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-rw-r--r--sci-chemistry/dssp/dssp-3.0.11.ebuild4
-rw-r--r--sci-chemistry/gromacs/Manifest6
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.7.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.5.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.9999.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2022.1.ebuild5
-rw-r--r--sci-chemistry/gromacs/gromacs-2022.2.ebuild (renamed from sci-chemistry/gromacs/gromacs-2022.ebuild)5
-rw-r--r--sci-chemistry/gromacs/gromacs-2022.9999.ebuild5
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild5
-rw-r--r--sci-chemistry/mdtraj/metadata.xml11
-rw-r--r--sci-chemistry/molden/molden-6.9-r1.ebuild (renamed from sci-chemistry/molden/molden-6.9.ebuild)16
-rw-r--r--sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild12
-rw-r--r--sci-chemistry/molsketch/Manifest1
-rw-r--r--sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch11
-rw-r--r--sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild60
-rw-r--r--sci-chemistry/molsketch/molsketch-0.7.2-r1.ebuild (renamed from sci-chemistry/molsketch/molsketch-0.7.2.ebuild)4
-rw-r--r--sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch32
-rw-r--r--sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild4
-rw-r--r--sci-chemistry/propka/Manifest2
-rw-r--r--sci-chemistry/propka/metadata.xml1
-rw-r--r--sci-chemistry/propka/propka-3.4.0.ebuild (renamed from sci-chemistry/propka/propka-3.2.0.ebuild)30
-rw-r--r--sci-chemistry/pymol/metadata.xml21
-rw-r--r--sci-chemistry/votca/votca-2022.ebuild2
25 files changed, 104 insertions, 143 deletions
diff --git a/sci-chemistry/dssp/dssp-3.0.11.ebuild b/sci-chemistry/dssp/dssp-3.0.11.ebuild
index 002c7d491d1..c072fd95aeb 100644
--- a/sci-chemistry/dssp/dssp-3.0.11.ebuild
+++ b/sci-chemistry/dssp/dssp-3.0.11.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/cmbi/${MY_PN}/archive/refs/tags/${PV}.tar.gz -> ${P}
LICENSE="Boost-1.0"
SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~arm ~arm64 x86 ~amd64-linux ~x86-linux"
# It's just cppcheck (at least in 3.0.11)
RESTRICT="test"
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 4e4bc921439..9b35e520e11 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -5,7 +5,7 @@ DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b091
DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5
DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5
DIST gromacs-2022.1.tar.gz 40375423 BLAKE2B fe28ec4c080500d0248bd3d37ec742e8cf51ba3520b5a7c3f640413b232fcf96354940c743e2a54a9fde04c98ecb2fd317863d8c06b008f516fefc0e9e1197dd SHA512 80c98badb7ebad171925486d1676b64e787cf8cbfb8f1b1cf1ccab8cbf8d8340f7fdd084dfb7388afc7a3aef23b95d603265305faf82125324307d86460c6f17
-DIST gromacs-2022.tar.gz 40353044 BLAKE2B e9ba72092467c143be7de0739e71181f384a6bb463338c58c60a5d56f30b960651bda60c1df4fa424e237f1ae90d5d7bab19670ec22cd21bba3cb638f8e5b1ba SHA512 f256b032b226c14407ba21c7b825b6bf3f7b3595318b8638594d81ed6346b0b8563098f6ff7005c2ba125447c5d2dff750829b24781c8f1ea266e6465f627db1
+DIST gromacs-2022.2.tar.gz 40350604 BLAKE2B 789c8abc13b5c64af6b9d66efcf70449330b7e6a4bc127ba299e36eea925e9485809c11480ffd857805d9b453df363ce9bb05bc54b439801334767651defc0ef SHA512 9f33518d2035afb37fc40377e575d497ff32bef2adb702669b35b1b51b1694b1113c5634fa6febd41955b6dfbfd055e7d523e1919bda1bf169a6d0c25700cef7
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed
@@ -13,7 +13,7 @@ DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426da
DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16
DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296
