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authorV3n3RiX <venerix@koprulu.sector>2021-12-22 14:08:05 +0000
committerV3n3RiX <venerix@koprulu.sector>2021-12-22 14:08:05 +0000
commit93a93e9a3b53c1a73142a305ea1f8136846942ee (patch)
treeb9791a06ab3284e27b568412c59316c66240c682 /sci-chemistry
parent2771f79232c273bc2a57d23bf335dd81ccf6af28 (diff)
gentoo resync : 22.12.2021
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/Manifest.gzbin10855 -> 11019 bytes
-rw-r--r--sci-chemistry/gnome-chemistry-utils/Manifest2
-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/Manifest7
-rw-r--r--sci-chemistry/openbabel/files/openbabel-python.cmake104
-rw-r--r--sci-chemistry/openbabel/metadata.xml4
-rw-r--r--sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild272
-rw-r--r--sci-chemistry/openbabel/openbabel-9999.ebuild272
-rw-r--r--sci-chemistry/votca/Manifest4
-rw-r--r--sci-chemistry/votca/metadata.xml18
-rw-r--r--sci-chemistry/votca/votca-2022_rc2.ebuild70
-rw-r--r--sci-chemistry/votca/votca-9999.ebuild70
12 files changed, 828 insertions, 7 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 7940614ab228..44e11544063e 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
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
+}