 files changed, 433 insertions, 192 deletions
diff --git a/science/InsightToolkit/Makefile b/science/InsightToolkit/Makefile index 9eb3fc1d6439..c5ebe50b238f 100644 --- a/science/InsightToolkit/Makefile +++ b/science/InsightToolkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= InsightToolkit DISTVERSIONPREFIX= v DISTVERSION= 5.3.0 -PORTREVISION= 4 +PORTREVISION= 6 CATEGORIES= science biology MASTER_SITES= https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${DISTVERSION}/:data DISTFILES= InsightData-${DISTVERSION}.tar.gz:data diff --git a/science/InsightToolkit/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx b/science/InsightToolkit/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx new file mode 100644 index 000000000000..cd13183d7c5f --- /dev/null +++ b/science/InsightToolkit/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx @@ -0,0 +1,14 @@ +Fix build with CMake >= 3.29.0. Support for the Comeau compiler was removed. + +--- Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx.orig 2022-11-24 13:15:41 UTC ++++ Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx +@@ -9,8 +9,7 @@ int test_preprocessor_main(int /*argc*/,char* /*argv*/ + int test_preprocessor_main(int /*argc*/,char* /*argv*/[]) + { + constexpr unsigned compiler_count +- = VXL_COMPILER_IS_Comeau +- + VXL_COMPILER_IS_Intel ++ = VXL_COMPILER_IS_Intel + + VXL_COMPILER_IS_PathScale + + VXL_COMPILER_IS_Embarcadero + + VXL_COMPILER_IS_Borland diff --git a/science/InsightToolkit501/Makefile b/science/InsightToolkit501/Makefile index b062991236c1..36263cbac051 100644 --- a/science/InsightToolkit501/Makefile +++ b/science/InsightToolkit501/Makefile @@ -1,6 +1,6 @@ PORTNAME= InsightToolkit PORTVERSION= 5.0.1 -PORTREVISION= 2 +PORTREVISION= 3 DISTVERSIONPREFIX=v CATEGORIES= science biology MASTER_SITES= https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0.1/:data diff --git a/science/InsightToolkit501/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx b/science/InsightToolkit501/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx new file mode 100644 index 000000000000..cd13183d7c5f --- /dev/null +++ b/science/InsightToolkit501/files/patch-Modules_ThirdParty_VNL_src_vxl_vcl_tests_test__preprocessor.cxx @@ -0,0 +1,14 @@ +Fix build with CMake >= 3.29.0. Support for the Comeau compiler was removed. + +--- Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx.orig 2022-11-24 13:15:41 UTC ++++ Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx +@@ -9,8 +9,7 @@ int test_preprocessor_main(int /*argc*/,char* /*argv*/ + int test_preprocessor_main(int /*argc*/,char* /*argv*/[]) + { + constexpr unsigned compiler_count +- = VXL_COMPILER_IS_Comeau +- + VXL_COMPILER_IS_Intel ++ = VXL_COMPILER_IS_Intel + + VXL_COMPILER_IS_PathScale + + VXL_COMPILER_IS_Embarcadero + + VXL_COMPILER_IS_Borland diff --git a/science/Makefile b/science/Makefile index 3fc8ac08b67d..0455d6c14621 100644 --- a/science/Makefile +++ b/science/Makefile @@ -383,6 +383,7 @@ SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-penaltymodel + SUBDIR += py-periodictable SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere diff --git a/science/PETSc/Makefile b/science/PETSc/Makefile index 17133cc86e4f..e76d917643b4 100644 --- a/science/PETSc/Makefile +++ b/science/PETSc/Makefile @@ -1,5 +1,5 @@ PORTNAME= PETSc -DISTVERSION= 3.21.0 +DISTVERSION= 3.21.1 CATEGORIES= science devel MASTER_SITES= http://web.cels.anl.gov/projects/petsc/download/release-snapshots/ # was: https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} diff --git a/science/PETSc/distinfo b/science/PETSc/distinfo index be769f739348..55d6656d71d3 100644 --- a/science/PETSc/distinfo +++ b/science/PETSc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711870730 -SHA256 (petsc-3.21.0.tar.gz) = 1e0c2f92514c72f80d4a4d0e6439a3aba0ceda7a0bcbc7ad9c44ce4cd8b14c28 -SIZE (petsc-3.21.0.tar.gz) = 17315509 +TIMESTAMP = 1714199164 +SHA256 (petsc-3.21.1.tar.gz) = 7ff8b692bceb7d7a8f51e2f45ccb20af00ba9395d7e1eee8816d46eb1c4c4b27 +SIZE (petsc-3.21.1.tar.gz) = 17324803 diff --git a/science/PETSc/pkg-plist b/science/PETSc/pkg-plist index 59a8ef000466..1b35552d6ed1 100644 --- a/science/PETSc/pkg-plist +++ b/science/PETSc/pkg-plist @@ -3905,6 +3905,7 @@ libdata/pkgconfig/petsc.pc %%DATADIR%%/examples/src/mat/tests/ex261.c %%DATADIR%%/examples/src/mat/tests/ex262f.F90 %%DATADIR%%/examples/src/mat/tests/ex263.c +%%DATADIR%%/examples/src/mat/tests/ex264.c %%DATADIR%%/examples/src/mat/tests/ex27.c %%DATADIR%%/examples/src/mat/tests/ex28.c %%DATADIR%%/examples/src/mat/tests/ex29.c diff --git a/science/R-cran-cmprsk/Makefile b/science/R-cran-cmprsk/Makefile index 86bb1edc9a1b..4526a7a46f55 100644 --- a/science/R-cran-cmprsk/Makefile +++ b/science/R-cran-cmprsk/Makefile @@ -1,6 +1,5 @@ PORTNAME= cmprsk -DISTVERSION= 2.2-11 -PORTREVISION= 1 +DISTVERSION= 2.2-12 CATEGORIES= science DISTNAME= ${PORTNAME}_${DISTVERSION} diff --git a/science/R-cran-cmprsk/distinfo b/science/R-cran-cmprsk/distinfo index 6815acc3861c..b259dbf70b55 100644 --- a/science/R-cran-cmprsk/distinfo +++ b/science/R-cran-cmprsk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1641692161 -SHA256 (cmprsk_2.2-11.tar.gz) = 844027cb2c162cf7ef97034d01237ad7b81aa192fe302250d22d2c5528110e14 -SIZE (cmprsk_2.2-11.tar.gz) = 45799 +TIMESTAMP = 1716184049 +SHA256 (cmprsk_2.2-12.tar.gz) = 773ecb93be0eac7bb5dfe9ea1480380da89ea95497b7b2febb08fd7c5104acdc +SIZE (cmprsk_2.2-12.tar.gz) = 45824 diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 0dbf5ddee359..76cb4fb074db 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,5 +1,5 @@ PORTNAME= abinit -DISTVERSION= 10.0.3 +DISTVERSION= 10.0.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/abinit/distinfo b/science/abinit/distinfo index d2b8c03f6c68..a10df3049ad1 100644 --- a/science/abinit/distinfo +++ b/science/abinit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713294583 -SHA256 (abinit-abinit-10.0.3_GH0.tar.gz) = bd3d319dd6146890d2428a80da5eba1280e07f6e72489612dbad73bbf3043c9d -SIZE (abinit-abinit-10.0.3_GH0.tar.gz) = 132478613 +TIMESTAMP = 1714624590 +SHA256 (abinit-abinit-10.0.5_GH0.tar.gz) = 27b51b5c9c21192b6d8321f30c9c8699ec852811589cdfcc94199a5fdd505527 +SIZE (abinit-abinit-10.0.5_GH0.tar.gz) = 132497323 diff --git a/science/afni/Makefile b/science/afni/Makefile index 445d0cba8434..7119669a6127 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 24.1.03 +DISTVERSION= 24.1.11 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index dbddded3e16c..6f25bcb0bf1c 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713542956 -SHA256 (afni-afni-AFNI_24.1.03_GH0.tar.gz) = d03981f34cb6294aef9b82d722142e503867e015585ab3dbc23c795301a4b9ec -SIZE (afni-afni-AFNI_24.1.03_GH0.tar.gz) = 52964586 +TIMESTAMP = 1715433548 +SHA256 (afni-afni-AFNI_24.1.11_GH0.tar.gz) = fa89b59ace84e38abd74818721fc2edb25b877ca27cc84d5de32295e254ab17b +SIZE (afni-afni-AFNI_24.1.11_GH0.tar.gz) = 53013046 diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index fea30274da83..a0a5e923d7b5 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -112,6 +112,8 @@ bin/3dKruskalWallis bin/3dLFCD bin/3dLME bin/3dLME.R +bin/3dLME2 +bin/3dLME2.R bin/3dLMEr bin/3dLMEr.R bin/3dLRflip @@ -501,6 +503,7 @@ bin/adjunct_combine_str.py bin/adjunct_deob_around_origin bin/adjunct_is_label.py bin/adjunct_make_script_and_rst.py +bin/adjunct_middle_pair_mask bin/adjunct_select_str.py bin/adjunct_simplify_cost.py bin/adjunct_suma_fs_mask_and_qc @@ -547,6 +550,7 @@ bin/column_cat bin/compute_ROI_stats.tcsh bin/convert_cdiflist_to_grads.py bin/count +bin/count_afni bin/dcm2niix_afni bin/demo.fixed.niml.do bin/demo.mobile.niml.do @@ -682,6 +686,7 @@ bin/unWarpEPI.py bin/uniq_images bin/waver bin/whereami +bin/whereami_afni bin/whirlgif bin/xmat_tool.py etc/mri/afni.cshrc