DIST manual-2022.1.pdf 13069337 BLAKE2B fed4d5b5ddc2b91dd2de2873c3efc01f6ce65b033840a79fda471b4481920fa6c5f5d9f23660d97ba4c84e0c7b75dc4c8723ed51413ad55c980818c394e9fde1 SHA512 73455190aec62aaffe760dddac4de26ea148d825f4c2d0e04d38c88b87fe15b7138b5a872bf9757452ac39e68942943c73e19025730ece8052d4a6a1873ca40e
-DIST manual-2022.pdf 13060966 BLAKE2B e1684d22e16d2bad878cd0adbac0df74a268f89034756a34374908afc7f2562a05dbdf91b3dcbdb98a45b3d21140b02a2df26e0f997c1f501347e102069f22c2 SHA512 0d9bd1fbe2db122f434df1565ba7c9ea5ad168f73855724a6cb488244eda13d8d47b2d534a6873dc7204012156fbf669bdaf7ca7d03a914745f60950392e6d28
+DIST manual-2022.2.pdf 13075063 BLAKE2B 1c9e525d45f1b9955f1aa2c4afa8c958b8ea62c51c28fafdebe302e3e5f6e04c97d1852e4ab2ba18149778d62959d9e7e42be9e4cd98f8187029cc590b1dfd9a SHA512 9b4d9b13547e0210b633394e0c9cba183a827409b08d3b2995a4b64df7b7e7aef0441af240bf4cfcb2e24594ade27c25fee454b9fcf4bb5df0ded464c4f6368d
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
@@ -21,4 +21,4 @@ DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf07
DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2
DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e
DIST regressiontests-2022.1.tar.gz 48613957 BLAKE2B 57113b1030baed0d4a635c4c4c7123e77640223dddc4e3d7b40d9a2b3805be85fcc3ca0dfc5f3d92f2dce9b962b67ca8732db2c782953c9a5ed1381bf6f02357 SHA512 44633e7497601a4cf11dd6af9d043ca132efe43246b6d924c57f879d2e6f7a6379390d9897e03d7a8f645e7bdbb76a81586b56c5e61846d9f40c137a4de216c2
-DIST regressiontests-2022.tar.gz 48616817 BLAKE2B 5d303f365a8b3c4554232ca3e583f0eacc1973dd62faaed769d297efb5d7dde3ca04b8071786ecee992a83d7980aa244965212856f48c8832ca55805af61b1c1 SHA512 4566b76b5eb3bbdcdfed8330d4fcd7ada02eb6802434aa9f2ed4f775da780e4bde7daa35d79a72b3f25c540cb1c2b347aa2e6d504a77c095830da024a933fab5
+DIST regressiontests-2022.2.tar.gz 48614810 BLAKE2B d39a9b29a023fa2462918206457bb222bf56f0c530b311a1e5572e8af6c561a9ba5cf7a445425a36f89804d120a5d05cb778998818ba11357ec67bfb05297de3 SHA512 6cd4b59515648aa5f9deec130454b4d667cce20a95d389b46883865d39a164ec23da303a52afb4459dda3c6b6a7804d0763c05424ea512e6c0725ce1ca684dc2
diff --git a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild
index 3d38fc4523b..178926f0014 100644
--- a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8,9} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
diff --git a/sci-chemistry/gromacs/gromacs-2020.7.ebuild b/sci-chemistry/gromacs/gromacs-2020.7.ebuild
index 2e38306eb66..de3335b0e75 100644
--- a/sci-chemistry/gromacs/gromacs-2020.7.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.7.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
diff --git a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
index 1ea7d0f255b..68d9a92c288 100644
--- a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8,9} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild
index b797cea596b..2f7f4f77115 100644
--- a/sci-chemistry/gromacs/gromacs-2021.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index 8e32fc1644e..af0fa65d05e 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
diff --git a/sci-chemistry/gromacs/gromacs-2022.1.ebuild b/sci-chemistry/gromacs/gromacs-2022.1.ebuild
index 80afa36142d..61b5edc51f1 100644
--- a/sci-chemistry/gromacs/gromacs-2022.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2022.1.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
@@ -24,7 +24,8 @@ else
http://ftp.gromacs.org/gromacs/${P}.tar.gz
doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ # since 2022 arm support was dropped (but not arm64)
+ KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-2022.ebuild b/sci-chemistry/gromacs/gromacs-2022.2.ebuild
index 80afa36142d..c10e8995787 100644
--- a/sci-chemistry/gromacs/gromacs-2022.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2022.2.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
