diff options
Diffstat (limited to 'science')
78 files changed, 421 insertions, 532 deletions
diff --git a/science/Makefile b/science/Makefile index 0fd8eb49e6d3..7a7615c8776f 100644 --- a/science/Makefile +++ b/science/Makefile @@ -321,6 +321,7 @@ SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client + SUBDIR += py-dwave-gate SUBDIR += py-dwave-greedy SUBDIR += py-dwave-hybrid SUBDIR += py-dwave-inspector diff --git a/science/afni/Makefile b/science/afni/Makefile index c555c6c25e04..74ad2cbe7f50 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.09 +DISTVERSION= 25.2.17 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 4ec769ac8338..a69fa3d8ee34 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1756108500 -SHA256 (afni-afni-AFNI_25.2.09_GH0.tar.gz) = ff6aacf8a4f2b0b60ea584ece08e23db665488bfb1978957f05f30df6c394e05 -SIZE (afni-afni-AFNI_25.2.09_GH0.tar.gz) = 53321640 +TIMESTAMP = 1758872368 +SHA256 (afni-afni-AFNI_25.2.17_GH0.tar.gz) = e97fba22be67fd931b753047e536f5cb919a507a2e2769f258a82ad0f0dec959 +SIZE (afni-afni-AFNI_25.2.17_GH0.tar.gz) = 53342709 diff --git a/science/agrum/Makefile b/science/agrum/Makefile index e65dbffd8d4e..761cac949744 100644 --- a/science/agrum/Makefile +++ b/science/agrum/Makefile @@ -1,6 +1,5 @@ PORTNAME= agrum -DISTVERSION= 2.2.0 -PORTREVISION= 1 +DISTVERSION= 2.2.1 CATEGORIES= science math MAINTAINER= yuri@FreeBSD.org @@ -9,7 +8,7 @@ WWW= https://agrum.gitlab.io \ https://gitlab.com/agrumery/aGrUM LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md TEST_DEPENDS= swig:devel/swig @@ -21,7 +20,7 @@ LLD_UNSAFE= yes USE_GITLAB= yes GL_ACCOUNT= agrumery GL_PROJECT= aGrUM -GL_TAGNAME= cf1283f783aa6803bafbd9a3fb4991316c1b52d9 +GL_TAGNAME= 40993102 SHEBANG_FILES= act @@ -44,16 +43,14 @@ PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_USES= python PYTHON_PLIST_SUB= PYTHON_VER_MAJ=${PYTHON_VER:R} PYTHON_RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}configparser>0:devel/py-configparser@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib-inline>0:math/py-matplotlib-inline@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbconvert>0:devel/py-nbconvert@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbformat>0:devel/py-nbformat@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydotplus>0:graphics/py-pydotplus@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} # see wrappers/pyAgrum/requirements.txt and wrappers/pyAgrum/testunits/optional_requirements.txt @@ -63,6 +60,6 @@ do-test: @cd ${WRKSRC} && \ ${SETENV} ${MAKE_ENV} ./act test release agrum -t all -# tests as of 2.2.0: Failed 0 of 1483 tests +# tests as of 2.2.1: Failed 0 of 1485 tests .include <bsd.port.mk> diff --git a/science/agrum/distinfo b/science/agrum/distinfo index 62c51836a6d8..03113cb380cc 100644 --- a/science/agrum/distinfo +++ b/science/agrum/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753632410 -SHA256 (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 57f7274925f64129c2f3bfcd178f75edd4cb6eaff1d06c30f20c85c41e6ca3d9 -SIZE (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 29175753 +TIMESTAMP = 1759029558 +SHA256 (aGrUM-40993102.tar.bz2) = f0a4174d7854ea4e045e79c9c6a85c40f2d017906beca221a95fba3a1f233e08 +SIZE (aGrUM-40993102.tar.bz2) = 21812219 diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist index 9fe1f9999703..bdc68b53969c 100644 --- a/science/agrum/pkg-plist +++ b/science/agrum/pkg-plist @@ -956,9 +956,9 @@ lib/libagrumID.so.%%VERSION%% lib/libagrumMRF.so lib/libagrumMRF.so.2 lib/libagrumMRF.so.%%VERSION%% -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.LGPL -%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.MIT +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.md +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/LGPL-3.0-or-later.txt +%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/MIT.txt %%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/METADATA %%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/WHEEL %%PYTHON_SITELIBDIR%%/pyagrum/__init__.py diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile index 46e7081d3302..e886894e59e5 100644 --- a/science/cp2k/Makefile +++ b/science/cp2k/Makefile @@ -5,7 +5,8 @@ CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry and solid state physics software package -WWW= https://www.cp2k.org/ +WWW= https://www.cp2k.org/ \ + https://github.com/cp2k/cp2k LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/science/dakota/Makefile b/science/dakota/Makefile index 96e46b04e23b..059d349e1323 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,5 +1,6 @@ PORTNAME= dakota DISTVERSION= 6.22.0 +PORTEVISION= 1 CATEGORIES= science MASTER_SITES= https://github.com/snl-dakota/dakota/releases/download/v${DISTVERSION}/ DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli @@ -15,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nanoflann>0:math/nanoflann LIB_DEPENDS= libblas.so:math/blas \ - libboost_system.so:devel/boost-libs \ + libboost_program_options.so:devel/boost-libs \ libexpat.so:textproc/expat2 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ @@ -74,6 +75,11 @@ post-extract: @${FIND} ${WRKSRC} -name "*.orig" -delete @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target +post-patch: + @${REINPLACE_CMD} -e 's| Boost::system||' \ + ${WRKSRC}/cmake/DakotaFindSystemTPLs.cmake \ + ${WRKSRC}/src/surrogates/unit/CMakeLists.txt + pre-configure: # MUQ_STANMATH_DIR is lost otherwise @${REINPLACE_CMD} 's|find_package(PkgConfig)|set(MUQ_STANMATH_DIR ${WRKSRC}/stanmath)|' ${WRKSRC}/packages/external/muq2/cmake/finds/FindSTANMATH.cmake diff --git a/science/dftd4/pkg-descr b/science/dftd4/pkg-descr index 19ae190643e6..5d459c6d9dff 100644 --- a/science/dftd4/pkg-descr +++ b/science/dftd4/pkg-descr @@ -1,2 +1,12 @@ -D4 is a generally applicable atomic-charge dependent london dispersion -correction calculator. +DFTD4 provides a generally applicable, charge-dependent London-dispersion +correction for Density Functional Theory (DFT) calculations and other +atomistic modeling methods. It addresses the missing van-der-Waals (vdW) +interactions from standard exchange-correlation functionals by approximating +them based solely on the system's structure, enabling rapid computation. + +This software can be linked as an external package to various DFT codes, +such as VASP, to add vdW energies, forces, and stresses for structure +relaxation and molecular dynamics simulations. It features functional-specific +parameters for numerous density functionals and offers API support for +Fortran, C, and Python, making it a versatile tool for computational +chemistry and physics. diff --git a/science/dimod/Makefile b/science/dimod/Makefile index f535bbdf1040..1605f697e49c 100644 --- a/science/dimod/Makefile +++ b/science/dimod/Makefile @@ -1,5 +1,5 @@ PORTNAME= dimod -DISTVERSION= 0.12.20 +DISTVERSION= 0.12.21 CATEGORIES= science python MAINTAINER= yuri@FreeBSD.org @@ -28,6 +28,6 @@ do-install: do-test: @cd ${WRKSRC}/testscpp && ${SETENV} ${MAKE_ENV} ${MAKE} -# tests as of 0.12.20: All tests passed (104295 assertions in 35 test cases) +# tests as of 0.12.21: All tests passed (104295 assertions in 35 test cases) .include <bsd.port.mk> diff --git a/science/dimod/distinfo b/science/dimod/distinfo index 8af012b9d278..93ff5101cd57 100644 --- a/science/dimod/distinfo +++ b/science/dimod/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742619271 -SHA256 (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 33c06ca8a9f0ab9be5edc3ef2ea065c908fa1e3847c20a20598b1bc1674eafa6 -SIZE (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 582646 +TIMESTAMP = 1758994255 +SHA256 (dwavesystems-dimod-0.12.21_GH0.tar.gz) = c7639f66a4270cc49ee2933b20ddca203e9b0e908b75ba1182fc2ff40e85f7ab +SIZE (dwavesystems-dimod-0.12.21_GH0.tar.gz) = 582916 diff --git a/science/feff10/Makefile b/science/feff10/Makefile index 0eb2b3ea71bd..184eea6011ad 100644 --- a/science/feff10/Makefile +++ b/science/feff10/Makefile @@ -26,12 +26,16 @@ WRKSRC_SUBDIR= src SHEBANG_GLOB= *.script -FFLAGS+= -ffree-line-length-512 -fallow-argument-mismatch - MAKE_ARGS= FLAGS="${FFLAGS}" BINARY_ALIAS= make=${GMAKE} ifort=${FC} +.include <bsd.port.pre.mk> + +.if ${FORTRAN_DEFAULT} != flang +FFLAGS= -ffree-line-length-512 -fallow-argument-mismatch +.endif + do-install: for f in ${WRKSRC}/../bin/Seq/*; do \ if readelf -V $${f} > /dev/null 2>&1; then \ @@ -41,4 +45,4 @@ do-install: fi \ done -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/science/kalzium/distinfo b/science/kalzium/distinfo index dc9bdf4527dc..2ed98aa072cd 100644 --- a/science/kalzium/distinfo +++ b/science/kalzium/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1754646547 -SHA256 (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 8765737e7baeb7fb0d0c16112ce11694ddb90a102e8e6b3e723dae9d595b8529 -SIZE (KDE/release-service/25.08.0/kalzium-25.08.0.tar.xz) = 22650880 +TIMESTAMP = 1757410249 +SHA256 (KDE/release-service/25.08.1/kalzium-25.08.1.tar.xz) = 64ecba7f0cc8333ee528fc951e500e591d263380e72af59e36b37654a8e1ae8b +SIZE (KDE/release-service/25.08.1/kalzium-25.08.1.tar.xz) = 22661180 diff --git a/science/libccp4/pkg-descr b/science/libccp4/pkg-descr index 8e24c34b4c17..a88f627c63b9 100644 --- a/science/libccp4/pkg-descr +++ b/science/libccp4/pkg-descr @@ -1,10 +1,13 @@ -CCP4 