gentoo resync : 16.04.2022

7 files changed, 113 insertions, 22 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index ddccaf21679d..b4bd1f64e1d1 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
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
-#}