@@ -24,7 +24,8 @@ else
http://ftp.gromacs.org/gromacs/${P}.tar.gz
doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ # since 2022 arm support was dropped (but not arm64)
+ KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild
index 101a76d94cf..2b70114b7ad 100644
--- a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
@@ -24,7 +24,8 @@ else
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ # since 2022 arm support was dropped (but not arm64)
+ KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 101a76d94cf..2b70114b7ad 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -5,7 +5,7 @@ EAPI=8
CMAKE_MAKEFILE_GENERATOR="ninja"
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
@@ -24,7 +24,8 @@ else
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+ # since 2022 arm support was dropped (but not arm64)
+ KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
index 7d3acaf5d25..950fb315228 100644
--- a/sci-chemistry/mdtraj/metadata.xml
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mdtraj/mdtraj</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/molden/molden-6.9.ebuild b/sci-chemistry/molden/molden-6.9-r1.ebuild
index df6e76dbfe7..e3ff6d0a079 100644
--- a/sci-chemistry/molden/molden-6.9.ebuild
+++ b/sci-chemistry/molden/molden-6.9-r1.ebuild
@@ -17,7 +17,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="opengl"
-RDEPEND="
+DEPEND="
x11-libs/libXmu
opengl? (
media-libs/freeglut
@@ -25,10 +25,9 @@ RDEPEND="
virtual/glu
)
"
-DEPEND="${RDEPEND}
- x11-misc/gccmakedep
- app-editors/vim"
- # vim provides ex, which the build system uses (surf/Makefile, at least)
+RDEPEND="${DEPEND}
+ sci-chemistry/surf
+"
PATCHES=(
"${FILESDIR}/${P}-ldflags.patch"
@@ -36,9 +35,6 @@ PATCHES=(
src_prepare() {
default
- sed \
- -e 's:makedepend:gccmakedep:g' \
- -i src/surf/Makefile || die
sed 's:shell g77:shell $(FC):g' -i makefile || die
}
@@ -60,7 +56,7 @@ src_compile() {
)
einfo "Building Molden..."
- emake -j1 molden ambfor/ambfor ambfor/ambmd surf/surf "${args[@]}"
+ emake -j1 molden ambfor/ambfor ambfor/ambmd "${args[@]}"
if use opengl ; then
einfo "Building Molden OpenGL helper..."
emake -j1 "${args[@]}" gmolden
@@ -68,7 +64,7 @@ src_compile() {
}
src_install() {
- dobin bin/molden bin/ambfor bin/ambmd bin/surf
+ dobin bin/molden bin/ambfor bin/ambmd
if use opengl; then
dobin bin/gmolden
doicon -s 64 haux/gmolden.png
diff --git a/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild
index 5c4f667b458..8901b0f81ce 100644
--- a/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild
+++ b/sci-chemistry/molequeue/molequeue-0.9.0-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2020 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_{8..11} )
inherit cmake python-r1 virtualx
@@ -66,9 +66,14 @@ src_configure() {
src_compile() {
if use zeromq; then
- python_foreach_impl run_in_build_dir cmake_src_compile all $(usex doc documentation "")
+ my_src_compile() {
+ run_in_build_dir cmake_src_compile all $(usex doc documentation "")
+ use doc && export HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
+ }
+ python_foreach_impl my_src_compile
else
cmake_src_compile all $(usex doc documentation "")
+ use doc && export HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
fi
}
@@ -81,7 +86,6 @@ src_test() {
}
src_install() {
- use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
if use zeromq; then
python_foreach_impl run_in_build_dir cmake_src_install
python_foreach_impl run_in_build_dir python_optimize
diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest
index adf2a2ef327..3dd6281fb47 100644
--- a/sci-chemistry/molsketch/Manifest
+++ b/sci-chemistry/molsketch/Manifest
