From 0c100b7dd2b30e75b799d806df4ef899fd98e1ea Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 16 Apr 2022 13:07:24 +0100 Subject: gentoo resync : 16.04.2022 --- sci-chemistry/Manifest.gz | Bin 10380 -> 10381 bytes sci-chemistry/modeller/Manifest | 2 +- sci-chemistry/modeller/modeller-9.25.ebuild | 6 +- sci-chemistry/openbabel/Manifest | 1 + .../openbabel/files/openbabel-python.cmake | 104 +++++++++++++++++++++ sci-chemistry/pymol/Manifest | 2 +- sci-chemistry/pymol/pymol-2.5.0.ebuild | 20 +--- 7 files changed, 113 insertions(+), 22 deletions(-) create mode 100644 sci-chemistry/openbabel/files/openbabel-python.cmake (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index ddccaf21679d..b4bd1f64e1d1 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index 81bceea7f910..633dc8b4ed43 100644 --- a/sci-chemistry/modeller/Manifest +++ b/sci-chemistry/modeller/Manifest @@ -1,3 +1,3 @@ DIST modeller-9.25.tar.gz 44820658 BLAKE2B b3e8a3cc8cc70689a25bc5ed2eee294d67bef8eea9ed4b64d41aba3a27c0bc428ae58e74d734da0eaab7e4fabb213d098b9ba66b9569557159ac7d4a58244b0a SHA512 93f273aba0ec0f884cde5bbcc24769a09386bfc6bf1744d80001e41924b1a682225ba3c554fb9898ef3bfd1fd8451f9458bb92431b20f2f51b01781e79686c91 -EBUILD modeller-9.25.ebuild 3847 BLAKE2B 410b9f2e700d683f4e08fc973096fab394707b718a36c1266a157ac5778b9210b725db00aabc541ac0f361fb5e3d6b728c218ad9b2bd277247d8c787b8ff5de3 SHA512 6b5d1b11aa56a2fc552ea41c41c9aea023bb3a782af21a498e042c96599d47dc84058137f03e25e16177d5ce1be59af3fce9b09043b15cb9433685ab86119785 +EBUILD modeller-9.25.ebuild 3838 BLAKE2B 6e63af63ae1a127f6477d2c53de249b43131fab56f1610864a17a6455f48f989ed1f7ec357142fb7f46e951fdfdd886d409e059be798b4045ebff39e70aee216 SHA512 0d0797812ab7af724ada4747b4cf9cff0f99291b65bfc023f1d8a9b303de04b8f90aea2889e43da215a6e9c9831057860489db8fbad8dfba0629599f49d00ba2 MISC metadata.xml 375 BLAKE2B 949d039d3cd24da52efe20f58e7da07b4371e90ef72f314d076110b4604af1c0b7a77c1241172cf5e0a1c40363a00728d14d6faf30af73d27317f24d5a6c2289 SHA512 52791b3cb6a3998676f23e16346b9c4f447f42de8a58e612eebdf8ebfd34bc724c4994c3accebf00d552187bc80d1c097f73bd02b6fd6874a84441627eb785ca diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild index 3e44bd99585c..f791a3104661 100644 --- a/sci-chemistry/modeller/modeller-9.25.ebuild +++ b/sci-chemistry/modeller/modeller-9.25.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{7..10} ) DISTUTILS_USE_SETUPTOOLS=no -inherit distutils-r1 multilib +inherit distutils-r1 DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" HOMEPAGE="https://salilab.org/modeller/" diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index c26e4e5832f4..85e159ec9039 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -1,3 +1,4 @@ +AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b6a7415fc197713d3df8f1703475bf2f2c53b546b7915466ce30b6b3c72c505ea72443dd23a17a7f9131f4f6e SHA512 a7bcdf90588930b05d11312429e735d3cc6a94053e67117bef6c1614932651abee7c4e082916482a9012622c0f29c3ba62dd7788b72aca6c88293660c7f2a3db DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 diff --git a/sci-chemistry/openbabel/files/openbabel-python.cmake b/sci-chemistry/openbabel/files/openbabel-python.cmake new file mode 100644 index 000000000000..425b4656a9d2 --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-python.cmake @@ -0,0 +1,104 @@ +# The following is a cmake fragment taken from scripts/CMakeLists.txt and +# edited for Gentoo python multibuild compatibility. + +if (PYTHON_BINDINGS) + # Tags should be edited to reflect the active python implementation + set(EPYTHON @@EPYTHON@@) + set(PYTHON_INCUDE_DIR @@PYTHON_INCUDE_DIR@@) + set(PYTHON_LIBS @@PYTHON_LIBS@@) + set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@) + + include_directories(${PYTHON_INCUDE_DIR}) + + add_custom_command( + OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py + COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i + MAIN_DEPENDENCY openbabel-python.i + VERBATIM + ) + + configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in + ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py) + + add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp) + target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY}) + + set_target_properties(bindings_python_${EPYTHON} + PROPERTIES + OUTPUT_NAME _openbabel + LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel + PREFIX "" + SUFFIX .so ) + + add_dependencies(bindings_python_${EPYTHON} openbabel) + + install(TARGETS bindings_python_${EPYTHON} + LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel + COMPONENT