diff options
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/Manifest.gz | bin | 10855 -> 11019 bytes | |||
-rw-r--r-- | sci-chemistry/gnome-chemistry-utils/Manifest | 2 | ||||
-rw-r--r-- | sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r1.ebuild (renamed from sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6.ebuild) | 12 | ||||
-rw-r--r-- | sci-chemistry/openbabel/Manifest | 7 | ||||
-rw-r--r-- | sci-chemistry/openbabel/files/openbabel-python.cmake | 104 | ||||
-rw-r--r-- | sci-chemistry/openbabel/metadata.xml | 4 | ||||
-rw-r--r-- | sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild | 272 | ||||
-rw-r--r-- | sci-chemistry/openbabel/openbabel-9999.ebuild | 272 | ||||
-rw-r--r-- | sci-chemistry/votca/Manifest | 4 | ||||
-rw-r--r-- | sci-chemistry/votca/metadata.xml | 18 | ||||
-rw-r--r-- | sci-chemistry/votca/votca-2022_rc2.ebuild | 70 | ||||
-rw-r--r-- | sci-chemistry/votca/votca-9999.ebuild | 70 |
12 files changed, 828 insertions, 7 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 7940614ab228..44e11544063e 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/gnome-chemistry-utils/Manifest b/sci-chemistry/gnome-chemistry-utils/Manifest index b3fba415d489..56f55d5e4651 100644 --- a/sci-chemistry/gnome-chemistry-utils/Manifest +++ b/sci-chemistry/gnome-chemistry-utils/Manifest @@ -1,4 +1,4 @@ DIST gnome-chemistry-utils-0.14.17.tar.xz 5911248 BLAKE2B 5d3bb4afbe3d3f620912e810717f08674d56a11c384b1fb239788cfbbb625797e8c52de2b6d940ae7f3d83847533afedd6ed961b1fa0ea1cec62dda88de1a6df SHA512 01bb964e1484e028c5965f1de74798422b448823047fcadf668dc76e98b3e214939a2f031d0182c717c4376f490e5969a4604ee66d1763e6b480032d7ae97468 DIST gnome-chemistry-utils_0.14.17-6.debian.tar.xz 68528 BLAKE2B 2e4d318a5b91ca7963829c40c5d732a0ffa7fd9f4a32a6727f4926d2d4ec57989f50bd6839da49b4fa71dc533830bd0926205e952f08d04c08320e76ab51914c SHA512 8c6fad95c5d5e0895666fb9fb880364a9e3ab89761893b812c2cf835265acb40abe6b40def0960e1b38a0eea441310a3c1af608a2bcea37d5558533c9151e309 -EBUILD gnome-chemistry-utils-0.14.17_p6.ebuild 1669 BLAKE2B 319dedd70e4c2bb4bceea014e8f300e44bf6bde9b112acb375d8d438b3584da646247b405e854bc5134a14cf328d621f77d91bf0c20c8245b41ec18df37d39b0 SHA512 86b78111a15981c72ad9627c3d61d4d2defe3771bd73d728c15d8fb36d5509a79b424b7c49ab53eafdcc27a0fcc80b48f79d067400b65969ea67ac3d4070efa5 +EBUILD gnome-chemistry-utils-0.14.17_p6-r1.ebuild 1687 BLAKE2B 60d754b891f66ed4f75c92db29aef405fb892ba774ef1444a7866dd72a09e92f35c61ff324356ff8e893874f104f0ecdd58ba7d72788f0ad86ea6dcf939bf0fa SHA512 4723b5584d922725434094e688062ff0757cb672bf1df1071177dc405d27f95c79485d126ead6ea76828f2cbd8c474fec59a08337ec75fd55b412d544ff6ec22 MISC metadata.xml 337 BLAKE2B f6895ff4b84e03d81d69b69efe05fc3bf246153e09afa56323c853c7b9b8e775d25173d24c82e2f2e66f5db42430c433e82940d91d47a99b51679af13b0d17ae SHA512 8a22e6a36ad43faeb635a12d977eed127f30f977915bfed2379b2187d33e05f2bbbc937977e168b47af5adb3fe26f964439d5d16e7a44dcd7f12faf7b84e60b1 diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r1.ebuild index c7f9cff11050..28d4cf3e6b85 100644 --- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6.ebuild +++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r1.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit autotools flag-o-matic xdg DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry" @@ -22,7 +22,7 @@ RDEPEND=" >=gnome-extra/libgsf-1.14.9 >=sci-chemistry/bodr-5 >=sci-chemistry/chemical-mime-data-0.1.94 - >=sci-chemistry/openbabel-2.3.0:0 + >=sci-chemistry/openbabel-2.3.0:0= >=x11-libs/cairo-1.6.0 >=x11-libs/gdk-pixbuf-2.22.0 >=x11-libs/goffice-0.10.12 @@ -41,10 +41,12 @@ BDEPEND=" S="${WORKDIR}/${P/_p*}" src_prepare() { - xdg_src_prepare + default + + if has_version '<sci-chemistry/openbabel-3'; then + sed -i -e '/openbabel-v3/d' "${WORKDIR}"/debian/patches/series || die + fi - # We don't have openbabel3 yet - sed -i -e '/openbabel-v3/d' "${WORKDIR}"/debian/patches/series || die # Debian patches for p in $(<"${WORKDIR}"/debian/patches/series) ; do eapply -p1 "${WORKDIR}/debian/patches/${p}" diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index 267e0dff1be3..9b3acc76b6cf 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -1,5 +1,10 @@ AUX openbabel-2.4.1-gcc10.patch 2317 BLAKE2B a76a4ef8b7502f8a80ebb807d2874d77f2ef5f532fa7b71a398245b737d1d55387121f4c24fc7dda7df47ddac4ad16e9cd12076787bedf0f63872708e9516d99 SHA512 ea37e5c53360728455be3d819c29fc27aa10556451a437e05c71c6a5e2bd5e1cfb4c229ff0e67e6c8ae7554f08b7bb16ad4be9ace36991c9c9f2417574b373f2 +AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b6a7415fc197713d3df8f1703475bf2f2c53b546b7915466ce30b6b3c72c505ea72443dd23a17a7f9131f4f6e SHA512 a7bcdf90588930b05d11312429e735d3cc6a94053e67117bef6c1614932651abee7c4e082916482a9012622c0f29c3ba62dd7788b72aca6c88293660c7f2a3db DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 +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 EBUILD openbabel-2.4.1-r2.ebuild 2178 BLAKE2B fd0d324a28dac54a6b67359b9250ab4331195eeb32c10de46d9d5d4e5c4bce44298eb0953eb06006823b7c6bdc5ab0b7f22b0b3334800e2f06d080a3e24fe311 SHA512 494acf7a358eb01a8bc77713da9135195013833c8bc993adad25221715238e53309719c0e42bdcd8ee076d35b26228946cfad5e08aab3259119db741c27ae5bd -MISC metadata.xml 666 BLAKE2B 717970113d4ce316eb1d4504a9b3f2e8137edad184e6f6f8d169d9c45ae781048ecb13c6e3bfcd334480cfb67ccc8055e1f34a22f706a3a3ccd19dda3538d143 SHA512 ae12c4813154b6571eddad77e7da986f2c341b32bc3ebcf13e63cf058ffac5cabc458ce8dd3d1bf761453ef7936260a07aaec7f50fe46c2b710b92e8833d7b96 +EBUILD openbabel-3.1.1_p20210225.ebuild 7237 BLAKE2B f0825a4ce1a6f2c504d8ea7b308cd5aa65e53be15055f92383e563cb38a5fb504d9bd2bcfd4c4b00e67673b2ca1e6ba85804f9fbd5d33a62ffa0f40369046282 SHA512 dec2f95380a9250941b743bffffca3fd83507137cd21daa87211327cc42ce8e7b77474c6d17b0b67a148832b81b44e1f245277226461c362e6a9809cbc6d5c3c +EBUILD openbabel-9999.ebuild 7197 BLAKE2B 77bfe052690916bda80ba7d38993f38fb1bff632f27d7d7d352bff6eddabe38cda89fe0f5574a37744091c80e59f1b575fea5a00da9c5a60f594a6c94ea4f9f2 SHA512 79781c3bff2a795c85dc4ca99640ee52c59130ddfd49c8452473fd2cb544991759f3c76f3cb9afa5a9671ee91508706707e9e02d8a95668f544274f315e4be03 +MISC metadata.xml 862 BLAKE2B 56a35c050142f5a8939441d6a669986ad58321154f1a46fb78dcf6b861311bbb28d6f49507fff673519396533fbbfb8bf0214aa9dbdf1041ae7497c3287a3eb3 SHA512 7d289c49a91b4ae9a3910c6feb1014fa307ccc01b1e041e1aece7c8f135ac2eb1f5aae562dfd25d17e38d88c5747786a7406d6c09d10f74e80c08691599dec80 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 ${pybindtests}) + endif (ENABLE_TESTS) +endif(PYTHON_BINDINGS) diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml index 88ffa5eb106b..f31c73d435ac 100644 --- a/sci-chemistry/openbabel/metadata.xml +++ b/sci-chemistry/openbabel/metadata.xml @@ -14,4 +14,8 @@ <upstream> <remote-id type="sourceforge">openbabel</remote-id> </upstream> + <use> + <flag name="inchi">Build support for IUPAC International Chemical Identifier format</flag> + <flag name="json">Build support for JSON formats (ChemDoodle, PubChem, etc...)</flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild new file mode 100644 index 000000000000..67ac61c1741b --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild @@ -0,0 +1,272 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +WX_GTK_VER=3.0-gtk3 + +inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="https://openbabel.org/" + +if [[ "${PV}" == *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/openbabel/${PN}.git" +else + if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325 + # Set to commit hash + OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b + SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz" + S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}" + else + MY_P="${PN}-$(ver_rs 1- -)" + SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz" + S="${WORKDIR}/${PN}-${MY_P}" + fi + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +fi + +SRC_URI="${SRC_URI} + https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png + http://openbabel.org/OBTitle.jpg -> ${PN}.jpg" + +# See src/CMakeLists.txt for LIBRARY_VERSION +SLOT="0/7.0.0" +LICENSE="GPL-2" +IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets" + +RESTRICT="!test? ( test )" + +# Inaccurate dependency logic upstream +REQUIRED_USE=" + python? ( ${PYTHON_REQUIRED_USE} ) + test? ( inchi json !minimal wxwidgets ) +" + +BDEPEND=" + dev-lang/perl + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + ) + perl? ( >=dev-lang/swig-2 ) + python? ( >=dev-lang/swig-2 ) + test? ( dev-lang/python ) +" + +COMMON_DEPEND=" + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sys-libs/zlib:= + inchi? ( sci-libs/inchi ) + json? ( >=dev-libs/rapidjson-1.1.0 ) + png? ( x11-libs/cairo ) + python? ( ${PYTHON_DEPS} ) + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] ) +" + +DEPEND=" + ${COMMON_DEPEND} + perl? ( dev-lang/perl ) +" + +RDEPEND=" + ${COMMON_DEPEND} + perl? ( + dev-lang/perl:= + !sci-chemistry/openbabel-perl + ) +" + +pkg_setup() { + use openmp && tc-check-openmp +} + +prepare_python_bindings() { + mkdir -p scripts/${EPYTHON} || die + # Appends to scripts/CMakeLists.txt, substituting the correct tags, for + # each valid python implementation, + cat "${FILESDIR}"/${PN}-python.cmake | \ + sed -e "s|@@EPYTHON@@|${EPYTHON}|" \ + -e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \ + -e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \ + -e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \ + scripts/CMakeLists.txt || die +} + +src_prepare() { + cmake_src_prepare + + if use perl; then + perl_set_version + + sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \ + -e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \ + -i scripts/CMakeLists.txt || die + fi + + if use python; then + # Skip the python bindings sections as we'll append our own + sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \ + -i {scripts,test}/CMakeLists.txt || die + if use test; then + # Problems with testbindings built with -O2 + local test_skip="@unittest.skip('Similar to Issue #2138')" + sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \ + -i test/testbindings.py || die + test_skip="@unittest.skip('Similar to Issue #2246')" + sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \ + -i test/testobconv_writers.py || die + fi + python_foreach_impl prepare_python_bindings + fi + + # Remove dependency automagic + if ! use png; then + sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die + fi + if ! use wxwidgets; then + sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die + fi + if ! use inchi; then + sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \ + -i cmake/modules/FindInchi.cmake || die + fi + + # Don't install example bins to /usr/bin + if use examples; then + sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \ + -i doc/examples/CMakeLists.txt || die + fi + + # boost is only used if building with gcc-3.x, which isn't supported in + # Gentoo. Still, it shouldn't look for, and include, its headers + sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die +} + +src_configure() { + if use json; then + # -DOPTIMIZE_NATIVE=ON also forces -march=native so use + # cpu_flags to set defines instead + use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2 + use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42 + use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON + fi + + use wxwidgets && setup-wxwidgets + + use_bindings() { + (use perl || use python) && (echo 'yes' || die) || (echo 'no' || die) + } + + local mycmakeargs=( + -DBUILD_DOCS=$(usex doc) + -DBUILD_EXAMPLES=$(usex examples) + -DBUILD_GUI=$(usex wxwidgets) + -DENABLE_OPENMP=$(usex openmp) + -DENABLE_TESTS=$(usex test) + -DMINIMAL_BUILD=$(usex minimal) + # Set this, otherwise it defaults to true and forces WITH_INCHI=true + -DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi) + -DOPTIMIZE_NATIVE=OFF + -DPERL_BINDINGS=$(usex perl) + -DPYTHON_BINDINGS=$(usex python) + -DRUN_SWIG=$(use_bindings) + -DWITH_COORDGEN=false + -DWITH_INCHI=$(usex inchi) + -DWITH_JSON=$(usex json) + -DWITH_MAEPARSER=false + ) + + if use test; then + # Help cmake find the python interpreter when dev-lang/python-exec is built + # without native-symlinks support. + python_setup + mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" ) + fi + + cmake_src_configure +} + +src_test() { + # Wierd deadlock causes system_load to keep rising + cmake_src_test -j1 +} + +openbabel-optimize() { + python_optimize "${D}/$(python_get_sitedir)"/openbabel || die +} + +src_install() { + cmake_src_install + + docinto html + for x in doc/*.html; do + [[ ${x} != doc/api*.html ]] && dodoc ${x} + done + # Rendered in some html pages + newdoc "${DISTDIR}"/${PN}.png babel130.png + newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg + + if use doc; then + cmake_src_install docs + docinto html/API + dodoc -r doc/API/html/. + fi + + if use examples; then + # no compression since we want ready-to-run scripts + docompress -x /usr/share/doc/${PF}/examples + + # ${PV} doesn't correspond to the internal BABEL_VERSION for + # live or patch release builds so we grep it + local babel_ver=$( + grep '^#define BABEL_VERSION' < \ + "${BUILD_DIR}"/include/openbabel/babelconfig.h | \ + cut -d \" -f 2 || die + ) + docinto examples/povray + dodoc doc/dioxin.* doc/README*.pov* + # Needed by the povray example + dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \ + /usr/share/doc/${PF}/examples/povray/babel31.inc + + fi + + if use perl; then + docinto / + newdoc scripts/perl/Changes Changes.perl + newdoc scripts/perl/README README.perl + if use examples; then + docinto examples/perl + dodoc -r scripts/perl/examples/. + fi + fi + + if use python; then + python_foreach_impl openbabel-optimize + docinto / + newdoc scripts/python/README.rst README.python.rst + docinto html + dodoc scripts/python/*.html + if use examples; then + docinto examples/python + dodoc -r scripts/python/examples/. + fi + fi + + if use wxwidgets; then + make_desktop_entry obgui "Open Babel" ${PN} + doicon "${DISTDIR}"/${PN}.png + fi +} + +pkg_postinst() { + use wxwidgets && xdg_desktop_database_update +} + +pkg_postrm() { + use wxwidgets && xdg_desktop_database_update +} diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild new file mode 100644 index 000000000000..baf793cb651c --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-9999.ebuild @@ -0,0 +1,272 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +WX_GTK_VER=3.0-gtk3 + +inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="https://openbabel.org/" + +if [[ "${PV}" == *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/openbabel/${PN}.git" +else + if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325 + # Set to commit hash + OPENBABEL_COMMIT= + SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz" + S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}" + else + MY_P="${PN}-$(ver_rs 1- -)" + SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz" + S="${WORKDIR}/${PN}-${MY_P}" + fi + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +fi + +SRC_URI="${SRC_URI} + https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png + http://openbabel.org/OBTitle.jpg -> ${PN}.jpg" + +# See src/CMakeLists.txt for LIBRARY_VERSION +SLOT="0/7.0.0" +LICENSE="GPL-2" +IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets" + +RESTRICT="!test? ( test )" + +# Inaccurate dependency logic upstream +REQUIRED_USE=" + python? ( ${PYTHON_REQUIRED_USE} ) + test? ( inchi json !minimal wxwidgets ) +" + +BDEPEND=" + dev-lang/perl + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + ) + perl? ( >=dev-lang/swig-2 ) + python? ( >=dev-lang/swig-2 ) + test? ( dev-lang/python ) +" + +COMMON_DEPEND=" + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sys-libs/zlib:= + inchi? ( sci-libs/inchi ) + json? ( >=dev-libs/rapidjson-1.1.0 ) + png? ( x11-libs/cairo ) + python? ( ${PYTHON_DEPS} ) + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] ) +" + +DEPEND=" + ${COMMON_DEPEND} + perl? ( dev-lang/perl ) +" + +RDEPEND=" + ${COMMON_DEPEND} + perl? ( + dev-lang/perl:= + !sci-chemistry/openbabel-perl + ) +" + +pkg_setup() { + use openmp && tc-check-openmp +} + +prepare_python_bindings() { + mkdir -p scripts/${EPYTHON} || die + # Appends to scripts/CMakeLists.txt, substituting the correct tags, for + # each valid python implementation, + cat "${FILESDIR}"/${PN}-python.cmake | \ + sed -e "s|@@EPYTHON@@|${EPYTHON}|" \ + -e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \ + -e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \ + -e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \ + scripts/CMakeLists.txt || die +} + +src_prepare() { + cmake_src_prepare + + if use perl; then + perl_set_version + + sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \ + -e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \ + -i scripts/CMakeLists.txt || die + fi + + if use python; then + # Skip the python bindings sections as we'll append our own + sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \ + -i {scripts,test}/CMakeLists.txt || die + if use test; then + # Problems with testbindings built with -O2 + local test_skip="@unittest.skip('Similar to Issue #2138')" + sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \ + -i test/testbindings.py || die + test_skip="@unittest.skip('Similar to Issue #2246')" + sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \ + -i test/testobconv_writers.py || die + fi + python_foreach_impl prepare_python_bindings + fi + + # Remove dependency automagic + if ! use png; then + sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die + fi + if ! use wxwidgets; then + sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die + fi + if ! use inchi; then + sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \ + -i cmake/modules/FindInchi.cmake || die + fi + + # Don't install example bins to /usr/bin + if use examples; then + sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \ + -i doc/examples/CMakeLists.txt || die + fi + + # boost is only used if building with gcc-3.x, which isn't supported in + # Gentoo. Still, it shouldn't look for, and include, its headers + sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die +} + +src_configure() { + if use json; then + # -DOPTIMIZE_NATIVE=ON also forces -march=native so use + # cpu_flags to set defines instead + use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2 + use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42 + use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON + fi + + use wxwidgets && setup-wxwidgets + + use_bindings() { + (use perl || use python) && (echo 'yes' || die) || (echo 'no' || die) + } + + local mycmakeargs=( + -DBUILD_DOCS=$(usex doc) + -DBUILD_EXAMPLES=$(usex examples) + -DBUILD_GUI=$(usex wxwidgets) + -DENABLE_OPENMP=$(usex openmp) + -DENABLE_TESTS=$(usex