@@ -1,2 +1 @@
-DIST Molsketch-0.4.1-src.tar.gz 1499842 BLAKE2B 22584f012e838037f9e23c16da6c63984604002884d279b2b6012d80eb08af9ee18b4d364fa29327572854fccad34840f97413b29b487cfbeb6496a2a8003d17 SHA512 263b088c2b8d01c1f13802b18aea6f6784580fe1a806de45b0e1ecd9f29024350e01a611bdeed1891938acc733a42746203d345d3be13ebaf4c309413e86bf26
DIST Molsketch-0.7.2-src.tar.gz 1907992 BLAKE2B 6bd099d963f352e66f73741273e9dee17f2fb299aec32b053ca39aa731a27f6a73093f98a4dbde2b6a97b85015016d1136fa4ead5f564006991b83072009ee6a SHA512 5e06f177ed4e7e8457215e07b623b1d92fa111f696fd7a106b0a6e8c56cc9c7d953fc33e0c0955c19766599d41a82519db95e12c0c49d3e4d3392311af3cc034
diff --git a/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch
deleted file mode 100644
index c32b975778e..00000000000
--- a/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/libmolsketch/src/molscene.cpp
-+++ b/libmolsketch/src/molscene.cpp
-@@ -842,7 +842,7 @@
- void MolScene::dragEnterEvent(QGraphicsSceneDragDropEvent *event)
- {
- if (!event->mimeData() || !event->mimeData()->hasFormat(mimeType())) return;
-- if (!event->proposedAction() == Qt::CopyAction) return;
-+ if ((!event->proposedAction()) == Qt::CopyAction) return;
- event->accept();
- for (genericAction* action : sceneActions())
- action->setChecked(false);
diff --git a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild
deleted file mode 100644
index 5b997ba272b..00000000000
--- a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake qmake-utils xdg-utils
-
-DESCRIPTION="A drawing tool for 2D molecular structures"
-HOMEPAGE="http://molsketch.sourceforge.net/"
-SRC_URI="mirror://sourceforge/project/${PN}/Molsketch/Beryllium-7%20${PV}/${P^}-src.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
- >=sci-chemistry/openbabel-2.2
- dev-qt/qtcore:5
- dev-qt/qtgui:5
- dev-qt/qtprintsupport:5
- dev-qt/qtsvg:5
- dev-qt/qtwidgets:5
-"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P^}"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-0.3.0-_DEFAULT_SOURCE.patch
- "${FILESDIR}"/${P}-more-quotes.patch
-)
-
-src_prepare() {
- sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \
- -i {obabeliface,libmolsketch/src}/CMakeLists.txt || die #351246
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}"/usr/include/openbabel-2.0
- -DMSK_INSTALL_PREFIX=/usr
- -DMSK_INSTALL_DOCS="${EPREFIX}"/usr/share/doc/${PF}
- )
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
- dosym ${PN}-qt5 /usr/bin/${PN}
-}
-
-pkg_postinst() {
- xdg_desktop_database_update
-}
-
-pkg_postrm() {
- xdg_desktop_database_update
-}
diff --git a/sci-chemistry/molsketch/molsketch-0.7.2.ebuild b/sci-chemistry/molsketch/molsketch-0.7.2-r1.ebuild
index 7dee9f3ea94..b35ceeca43b 100644
--- a/sci-chemistry/molsketch/molsketch-0.7.2.ebuild
+++ b/sci-chemistry/molsketch/molsketch-0.7.2-r1.ebuild
@@ -15,8 +15,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
DEPEND="
- >=sci-chemistry/openbabel-3
- dev-qt/linguist-tools:5
+ >=sci-chemistry/openbabel-3:=
dev-qt/qtcore:5
dev-qt/qtgui:5
dev-qt/qtnetwork:5
@@ -25,6 +24,7 @@ DEPEND="
dev-qt/qtwidgets:5
"
RDEPEND="${DEPEND}"
+BDEPEND="dev-qt/linguist-tools:5"
PATCHES=(
"${FILESDIR}"/${PN}-0.3.0-_DEFAULT_SOURCE.patch
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch
new file mode 100644
index 00000000000..69e41211023
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch
@@ -0,0 +1,32 @@
+https://github.com/openbabel/openbabel/pull/2493
+
+From: Sam James <sam@gentoo.org>
+Date: Sun, 12 Jun 2022 11:23:59 +0100
+Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Without this fixed check, we get a build failure with GCC 12:
+```
+/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope; did you mean ‘clock_t’?