bindings_python) + install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py + DESTINATION ${PYTHON_SITEDIR}/openbabel + COMPONENT bindings_python) + install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py + DESTINATION ${PYTHON_SITEDIR}/openbabel + COMPONENT bindings_python) + install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py + DESTINATION ${PYTHON_SITEDIR}/openbabel + COMPONENT bindings_python) + + if (ENABLE_TESTS) + # Make sure all module files are together in the same directory for testing + add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD + COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/ + COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/) + set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test) + # define TESTDATADIR for tests that need input files + add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/") + # define FORMATDIR for location of format plugin binaries + set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/") + add_definitions(-DFORMATDIR="${FORMATDIR}/") + include_directories(${TEST_SOURCE_DIR}) + + # The macro is modified from cmake/modules/UsePythonTest.cmake + MACRO(ADD_PYTHON_TEST TESTNAME FILENAME) + GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION) + STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}") + FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake +" + MESSAGE(\"${PYTHONPATH}\") + EXECUTE_PROCESS( + COMMAND ${EPYTHON} ${loc} ${wo_semicolumn} + RESULT_VARIABLE import_res + OUTPUT_VARIABLE import_output + ERROR_VARIABLE import_output + ) + + # Pass the output back to ctest + IF(import_output) + MESSAGE(\${import_output}) + ENDIF(import_output) + IF(import_res) + MESSAGE(SEND_ERROR \${import_res}) + ENDIF(import_res) +" + ) + ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake) + ENDMACRO(ADD_PYTHON_TEST) + + set(pybindtests + bindings + _pybel + example + obconv_writers + cdjsonformat + pcjsonformat + roundtrip + ) + foreach(pybindtest ${pybindtests}) + ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py) + set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES + ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data" + FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" + ) + endforeach(pybindtest ${pybindtests}) + endif (ENABLE_TESTS) +endif(PYTHON_BINDINGS) diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 7fa22a257f67..5ad4d5152a40 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,4 +1,4 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91 -EBUILD pymol-2.5.0.ebuild 3092 BLAKE2B 911add60f71e41659a1bf0754fa1e263ed3b8bb1222b83401ed192db2c4679629b41ec4476e552e23d0c7f85063adcc4380be16cd920a50ce1ba5ef7ee4da1c1 SHA512 2326993a095b2dda7de7b0049d192a57c5a4e28cd323629344e8723090c621fe10b1e767c50c50a3941d2241bb06a7c393210c0093bf0d5810e20419737ca30e +EBUILD pymol-2.5.0.ebuild 2551 BLAKE2B 478607dae22f4715cfc3cae170a7154dd83c6fd84c69ac1b456c85de6e767b95b99b5f333c1a41c8b43ad85189ba8cc94f8e6137d0360d87edecdc7b41c72356 SHA512 8908ac67fdc6a94cc61dcc90a3f96b450b0f2509aa59107a9f1931c89a8f448be3056e5715bc0230243f84aaae769fea15257ac6e8f759675bc41335b9f72eec MISC metadata.xml 440 BLAKE2B ee3a427d21cd25ce455b61c40767eec9ded9718fa835f545b0849e24451d2004a149bd25df36e59c94d53f3fc27b3d747ac051f82db6aec593645e54a335d884 SHA512 848b215441a66d3ebcda4c06733dc6ce879b738e5210f9e20d309d2aed11f1dd6f2d267e0a4ecb702b43dc5cc9925cb026aff2a16ded4b35dce7c38607438417 diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild b/sci-chemistry/pymol/pymol-2.5.0.ebuild index a7fc5fdc127c..93464f4a28be 100644 --- a/sci-chemistry/pymol/pymol-2.5.0.ebuild +++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{7..10} ) DISTUTILS_USE_SETUPTOOLS=no -inherit desktop optfeature flag-o-matic xdg distutils-r1 +inherit desktop flag-o-matic xdg distutils-r1 DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="https://www.pymol.org/" @@ -65,15 +65,6 @@ python_prepare_all() { python_install() { distutils-r1_python_install \ --pymol-path="${EPREFIX}/usr/share/pymol" - -# File is not created as apbs was dropped from the tree -# https://bugs.gentoo.org/790629 -# sed \ -# -e '1d' \ -# -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ -# -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ -# -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ -# -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die } python_install_all() { @@ -106,8 +97,3 @@ python_install_all() { rm -f "${ED}"/usr/share/${PN}/LICENSE || die } - -#pkg_postinst() { -# xdg_pkg_postinst -# optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -#} -- cgit v1.2.3