exists to produce and support a world-leading, integrated suite of programs -that allows researchers to determine macromolecular structures by X-ray -crystallography, and other biophysical techniques. CCP4 aims to develop and -support the development of cutting edge approaches to experimental determination -and analysis of protein structure, and integrate these approaches into the -suite. CCP4 is a community based resource that supports the widest possible -researcher community, embracing academic, not for profit, and for profit -research. CCP4 aims to play a key role in the education and training of -scientists in experimental structural biology. It encourages the wide -dissemination of new ideas, techniques and practice. +CCP4 is a world-leading, integrated software suite for macromolecular +structure determination using X-ray crystallography and other biophysical +techniques. It provides a comprehensive collection of programs covering +all stages of the process, from data processing and phasing (e.g., Crank) +to molecular replacement (e.g., Beast, AMPLE), model building (e.g., +Buccaneer), refinement (e.g., REFMAC), and validation. + +The suite features automated structure solution pipelines and modern +graphical user interfaces like CCP4i2. As a community-based resource, +CCP4 supports a wide research community and plays a key role in the +education and training of scientists in experimental structural biology. +Its modular design and Coordinate Library offer flexibility and extensive +functionality for structural biologists. diff --git a/science/maeparser/pkg-descr b/science/maeparser/pkg-descr index 5a07dac6de9a..f381e9c79480 100644 --- a/science/maeparser/pkg-descr +++ b/science/maeparser/pkg-descr @@ -1,5 +1,13 @@ -maeparser is a parser for Schrodinger Maestro files. +maeparser is a C++ library developed by Schrodinger for efficiently and +losslessly parsing Maestro files, which serve as Schrodinger's primary +output format for storing molecular structures and data. This parser is +crucial for any software package needing to interact with Schrodinger's +physics-based modeling outputs. -Structure files (.mae,.maegz,.mae.gz) can contain multiple structures -delimited by "f_m_ct". See MaeConstants.hpp for standard block and property -names. +It supports various applications in computational chemistry, including +molecular dynamics, ligand-protein docking, and quantum mechanics. The +library utilizes a recursive descent approach, prioritizing parsing speed +to ensure quick and accurate extraction of data from .mae, .maegz, and +.mae.gz structure files. These files can contain multiple structures, +delimited by "f_m_ct", with standard block and property names defined in +MaeConstants.hpp. diff --git a/science/mopac/pkg-descr b/science/mopac/pkg-descr index 18229a7d331d..a510745aeb45 100644 --- a/science/mopac/pkg-descr +++ b/science/mopac/pkg-descr @@ -1,2 +1,14 @@ -MOPAC7, semi-empirical (MNDO, AM1, PM3, MINDO/3) quantum-chemical -calculation written by James J. P. Stewart and co-workers. +MOPAC (Molecular Orbital PACkage) is a powerful computational chemistry +software that employs semi-empirical quantum chemistry methods to study +molecular and periodic structures. Developed since 1981, it offers a +balance of computational speed and accuracy for a wide range of +applications in chemistry and materials science. + +MOPAC implements various semi-empirical models, including AM1, PM3, PM6, +and PM7. It performs geometry optimization, transition-state optimization, +and vibrational analysis. Key features include solvation models (COSMO), +support for periodic boundary conditions, and the unique MOZYME solver +for rapid calculations on large systems, such as biomolecules and +materials. MOPAC also calculates gas-phase thermodynamics, molecular +polarizability, and integrates with numerous graphical user interfaces +and other chemistry software. It supports 83 elements of the periodic table. diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index fd76e7f0a190..20193cb276c9 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,6 +1,6 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v -DISTVERSION= 1.25.2 +DISTVERSION= 1.25.4 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} diff --git a/science/openmodelica/distinfo b/science/openmodelica/distinfo index 56ac7fddde4b..2597c4be9261 100644 --- a/science/openmodelica/distinfo +++ b/science/openmodelica/distinfo @@ -1,19 +1,19 @@ -TIMESTAMP = 1756357301 -SHA256 (openmodelica-1.25.2/OpenModelica-OpenModelica-v1.25.2_GH0.tar.gz) = a56f60074842f8b10c05d8ad323e89937b38ecbea0c9f062858f57d5ab8dbf7c -SIZE (openmodelica-1.25.2/OpenModelica-OpenModelica-v1.25.2_GH0.tar.gz) = 148277183 -SHA256 (openmodelica-1.25.2/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 -SIZE (openmodelica-1.25.2/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 -SHA256 (openmodelica-1.25.2/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 -SIZE (openmodelica-1.25.2/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 -SHA256 (openmodelica-1.25.2/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d -SIZE (openmodelica-1.25.2/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 -SHA256 (openmodelica-1.25.2/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 -SIZE (openmodelica-1.25.2/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 -SHA256 (openmodelica-1.25.2/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b -SIZE (openmodelica-1.25.2/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 -SHA256 (openmodelica-1.25.2/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa -SIZE (openmodelica-1.25.2/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 -SHA256 (openmodelica-1.25.2/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a -SIZE (openmodelica-1.25.2/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 -SHA256 (openmodelica-1.25.2/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 -SIZE (openmodelica-1.25.2/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 +TIMESTAMP = 1757658835 +SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = b9d50f8321f4537735d70368b2ca105e35ad118797d71b0107b24eb660387ad4 +SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = 148278628 +SHA256 (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 +SIZE (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 +SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d +SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 +SHA256 (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 +SIZE (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b +SIZE (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 +SHA256 (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa +SIZE (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 +SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a +SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 +SHA256 (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 +SIZE (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 diff --git a/science/opsin/pkg-descr b/science/opsin/pkg-descr index f49b9052d4ca..efc128011b63 100644 --- a/science/opsin/pkg-descr +++ b/science/opsin/pkg-descr @@ -1,4 +1,13 @@ -OPSIN is a Java library for IUPAC name-to-structure conversion offering high -recall and precision on organic chemical nomenclature. -Supported outputs are SMILES, CML (Chemical Markup Language) and InChI (IUPAC -International Chemical Identifier). +OPSIN (Open Parser for Systematic IUPAC Nomenclature) is a freely +available, open-source Java library designed to accurately interpret +systematic IUPAC chemical nomenclature and convert it into chemical +structures. It offers high precision and recall for organic chemical +names, including complex heterocycles and stereochemistry. + +OPSIN supports multiple output formats such as SMILES, InChI, and CML, +and can also generate PNG, SVG, and JSON. It can be deployed as a web +service, a local command-line application for bulk conversion, or +integrated into other systems via third-party Python libraries. Its +extensible design and robust parsing mechanism make it a valuable tool +for chemical information extraction from scientific literature and +patents, research and development, and populating chemical databases. diff --git a/science/plumed/pkg-descr b/science/plumed/pkg-descr index a4e5b42106c3..9d390c7b6028 100644 --- a/science/plumed/pkg-descr +++ b/science/plumed/pkg-descr @@ -1,6 +1,13 @@ -PLUMED is an open-source, community-developed library that provides a wide -range of different methods, which include: -* enhanced-sampling algorithms -* free-energy methods -* tools to analyze the vast amounts of data produced by molecular dynamics (MD) - simulations. +PLUMED is an open-source, community-developed library designed to work +with molecular dynamics (MD) simulations. It provides a comprehensive +toolbox of methods, including enhanced-sampling algorithms, free-energy +methods, and advanced tools for analyzing the vast amounts of data +produced by MD simulations. + +This versatile library offers a wide range of collective variables, +making it suitable for studying complex processes across various scientific +disciplines such as physics, chemistry, material science, and biology. +PLUMED seamlessly integrates with popular MD engines like GROMACS and +LAMMPS, as well as analysis tools such as VMD. Its API supports multiple +programming languages (C, C++, Fortran, Python) and its L-GPL license +ensures compatibility with proprietary software. diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile index 54a52b7b7205..32fa25a62689 100644 --- a/science/py-OpenMC/Makefile +++ b/science/py-OpenMC/Makefile @@ -1,7 +1,7 @@ PORTNAME= OpenMC DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile index 398ade237318..150580aa2496 100644 --- a/science/py-asdf/Makefile +++ b/science/py-asdf/Makefile @@ -1,5 +1,5 @@ PORTNAME= asdf -PORTVERSION= 4.4.0 +PORTVERSION= 4.5.