diff --git a/science/agrum/Makefile b/science/agrum/Makefile index 9b88a0ced396..52f51d2f8dc0 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,5 +1,6 @@ PORTNAME= agrum DISTVERSION= 1.13.1 +PORTREVISION= 1 CATEGORIES= science math MAINTAINER= yuri@FreeBSD.org diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile index b1846fae3beb..28249c21f5f5 100644 --- a/science/csvtk/Makefile +++ b/science/csvtk/Makefile @@ -1,7 +1,7 @@ PORTNAME= csvtk DISTVERSIONPREFIX= v DISTVERSION= 0.24.0 -PORTREVISION= 19 +PORTREVISION= 20 CATEGORIES= science MAINTAINER= jwb@FreeBSD.org diff --git a/science/dirac/Makefile b/science/dirac/Makefile index ba9e9416ebf9..8e45f51f7850 100644 --- a/science/dirac/Makefile +++ b/science/dirac/Makefile @@ -14,6 +14,7 @@ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: Error: Old-style type declaration REAL*16 not supported at (1) +BROKEN_i386= compilation fails: Error: Type mismatch in argument 'lu' at (1); passed INTEGER(8) to INTEGER(4) (and similar) BROKEN_powerpc64= compilation fails: Error: Old-style type declaration REAL*16 not supported at (1) BROKEN_powerpc64le= compilation fails: Error: Old-style type declaration REAL*16 not supported at (1) diff --git a/science/dynare/Makefile b/science/dynare/Makefile index aec9a20139b3..adc5d12ea3f3 100644 --- a/science/dynare/Makefile +++ b/science/dynare/Makefile @@ -1,6 +1,6 @@ PORTNAME= dynare DISTVERSION= 5.4 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science # economics MASTER_SITES= https://www.dynare.org/release/source/ diff --git a/science/elmerfem/Makefile b/science/elmerfem/Makefile index 3f807b3cb60c..cc50530a1088 100644 --- a/science/elmerfem/Makefile +++ b/science/elmerfem/Makefile @@ -1,7 +1,7 @@ PORTNAME= elmerfem DISTVERSIONPREFIX= release- DISTVERSION= 9.0 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= science PATCH_SITES= https://github.com/ElmerCSC/${PORTNAME}/commit/ diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index a984adf2db50..15237333237f 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -1,6 +1,6 @@ PORTNAME= gnudatalanguage PORTVERSION= 1.0.4 -PORTREVISION= 2 +PORTREVISION= 3 DISTVERSIONPREFIX= v CATEGORIES= science lang .if defined(BUILD_PYTHON_MODULE) diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index 092fd88d9f0a..0c4668c264c1 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,5 +1,5 @@ PORTNAME= gromacs -DISTVERSION= 2024.1 +DISTVERSION= 2024.2 CATEGORIES= science MASTER_SITES= https://ftp.gromacs.org/pub/gromacs/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} # only for googletest @@ -33,13 +33,20 @@ CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD} \ TEST_TARGET= check -OPTIONS_DEFINE= ATLAS FLOAT HWLOC LEGACY OPENMP SIMD +OPTIONS_DEFINE= ATLAS FLOAT HWLOC LEGACY SIMD OPTIONS_SINGLE= MP OPENCL OPTIONS_SINGLE_MP= NOMP MPICH OPENMPI THREAD_MPI OPTIONS_SINGLE_OPENCL= OPENCL_NONE OPENCL_ICD OPENCL_SYCL -OPTIONS_DEFAULT= HWLOC LEGACY OPENCL_NONE OPENMP THREAD_MPI # FLOAT should not be a default because science/votca needs double precision. This is likely the same for many other uses. +OPTIONS_DEFAULT= HWLOC LEGACY OPENCL_NONE THREAD_MPI # FLOAT should not be a default because science/votca needs double precision. This is likely the same for many other uses. OPTIONS_SUB= yes +.if exists(/usr/include/omp.h) +OPTIONS_DEFINE+= OPENMP +OPTIONS_DEFAULT+= OPENMP +.else +CMAKE_OFF+= GMX_OPENMP +.endif + ATLAS_DESC= Use ATLAS for BLAS and LAPACK ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack @@ -80,8 +87,6 @@ OPENCL_SYCL_LIB_DEPENDS= libhipSYCL-rt.so:lang/opensycl OPENCL_SYCL_IMPLIES= FLOAT OPENCL_SYCL_BROKEN= configure uses a wrong namespace to find CYCL, see https://gitlab.com/gromacs/gromacs/-/issues/4838 -OPENMP_CMAKE_BOOL= GMX_OPENMP - SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" SIMD_CMAKE_ON= -DGMX_SIMD:STRING="AUTO" @@ -95,6 +100,7 @@ MPICH_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" MPICH_PLIST_SUB= SUFFIX_MPI="_mpi" +OPENMP_CMAKE_BOOL= GMX_OPENMP OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_CMAKE_ON= -DGMX_MPI:BOOL=ON \ diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index 4fb8730e39d5..02919da2bde2 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1711660510 -SHA256 (gromacs-2024.1.tar.gz) = 937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7 -SIZE (gromacs-2024.1.tar.gz) = 42324773 +TIMESTAMP = 1715436343 +SHA256 (gromacs-2024.2.tar.gz) = 802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b +SIZE (gromacs-2024.2.tar.gz) = 42367929 SHA256 (google-googletest-v1.13.0_GH0.tar.gz) = ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363 SIZE (google-googletest-v1.13.0_GH0.tar.gz) = 862871 diff --git a/science/kst2/Makefile b/science/kst2/Makefile index 42a9e6ca1d7e..8c04253c5353 100644 --- a/science/kst2/Makefile +++ b/science/kst2/Makefile @@ -1,6 +1,6 @@ PORTNAME= kst DISTVERSION= ${KST_VERSION}.${KST_DATE} -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= makc@FreeBSD.org diff --git a/science/lammps/Makefile b/science/lammps/Makefile index f5ba7266778e..512d351e9ae6 100644 --- a/science/lammps/Makefile +++ b/science/lammps/Makefile @@ -1,6 +1,6 @@ PORTNAME= lammps PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/S/_update/./:C/\.([1-9])$/.0\1/} -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/liggghts/Makefile b/science/liggghts/Makefile index 5a97ce18869c..dadf1e6ed49b 100644 --- a/science/liggghts/Makefile +++ b/science/liggghts/Makefile @@ -1,6 +1,6 @@ PORTNAME= liggghts DISTVERSION= 3.8.0-58 -PORTREVISION= 5 +PORTREVISION= 6 DISTVERSIONSUFFIX= -g6e28cfe3 CATEGORIES= science diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile index a601b39b80e0..6948babf6a4d 100644 --- a/science/mbdyn/Makefile +++ b/science/mbdyn/Makefile @@ -1,6 +1,6 @@ PORTNAME= mbdyn DISTVERSION= 1.7.3 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= science MASTER_SITES= https://www.mbdyn.org/userfiles/downloads/ diff --git a/science/molgif/Makefile b/science/molgif/Makefile index d78783dcf938..eaf72a36512e 100644 --- a/science/molgif/Makefile +++ b/science/molgif/Makefile @@ -1,6 +1,6 @@ PORTNAME= molgif DISTVERSION= g20180108 -PORTREVISION= 19 +PORTREVISION= 20 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/multiwfn/files/patch-Makefile b/science/multiwfn/files/patch-Makefile index 00ff10bae181..9c38fc1f94f2 100644 --- a/science/multiwfn/files/patch-Makefile +++ b/science/multiwfn/files/patch-Makefile @@ -1,6 +1,6 @@ --- Makefile.orig 2023-02-06 10:17:38 UTC +++ Makefile -@@ -1,6 +1,6 @@ +@@ -1,6 +1,6 @@ SIMD = -msse3 SIMD = -msse3 -OPT = -O2 -qopenmp -qopenmp-link=static -threads -qopt-matmul $(SIMD) -diag-disable 8290,8291,6371,10316,6178 -fpp -mkl -static-intel -DINTEL_MKL -OPT1 = -O1 -qopenmp -qopenmp-link=static -threads $(SIMD) -diag-disable 8290,8291,6371,10316,6178 -fpp -mkl -static-intel -DINTEL_MKL @@ -9,7 +9,7 @@ #Options in the next line is for debugging purpose #OPTDBG = -O0 -qopenmp -diag-disable 8290,8291,6371 -threads -qopenmp-link=static -debug all -g -traceback -check all -fstack-protector -fpp -mkl -static-intel -@@ -43,10 +43,10 @@ default : $(objects) +@@ -43,10 +43,10 @@ GUI: $(objects) @echo " ------------------------------------------------------ " GUI: $(objects) @@ -22,7 +22,16 @@ clean: rm -f $(EXE) *.o *.mod -@@ -230,7 +230,7 @@ cp2kmate.o : cp2kmate.f90 $(modules) +@@ -80,7 +80,7 @@ util.o : util.f90 define.o + util.o : util.f90 define.o + $(FC) $(OPT) -c util.f90 + +-function.o : function.f90 define.o util.o Bspline.o libreta.o ++function.o : function.f90 define.o util.o Bspline.o libreta.o 2F2.f90.o # add 2F2.f90.o to fix dependency problem when mod_2f2.mod isn't found + $(FC) $(OPT) -c function.f90 + + plot.o : plot.f90 define.o util.o +@@ -230,7 +230,7 @@ noGUI/dislin_d_empty.o : noGUI/dislin_d_empty.f90 noGUI/dislin_d_empty.o : noGUI/dislin_d_empty.f90 @@ -31,7 +40,7 @@ # Interfaces of libreta-ESP to Multiwfn -@@ -241,10 +241,10 @@ libreta.o: ${LIBRETAPATH}/libreta.f90 hrr_012345.o blo +@@ -241,10 +241,10 @@ hrr_012345.o: ${LIBRETAPATH}/hrr_012345.f90 # Pure libreta files for ESP hrr_012345.o: ${LIBRETAPATH}/hrr_012345.f90 diff --git a/science/octopus/Makefile b/science/octopus/Makefile index 1917149d40f2..617631675471 100644 --- a/science/octopus/Makefile +++ b/science/octopus/Makefile @@ -1,6 +1,6 @@ PORTNAME= octopus DISTVERSION= 13.