test) + -DMINIMAL_BUILD=$(usex minimal) + # Set this, otherwise it defaults to true and forces WITH_INCHI=true + -DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi) + -DOPTIMIZE_NATIVE=OFF + -DPERL_BINDINGS=$(usex perl) + -DPYTHON_BINDINGS=$(usex python) + -DRUN_SWIG=$(use_bindings) + -DWITH_COORDGEN=false + -DWITH_INCHI=$(usex inchi) + -DWITH_JSON=$(usex json) + -DWITH_MAEPARSER=false + ) + + if use test; then + # Help cmake find the python interpreter when dev-lang/python-exec is built + # without native-symlinks support. + python_setup + mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" ) + fi + + cmake_src_configure +} + +src_test() { + # Wierd deadlock causes system_load to keep rising + cmake_src_test -j1 +} + +openbabel-optimize() { + python_optimize "${D}/$(python_get_sitedir)"/openbabel || die +} + +src_install() { + cmake_src_install + + docinto html + for x in doc/*.html; do + [[ ${x} != doc/api*.html ]] && dodoc ${x} + done + # Rendered in some html pages + newdoc "${DISTDIR}"/${PN}.png babel130.png + newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg + + if use doc; then + cmake_src_install docs + docinto html/API + dodoc -r doc/API/html/. + fi + + if use examples; then + # no compression since we want ready-to-run scripts + docompress -x /usr/share/doc/${PF}/examples + + # ${PV} doesn't correspond to the internal BABEL_VERSION for + # live or patch release builds so we grep it + local babel_ver=$( + grep '^#define BABEL_VERSION' < \ + "${BUILD_DIR}"/include/openbabel/babelconfig.h | \ + cut -d \" -f 2 || die + ) + docinto examples/povray + dodoc doc/dioxin.* doc/README*.pov* + # Needed by the povray example + dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \ + /usr/share/doc/${PF}/examples/povray/babel31.inc + + fi + + if use perl; then + docinto / + newdoc scripts/perl/Changes Changes.perl + newdoc scripts/perl/README README.perl + if use examples; then + docinto examples/perl + dodoc -r scripts/perl/examples/. + fi + fi + + if use python; then + python_foreach_impl openbabel-optimize + docinto / + newdoc scripts/python/README.rst README.python.rst + docinto html + dodoc scripts/python/*.html + if use examples; then + docinto examples/python + dodoc -r scripts/python/examples/. + fi + fi + + if use wxwidgets; then + make_desktop_entry obgui "Open Babel" ${PN} + doicon "${DISTDIR}"/${PN}.png + fi +} + +pkg_postinst() { + use wxwidgets && xdg_desktop_database_update +} + +pkg_postrm() { + use wxwidgets && xdg_desktop_database_update +} diff --git a/sci-chemistry/votca/Manifest b/sci-chemistry/votca/Manifest new file mode 100644 index 000000000000..b755470d6d3f --- /dev/null +++ b/sci-chemistry/votca/Manifest @@ -0,0 +1,4 @@ +DIST votca-2022_rc2.tar.gz 61692061 BLAKE2B 9fdf016267ff6657bfbbd51c79c2c38cb7064635d26e80b905eeeb8326ca1780f7a9c711802491f3ec7a216dbd53b86fe08da2c969a6a10db110168a02ac0d0f SHA512 3bfd108df7499c21ad290955672ab042b9a11b7a868f0eb49fdbd94365e35ed7ffc8b8b44c9b7dd74b7504b8fd30cc6bacfed443068f2bb3702e272aad26c961 +EBUILD votca-2022_rc2.ebuild 1599 BLAKE2B 709252689e526e83d5b9f0933e44d7b83b6d2e02fd3cbae0938630e87c99a83ac2179ccc06d2d2843f7fca039305f6aff4793357ea44ef2f8db9ff2edee87f90 SHA512 9b41346126363598de2174c9e06a4c7550e82dc4ec22f2fcc0a6b8948731831ae871a2b30988dfcd5d3c5ebdd1e6a377946374bc2d3a2b25c6c3a7732b04ac71 +EBUILD votca-9999.ebuild 1599 BLAKE2B 709252689e526e83d5b9f0933e44d7b83b6d2e02fd3cbae0938630e87c99a83ac2179ccc06d2d2843f7fca039305f6aff4793357ea44ef2f8db9ff2edee87f90 SHA512 9b41346126363598de2174c9e06a4c7550e82dc4ec22f2fcc0a6b8948731831ae871a2b30988dfcd5d3c5ebdd1e6a377946374bc2d3a2b25c6c3a7732b04ac71 +MISC metadata.xml 579 BLAKE2B fc22a14bfa99c926b2c5b2071a10b6dd78baab670551c817c4c4f2e5e6a2e13c5fa216fe7a2aa455f15fbf1c8ae488a06b99960830a2d4fb6a82a6a0a277e233 