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-asdf/distinfo b/science/py-asdf/distinfo index f4e9bc88b54d..cf61646370fe 100644 --- a/science/py-asdf/distinfo +++ b/science/py-asdf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1757120806 -SHA256 (asdf-4.4.0.tar.gz) = f7146119e3d217f0b83d125e2fd657c1b2427caf6faeaf7ceedcd81db464363e -SIZE (asdf-4.4.0.tar.gz) = 899576 +TIMESTAMP = 1757436539 +SHA256 (asdf-4.5.0.tar.gz) = 1f37979263cac53b8f7b078c521fda8aa9a08cd5d2badb9aacec34d6badd2dc1 +SIZE (asdf-4.5.0.tar.gz) = 900039 diff --git a/science/py-dimod/Makefile b/science/py-dimod/Makefile index 74fe1a102445..7d5302b9ef4f 100644 --- a/science/py-dimod/Makefile +++ b/science/py-dimod/Makefile @@ -1,5 +1,5 @@ PORTNAME= dimod -DISTVERSION= 0.12.20 +DISTVERSION= 0.12.21 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -27,6 +27,6 @@ TEST_WRKSRC= ${WRKSRC}/tests post-install: @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} -# tests as of 0.12.20: Ran 2913 tests in 34.742s +# tests as of 0.12.21: Ran 2914 tests in 35.706s .include <bsd.port.mk> diff --git a/science/py-dimod/distinfo b/science/py-dimod/distinfo index e0aa99e8e9ee..b3ff37953dd7 100644 --- a/science/py-dimod/distinfo +++ b/science/py-dimod/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742619329 -SHA256 (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 33c06ca8a9f0ab9be5edc3ef2ea065c908fa1e3847c20a20598b1bc1674eafa6 -SIZE (dwavesystems-dimod-0.12.20_GH0.tar.gz) = 582646 +TIMESTAMP = 1758994821 +SHA256 (dwavesystems-dimod-0.12.21_GH0.tar.gz) = c7639f66a4270cc49ee2933b20ddca203e9b0e908b75ba1182fc2ff40e85f7ab +SIZE (dwavesystems-dimod-0.12.21_GH0.tar.gz) = 582916 diff --git a/science/py-dwave-cloud-client/Makefile b/science/py-dwave-cloud-client/Makefile index c9b36c967a07..6a79a590dca2 100644 --- a/science/py-dwave-cloud-client/Makefile +++ b/science/py-dwave-cloud-client/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-cloud-client -DISTVERSION= 0.12.0 -PORTREVISION= 2 +DISTVERSION= 0.14.0 CATEGORIES= science python www # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,19 +11,21 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}authlib>=1.2:security/py-authlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}click>=7:devel/py-click@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}click>=7.0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}python-dateutil>=2.7:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}diskcache>=5.2.1:devel/py-diskcache@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.9:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0:devel/py-homebase@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}http-sf>=1.0.4:www/py-http-sf@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}importlib-metadata>=5.0.0:devel/py-importlib-metadata@${PY_FLAVOR} \ ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}orjson>=3.10:devel/py-orjson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=19:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydantic2>=2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.25:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.5.0:devel/py-typing-extensions@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}urllib3>=1.26,1<3.0,1:net/py-urllib3@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}urllib3>=1.26:net/py-urllib3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}werkzeug>=2.2:www/py-werkzeug@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-dwave-cloud-client/distinfo b/science/py-dwave-cloud-client/distinfo index b26ca956e0e1..b69fa4d5c43d 100644 --- a/science/py-dwave-cloud-client/distinfo +++ b/science/py-dwave-cloud-client/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721011778 -SHA256 (dwavesystems-dwave-cloud-client-0.12.0_GH0.tar.gz) = 392a65fdeead193bd5e018b408a1379259297950e23b5706f44ab14afd0a3796 -SIZE (dwavesystems-dwave-cloud-client-0.12.0_GH0.tar.gz) = 215318 +TIMESTAMP = 1759002074 +SHA256 (dwavesystems-dwave-cloud-client-0.14.0_GH0.tar.gz) = 1bb21f5c65f598b6aefff4bc1dfafc698572428501d60267b6f5ea19e4e23614 +SIZE (dwavesystems-dwave-cloud-client-0.14.0_GH0.tar.gz) = 257192 diff --git a/science/py-dwave-gate/Makefile b/science/py-dwave-gate/Makefile new file mode 100644 index 000000000000..cd726d2113cb --- /dev/null +++ b/science/py-dwave-gate/Makefile @@ -0,0 +1,25 @@ +PORTNAME= dwave-gate +DISTVERSION= 0.3.4 +CATEGORIES= science python # quantum-computing +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= DWave: Gate model library +WWW= https://github.com/dwavesystems/dwave-gate + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} + +USES= python +USE_PYTHON= pep517 cython3 autoplist pytest + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} + +.include <bsd.port.mk> diff --git a/science/py-dwave-gate/distinfo b/science/py-dwave-gate/distinfo new file mode 100644 index 000000000000..aeb63b7147d2 --- /dev/null +++ b/science/py-dwave-gate/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1758999333 +SHA256 (dwave_gate-0.3.4.tar.gz) = 17e193da453724c427448e3d7beeb8260c804404ac0ab43ed2d0abcbb0d55b5e +SIZE (dwave_gate-0.3.4.tar.gz) = 367210 diff --git a/science/py-dwave-gate/files/example.py b/science/py-dwave-gate/files/example.py new file mode 100644 index 000000000000..1148e23e9b0a --- /dev/null +++ b/science/py-dwave-gate/files/example.py @@ -0,0 +1,3 @@ +from tabu import TabuSampler +response = TabuSampler().sample_ising({'a': -0.5, 'b': 1.0}, {('a', 'b'): -1}) +print(response) diff --git a/science/py-dwave-gate/files/patch-pyproject.toml b/science/py-dwave-gate/files/patch-pyproject.toml new file mode 100644 index 000000000000..02f8f28f6143 --- /dev/null +++ b/science/py-dwave-gate/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-09-27 18:57:44 UTC ++++ pyproject.toml +@@ -3,7 +3,7 @@ requires = [ + "setuptools>=46.4.0", # PEP-420 support, PEP-517/518 support + "wheel>=0.30.0", # limited python api support + "cython~=3.0", +- "numpy~=2.0", ++ "numpy", + ] + build-backend = "setuptools.build_meta" + diff --git a/science/py-dwave-gate/pkg-descr b/science/py-dwave-gate/pkg-descr new file mode 100644 index 000000000000..929fb4be2268 --- /dev/null +++ b/science/py-dwave-gate/pkg-descr @@ -0,0 +1,2 @@ +dwave-gate is a software package for constructing, modifying and running quantum +circuits on the provided state-vector simulator. diff --git a/science/py-dwave-hybrid/Makefile b/science/py-dwave-hybrid/Makefile index e56c2779f488..e4f3e04da77e 100644 --- a/science/py-dwave-hybrid/Makefile +++ b/science/py-dwave-hybrid/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-hybrid -DISTVERSION= 0.6.11 -PORTREVISION= 2 +DISTVERSION= 0.6.14 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,17 +11,15 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>5:devel/py-click@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dimod>=0.10.13:science/py-dimod@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.2:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.10.6:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.1.0:science/py-dwave-greedy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.8:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-neal>=0.5.4:science/py-dwave-neal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>0:science/py-dwave-preprocessing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.13.0:science/py-dwave-system@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-tabu>=0.2.0:science/py-dwave-tabu@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.4:science/py-dwave-preprocessing@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.16.0:science/py-dwave-system@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.7:math/py-minorminer@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.1.7:math/py-minorminer@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-dwave-hybrid/distinfo b/science/py-dwave-hybrid/distinfo index 28edf5d6a7c0..3ca4e02ba017 100644 --- a/science/py-dwave-hybrid/distinfo +++ b/science/py-dwave-hybrid/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709582741 -SHA256 (dwavesystems-dwave-hybrid-0.6.11_GH0.tar.gz) = 3f0bff143bd43039c81108b5a78bcd91e306ce98313107915e391b8b4266ac97 -SIZE (dwavesystems-dwave-hybrid-0.6.11_GH0.tar.gz) = 21334393 +TIMESTAMP = 1758900792 +SHA256 (dwavesystems-dwave-hybrid-0.6.14_GH0.tar.gz) = 48592f46150bc863de6fd50a2a80589f1184e54dc0f4a310f613340108b13f0d +SIZE (dwavesystems-dwave-hybrid-0.6.14_GH0.tar.gz) = 21327352 diff --git a/science/py-dwave-inspector/Makefile b/science/py-dwave-inspector/Makefile index 4fdbfa6b5b88..b583ab95b573 100644 --- a/science/py-dwave-inspector/Makefile +++ b/science/py-dwave-inspector/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-inspector -DISTVERSION= 0.5.1 -PORTREVISION= 2 +DISTVERSION= 0.5.5 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.10.0:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.11.