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry MASTER_SITES= https://octopus-code.org/download/${DISTVERSION}/ diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index a01b3aa7bd56..17b96314a9f5 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,8 +1,7 @@ PORTNAME= orthanc -DISTVERSION= 1.11.0 -PORTREVISION= 12 +DISTVERSION= 1.12.3 CATEGORIES= science -MASTER_SITES= https://www.orthanc-server.com/downloads/get.php?path=/orthanc/ +MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc/ DISTNAME= Orthanc-${PORTVERSION} MAINTAINER= maintainer.freebsd@xpoundit.com @@ -12,6 +11,8 @@ WWW= https://www.orthanc-server.com/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING +BUILD_DEPENDS= protoc:devel/protobuf + LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libcivetweb.so:www/civetweb \ libcurl.so:ftp/curl \ @@ -20,9 +21,10 @@ LIB_DEPENDS= libboost_atomic.so:devel/boost-libs \ libicuuc.so:devel/icu \ libjsoncpp.so:devel/jsoncpp \ libpng16.so:graphics/png \ + libprotobuf.so:devel/protobuf \ libpugixml.so:textproc/pugixml \ libtiff.so:graphics/tiff \ - libuuid.so:misc/e2fsprogs-libuuid + libuuid.so:misc/e2fsprogs-libuuid \ USES= cmake gnome iconv jpeg lua python:build sqlite ssl USE_GNOME= libxml2 diff --git a/science/orthanc/distinfo b/science/orthanc/distinfo index f28286e4fad0..66007b6a7195 100644 --- a/science/orthanc/distinfo +++ b/science/orthanc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1652266484 -SHA256 (Orthanc-1.11.0.tar.gz) = 23949a70562487fd6e79d6f3f13c71a0fc90aa25e492fb3a99575fee0722c5af -SIZE (Orthanc-1.11.0.tar.gz) = 1899829 +TIMESTAMP = 1714974143 +SHA256 (Orthanc-1.12.3.tar.gz) = 64b7ed7506a60e52f52121efb14961485b710fd092ab73d6c550fa25a01f516b +SIZE (Orthanc-1.12.3.tar.gz) = 2043176 diff --git a/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake index 0237ef13ed79..e0ac6558feb7 100644 --- a/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake +++ b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_CivetwebConfiguration.cmake @@ -1,6 +1,6 @@ ---- OrthancFramework/Resources/CMake/CivetwebConfiguration.cmake.orig 2021-08-30 20:14:33 UTC +--- OrthancFramework/Resources/CMake/CivetwebConfiguration.cmake.orig 2023-07-04 14:39:31 UTC +++ OrthancFramework/Resources/CMake/CivetwebConfiguration.cmake -@@ -109,32 +109,38 @@ else() +@@ -110,32 +110,38 @@ else() cmake_reset_check_state() set(CMAKE_REQUIRED_LIBRARIES dl pthread) diff --git a/science/orthanc/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake new file mode 100644 index 000000000000..e6d9c8ff88cf --- /dev/null +++ b/science/orthanc/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake @@ -0,0 +1,37 @@ +--- OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake.orig 2023-12-05 11:17:50 UTC ++++ OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake +@@ -64,22 +64,26 @@ else() + message(FATAL_ERROR "Please install the libprotobuf-dev package") + endif() + +- set(CMAKE_REQUIRED_LIBRARIES "protobuf") ++ if (${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") ++ find_package(Protobuf REQUIRED) ++ else() ++ set(CMAKE_REQUIRED_LIBRARIES "protobuf") + +- include(CheckCXXSourceCompiles) +- check_cxx_source_compiles( +- " ++ include(CheckCXXSourceCompiles) ++ check_cxx_source_compiles( ++ " + #include <google/protobuf/descriptor.h> + int main() + { + google::protobuf::FieldDescriptor::TypeName(google::protobuf::FieldDescriptor::TYPE_FLOAT); + } + " HAVE_PROTOBUF_LIB) +- if (NOT HAVE_PROTOBUF_LIB) +- message(FATAL_ERROR "Cannot find the protobuf library") ++ if (NOT HAVE_PROTOBUF_LIB) ++ message(FATAL_ERROR "Cannot find the protobuf library") ++ endif() ++ ++ unset(CMAKE_REQUIRED_LIBRARIES) + endif() +- +- unset(CMAKE_REQUIRED_LIBRARIES) + + link_libraries(protobuf) + endif() diff --git a/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json index 91f978822db2..73c17f35620f 100644 --- a/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json +++ b/science/orthanc/files/patch-OrthancServer_Resources_Configuration.json @@ -1,6 +1,6 @@ ---- OrthancServer/Resources/Configuration.json.orig 2021-01-29 09:36:16 UTC +--- OrthancServer/Resources/Configuration.json.orig 2023-07-04 14:39:31 UTC +++ OrthancServer/Resources/Configuration.json -@@ -10,12 +10,12 @@ +@@ -15,12 +15,12 @@ // Path to the directory that holds the heavyweight files (i.e. the // raw DICOM instances). Backslashes must be either escaped by // doubling them, or replaced by forward slashes "/". @@ -15,7 +15,7 @@ // Path to the directory where Orthanc stores its large temporary // files. The content of this folder can be safely deleted once -@@ -53,6 +53,7 @@ +@@ -83,6 +83,7 @@ // find shared libraries. Backslashes must be either escaped by // doubling them, or replaced by forward slashes "/". "Plugins" : [ diff --git a/science/orthanc/pkg-plist b/science/orthanc/pkg-plist index b44ca2376c94..293f39bc83d4 100644 --- a/science/orthanc/pkg-plist +++ b/science/orthanc/pkg-plist @@ -11,10 +11,15 @@ bin/OrthancRecoverCompressedFile include/orthanc/OrthancCDatabasePlugin.h include/orthanc/OrthancCPlugin.h +include/orthanc/OrthancDatabasePlugin.proto sbin/Orthanc +%%DATADIR%%/plugins/libDelayedDeletion.so +%%DATADIR%%/plugins/libDelayedDeletion.so.%%DISTVERSION%% %%DATADIR%%/plugins/libHousekeeper.so %%DATADIR%%/plugins/libHousekeeper.so.%%DISTVERSION%% %%DATADIR%%/plugins/libModalityWorklists.so %%DATADIR%%/plugins/libModalityWorklists.so.%%DISTVERSION%% +%%DATADIR%%/plugins/libMultitenantDicom.so +%%DATADIR%%/plugins/libMultitenantDicom.so.%%DISTVERSION%% %%DATADIR%%/plugins/libServeFolders.so %%DATADIR%%/plugins/libServeFolders.so.%%DISTVERSION%% diff --git a/science/paraview/Makefile b/science/paraview/Makefile index bd1960bd233f..d87fa2fa70b1 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.0 -PORTREVISION= 2 +PORTREVISION= 4 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile index 03eaa997c5c9..04afa1c3a63a 100644 --- a/science/phonopy/Makefile +++ b/science/phonopy/Makefile @@ -1,6 +1,6 @@ PORTNAME= phonopy DISTVERSIONPREFIX= v -DISTVERSION= 2.22.1 +DISTVERSION= 2.23.1 CATEGORIES= science python MAINTAINER= yuri@FreeBSD.org diff --git a/science/phonopy/distinfo b/science/phonopy/distinfo index 33d1818e7990..cb3120f023b3 100644 --- a/science/phonopy/distinfo +++ b/science/phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711741734 -SHA256 (phonopy-phonopy-v2.22.1_GH0.tar.gz) = d37cbf5334958e32774c3ff10c87d42353fac474fc39f92ae571a774fd0162c4 -SIZE (phonopy-phonopy-v2.22.1_GH0.tar.gz) = 6873299 +TIMESTAMP = 1714796182 +SHA256 (phonopy-phonopy-v2.23.1_GH0.tar.gz) = 07e002da4231b37587e651fe0140fdc80199171245e0f43638bcf96cc00ef66f +SIZE (phonopy-phonopy-v2.23.1_GH0.tar.gz) = 6902364 diff --git a/science/psi4/Makefile b/science/psi4/Makefile index 1a79ca363d60..4f0cad2b0dde 100644 --- a/science/psi4/Makefile +++ b/science/psi4/Makefile @@ -1,6 +1,7 @@ PORTNAME= psi4 DISTVERSIONPREFIX= v DISTVERSION= 1.9.1 +PORTREVISION= 1 CATEGORIES= science # quantum-chemistry EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} diff --git a/science/py-MDAnalysis/Makefile b/science/py-MDAnalysis/Makefile index acb635f24fb4..70b9478a111a 100644 --- a/science/py-MDAnalysis/Makefile +++ b/science/py-MDAnalysis/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysis -DISTVERSION= 2.3.0 -PORTREVISION= 1 +DISTVERSION= 2.7.