SHA512 89a2c88dc5dc5e06ccd4e1830caa58e0d74f93e1742f4658ed27b6f41be3bd6924da47dc70cd7fcdce9837ceac4012dfeca39e8bf19d0451f044568d00743539 diff --git a/sci-chemistry/votca/metadata.xml b/sci-chemistry/votca/metadata.xml new file mode 100644 index 000000000000..137114c8f259 --- /dev/null +++ b/sci-chemistry/votca/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="gromacs">Add support for gromacs file formats through <pkg>sci-chemistry/gromacs</pkg></flag> + </use> + <upstream> + <remote-id type="github">votca/votca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca/votca-2022_rc2.ebuild b/sci-chemistry/votca/votca-2022_rc2.ebuild new file mode 100644 index 000000000000..6a1ae090460b --- /dev/null +++ b/sci-chemistry/votca/votca-2022_rc2.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit bash-completion-r1 cmake + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/votca/votca.git" +else + if [[ ${PV} = *_rc[1-9] ]]; then + MY_PV="${PV%%_rc*}-rc.${PV##*_rc}" + else + MY_PV="${PV}" + fi + SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux" + S="${WORKDIR}/votca-${MY_PV}" +fi + +DESCRIPTION="Versatile Object-oriented Toolkit for Coarse-graining Applications" +HOMEPAGE="https://www.votca.org/" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="+gromacs test" +RESTRICT="!test? ( test )" + +RDEPEND=" + !sci-libs/votca-tools + !sci-chemistry/votca-csg + !sci-chemistry/votca-xtp + app-shells/bash:* + >=dev-cpp/eigen-3.3 + dev-libs/boost:= + dev-libs/expat + sci-libs/fftw:3.0= + dev-lang/perl + gromacs? ( sci-chemistry/gromacs:= ) + sci-libs/hdf5[cxx] + sci-libs/libxc + sci-libs/libint:2 +" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +DOCS=( README.rst NOTICE.rst CHANGELOG.rst ) + +src_configure() { + local mycmakeargs=( + -DENABLE_TESTING=$(usex test) + -DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=$(usex !gromacs) + -DBUILD_CSGAPPS=ON + -DINSTALL_RC_FILES=OFF + -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON + ) + cmake_src_configure +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)" + einfo "https://doi.org/10.1021/acs.jctc.8b00617" + einfo + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca/votca-9999.ebuild b/sci-chemistry/votca/votca-9999.ebuild new file mode 100644 index 000000000000..6a1ae090460b --- /dev/null +++ b/sci-chemistry/votca/votca-9999.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit bash-completion-r1 cmake + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/votca/votca.git" +else + if [[ ${PV} = *_rc[1-9] ]]; then + MY_PV="${PV%%_rc*}-rc.${PV##*_rc}" + else + MY_PV="${PV}" + fi + SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux" + S="${WORKDIR}/votca-${MY_PV}" +fi + +DESCRIPTION="Versatile Object-oriented Toolkit for Coarse-graining Applications" +HOMEPAGE="https://www.votca.org/" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="+gromacs test" +RESTRICT="!test? ( test )" + +RDEPEND=" + !sci-libs/votca-tools + !sci-chemistry/votca-csg + !sci-chemistry/votca-xtp + app-shells/bash:* + >=dev-cpp/eigen-3.3 + dev-libs/boost:= + dev-libs/expat + sci-libs/fftw:3.0= + dev-lang/perl + gromacs? ( sci-chemistry/gromacs:= ) + sci-libs/hdf5[cxx] + sci-libs/libxc + sci-libs/libint:2 +" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +DOCS=( README.rst NOTICE.rst CHANGELOG.rst ) + +src_configure() { + local mycmakeargs=( + -DENABLE_TESTING=$(usex test) + -DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=$(usex !gromacs) + -DBUILD_CSGAPPS=ON + -DINSTALL_RC_FILES=OFF + -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON + ) + cmake_src_configure +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)" + einfo "https://doi.org/10.1021/acs.jctc.8b00617" + einfo + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} |