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.13.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.3.0:science/py-dwave-system@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}flask>=2.2:www/py-flask@${PY_FLAVOR} \ ${PYNUMPY} \ diff --git a/science/py-dwave-inspector/distinfo b/science/py-dwave-inspector/distinfo index 46a2556a8d09..fe7ec0bf2296 100644 --- a/science/py-dwave-inspector/distinfo +++ b/science/py-dwave-inspector/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725082475 -SHA256 (dwavesystems-dwave-inspector-0.5.1_GH0.tar.gz) = cfc67472572e4dffd3ab40bae9b000a0efbf4f147a477ee7f2df39c4c11f7b9f -SIZE (dwavesystems-dwave-inspector-0.5.1_GH0.tar.gz) = 1551148 +TIMESTAMP = 1758901017 +SHA256 (dwavesystems-dwave-inspector-0.5.5_GH0.tar.gz) = 9426ba5515079b7d704c1ae951f602ef67119add3ab2f811a1e1901a40f3ea6b +SIZE (dwavesystems-dwave-inspector-0.5.5_GH0.tar.gz) = 1474496 diff --git a/science/py-dwave-networkx/Makefile b/science/py-dwave-networkx/Makefile index d86d538ab3e1..ea480887bd30 100644 --- a/science/py-dwave-networkx/Makefile +++ b/science/py-dwave-networkx/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-networkx -DISTVERSION= 0.8.15 -PORTREVISION= 2 +DISTVERSION= 0.8.18 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} @@ -13,7 +12,8 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.0:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ + ${PYNUMPY} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} \ diff --git a/science/py-dwave-networkx/distinfo b/science/py-dwave-networkx/distinfo index 9bf974558485..9ac31a859a25 100644 --- a/science/py-dwave-networkx/distinfo +++ b/science/py-dwave-networkx/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1718437530 -SHA256 (dwavesystems-dwave-networkx-0.8.15_GH0.tar.gz) = 101eb8179c27fc3c95f7759922c295004063b06de673a17a3f7dae15c83be806 -SIZE (dwavesystems-dwave-networkx-0.8.15_GH0.tar.gz) = 1414577 +TIMESTAMP = 1759003300 +SHA256 (dwavesystems-dwave-networkx-0.8.18_GH0.tar.gz) = c136b4c30dbb1f4d7baa435627fa1043dfa0faca44ff4a2c7a04f5e9ed69ad99 +SIZE (dwavesystems-dwave-networkx-0.8.18_GH0.tar.gz) = 1416959 diff --git a/science/py-dwave-ocean-sdk/Makefile b/science/py-dwave-ocean-sdk/Makefile index bf09ca76c0db..c7dd59b5b1bb 100644 --- a/science/py-dwave-ocean-sdk/Makefile +++ b/science/py-dwave-ocean-sdk/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-ocean-sdk -DISTVERSION= 6.9.0 -PORTREVISION= 2 +DISTVERSION= 9.0.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,26 +10,26 @@ WWW= https://docs.ocean.dwavesys.com/en/stable/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.14:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.11.3:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.3.0:science/py-dwave-greedy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-hybrid>=0.6.11:science/py-dwave-hybrid@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-inspector>=0.4.4:science/py-dwave-inspector@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-neal>=0.6.0:science/py-dwave-neal@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.14:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.6.5:science/py-dwave-preprocessing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.2.0:science/py-dwave-samplers@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.23.0:science/py-dwave-system@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-tabu>=0.5.0:science/py-dwave-tabu@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwavebinarycsp>=0.3.0:science/py-dwavebinarycsp@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.13:math/py-minorminer@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}penaltymodel>=1.1.0:science/py-penaltymodel@${PY_FLAVOR} +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.21:science/py-dimod@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.14.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-gate>=0.3.4:science/py-dwave-gate@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-hybrid>=0.6.14:science/py-dwave-hybrid@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-inspector>=0.5.5:science/py-dwave-inspector@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.18:science/py-dwave-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.6.4:science/py-dwave-optimization@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.6.10:science/py-dwave-preprocessing@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.6.0:science/py-dwave-samplers@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.33.0:science/py-dwave-system@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.19:math/py-minorminer@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}penaltymodel>=1.3.0:science/py-penaltymodel@${PY_FLAVOR} #${PYTHON_PKGNAMEPREFIX}pyqubo>=1.4.0:science/py-pyqubo@${PY_FLAVOR} # exclude pyqubo until it supports py312 -BUILD_DEPENDS= ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= python -USE_PYTHON= distutils autoplist unittest +USE_PYTHON= pep517 autoplist unittest USE_GITHUB= yes GH_ACCOUNT= dwavesystems diff --git a/science/py-dwave-ocean-sdk/distinfo b/science/py-dwave-ocean-sdk/distinfo index cbd8a9aa1a24..c9e61347cfb0 100644 --- a/science/py-dwave-ocean-sdk/distinfo +++ b/science/py-dwave-ocean-sdk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709591130 -SHA256 (dwavesystems-dwave-ocean-sdk-6.9.0_GH0.tar.gz) = 369170b1f92248f97621098f19647649bec14f1b407fa8861d0ef0407d6f6fdc -SIZE (dwavesystems-dwave-ocean-sdk-6.9.0_GH0.tar.gz) = 12689356 +TIMESTAMP = 1758900842 +SHA256 (dwavesystems-dwave-ocean-sdk-9.0.0_GH0.tar.gz) = 84af7387adf9f9fa63f506daa00b381450542d6bb0967d5186d66e45bdda303c +SIZE (dwavesystems-dwave-ocean-sdk-9.0.0_GH0.tar.gz) = 43904011 diff --git a/science/py-dwave-optimization/Makefile b/science/py-dwave-optimization/Makefile index 9afc4936d88d..116210d8c460 100644 --- a/science/py-dwave-optimization/Makefile +++ b/science/py-dwave-optimization/Makefile @@ -1,8 +1,9 @@ PORTNAME= dwave-optimization -DISTVERSION= 0.1.0 +DISTVERSION= 0.6.6 CATEGORIES= science python # quantum-computing MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Nonlinear models for industrial optimization problems @@ -12,31 +13,19 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}setuptools-dso>=2.10:devel/py-setuptools-dso@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}reno>=4.1.0:textproc/py-reno@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}meson-python>=0.18.0:devel/meson-python@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} USES= python -USE_PYTHON= autoplist cython3 pep517 - -POST_PLIST= fix-plist +USE_PYTHON= pep517 cython3 autoplist pytest post-install: # strip binaries @${STRIP_CMD} \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/_model${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/_utilities${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/libdwave-optimization.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/model${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/states${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/optimization/symbols${PYTHON_TAG}.so - # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 - @${RM} -r \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__pycache__ - -fix-plist: - @${REINPLACE_CMD} -e " \ - s|.*dwave/__init__\.py||; \ - s|.*dwave/__pycache__/.*|| \ - " ${TMPPLIST} .include <bsd.port.mk> diff --git a/science/py-dwave-optimization/distinfo b/science/py-dwave-optimization/distinfo index f0f7d3875377..02983f9df619 100644 --- a/science/py-dwave-optimization/distinfo +++ b/science/py-dwave-optimization/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721017559 -SHA256 (dwave-optimization-0.1.0.tar.gz) = 585b69026d26e9f99b9c8552a68dae794960cd94582ccdf973d2eb30a6303b9e -SIZE (dwave-optimization-0.1.0.tar.gz) = 725660 +TIMESTAMP = 1759005736 +SHA256 (dwave_optimization-0.6.6.tar.gz) = f50fd9cff71b259487212f88c793348e26ebe785e6c2a50ec2b62486c2060ee4 +SIZE (dwave_optimization-0.6.6.tar.gz) = 341092 diff --git a/science/py-dwave-optimization/files/patch-pyproject.toml b/science/py-dwave-optimization/files/patch-pyproject.toml index 266f645a6998..3ee77e1a76e5 100644 --- a/science/py-dwave-optimization/files/patch-pyproject.toml +++ b/science/py-dwave-optimization/files/patch-pyproject.toml @@ -1,13 +1,11 @@ ---- pyproject.toml.orig 2024-07-15 16:16:29 UTC +--- pyproject.toml.orig 2025-09-27 21:16:33 UTC +++ pyproject.toml -@@ -1,8 +1,8 @@ requires = [ +@@ -1,7 +1,7 @@ requires = [ [build-system] requires = [ -- "cython==3.0.8", -+ "cython>=3.0.8", - 'numpy==1.19.0;python_version<"3.9"', # C API for numpy.random -- 'oldest-supported-numpy;python_version>="3.9"', -+ 'numpy;python_version>="3.9"', - "setuptools>=46.4.0", - "setuptools_dso>=2.10,<3.0;platform_system != 'Windows'", # On Windows we don't distribute a dynamic library - "wheel>=0.30.0", + "cython~=3.1.0", +- "meson-python~=0.18.0", ++ "meson-python", + ] + build-backend = 'mesonpy' + diff --git a/science/py-dwave-preprocessing/Makefile b/science/py-dwave-preprocessing/Makefile index a7fc27a649bb..c9a03c027f18 100644 --- a/science/py-dwave-preprocessing/Makefile +++ b/science/py-dwave-preprocessing/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-preprocessing -DISTVERSION= 0.6.6 -PORTREVISION= 1 +DISTVERSION= 0.6.10 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.6:science/py-dimod@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.6:science/py-dimod@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.20:science/py-dimod@${PY_FLAVOR} \ ${PYNUMPY} USES= localbase:ldflags python diff --git a/science/py-dwave-preprocessing/distinfo b/science/py-dwave-preprocessing/distinfo index da8873cbb9b2..281af1f3ac64 100644 --- a/science/py-dwave-preprocessing/distinfo +++ b/science/py-dwave-preprocessing/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721009063 -SHA256 (dwavesystems-dwave-preprocessing-0.6.6_GH0.tar.gz) = 3ffbf8694997f2527380e6080f7f6fa7501a85927ca98ace87672e9b0d251438 -SIZE (dwavesystems-dwave-preprocessing-0.6.6_GH0.tar.gz) = 126646 +TIMESTAMP = 1758901068 +SHA256 (dwavesystems-dwave-preprocessing-0.6.10_GH0.tar.gz) = 95c1f7a0508c11fe17d37461cf27d267592dbc4a5233194fe5ac645539ab81f0 +SIZE (dwavesystems-dwave-preprocessing-0.6.10_GH0.tar.gz) = 128447 diff --git a/science/py-dwave-samplers/Makefile b/science/py-dwave-samplers/Makefile index b51248d1ef3a..26518e9c6501 100644 --- a/science/py-dwave-samplers/Makefile +++ b/science/py-dwave-samplers/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-samplers -DISTVERSION= 1.3.0 -PORTREVISION= 2 +DISTVERSION= 1.6.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,7 +11,7 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.6.3:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}reno>0:textproc/py-reno@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} @@ -20,7 +19,7 @@ RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} USES= python -USE_PYTHON= cython3 distutils unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-samplers/issues/66 +USE_PYTHON= cython3 distutils autoplist unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-samplers/issues/66 USE_GITHUB= yes GH_ACCOUNT= dwavesystems @@ -46,4 +45,6 @@ post-install: post-test: @${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${FILESDIR}/example.py +# tests as of 1.6.0: Ran 522 tests in 102.085s + .include <bsd.port.mk> diff --git a/science/py-dwave-samplers/distinfo b/science/py-dwave-samplers/distinfo index 17abea740f3f..cc7fd1115361 100644 --- a/science/py-dwave-samplers/distinfo +++ b/science/py-dwave-samplers/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721009758 -SHA256 (dwavesystems-dwave-samplers-1.3.0_GH0.tar.gz) = ed4b3a4e3da76c35dfb3d70e4bb45fe3c0b5eb277115d41894381cf8c9cd5999 -SIZE (dwavesystems-dwave-samplers-1.3.0_GH0.tar.gz) = 147340 +TIMESTAMP = 1758900891 +SHA256 (dwavesystems-dwave-samplers-1.6.0_GH0.tar.gz) = 4d16e1262e8a93adbf27d8a2bcab48f5f53927396c751cec0ecc1b38a7a3c269 +SIZE (dwavesystems-dwave-samplers-1.6.0_GH0.tar.gz) = 193371 diff --git a/science/py-dwave-samplers/pkg-plist b/science/py-dwave-samplers/pkg-plist deleted file mode 100644 index d9aa3ff38972..000000000000 --- a/science/py-dwave-samplers/pkg-plist +++ /dev/null @@ -1,105 +0,0 @@ -%%PYTHON_SITELIBDIR%%/dwave/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/composite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/composite.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/decl.pxd -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/descent.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/greedy/src/descent.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/planar%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/util%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/__pycache__/util%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/planar.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/planar/util.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/random/cyrandom.cpp 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-%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/utils%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/__pycache__/utils%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/sampler.py -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/bqp.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/bqp.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/common.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_search.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_search.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_utils.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tabu/src/tabu_utils.h 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-%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/solve.pyx -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/base.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/buckettree.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/combine.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/exception.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/graph.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/marginalizer.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/merger.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/count.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/dummy.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/logsumprod.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/operations/min.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/orang.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/sample.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/solve.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/table.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/task.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/treedecomp.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/utils.hpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/src/include/varorder.h -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.cpp -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities%%PYTHON_TAG%%.so -%%PYTHON_SITELIBDIR%%/dwave/samplers/tree/utilities.pyx diff --git a/science/py-dwave-system/Makefile b/science/py-dwave-system/Makefile index c9ce8f85f894..0039e8028bfb 100644 --- a/science/py-dwave-system/Makefile +++ b/science/py-dwave-system/Makefile @@ -1,6 +1,5 @@ PORTNAME= dwave-system -DISTVERSION= 1.25.0 -PORTREVISION= 2 +DISTVERSION= 1.33.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,23 +10,21 @@ WWW= https://github.com/dwavesystems/dwave-system LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE -PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.20:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.12.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-greedy>=0.2.5:science/py-dwave-greedy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.10:science/py-dwave-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.1.0:science/py-dwave-optimization@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.6.6:science/py-dwave-optimization@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.0:science/py-dwave-preprocessing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.0:devel/py-homebase@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.8:math/py-minorminer@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=2.8.8:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.19:math/py-minorminer@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python -USE_PYTHON= distutils unittest # 1 test fails because the closed source dwave.drivers optional dependency is missing +USE_PYTHON= distutils unittest autoplist # 1 test fails because the closed source dwave.drivers optional dependency is missing USE_GITHUB= yes GH_ACCOUNT= dwavesystems diff --git a/science/py-dwave-system/distinfo b/science/py-dwave-system/distinfo index 10c14a5f509b..9024afa5cadc 100644 --- a/science/py-dwave-system/distinfo +++ b/science/py-dwave-system/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1721015341 -SHA256 (dwavesystems-dwave-system-1.25.0_GH0.tar.gz) = ab33c625f588f7197ce82bcee634305717afe537ba4a8662e41ffc659dc8e775 -SIZE (dwavesystems-dwave-system-1.25.0_GH0.tar.gz) = 685604 +TIMESTAMP = 1759022035 +SHA256 (dwavesystems-dwave-system-1.33.0_GH0.tar.gz) = e34f9df6d48140ac2a3f8e73457991b783ae47f34d8fb41478ac5b6540734920 +SIZE (dwavesystems-dwave-system-1.33.0_GH0.tar.gz) = 707773 diff --git a/science/py-dwave-system/pkg-plist b/science/py-dwave-system/pkg-plist deleted file mode 100644 index b55d9993ee26..000000000000 --- a/science/py-dwave-system/pkg-plist +++ /dev/null @@ -1,108 +0,0 @@ -%%PYTHON_SITELIBDIR%%/dwave/embedding/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_breaks%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_breaks%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_strength%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chain_strength%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chimera%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/chimera%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/diagnostic%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/diagnostic%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/drawing%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/drawing%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/exceptions%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/exceptions%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/pegasus%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/pegasus%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/polynomialembedder%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/polynomialembedder%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/transforms%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/transforms%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/utils%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/utils%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/zephyr%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/__pycache__/zephyr%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/embedding/chain_breaks.