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysis/distinfo b/science/py-MDAnalysis/distinfo index eefa396a1fd7..904a4e724ecb 100644 --- a/science/py-MDAnalysis/distinfo +++ b/science/py-MDAnalysis/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1662095086 -SHA256 (MDAnalysis-2.3.0.tar.gz) = 29579433c4ea87048278dc1d4019b52e6a19504162659447be7c79fbdbf508ff -SIZE (MDAnalysis-2.3.0.tar.gz) = 3701615 +TIMESTAMP = 1714979275 +SHA256 (MDAnalysis-2.7.0.tar.gz) = 572e82945e5d058e3749ec5f18e6b3831ef7f2119cb54672567ae9a977201e93 +SIZE (MDAnalysis-2.7.0.tar.gz) = 3938260 diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt index 863978e58ce8..ec795498a023 100644 --- a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt +++ b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt @@ -1,10 +1,10 @@ ---- MDAnalysis.egg-info/requires.txt.orig 2022-06-02 18:49:39 UTC +--- MDAnalysis.egg-info/requires.txt.orig 2023-12-26 20:46:12 UTC +++ MDAnalysis.egg-info/requires.txt -@@ -7,7 +7,6 @@ joblib>=0.12 +@@ -5,7 +5,6 @@ tqdm>=4.43.0 scipy>=1.5.0 matplotlib>=1.5.1 tqdm>=4.43.0 -threadpoolctl packaging fasteners - gsd>=1.9.3 + mda-xdrlib diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c b/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c new file mode 100644 index 000000000000..e64cd135c92c --- /dev/null +++ b/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c @@ -0,0 +1,46 @@ +- workaround for invalid C/C++ code, see https://github.com/MDAnalysis/mdanalysis/issues/4589 + +--- MDAnalysis/lib/formats/src/xdrfile.c.orig 2024-05-06 20:07:19 UTC ++++ MDAnalysis/lib/formats/src/xdrfile.c +@@ -132,8 +132,8 @@ struct XDR + int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len); + int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len); + /* two next routines are not 64-bit IO safe - don't use! */ +- unsigned int (*x_getpostn) (XDR *__xdrs); +- int (*x_setpostn) (XDR *__xdrs, unsigned int __pos); ++ off_t (*x_getpostn) (XDR *__xdrs); ++ off_t (*x_setpostn) (XDR *__xdrs, off_t __pos, int); + void (*x_destroy) (XDR *__xdrs); + } + *x_ops; +@@ -2519,8 +2519,8 @@ static int xdrstdio_putbytes (XDR *, char *, unsigned + static int xdrstdio_putlong (XDR *, int32_t *); + static int xdrstdio_getbytes (XDR *, char *, unsigned int); + static int xdrstdio_putbytes (XDR *, char *, unsigned int); +-static int64_t xdrstdio_getpos (XDR *); +-static int xdrstdio_setpos (XDR *, int64_t, int); ++static off_t xdrstdio_getpos (XDR *); ++static off_t xdrstdio_setpos (XDR *, int64_t, int); + static void xdrstdio_destroy (XDR *); + + /* +@@ -2602,7 +2602,7 @@ xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int + } + + +-static int64_t ++static off_t + xdrstdio_getpos (XDR *xdrs) + { + #ifdef _WIN32 +@@ -2612,8 +2612,8 @@ xdrstdio_getpos (XDR *xdrs) + #endif + } + +-static int +-xdrstdio_setpos (XDR *xdrs, int64_t pos, int whence) ++static off_t ++xdrstdio_setpos (XDR *xdrs, off_t pos, int whence) + { + /* A reason for failure can be filesystem limits on allocation units, + * before the actual off_t overflow (ext3, with a 4K clustersize, diff --git a/science/py-MDAnalysis/files/patch-setup.py b/science/py-MDAnalysis/files/patch-setup.py index 21db43b92b78..b418f13e5dbc 100644 --- a/science/py-MDAnalysis/files/patch-setup.py +++ b/science/py-MDAnalysis/files/patch-setup.py @@ -1,19 +1,19 @@ ---- setup.py.orig 2022-06-02 18:49:09 UTC +--- setup.py.orig 2023-12-26 20:45:53 UTC +++ setup.py -@@ -274,7 +274,7 @@ def extensions(config): - use_cython = config.get('use_cython', default=cython_found) +@@ -266,7 +266,7 @@ def extensions(config): use_openmp = config.get('use_openmp', default=True) + annotate_cython = config.get('annotate_cython', default=False) -- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops', -+ extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops', +- extra_compile_args = ['-std=c99', '-O3', '-funroll-loops', ++ extra_compile_args = ['-std=c99', '-funroll-loops', '-fsigned-zeros'] # see #2722 define_macros = [] if config.get('debug_cflags', default=False): -@@ -599,7 +599,6 @@ if __name__ == '__main__': +@@ -598,7 +598,6 @@ if __name__ == '__main__': 'scipy>=1.5.0', 'matplotlib>=1.5.1', 'tqdm>=4.43.0', - 'threadpoolctl', 'packaging', 'fasteners', - 'gsd>=1.9.3', + 'mda-xdrlib', diff --git a/science/py-MDAnalysisTests/Makefile b/science/py-MDAnalysisTests/Makefile index ee722a2cd5b2..b560f72a9b9f 100644 --- a/science/py-MDAnalysisTests/Makefile +++ b/science/py-MDAnalysisTests/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysisTests -DISTVERSION= 2.3.0 -PORTREVISION= 1 +DISTVERSION= 2.7.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysisTests/distinfo b/science/py-MDAnalysisTests/distinfo index 28d4454038e0..f39c637c7f98 100644 --- a/science/py-MDAnalysisTests/distinfo +++ b/science/py-MDAnalysisTests/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1662099346 -SHA256 (MDAnalysisTests-2.3.0.tar.gz) = b4dcdbbc6e216a59feb7c3e8cb5c7d9251dbd7aa7ab35f04ad81e93a301c12dc -SIZE (MDAnalysisTests-2.3.0.tar.gz) = 52461472 +TIMESTAMP = 1715029181 +SHA256 (MDAnalysisTests-2.7.0.tar.gz) = 326d65d7f14da8d1b047aab87ca312a68459a5fd18ddf6d8cb9ac9c3ca51d9e5 +SIZE (MDAnalysisTests-2.7.0.tar.gz) = 55704756 diff --git a/science/py-OpenFermion/Makefile b/science/py-OpenFermion/Makefile index 488adbbe68a1..bfd3021135c5 100644 --- a/science/py-OpenFermion/Makefile +++ b/science/py-OpenFermion/Makefile @@ -1,6 +1,6 @@ PORTNAME= OpenFermion DISTVERSIONPREFIX= v -DISTVERSION= 1.6.0 +DISTVERSION= 1.6.1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,7 +11,7 @@ WWW= https://github.com/quantumlib/OpenFermion LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cirq-core>=1.0:science/py-cirq-core@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cirq-core>=1.0:science/py-cirq-core@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cirq-google>=0.15.0:science/py-cirq-google@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}deprecation>0:devel/py-deprecation@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>=2.8:science/py-h5py@${PY_FLAVOR} \ @@ -21,15 +21,15 @@ PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cirq-core>=1.0:science/py-cirq-core@${PY_FLAV ${PYTHON_PKGNAMEPREFIX}requests>=2.18:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>0:math/py-sympy@${PY_FLAVOR} -BUILD_DEPENDS= ${PY_DEPENDS} -RUN_DEPENDS= ${PY_DEPENDS} USES= python -USE_PYTHON= distutils autoplist pytest # 91 tests fail, see https://github.com/quantumlib/OpenFermion/issues/851 +USE_PYTHON= distutils autoplist pytest # 1 tests fails, see https://github.com/quantumlib/OpenFermion/issues/879 USE_GITHUB= yes GH_ACCOUNT= quantumlib NO_ARCH= yes +BINARY_ALIAS= python3=${PYTHON_CMD} # only for tests + .include <bsd.port.mk> diff --git a/science/py-OpenFermion/distinfo b/science/py-OpenFermion/distinfo index 07a1a76fe1e5..82454570bd5e 100644 --- a/science/py-OpenFermion/distinfo +++ b/science/py-OpenFermion/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1698636606 -SHA256 (quantumlib-OpenFermion-v1.6.0_GH0.tar.gz) = 4a346a5e308be2383993a202fdb901e4b85d586aa756678f42907c65eb5dd30e -SIZE (quantumlib-OpenFermion-v1.6.0_GH0.tar.gz) = 45091606 +TIMESTAMP = 1714198243 +SHA256 (quantumlib-OpenFermion-v1.6.1_GH0.tar.gz) = d1b6fd254efa12dd3eb08c7877c4b9e04bb12e4ead4ec809b8e370b25c898ed6 +SIZE (quantumlib-OpenFermion-v1.6.1_GH0.tar.gz) = 45081688 diff --git a/science/py-PyNE/Makefile b/science/py-PyNE/Makefile index 8630a8f24b48..1eda9655b2d2 100644 --- a/science/py-PyNE/Makefile +++ b/science/py-PyNE/Makefile @@ -1,5 +1,6 @@ PORTNAME= PyNE DISTVERSION= 0.7.8 +PORTREVISION= 1 CATEGORIES= science # physics MASTER_SITES= https://raw.githubusercontent.com/pyne/data/master/:decay \ https://raw.githubusercontent.com/pyne/data/master/:cram \ @@ -81,4 +82,7 @@ do-install: ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/xs/models.so +# CAVEAT: due to the failure to find MOAB-5.5.1 the file pyne/source_sampling.so isn't built, and is removed from plist +# - see https://github.com/pyne/pyne/issues/1537 + .include <bsd.port.mk> diff --git a/science/py-PyNE/pkg-plist b/science/py-PyNE/pkg-plist index c429e2018ed7..5e6baa1151b7 100644 --- a/science/py-PyNE/pkg-plist +++ b/science/py-PyNE/pkg-plist @@ -231,7 +231,6 @@ lib/libpyne.so %%PYTHON_SITELIBDIR%%/pyne/source.pxd %%PYTHON_SITELIBDIR%%/pyne/source.so %%PYTHON_SITELIBDIR%%/pyne/source_sampling.pxd -%%PYTHON_SITELIBDIR%%/pyne/source_sampling.so %%PYTHON_SITELIBDIR%%/pyne/spatialsolver.py %%PYTHON_SITELIBDIR%%/pyne/spectanalysis.py %%PYTHON_SITELIBDIR%%/pyne/stlcontainers.pxd diff --git a/science/py-access/Makefile b/science/py-access/Makefile index 79a2de91ddbd..0cdd6cbb8fa5 100644 --- a/science/py-access/Makefile +++ b/science/py-access/Makefile @@ -1,6 +1,6 @@ PORTNAME= access PORTVERSION= 1.1.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,13 +13,15 @@ WWW= https://pysal.org/access/ \ LICENSE= BSD3CLAUSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.3,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.23.4,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2:www/py-requests@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-atomium/Makefile b/science/py-atomium/Makefile index 6270e74da9cf..b2b0caef95d0 100644 --- a/science/py-atomium/Makefile +++ b/science/py-atomium/Makefile @@ -1,7 +1,7 @@ PORTNAME= atomium DISTVERSIONPREFIX= v DISTVERSION= 1.0.11 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-cdo/Makefile b/science/py-cdo/Makefile index 2c2feee18daa..60fbea7f0adf 100644 --- a/science/py-cdo/Makefile +++ b/science/py-cdo/Makefile @@ -1,5 +1,6 @@ PORTNAME= cdo PORTVERSION= 1.6.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,11 +11,13 @@ WWW= https://code.mpimet.mpg.de/projects/cdo/wiki/Cdo%7Brbpy%7D LICENSE= GPLv2 +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= cdo:science/cdo \ ${PYTHON_PKGNAMEPREFIX}six>=0:devel/py-six@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-chempy/Makefile b/science/py-chempy/Makefile index e3f9a333329c..ba18fce502b5 100644 --- a/science/py-chempy/Makefile +++ b/science/py-chempy/Makefile @@ -1,5 +1,6 @@ PORTNAME= chempy -DISTVERSION= 0.8.3 +DISTVERSION= 0.9.0 +PORTREVISION= 1 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-chempy/distinfo b/science/py-chempy/distinfo index e3ed0aed9cb4..1ac919ccffb9 100644 --- a/science/py-chempy/distinfo +++ b/science/py-chempy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1689572688 -SHA256 (chempy-0.8.3.tar.gz) = 8f7bfb5066969019556d6191b391794742214430bf330bbc9929f5d454ca072b -SIZE (chempy-0.8.3.tar.gz) = 184646 +TIMESTAMP = 1714020842 +SHA256 (chempy-0.9.0.tar.gz) = 3ba07d597fef672f3dea4c3ce81e64683f90afd263a7962a6d0db2ab8d9a0204 +SIZE (chempy-0.9.0.tar.gz) = 184714 diff --git a/science/py-cirq-rigetti/Makefile b/science/py-cirq-rigetti/Makefile index 5ce88b24121e..92e9702b1355 100644 --- a/science/py-cirq-rigetti/Makefile +++ b/science/py-cirq-rigetti/Makefile @@ -1,6 +1,7 @@ PORTNAME= cirq-rigetti DISTVERSIONPREFIX= v DISTVERSION= 1.3.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-coards/Makefile b/science/py-coards/Makefile index 5c717e7e63c7..0d4d730643ce 100644 --- a/science/py-coards/Makefile +++ b/science/py-coards/Makefile @@ -1,6 +1,6 @@ PORTNAME= coards PORTVERSION= 1.0.5 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,8 +11,11 @@ WWW= https://pypi.org/project/coards/ LICENSE= MIT +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} + USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-eccodes/Makefile b/science/py-eccodes/Makefile index e7611a9e8d6e..9a692299f5db 100644 --- a/science/py-eccodes/Makefile +++ b/science/py-eccodes/Makefile @@ -1,5 +1,6 @@ PORTNAME= eccodes PORTVERSION= 1.7.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,6 +12,8 @@ WWW= https://github.com/ecmwf/eccodes-python LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} LIB_DEPENDS= libeccodes.so:science/eccodes RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}attrs>=0:devel/py-attrs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cffi>=0:devel/py-cffi@${PY_FLAVOR} \ @@ -22,7 +25,7 @@ TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=0:devel/py-typing-extensions@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils pytest +USE_PYTHON= autoplist concurrent pep517 pytest NO_ARCH= yes diff --git a/science/py-geolinks/Makefile b/science/py-geolinks/Makefile index 058539936196..8315c877932b 100644 --- a/science/py-geolinks/Makefile +++ b/science/py-geolinks/Makefile @@ -1,5 +1,6 @@ PORTNAME= geolinks PORTVERSION= 0.2.3 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,10 +12,12 @@ WWW= https://github.com/geopython/geolinks LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.md +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-geometer/Makefile b/science/py-geometer/Makefile index 38b8e351574b..22d1404b8f58 100644 --- a/science/py-geometer/Makefile +++ b/science/py-geometer/Makefile @@ -1,6 +1,6 @@ PORTNAME= geometer PORTVERSION= 0.3.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,10 +12,12 @@ WWW= https://github.com/jan-mue/geometer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.15,1:math/py-numpy@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-ipygany/Makefile b/science/py-ipygany/Makefile index f3bfddae1a4f..6f4ef2ebcdf0 100644 --- a/science/py-ipygany/Makefile +++ b/science/py-ipygany/Makefile @@ -1,6 +1,6 @@ PORTNAME= ipygany DISTVERSION= 0.5.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-jupyter_jsmol/Makefile b/science/py-jupyter_jsmol/Makefile index 5a720c164701..6ac713a79cde 100644 --- a/science/py-jupyter_jsmol/Makefile +++ b/science/py-jupyter_jsmol/Makefile @@ -1,5 +1,6 @@ PORTNAME= jupyter-jsmol PORTVERSION= 2022.1.0 +PORTREVISION= 1 CATEGORIES= science devel python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-kinematics/Makefile b/science/py-kinematics/Makefile index e361c2df533f..85341adb5cc1 100644 --- a/science/py-kinematics/Makefile +++ b/science/py-kinematics/Makefile @@ -1,6 +1,6 @@ PORTNAME= kinematics PORTVERSION= 0.1.7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,13 +11,15 @@ WWW= https://github.com/skulumani/kinematics LICENSE= GPLv3 +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}coverage>=0:devel/py-coverage@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>=0:devel/py-pytest-cov@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-liac-arff/Makefile b/science/py-liac-arff/Makefile index bb6919ac8b10..416df22f4459 100644 --- a/science/py-liac-arff/Makefile +++ b/science/py-liac-arff/Makefile @@ -1,5 +1,6 @@ PORTNAME= liac-arff PORTVERSION= 2.5.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,10 +11,12 @@ WWW= https://github.com/renatopp/liac-arff LICENSE= MIT +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mock>=0:devel/py-mock@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-netcdf-flattener/Makefile b/science/py-netcdf-flattener/Makefile index fa2f608bade7..0b9fc4d162db 100644 --- a/science/py-netcdf-flattener/Makefile +++ b/science/py-netcdf-flattener/Makefile @@ -1,6 +1,6 @@ PORTNAME= netcdf-flattener PORTVERSION= 1.2.