+ 65 | start= clock();
+ | ^~~~~
+ | clock_t
+```
+
+Bug: https://bugs.gentoo.org/851510
+--- a/src/config.h.cmake
++++ b/src/config.h.cmake
+@@ -182,8 +182,8 @@
+ #define OB_MODULE_PATH "@OB_MODULE_PATH@"
+
+ #ifndef TIME_WITH_SYS_TIME
+- #ifdef HAVE_SYS_TIME
+- #ifdef HAVE_TIME
++ #ifdef HAVE_SYS_TIME_H
++ #ifdef HAVE_TIME_H
+ #define TIME_WITH_SYS_TIME 1
+ #else
+ #define TIME_WITH_SYS_TIME 0
+
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
index 61a6ad498b6..0eb8ddaa0cf 100644
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
@@ -80,6 +80,10 @@ RDEPEND="
)
"
+PATCHES=(
+ "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+)
+
pkg_pretend() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}
diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest
index 4141de90904..a3ae32cc089 100644
--- a/sci-chemistry/propka/Manifest
+++ b/sci-chemistry/propka/Manifest
@@ -1 +1 @@
-DIST propka-3.2.0.tar.gz 73746 BLAKE2B f79e493d5a195b81dc5d11cc21b9ab16c8d1fa48f15f7e23e2b2936dfb8634fdb00c7838b8dbdb4a68726dab0f16e54522ad71d71b3273ac93c03a737ae06f04 SHA512 98f2240b28b33bab94cdbe9392062bb7f6b87e75b94c2af91e178f874a74d210601161ebc835c4d751b89d37b32348fdfb096e28cbf8e9237b3f472d3fb6b4fc
+DIST propka-3.4.0.gh.tar.gz 363641 BLAKE2B 87f495ba69028593cf3ebf98ed33da0944f7a3833f2d08cae4f0a0b5cbe2f3a67e9812685b896a7d89c88ba25653861f135dbac53dc6df7af426a290bacb3d22 SHA512 2ce431c66374d0692acb7504661caa870ab6460ace3a6478f88c1d46a7bfcd82c748bf153a1ce2ea6d1611bc4bbf2351c4f5149f4578e5f8a9f9ec8385298fe9
diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml
index 03810a21807..5153791d236 100644
--- a/sci-chemistry/propka/metadata.xml
+++ b/sci-chemistry/propka/metadata.xml
@@ -9,4 +9,5 @@
<remote-id type="pypi">propka</remote-id>
<remote-id type="github">jensengroup/propka</remote-id>
</upstream>
+ <stabilize-allarches/>
</pkgmetadata>
diff --git a/sci-chemistry/propka/propka-3.2.0.ebuild b/sci-chemistry/propka/propka-3.4.0.ebuild
index b5dadd1825d..81b20fbee2e 100644
--- a/sci-chemistry/propka/propka-3.2.0.ebuild
+++ b/sci-chemistry/propka/propka-3.4.0.ebuild
@@ -1,40 +1,28 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes"
HOMEPAGE="https://github.com/jensengroup/propka"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
SLOT="0"
LICENSE="LGPL-2.1"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RESTRICT="!test? ( test )"
RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-BDEPEND="test? (
- ${RDEPEND}
- dev-python/pandas[${PYTHON_USEDEP}]
-)"
+
+distutils_enable_tests pytest
python_prepare_all() {
- sed -e "/exclude/s:scripts:\', \'Tests:g" \
+ # Do not install the tests
+ sed -e "/exclude/s:scripts:\', \'tests:g" \
-i setup.py || die
distutils-r1_python_prepare_all
}
-
-python_test() {
- cd Tests || die
- ${PYTHON} runtest.py || die
-}
-
-python_install_all() {
- distutils-r1_python_install_all
-}
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index d28a87c8e56..8a087408c33 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,14 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
- <use>
- <flag name="web">Install Pymodule needed for web app support</flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">pymol</remote-id>
- </upstream>
+ <maintainer type="project">
+ <email>sci-chemistry@gentoo.org</email>
+ <name>Gentoo Chemistry Project</name>
+ </maintainer>
+ <use>
+ <flag name="web">Install Pymodule needed for web app support</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">schrodinger/pymol-open-source</remote-id>
+ <remote-id type="sourceforge">pymol</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/votca/votca-2022.ebuild b/sci-chemistry/votca/votca-2022.ebuild
index 0962e065f91..95c32eda807 100644
--- a/sci-chemistry/votca/votca-2022.ebuild
+++ b/sci-chemistry/votca/votca-2022.ebuild
@@ -16,7 +16,7 @@ else
MY_PV="${PV}"
fi
SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86 ~amd64-linux"
+ KEYWORDS="amd64 x86 ~amd64-linux"
S="${WORKDIR}/votca-${MY_PV}"
fi