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/chain_strength.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/chimera.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/diagnostic.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/drawing.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/exceptions.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/pegasus.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/polynomialembedder.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/transforms.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/utils.py -%%PYTHON_SITELIBDIR%%/dwave/embedding/zephyr.py -%%PYTHON_SITELIBDIR%%/dwave/system/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/coupling_groups%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/exceptions%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/flux_bias_offsets%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/package_info%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/package_info%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/schedules%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/schedules%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/temperatures%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/temperatures%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/testing%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/testing%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/utilities%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/utilities%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/warnings%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/__pycache__/warnings%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/cache_manager%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/database_manager%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/__pycache__/schema%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/cache/cache_manager.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/database_manager.py -%%PYTHON_SITELIBDIR%%/dwave/system/cache/schema.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/cutoffcomposite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/embedding%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/reversecomposite%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/tiling%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/__pycache__/virtual_graph%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/composites/cutoffcomposite.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/embedding.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/reversecomposite.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/tiling.py -%%PYTHON_SITELIBDIR%%/dwave/system/composites/virtual_graph.py -%%PYTHON_SITELIBDIR%%/dwave/system/coupling_groups.py -%%PYTHON_SITELIBDIR%%/dwave/system/exceptions.py -%%PYTHON_SITELIBDIR%%/dwave/system/flux_bias_offsets.py -%%PYTHON_SITELIBDIR%%/dwave/system/package_info.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__init__.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/__init__%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/clique%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/dwave_sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/__pycache__/leap_hybrid_sampler%%PYTHON_TAG%%.pyc -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/clique.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/dwave_sampler.py -%%PYTHON_SITELIBDIR%%/dwave/system/samplers/leap_hybrid_sampler.py -%%PYTHON_SITELIBDIR%%/dwave/system/schedules.py -%%PYTHON_SITELIBDIR%%/dwave/system/temperatures.py -%%PYTHON_SITELIBDIR%%/dwave/system/testing.py -%%PYTHON_SITELIBDIR%%/dwave/system/utilities.py -%%PYTHON_SITELIBDIR%%/dwave/system/warnings.py diff --git a/science/py-icet/Makefile b/science/py-icet/Makefile index b5a2b9177d5c..2a01864fa3b9 100644 --- a/science/py-icet/Makefile +++ b/science/py-icet/Makefile @@ -1,6 +1,5 @@ PORTNAME= icet -DISTVERSION= 3.0 -PORTREVISION= 1 +DISTVERSION= 3.1 CATEGORIES= science # chemistry, physics #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -29,7 +28,7 @@ USE_PYTHON= pep517 autoplist pytest USE_GITLAB= yes GL_ACCOUNT= materials-modeling -GL_TAGNAME= 769b5db248baa5146bdb294e963e061cf2dfd228 +GL_TAGNAME= 3.1 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} diff --git a/science/py-icet/distinfo b/science/py-icet/distinfo index bcff29135073..27b719b500bf 100644 --- a/science/py-icet/distinfo +++ b/science/py-icet/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737766451 -SHA256 (materials-modeling-icet-769b5db248baa5146bdb294e963e061cf2dfd228_GL0.tar.gz) = bec8c2a34bc8343e7e075460964c997228a1a8fe1a12ba449503c7e80b2b653a -SIZE (materials-modeling-icet-769b5db248baa5146bdb294e963e061cf2dfd228_GL0.tar.gz) = 3928095 +TIMESTAMP = 1758905344 +SHA256 (icet-3.1.tar.bz2) = b942fa3001fd53095cca9e19f4fdcea7c3716a69cf0bb2f4e735c8b997f1de5b +SIZE (icet-3.1.tar.bz2) = 3740838 diff --git a/science/py-icet/files/patch-pyproject.toml b/science/py-icet/files/patch-pyproject.toml new file mode 100644 index 000000000000..f1953b314896 --- /dev/null +++ b/science/py-icet/files/patch-pyproject.toml @@ -0,0 +1,10 @@ +--- pyproject.toml.orig 2025-09-28 03:59:57 UTC ++++ pyproject.toml +@@ -1,6 +1,6 @@ requires = [ + [build-system] + requires = [ +- "setuptools>=77.0", ++ "setuptools", + "wheel", + "pybind11>=2.10", + ] diff --git a/science/py-mp-api/Makefile b/science/py-mp-api/Makefile index 681bea4d9bc1..cda39e1cd11d 100644 --- a/science/py-mp-api/Makefile +++ b/science/py-mp-api/Makefile @@ -1,6 +1,6 @@ PORTNAME= mp-api DISTVERSION= 0.34.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -21,7 +21,7 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}boto3>0:www/py-boto3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}monty>=2022.3.12:devel/py-monty@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mpcontribs-client>=5.0.10:science/py-mpcontribs-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pydantic>=1.8.2:devel/py-pydantic@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pydantic2>=1.8.2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pymatgen-analysis-alloys>=0.0.3:science/py-pymatgen-analysis-alloys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pymatgen>=2022.3.7:science/py-pymatgen@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.27.1:www/py-requests@${PY_FLAVOR} \ diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile index 49e98776b6f4..a61d0fd9a229 100644 --- a/science/py-obspy/Makefile +++ b/science/py-obspy/Makefile @@ -1,6 +1,6 @@ PORTNAME= obspy PORTVERSION= 1.4.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +15,7 @@ BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.12.4:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=2.2:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=2.2:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}decorator>=0:devel/py-decorator@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=0:databases/py-sqlalchemy10@${PY_FLAVOR} diff --git a/science/py-penaltymodel/Makefile b/science/py-penaltymodel/Makefile index 08b126f5fb7d..a99d122fbb4e 100644 --- a/science/py-penaltymodel/Makefile +++ b/science/py-penaltymodel/Makefile @@ -1,6 +1,5 @@ PORTNAME= penaltymodel -DISTVERSION= 1.1.0 -PORTREVISION= 2 +DISTVERSION= 1.3.0 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,7 +14,6 @@ PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.1:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}reno>=3.3.0:textproc/py-reno@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} diff --git a/science/py-penaltymodel/distinfo b/science/py-penaltymodel/distinfo index f636f3095631..884d08c6d13f 100644 --- a/science/py-penaltymodel/distinfo +++ b/science/py-penaltymodel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1705599914 -SHA256 (dwavesystems-penaltymodel-1.1.0_GH0.tar.gz) = cdcfeac4b9682fed6118f28459d33acb6c302850e9c2952a413fe17378d8f640 -SIZE (dwavesystems-penaltymodel-1.1.0_GH0.tar.gz) = 38244 +TIMESTAMP = 1759022813 +SHA256 (dwavesystems-penaltymodel-1.3.0_GH0.tar.gz) = bb8874b2ca46c2250e3093abd2e531516b6304556f850ec280be43ec7b18d653 +SIZE (dwavesystems-penaltymodel-1.3.0_GH0.tar.gz) = 36574 diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile index 0e08e20fb106..0438efb397ae 100644 --- a/science/py-pycsw/Makefile +++ b/science/py-pycsw/Makefile @@ -1,6 +1,6 @@ PORTNAME= pycsw PORTVERSION= 2.6.