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,11 +12,13 @@ WWW= https://gitlab.eumetsat.int/open-source/netcdf-flattener LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}netCDF4>=0:science/py-netCDF4@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index af9c8413423b..832142d09e3c 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,6 +1,5 @@ PORTNAME= obspy -PORTVERSION= 1.4.0 -PORTREVISION= 1 +PORTVERSION= 1.4.1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-obspy/distinfo b/science/py-obspy/distinfo index d06007f0218e..939956a85f55 100644 --- a/science/py-obspy/distinfo +++ b/science/py-obspy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1669044620 -SHA256 (obspy-1.4.0.tar.gz) = 336a6e1d9a485732b08173cb5dc1dd720a8e53f3b54c180a62bb8ceaa5fe5c06 -SIZE (obspy-1.4.0.tar.gz) = 16984057 +TIMESTAMP = 1714976382 +SHA256 (obspy-1.4.1.tar.gz) = 9cf37b0ce03de43d80398703c006bfddbd709f32e8460a9404b27df998d3f747 +SIZE (obspy-1.4.1.tar.gz) = 17035765 diff --git a/science/py-optking/Makefile b/science/py-optking/Makefile index fcf289d15d42..c18a2056b1ac 100644 --- a/science/py-optking/Makefile +++ b/science/py-optking/Makefile @@ -1,6 +1,6 @@ PORTNAME= optking DISTVERSION= 0.2.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python # chemistry PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-periodictable/Makefile b/science/py-periodictable/Makefile new file mode 100644 index 000000000000..457fd07e33e7 --- /dev/null +++ b/science/py-periodictable/Makefile @@ -0,0 +1,22 @@ +PORTNAME= periodictable +DISTVERSION= 1.7.0 +CATEGORIES= science python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Extensible periodic table of the elements pre-populated with data +WWW= https://periodictable.readthedocs.io/en/latest/ + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} + +USES= python +USE_PYTHON= distutils autoplist + +NO_ARCH= yes + +.include <bsd.port.mk> diff --git a/science/py-periodictable/distinfo b/science/py-periodictable/distinfo new file mode 100644 index 000000000000..24a297f2245b --- /dev/null +++ b/science/py-periodictable/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1714797378 +SHA256 (periodictable-1.7.0.tar.gz) = 420e57c2b19d6a521b1c0b5e387da590a31a8456e4cc1c00bca5ce2dc5f05ea9 +SIZE (periodictable-1.7.0.tar.gz) = 1003080 diff --git a/science/py-periodictable/pkg-descr b/science/py-periodictable/pkg-descr new file mode 100644 index 000000000000..14e907d997b4 --- /dev/null +++ b/science/py-periodictable/pkg-descr @@ -0,0 +1,2 @@ +The periodictable package provides a periodic table of the elements with support +for mass, density and xray/neutron scattering information. diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile index 0e85642e69ba..76f23d93c8b3 100644 --- a/science/py-phonopy/Makefile +++ b/science/py-phonopy/Makefile @@ -1,5 +1,5 @@ PORTNAME= phonopy -DISTVERSION= 2.22.1 +DISTVERSION= 2.23.1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo index a134502b1d0c..b828dbfebf0f 100644 --- a/science/py-phonopy/distinfo +++ b/science/py-phonopy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711741758 -SHA256 (phonopy-2.22.1.tar.gz) = 9eec7aff5cf5c41afee3e7d6ad1fe839cfb354e23d8fad29fd21c700f67e8562 -SIZE (phonopy-2.22.1.tar.gz) = 3959442 +TIMESTAMP = 1714796317 +SHA256 (phonopy-2.23.1.tar.gz) = c49a2144e24d00f744213b4cfd59dc0182fc01291f81384acbc5d79ea892de15 +SIZE (phonopy-2.23.1.tar.gz) = 3988437 diff --git a/science/py-pupynere/Makefile b/science/py-pupynere/Makefile index a6e5b7434145..e873fb887dc4 100644 --- a/science/py-pupynere/Makefile +++ b/science/py-pupynere/Makefile @@ -1,6 +1,6 @@ PORTNAME= pupynere PORTVERSION= 1.0.15 -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,10 +11,12 @@ WWW= https://bitbucket.org/robertodealmeida/pupynere LICENSE= MIT +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pyaixi/Makefile b/science/py-pyaixi/Makefile index 94941316ea70..0b5696ea3a94 100644 --- a/science/py-pyaixi/Makefile +++ b/science/py-pyaixi/Makefile @@ -1,7 +1,7 @@ PORTNAME= pyaixi PORTVERSION= 1.0.4 DISTVERSIONSUFFIX= .post1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,8 +13,11 @@ WWW= https://github.com/sgkasselau/pyaixi LICENSE= CC-BY-SA-3.0 LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} + USES= dos2unix python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index 9d4cacd4ee16..57aaea79aec7 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,6 +1,6 @@ PORTNAME= pycsw PORTVERSION= 2.6.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,6 +12,8 @@ WWW= https://pycsw.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ @@ -20,7 +22,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${PY_FLAVOR} ${PYTHON_PKGNAMEPREFIX}xmltodict>=0:devel/py-xmltodict@${PY_FLAVOR} USES= cpe python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pygeodesy/Makefile b/science/py-pygeodesy/Makefile index 433427bb4d21..38999bdbee9d 100644 --- a/science/py-pygeodesy/Makefile +++ b/science/py-pygeodesy/Makefile @@ -1,5 +1,6 @@ PORTNAME= pygeodesy PORTVERSION= 23.4.23 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI \ https://github.com/mrJean1/PyGeodesy/raw/master/dist/ @@ -12,8 +13,11 @@ WWW= https://github.com/mrJean1/PyGeodesy LICENSE= MIT +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} + USES= python:3.9+ zip -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pygeodesy/files/patch-setup.py b/science/py-pygeodesy/files/patch-setup.py new file mode 100644 index 000000000000..456f14fdfa45 --- /dev/null +++ b/science/py-pygeodesy/files/patch-setup.py @@ -0,0 +1,11 @@ +--- setup.py.orig 2023-04-01 06:02:24 UTC ++++ setup.py +@@ -104,7 +104,7 @@ _KeyWords = ('AER', 'Albers', 'altitude', 'Andoyer', ' + 'Web-Mercator', 'Welford', 'WGRS', 'WGS', 'Whyatt', 'Wildberger', 'Witkam', 'winding-number', + 'XYZ', 'yaw', 'You') + +-setup(name='PyGeodesy', ++setup(name='pygeodesy', + packages=['pygeodesy', 'pygeodesy.deprecated', 'pygeodesy.geodesicx'], + description='Pure Python geodesy tools', + version=_version(), diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile index 62347dc2d76a..d04695972bd2 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,5 +1,6 @@ PORTNAME= pygeometa PORTVERSION= 0.15.3 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,6 +13,8 @@ WWW= https://geopython.github.io/pygeometa/ \ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.md +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>=0:devel/py-jsonschema@${PY_FLAVOR} \ @@ -20,7 +23,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=0:devel/py-yaml@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pysal/Makefile b/science/py-pysal/Makefile index 0a0895abed43..764e40f97df5 100644 --- a/science/py-pysal/Makefile +++ b/science/py-pysal/Makefile @@ -1,5 +1,6 @@ PORTNAME= pysal PORTVERSION= 23.1 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,6 +12,8 @@ WWW= https://pysal.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}access>=1.1.8:science/py-access@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}esda>=2.4.1:science/py-esda@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}giddy>=2.3.3:graphics/py-giddy@${PY_FLAVOR} \ @@ -31,7 +34,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}access>=1.1.8:science/py-access@${PY_FLAVOR} ${PYTHON_PKGNAMEPREFIX}tobler>=0.8.2:science/py-tobler@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile index 5866d95c9675..3a10902722e4 100644 --- a/science/py-pyteomics/Makefile +++ b/science/py-pyteomics/Makefile @@ -1,6 +1,5 @@ PORTNAME= pyteomics -PORTVERSION= 4.7.1 -PORTREVISION= 1 +PORTVERSION= 4.7.