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,7 +16,7 @@ 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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=0:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}shapely>=0:devel/py-shapely@${PY_FLAVOR} \ diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile index df12a82e2163..e5edb487276c 100644 --- a/science/py-pygeometa/Makefile +++ b/science/py-pygeometa/Makefile @@ -1,6 +1,6 @@ PORTNAME= pygeometa PORTVERSION= 0.15.3 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLA 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} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR} diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile index 0de34c07af0e..546b78099722 100644 --- a/science/py-pyteomics/Makefile +++ b/science/py-pyteomics/Makefile @@ -1,6 +1,6 @@ PORTNAME= pyteomics PORTVERSION= 4.7.5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -31,9 +31,9 @@ XML_DESC= XML support DF_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=0.17,1:math/py-pandas@${PY_FLAVOR} GRAPHICS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} TDA_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} -UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ +UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR} -XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \ +XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} .include <bsd.port.mk> diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index 98898e931d59..25eb454a3612 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,6 +1,5 @@ PORTNAME= qiskit -DISTVERSION= 2.1.1 -PORTREVISION= 1 +DISTVERSION= 2.1.2 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-qiskit/distinfo b/science/py-qiskit/distinfo index f1f98a1c4ce5..40086a88e8e1 100644 --- a/science/py-qiskit/distinfo +++ b/science/py-qiskit/distinfo @@ -1,4 +1,4 @@ -TIMESTAMP = 1753430083 +TIMESTAMP = 1757578345 SHA256 (rust/crates/ahash-0.7.0.crate) = efa60d2eadd8b12a996add391db32bd1153eac697ba4869660c0016353611426 SIZE (rust/crates/ahash-0.7.0.crate) = 55813 SHA256 (rust/crates/ahash-0.8.12.crate) = 5a15f179cd60c4584b8a8c596927aadc462e27f2ca70c04e0071964a73ba7a75 @@ -485,5 +485,5 @@ SHA256 (rust/crates/zerocopy-0.8.25.crate) = a1702d9583232ddb9174e01bb7c15a2ab8f SIZE (rust/crates/zerocopy-0.8.25.crate) = 252714 SHA256 (rust/crates/zerocopy-derive-0.8.25.crate) = 28a6e20d751156648aa063f3800b706ee209a32c0b4d9f24be3d980b01be55ef SIZE (rust/crates/zerocopy-derive-0.8.25.crate) = 87671 -SHA256 (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 96cd5725ea5f99a6527885e9ef4436bcb34e6388c6ab1bf43d48b9dab80f429f -SIZE (Qiskit-qiskit-2.1.1_GH0.tar.gz) = 7095152 +SHA256 (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 23559ca58042d263152b233843af24f6753d591500de5a84df14a68a54f4a7db +SIZE (Qiskit-qiskit-2.1.2_GH0.tar.gz) = 7100760 diff --git a/science/py-sarpy/Makefile b/science/py-sarpy/Makefile index f5421f78c28e..84ec18c8ecee 100644 --- a/science/py-sarpy/Makefile +++ b/science/py-sarpy/Makefile @@ -1,5 +1,6 @@ PORTNAME= sarpy PORTVERSION= 1.3.61 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,7 +15,7 @@ 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= ${PYTHON_PKGNAMEPREFIX}h5py>=0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>=4.1.1:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>=4.1.1:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.19.0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pillow>=0:graphics/py-pillow@${PY_FLAVOR} \ diff --git a/science/qwalk/pkg-descr b/science/qwalk/pkg-descr index f0e473e2929f..d3ad2e3f8fb3 100644 --- a/science/qwalk/pkg-descr +++ b/science/qwalk/pkg-descr @@ -1,4 +1,12 @@ -QWalk is a program developed to perform high accuracy quantum Monte Carlo -calculations of electronic structure in molecules and solids. It is specifically -designed as a research vehicle for new algorithms and method developments, as -well as being able to scale up to large system sizes. +QWalk is a high-accuracy quantum Monte Carlo (QMC) program designed for +electronic structure calculations in molecules and solids. It serves as a +research vehicle for developing new algorithms and methods, capable of +scaling up to large system sizes and finding very accurate solutions to +the stationary Schrodinger equation for atoms, molecules, solids, and +various model systems. + +Its primary application lies in computational condensed-matter physics +and chemistry, particularly for studying correlated electron systems and +determining both ground-state and excited-state properties of quantum +systems. QWalk provides a robust platform for advanced research in +quantum chemistry and materials science. diff --git a/science/salome-configuration/Makefile b/science/salome-configuration/Makefile index e9e82543ac64..de2ea9312b27 100644 --- a/science/salome-configuration/Makefile +++ b/science/salome-configuration/Makefile @@ -1,40 +1,28 @@ PORTNAME= salome-configuration DISTVERSIONPREFIX= V -DISTVERSION= 9_11_0 +DISTVERSION= 9_15_0 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Configuration -WWW= https://www.salome-platform.org/ +WWW= https://www.salome-platform.org/ \ + https://github.com/SalomePlatform/configuration/ -BROKEN= Unfetchable -DEPRECATED= Fails to fetch -EXPIRATION_DATE=2025-06-30 +LICENSE= LGPL21+ +LICENSE_FILE= ${WRKSRC}/COPYING -FETCH_DEPENDS= git:devel/git - -GIT_URL= https://git.salome-platform.org/gitpub/tools/configuration.git # all Salome repositories: https://git.salome-platform.org/gitweb/ +USE_GITHUB= yes +GH_ACCOUNT= SalomePlatform +GH_PROJECT= configuration DATADIR= ${PREFIX}/share/salome - -NO_BUILD= yes NO_ARCH= yes - -do-fetch: - @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ - ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ - cd ${DISTDIR}/${DIST_SUBDIR} && \ - git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=ustar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ - ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ - fi +NO_BUILD= yes do-install: ${MKDIR} ${STAGEDIR}${DATADIR}/configuration - cd ${WRKSRC} && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/configuration + cd ${WRKSRC} && \ + ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/configuration ${RM} ${STAGEDIR}${DATADIR}/configuration/.gitignore .include <bsd.port.mk> diff --git a/science/salome-configuration/distinfo b/science/salome-configuration/distinfo index 18910f5ff474..d3b5c510e961 100644 --- a/science/salome-configuration/distinfo +++ b/science/salome-configuration/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688414005 -SHA256 (salome-configuration-V9_11_0.tar.gz) = 5f19f22ea595e7f7e5cffc97386dc89ad8c0ed597e86c94f03924386a56815e4 -SIZE (salome-configuration-V9_11_0.tar.gz) = 90716 +TIMESTAMP = 1758452949 +SHA256 (SalomePlatform-configuration-V9_15_0_GH0.tar.gz) = 01dd367a167383fbc03ca8de47e127c87f4a9d4c826c68768ac3a2bfd5f998f7 +SIZE (SalomePlatform-configuration-V9_15_0_GH0.tar.gz) = 101578 diff --git a/science/salome-configuration/pkg-plist b/science/salome-configuration/pkg-plist index 3408d0ae8100..8a94f255db5d 100644 --- a/science/salome-configuration/pkg-plist +++ b/science/salome-configuration/pkg-plist @@ -1,3 +1,4 @@ +%%DATADIR%%/configuration/COPYING %%DATADIR%%/configuration/autotools/m4/ac_check_sizeof_fortran.m4 %%DATADIR%%/configuration/autotools/m4/ac_cxx_depend_flag.m4 %%DATADIR%%/configuration/autotools/m4/ac_cxx_have_sstream.m4 @@ -70,11 +71,14 @@ %%DATADIR%%/configuration/cmake/FindSIP.cmake %%DATADIR%%/configuration/cmake/FindSMESH.cmake %%DATADIR%%/configuration/cmake/FindSalomeBLSURFPLUGIN.cmake +%%DATADIR%%/configuration/cmake/FindSalomeBasicIterativeStatistics.cmake %%DATADIR%%/configuration/cmake/FindSalomeBoost.cmake +%%DATADIR%%/configuration/cmake/FindSalomeBootstrap.cmake %%DATADIR%%/configuration/cmake/FindSalomeCALCULATOR.cmake %%DATADIR%%/configuration/cmake/FindSalomeCAS.cmake %%DATADIR%%/configuration/cmake/FindSalomeCGNS.cmake %%DATADIR%%/configuration/cmake/FindSalomeCOMPONENT.cmake +%%DATADIR%%/configuration/cmake/FindSalomeCommonGeomLib.cmake %%DATADIR%%/configuration/cmake/FindSalomeCppUnit.cmake %%DATADIR%%/configuration/cmake/FindSalomeDoxygen.cmake %%DATADIR%%/configuration/cmake/FindSalomeFIELDS.cmake @@ -97,6 +101,7 @@ %%DATADIR%%/configuration/cmake/FindSalomeLibXml2.cmake %%DATADIR%%/configuration/cmake/FindSalomeMEDCoupling.cmake %%DATADIR%%/configuration/cmake/FindSalomeMEDFile.cmake +%%DATADIR%%/configuration/cmake/FindSalomeMEDFileWindows.cmake %%DATADIR%%/configuration/cmake/FindSalomeMESHGEMS.cmake %%DATADIR%%/configuration/cmake/FindSalomeMPI.cmake %%DATADIR%%/configuration/cmake/FindSalomeMetis.cmake @@ -157,3 +162,4 @@ %%DATADIR%%/configuration/copyright/modules.info %%DATADIR%%/configuration/tests/ListOfSalomeTestLabelsToBeOK %%DATADIR%%/configuration/tests/README.txt +%%DATADIR%%/configuration/tests/sod_test_config.json diff --git a/science/salome-kernel/Makefile b/science/salome-kernel/Makefile index 490e715aab60..11413201242a 100644 --- a/science/salome-kernel/Makefile +++ b/science/salome-kernel/Makefile @@ -1,64 +1,49 @@ PORTNAME= salome-kernel DISTVERSIONPREFIX= V DISTVERSION= 9_11_0 -PORTREVISION= 4 -CATEGORIES= science +PORTREVISION= 5 +CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Kernel -WWW= https://www.salome-platform.org/ +WWW= https://www.salome-platform.org/ \ + https://github.com/SalomePlatform/kernel/ -LICENSE= LGPL21 +LICENSE= LGPL21+ LICENSE_FILE= ${WRKSRC}/COPYING -DEPRECATED= Depends on expired science/salome-configuration -EXPIRATION_DATE=2025-09-30 - -FETCH_DEPENDS= git:devel/git PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}omniorb>0:devel/py-omniorb \ ${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} -BUILD_DEPENDS= salome-configuration>0:science/salome-configuration \ - swig:devel/swig \ - ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_DEPENDS} \ + salome-configuration>0:science/salome-configuration \ + swig:devel/swig LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libomniORB4.so:devel/omniORB -RUN_DEPENDS= bash:shells/bash \ - ${PY_DEPENDS} +RUN_DEPENDS= ${PY_DEPENDS} \ + bash:shells/bash USES= cmake compiler:c++11-lang gnome python shebangfix +USE_GITHUB= yes +GH_ACCOUNT= SalomePlatform +GH_PROJECT= kernel USE_GNOME= libxml2 USE_LDCONFIG= yes +SHEBANG_FILES= bin/appliskel/.bashrc bin/appliskel/.salome_run \ + bin/appliskel/salome bin/appliskel/salome_mesa SHEBANG_GLOB= *.py *.sh -SHEBANG_FILES= bin/appliskel/salome \ - bin/appliskel/salome_mesa \ - bin/appliskel/.salome_run \ - bin/appliskel/.bashrc - -GIT_URL= https://git.salome-platform.org/gitpub/modules/kernel # all Salome repositories: https://git.salome-platform.org/gitweb/ CMAKE_ARGS= -DCONFIGURATION_ROOT_DIR=${LOCALBASE}/share/salome/configuration \ -DOMNIORBPY_ROOT_DIR=${LOCALBASE} \ -DPython_EXECUTABLE=${PYTHON_CMD} -CMAKE_OFF= SALOME_BUILD_TESTS SALOME_BUILD_DOC +CMAKE_OFF= SALOME_BUILD_DOC SALOME_BUILD_TESTS + CFLAGS+= -DSIZEOF_INT=4 -DSIZEOF_LONG=4 LDFLAGS+= -lexecinfo DATADIR= ${PREFIX}/share/salome -do-fetch: - @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ - ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ - cd ${DISTDIR}/${DIST_SUBDIR} && \ - git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ - (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ - ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=ustar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ - ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ - fi - .include <bsd.port.mk> diff --git a/science/salome-kernel/distinfo b/science/salome-kernel/distinfo index 91a1299e3225..f80643ecdf7c 100644 --- a/science/salome-kernel/distinfo +++ b/science/salome-kernel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688418727 -SHA256 (salome-kernel-V9_11_0.tar.gz) = ab1ba2be6f48adc97497266f2b6db3b6878aceb8ce8732e496130bc4924ccb3d -SIZE (salome-kernel-V9_11_0.tar.gz) = 3435113 +TIMESTAMP = 1758456327 +SHA256 (SalomePlatform-kernel-V9_11_0_GH0.tar.gz) = cdbc752b1dc093f3a9d9509e68fe70437bb195baf37f9653f0e33a21ce75b935 +SIZE (SalomePlatform-kernel-V9_11_0_GH0.tar.gz) = 3437694 diff --git a/science/step/distinfo b/science/step/distinfo index b2a6ad4575c2..5db7278905a9 100644 --- a/science/step/distinfo +++ b/science/step/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1754646550 -SHA256 (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 994bab4d0750cfdeb3af1f92d6453ee173cd483e392ad170bf5250b23b4ddf3a -SIZE (KDE/release-service/25.08.0/step-25.08.0.tar.xz) = 1004072 +TIMESTAMP = 1757410252 +SHA256 (KDE/release-service/25.08.1/step-25.08.1.tar.xz) = d5ae8c25718f6a647556210f2d4055de1ccd342d3b948f14f9e2ee27ab48b154 +SIZE (KDE/release-service/25.08.1/step-25.08.1.tar.xz) = 1007604 diff --git a/science/tinker/Makefile b/science/tinker/Makefile index 2406c4c31a27..9249e98239ef 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,6 +1,5 @@ PORTNAME= tinker -DISTVERSION= 25.3 -PORTREVISION= 1 +DISTVERSION= 25.5 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ diff --git a/science/tinker/distinfo b/science/tinker/distinfo index 6ebb852d7522..327e627a7d9e 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1755934058 -SHA256 (tinker-25.3.tar.gz) = 84744d00e2936be23be6ed6acbbc251f07e016db53ead079a270280539a42145 -SIZE (tinker-25.3.tar.gz) = 80772560 +TIMESTAMP = 1758258766 +SHA256 (tinker-25.5.tar.gz) = 01b50ad3680c0bfb77c77e4f9c653c47a39da1510286cb8a5dbc14f8f7b86d18 +SIZE (tinker-25.5.tar.gz) = 81152948 diff --git a/science/tinker/pkg-descr b/science/tinker/pkg-descr index bd18a27c4744..1cd6d0590002 100644 --- a/science/tinker/pkg-descr +++ b/science/tinker/pkg-descr @@ -1,14 +1,15 @@ -Tinker is a set of small programs for doing general purpose molecular -modeling calculations. Tools are included for energy minimizations, -geometry calculations, simulated annealing, molecular dynamics, and -molecular analysis calculations. Tools for converting coordinate sets -are also provided. Tinker employs several force fields and minimization -techniques. +Tinker is a comprehensive and versatile molecular modeling software package +designed for molecular mechanics and dynamics simulations, with specialized +capabilities for biopolymers. It provides a complete set of tools for +energy minimizations, geometry calculations, simulated annealing, and +molecular dynamics. -This port sets the maxatm value to 2500 atoms. This should be -sufficient for most molecular systems. Should you need to work with -larger systems you can set the maxatm parameter in the sizes.i file -located in the tinker/source directory and recompile. Note that if it -is set too large that tinker programs will abort and core dump. - -For more information about Tinker see: +Tinker supports a wide array of force fields, including Amber, CHARMM, +OPLS, MMFF94, and advanced polarizable models like AMOEBA. It features +atomic multipole-based electrostatics with explicit dipole polarizability +and various continuum solvation treatments. The software offers efficient +truncated Newton optimization, normal mode vibrational analysis, and +free energy calculations. It also includes algorithms for conformational +searches, global optimization, and transition state location. Written in +Fortran 95, Tinker is a modular and extensible system, widely used in +computational chemistry and biophysics. diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index b0f9367ade44..723615e476ff 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -96,7 +96,9 @@ bin/xyzpdb %%DATADIR%%/params/mmff94.prm %%DATADIR%%/params/mmff94s.prm %%DATADIR%%/params/oplsaa08.prm +%%DATADIR%%/params/oplsaa24.prm %%DATADIR%%/params/oplsaal.prm +%%DATADIR%%/params/oplsaam.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm diff --git a/science/vmd/pkg-descr b/science/vmd/pkg-descr index 82404ecc97d5..a62978d88d97 100644 --- a/science/vmd/pkg-descr +++ b/science/vmd/pkg-descr @@ -1,2 +1,13 @@ -VMD is a molecular visualization program for displaying, animating, and -analyzing large biomolecular systems using 3-D graphics and built-in scripting. +VMD (Visual Molecular Dynamics) is a molecular visualization program for +displaying, animating, and analyzing large biomolecular systems. It +utilizes 3D graphics and built-in scripting (Tcl and Python) for +interactive exploration. + +Key features include: +- Visualization of molecular dynamics simulations. +- Support for over 60 molecular file formats and data types. +- Various rendering styles (licorice, ribbons, van der Waals spheres). +- High-quality rendering, animation, and stereo display. +- Integrated analysis tools and custom scripting for advanced analysis. +- GPU acceleration and no inherent limits on molecular size. +- Cross-platform availability (Windows, macOS, and Linux). diff --git a/science/votca/Makefile b/science/votca/Makefile index 03ee6bcbd1a4..07f97264f4bb 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,7 +1,7 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2025 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -16,7 +16,7 @@ BROKEN_i386= undefined reference to `__atomic_load' # ' PY_DEPENDS= \ ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ diff --git a/science/wannier90/pkg-descr b/science/wannier90/pkg-descr index b1bce64c43cd..9aa0b87cae34 100644 --- a/science/wannier90/pkg-descr +++ b/science/wannier90/pkg-descr @@ -1,2 +1,15 @@ -The computer program that calculates maximally-localized Wannier functions -(MLWFs) and Wannier90 for quantum chemistry and physics fields. +Wannier90 is an open-source software package for generating maximally- +localized Wannier functions (MLWFs) and utilizing them to calculate +advanced electronic properties of materials with high efficiency and +accuracy. It is widely used in computational materials science and +interfaced with numerous popular electronic structure codes such as +Quantum ESPRESSO, ABINIT, VASP, and Siesta. + +The program exploits the real-space localization of MLWFs for efficient +Wannier interpolation of spectral and Fermi-surface properties. Its +applications include calculating electronic band structures, densities +of states, Fermi surfaces, and various transport properties. Wannier90 +also supports advanced functionalities like symmetry-adapted MLWFs, +calculation of shift currents, and Berry-curvature dipole, making it a +versatile tool for analyzing chemical bonding, dielectric properties, +and topological features in materials. |