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-pyteomics/distinfo b/science/py-pyteomics/distinfo index 615dd3a60f5e..9fd96de6b800 100644 --- a/science/py-pyteomics/distinfo +++ b/science/py-pyteomics/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709764215 -SHA256 (pyteomics-4.7.1.tar.gz) = e5e5d3204af3050b9bf95bb64941b6156331335216e125ac253e7c8dfb1cf0ab -SIZE (pyteomics-4.7.1.tar.gz) = 233874 +TIMESTAMP = 1715842804 +SHA256 (pyteomics-4.7.2.tar.gz) = 9c2cc22f0e45574c62a8e8628a8412d7b5688ccdd679b2f6ddc6fbbee2abb26d +SIZE (pyteomics-4.7.2.tar.gz) = 235076 diff --git a/science/py-qcelemental/Makefile b/science/py-qcelemental/Makefile index 3a2388beb89d..33b81664b3a4 100644 --- a/science/py-qcelemental/Makefile +++ b/science/py-qcelemental/Makefile @@ -1,5 +1,6 @@ PORTNAME= qcelemental DISTVERSION= 0.27.1 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qcengine/Makefile b/science/py-qcengine/Makefile index 676ebde9fdc1..ae5d924cbb01 100644 --- a/science/py-qcengine/Makefile +++ b/science/py-qcengine/Makefile @@ -1,5 +1,6 @@ PORTNAME= qcengine DISTVERSION= 0.29.0 +PORTREVISION= 1 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-scikit-optimize/Makefile b/science/py-scikit-optimize/Makefile index 273ad1b2a592..66082d16ba43 100644 --- a/science/py-scikit-optimize/Makefile +++ b/science/py-scikit-optimize/Makefile @@ -1,5 +1,6 @@ PORTNAME= scikit-optimize PORTVERSION= 0.10.1 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -22,7 +23,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index 1143b32f5ece..f04fc9abc1e7 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,6 +1,6 @@ PORTNAME= scikit-sparse DISTVERSION= 0.4.8 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-sklearn-pandas/Makefile b/science/py-sklearn-pandas/Makefile index b4d1cd73bcdb..446dd48628c3 100644 --- a/science/py-sklearn-pandas/Makefile +++ b/science/py-sklearn-pandas/Makefile @@ -1,6 +1,6 @@ PORTNAME= sklearn-pandas PORTVERSION= 2.2.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,13 +13,15 @@ LICENSE= BSD2CLAUSE ZLIB LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.18.1,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.1.4,1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.23.0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.5.1:science/py-scipy@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-skrebate/Makefile b/science/py-skrebate/Makefile index 073d0ffac9c8..70e9e4e9c44d 100644 --- a/science/py-skrebate/Makefile +++ b/science/py-skrebate/Makefile @@ -1,6 +1,6 @@ PORTNAME= skrebate PORTVERSION= 0.62 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,12 +12,14 @@ WWW= https://github.com/EpistasisLab/scikit-rebate LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-tobler/Makefile b/science/py-tobler/Makefile index 4839ecacbf7f..d6c96beb13ca 100644 --- a/science/py-tobler/Makefile +++ b/science/py-tobler/Makefile @@ -1,16 +1,20 @@ PORTNAME= tobler PORTVERSION= 0.9.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Areal Interpolation -WWW= https://pysal.org/tobler/ +WWW= https://pysal.org/tobler/ \ + https://github.com/pysal/tobler LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}libpysal>=0:science/py-libpysal@${PY_FLAVOR} \ @@ -23,7 +27,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geopandas>=0:graphics/py-geopandas@${PY_FLAV ${PYTHON_PKGNAMEPREFIX}tqdm>=0:misc/py-tqdm@${PY_FLAVOR} USES= python -USE_PYTHON= autoplist concurrent distutils +USE_PYTHON= autoplist concurrent pep517 NO_ARCH= yes diff --git a/science/py-tobler/pkg-descr b/science/py-tobler/pkg-descr index f63914fc338a..f9f8fc74860e 100644 --- a/science/py-tobler/pkg-descr +++ b/science/py-tobler/pkg-descr @@ -1,4 +1,2 @@ tobler is a library for areal interpolation and dasymetric mapping. The name is an homage to the legendary geographer Waldo Tobler. - -See also: https://github.com/pysal/tobler diff --git a/science/pynn/Makefile b/science/pynn/Makefile index 3c74a2c27e67..f524f44a1db5 100644 --- a/science/pynn/Makefile +++ b/science/pynn/Makefile @@ -1,5 +1,5 @@ PORTNAME= pynn -PORTVERSION= 0.12.2 +PORTVERSION= 0.12.3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -17,6 +17,8 @@ LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} + NO_ARCH= yes USES= python diff --git a/science/pynn/distinfo b/science/pynn/distinfo index 8ef83437a6e9..807eb0644a15 100644 --- a/science/pynn/distinfo +++ b/science/pynn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1708679064 -SHA256 (PyNN-0.12.2.tar.gz) = 8039b68e3e5f98b537038c249dc42c027bd63f9ecc015c82f1f88bd30dfa28a9 -SIZE (PyNN-0.12.2.tar.gz) = 522125 +TIMESTAMP = 1715154234 +SHA256 (PyNN-0.12.3.tar.gz) = e196f9055c46fe5c0e23f491815d16dca8db9be599a226ee11fa67605cab153d +SIZE (PyNN-0.12.3.tar.gz) = 521282 diff --git a/science/qt6-quick3dphysics/distinfo b/science/qt6-quick3dphysics/distinfo index f124b0eca149..593b62984e53 100644 --- a/science/qt6-quick3dphysics/distinfo +++ b/science/qt6-quick3dphysics/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711663491 -SHA256 (KDE/Qt/6.6.3/qtquick3dphysics-everywhere-src-6.6.3.tar.xz) = 67e19b482ea1ac8ba14afda8f804e90e0a68ff68e7da58b454deffda3051f546 -SIZE (KDE/Qt/6.6.3/qtquick3dphysics-everywhere-src-6.6.3.tar.xz) = 4692928 +TIMESTAMP = 1712114589 +SHA256 (KDE/Qt/6.7.0/qtquick3dphysics-everywhere-src-6.7.0.tar.xz) = 80045f261109f3f3807c0b405d056e935210a36499c3a9aff78296d8940e04e6 +SIZE (KDE/Qt/6.7.0/qtquick3dphysics-everywhere-src-6.7.0.tar.xz) = 4702492 diff --git a/science/quantum-espresso/Makefile b/science/quantum-espresso/Makefile index bb9981633487..1bc200b9c6fc 100644 --- a/science/quantum-espresso/Makefile +++ b/science/quantum-espresso/Makefile @@ -11,6 +11,7 @@ WWW= https://www.quantum-espresso.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/License +BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory diff --git a/science/rubygem-rgeo-shapefile/Makefile b/science/rubygem-rgeo-shapefile/Makefile index 6e9915a0586b..32f43026fd85 100644 --- a/science/rubygem-rgeo-shapefile/Makefile +++ b/science/rubygem-rgeo-shapefile/Makefile @@ -1,5 +1,6 @@ PORTNAME= rgeo-shapefile PORTVERSION= 3.1.0 +PORTREVISION= 1 CATEGORIES= science rubygems MASTER_SITES= RG @@ -10,7 +11,7 @@ WWW= https://github.com/rgeo/rgeo-shapefile LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt -RUN_DEPENDS= rubygem-dbf>=4.0<5:databases/rubygem-dbf \ +RUN_DEPENDS= rubygem-dbf4>=4.0<5:databases/rubygem-dbf4 \ rubygem-rgeo>=1.0:science/rubygem-rgeo USES= gem diff --git a/science/shelxle/Makefile b/science/shelxle/Makefile index 4d680993faf2..187284c21391 100644 --- a/science/shelxle/Makefile +++ b/science/shelxle/Makefile @@ -1,5 +1,5 @@ PORTNAME= shelxle -DISTVERSION= 1.0.1636 +DISTVERSION= 1.0.1638 CATEGORIES= science # chemistry MASTER_SITES= SF/${PORTNAME}/code/ diff --git a/science/shelxle/distinfo b/science/shelxle/distinfo index 4fed8ef1f549..7d5e3f3137ba 100644 --- a/science/shelxle/distinfo +++ b/science/shelxle/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713601272 -SHA256 (shelxle-1.0.1636.tar.bz2) = d28973ca82ee95be45c76fae0bbbbfa0ef937fe012734de6cb1b86bfd3344947 -SIZE (shelxle-1.0.1636.tar.bz2) = 3953221 +TIMESTAMP = 1714104398 +SHA256 (shelxle-1.0.1638.tar.bz2) = e16f53e2473e5791746d56b2950ede315f952ef7f1d3fe961a99e54ff7f28c92 +SIZE (shelxle-1.0.1638.tar.bz2) = 3953512 diff --git a/science/siconos/Makefile b/science/siconos/Makefile index b98ee4ea1671..3eeefb2cf527 100644 --- a/science/siconos/Makefile +++ b/science/siconos/Makefile @@ -1,6 +1,6 @@ PORTNAME= siconos DISTVERSION= 4.4.0 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/smoldyn/Makefile b/science/smoldyn/Makefile index 94049c8e7936..73bd8471e015 100644 --- a/science/smoldyn/Makefile +++ b/science/smoldyn/Makefile @@ -1,5 +1,6 @@ PORTNAME= smoldyn DISTVERSION= 2.73 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://www.smoldyn.org/ diff --git a/science/step/Makefile b/science/step/Makefile index 2397e2aa0dc8..845243871bca 100644 --- a/science/step/Makefile +++ b/science/step/Makefile @@ -1,6 +1,6 @@ PORTNAME= step DISTVERSION= ${KDE_APPLICATIONS_VERSION} -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science education kde kde-applications MAINTAINER= kde@FreeBSD.org diff --git a/science/thermofun/Makefile b/science/thermofun/Makefile index f121cb363492..cca1c2936417 100644 --- a/science/thermofun/Makefile +++ b/science/thermofun/Makefile @@ -1,41 +1,42 @@ PORTNAME= thermofun DISTVERSIONPREFIX= v -DISTVERSION= 0.4.4 +DISTVERSION= 0.4.5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Code for calculating thermodynamic properties of materials -WWW= https://github.com/thermohub/thermofun +WWW= https://github.com/thermohub/thermofun/ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nlohmann-json>0:devel/nlohmann-json \ - spdlog>0:devel/spdlog \ - ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} + spdlog>0:devel/spdlog LIB_DEPENDS= libChemicalFun.so:science/chemicalfun -USES= cmake compiler:c++14-lang +USES= cmake USE_GITHUB= yes GH_ACCOUNT= thermohub +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + CXXFLAGS+= -DSPDLOG_FMT_EXTERNAL # see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=258073#c3 -TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC} OPTIONS_DEFINE= PYTHON OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes +PYTHON_BUILD_DEPENDS= pybind11>0:devel/pybind11 \ + ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} PYTHON_USES= python PYTHON_USE= PYTHON=pytest PYTHON_CMAKE_BOOL= TFUN_BUILD_PYTHON PYTHON_CMAKE_ON= -DFREEBSD_STAGEDIR=${STAGEDIR} -DFREEBSD_PREFIX=${PREFIX} -PYTHON_BUILD_DEPENDS= pybind11>0:devel/pybind11 \ - ${PY_SETUPTOOLS} post-install-PYTHON-on: # remove wrong *.pyc, see related bug https://bitbucket.org/gems4/chemicalfun/issues/1/please-support-stagedir diff --git a/science/thermofun/distinfo b/science/thermofun/distinfo index 9b6fa7e8a90e..0346934de012 100644 --- a/science/thermofun/distinfo +++ b/science/thermofun/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1686365234 -SHA256 (thermohub-thermofun-v0.4.4_GH0.tar.gz) = d5ca71461eeeb7e2343bad15131d7d5c0a271d495f869243b28677f82386ee6d -SIZE (thermohub-thermofun-v0.4.4_GH0.tar.gz) = 2084337 +TIMESTAMP = 1713550727 +SHA256 (thermohub-thermofun-v0.4.5_GH0.tar.gz) = 90519474d54ff91de61172cab0169c8a26a3dc7e2b0b6345237ed0d4e9787b30 +SIZE (thermohub-thermofun-v0.4.5_GH0.tar.gz) = 2079838 diff --git a/science/thermofun/pkg-descr b/science/thermofun/pkg-descr index 2ecc495e54fe..32c595adc9bf 100644 --- a/science/thermofun/pkg-descr +++ b/science/thermofun/pkg-descr @@ -1,2 +1,2 @@ -A code for calculating the standard state thermodynamic properties at a given -temperature and pressure. +A code for calculating the standard state thermodynamic properties +at a given temperature and pressure. diff --git a/science/thermofun/pkg-plist b/science/thermofun/pkg-plist index c11f3bece961..c70bdbb788a1 100644 --- a/science/thermofun/pkg-plist +++ b/science/thermofun/pkg-plist @@ -68,12 +68,12 @@ lib/cmake/ThermoFun/ThermoFunConfigVersion.cmake lib/cmake/ThermoFun/ThermoFunTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/ThermoFun/ThermoFunTargets.cmake lib/libThermoFun.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/INSTALLER -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/METADATA -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/RECORD -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/REQUESTED -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/WHEEL -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/direct_url.json -%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.3.dist-info/top_level.txt +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/INSTALLER +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/METADATA +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/RECORD +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/REQUESTED +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/WHEEL +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/direct_url.json +%%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun-0.4.5.dist-info/top_level.txt %%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun/PyThermoFun%%PYTHON_EXT_SUFFIX%%.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/thermofun/__init__.py diff --git a/science/tinker/Makefile b/science/tinker/Makefile index 6de3707bb4d7..3fac5bdbe5ec 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,5 +1,6 @@ PORTNAME= tinker -DISTVERSION= 8.11.1 +DISTVERSION= 8.11.2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 7f0aa845abc3..f2d658be468b 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713071651 -SHA256 (tinker-8.11.1.tar.gz) = cdbf2dfb5e43c3438b27ac8b767c9290ae2948e62333149babd72a6811963731 -SIZE (tinker-8.11.1.tar.gz) = 74273877 +TIMESTAMP = 1716143875 +SHA256 (tinker-8.11.2.tar.gz) = 1ffe22d0cfbe15ae714e4c260185322f789fd90f3f0aa4d4e8904a6ea6b1f949 +SIZE (tinker-8.11.2.tar.gz) = 72243545 diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index e1f412c1b22f..4b7b308532ab 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,14 +1,14 @@ ---- make/Makefile.orig 2024-04-08 01:19:41 UTC +--- make/Makefile.orig 2024-05-04 16:08:28 UTC +++ make/Makefile -@@ -86,7 +86,7 @@ F77FLAGS = -c +@@ -68,7 +68,7 @@ F77FLAGS = -c F77 = gfortran F77FLAGS = -c -OPTFLAGS = -Ofast -march=native -fopenmp +OPTFLAGS = -Ofast $(PORT_SIMD_FLAGS) -fopenmp - #OPTFLAGS = -Ofast -fopenmp - #OPTFLAGS = -Og -g -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized - LIBDIR = -L. -L$(TINKER_LIBDIR)/macos + OPTFLAGS = -Ofast -fopenmp + OPTFLAGS = -Og -g -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized + LIBDIR = -L. -L$(TINKER_LIBDIR)/linux -Wl,--no-as-needed -ldl @@ -829,138 +829,138 @@ rename_bin: cat *.f *.c > tinker.txt diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index 04f2dc7f3175..286fc0abcadd 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -71,8 +71,8 @@ bin/xyzpdb %%DATADIR%%/params/amber99sb.prm %%DATADIR%%/params/amoeba04.prm %%DATADIR%%/params/amoeba09.prm +%%DATADIR%%/params/amoebabio-hfc23.prm %%DATADIR%%/params/amoebabio09.prm -%%DATADIR%%/params/amoebabio18-hfc23.prm %%DATADIR%%/params/amoebabio18.prm %%DATADIR%%/params/amoebail22.prm %%DATADIR%%/params/amoebanuc17.prm @@ -84,6 +84,7 @@ bin/xyzpdb %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm22cmap.prm %%DATADIR%%/params/dang.prm +%%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm %%DATADIR%%/params/iwater.prm %%DATADIR%%/params/mm2.prm diff --git a/science/trilinos/Makefile b/science/trilinos/Makefile index 8a11a7d2bd86..44f10e85d9b2 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,6 +1,7 @@ PORTNAME= trilinos DISTVERSIONPREFIX= trilinos-release- DISTVERSION= 15-1-1 +PORTREVISION= 1 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/zotero/Makefile b/science/zotero/Makefile index dc55987cc707..8a07860c0ca5 100644 --- a/science/zotero/Makefile +++ b/science/zotero/Makefile @@ -1,5 +1,6 @@ PORTNAME= zotero DISTVERSION= 6.0.36 +PORTREVISION= 1 CATEGORIES= science deskutils MASTER_SITES= LOCAL/mikael DISTFILES= Zotero-${DISTVERSION}_FreeBSD-${ARCH}${EXTRACT_SUFX} diff --git a/science/zotero/distinfo b/science/zotero/distinfo index e96580ab90a5..c5c1ef39c55e 100644 --- a/science/zotero/distinfo +++ b/science/zotero/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1710752163 -SHA256 (Zotero-6.0.36_FreeBSD-amd64.tar.xz) = 2a075a892cec091c391fb7969385917dbd7038239a84e1626ccd6c27b2bacc93 -SIZE (Zotero-6.0.36_FreeBSD-amd64.tar.xz) = 60745092 -SHA256 (Zotero-6.0.36_FreeBSD-i386.tar.xz) = 95af0e0d624e5f07d34004f5f510799fee8d9ce9f617ca2ac3930e665f3a2142 -SIZE (Zotero-6.0.36_FreeBSD-i386.tar.xz) = 56653828 +TIMESTAMP = 1715608280 +SHA256 (Zotero-6.0.36_FreeBSD-amd64.tar.xz) = c978a95d2e1baa6209a185a90ed3d61ab7a333485229cf5b8f5174946c91f5e7 +SIZE (Zotero-6.0.36_FreeBSD-amd64.tar.xz) = 57026220 +SHA256 (Zotero-6.0.36_FreeBSD-i386.tar.xz) = b464f148f6ea052274ae4f6699b5b8ae69b7cb15347ec41b81f3a27dfe65cc30 +SIZE (Zotero-6.0.36_FreeBSD-i386.tar.xz) = 54587836 |