diff options
Diffstat (limited to 'sci-chemistry')
59 files changed, 1094 insertions, 332 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild index 1338b634d927..8f747a7a5acd 100644 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild @@ -3,9 +3,9 @@ EAPI=7 -PYTHON_COMPAT=( python3_7 ) +PYTHON_COMPAT=( python3_{7..9} ) -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then scm_eclass=git-r3 EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git" EGIT_BRANCH="develop" @@ -25,14 +25,16 @@ LICENSE="GPL-3 LGPL-3" SLOT="0" IUSE="" -BDEPEND=" +RDEPEND=" dev-python/six[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] sci-libs/numkit[${PYTHON_USEDEP}] +" +BDEPEND=" + ${RDEPEND} test? ( >=dev-python/pandas-0.17[${PYTHON_USEDEP}] ) " -RDEPEND="${DEPEND}" distutils_enable_tests pytest diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest index 3dc9888be4c9..354392f748c2 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,4 +1,4 @@ AUX GromacsWrapper-0.8.0-tests-package.patch 594 BLAKE2B 6b2c7c1aebebfbb5222c84e67805806aae714b8c96cbaad568b7ecb2959e38d504ea5a18a1de4bfcbfeea4488b04182d1cdbd0664511bfeb3cae2bd27534e8f7 SHA512 92b0232092ee9230050c114906ea61136d03de7b417d7267ef194c751bc801ab6f35d882681c36bb28949cddbea5e3c1c413df6ec949a073fcccd59b5433fefa DIST GromacsWrapper-0.8.0.tar.gz 1205837 BLAKE2B 3627e56df0dc6ba86caac67795416c7c8c187aaa4fac545600d17dcd799cb153feaab61a0f0632e051c4e9c0b4cd74f8e165156873e36bc53571bec78e5fca61 SHA512 da7215216c9a2b52094bb7e43e04f1b429c4893ba67b4bd850fe68e99f338813392fd9d0aa1b19d3398c694be964bc2badbf1b3623420da929ee4abcef18026f -EBUILD GromacsWrapper-0.8.0.ebuild 988 BLAKE2B 075465aa992911354809b14a183eaf960a1fed8ec30104a68f31fbe736beb9a0b5bbc012cd92935f2d20c80cb3ec6ab7a4fe1935636ab3f069737af4405d074e SHA512 c1ee2e69a58a6a0f6e1dc57bd9f56f5d5df2df72de7e30f3cac996379623b44288b6ece4a26c2401b1179f30244f83961787dfe33704c33e242c4c859f050890 +EBUILD GromacsWrapper-0.8.0-r1.ebuild 999 BLAKE2B 79622ebe01dd515f3f3697700a8493c7ddcbcf92bf64f81e61fbe7924a7ac37639dcb01794e5118e3f447bc5de3962f434610b41e3000961bd212a7261700adf SHA512 0941c46ab84522a06a6c26853ed593ca6ff315dc97d1bbbfe366d60e4aefb4221e10f2faa778030d0a19de9045a2d57ef94d37a0560f272e8ff876264dceecb0 MISC metadata.xml 482 BLAKE2B 2745b575ac325e9f8c53d53026ca0c67201f1519725c572813c0ad281b4a39399cbf93176e816646aa83f829c0981ee4457e3ab2232ed095f76d5a2068840912 SHA512 4f2efb8d263f20e50928e0c6f0913c65da746b5253a14658273c830b7f95ecc15620f92e87db9670adfd92792e96cc352af528ed4fa1e874977a744d2e15c6bf diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 330435993006..95348a04517a 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest index a0d491891151..8026a4a2d5f4 100644 --- a/sci-chemistry/avogadro2/Manifest +++ b/sci-chemistry/avogadro2/Manifest @@ -1,3 +1,3 @@ DIST avogadro2-1.93.0.tar.gz 2905461 BLAKE2B db51e4574fdf2a31657b8bef7b06eb0d563484deaae1a6d75649187d6f5fd7b02a99506cfb850e09792555d7c27d9937d0df0f7172fafc3ddcbccaa7502c5bb6 SHA512 8e4e15b6c2d1935f8c585c83761b28a6397bc1dc22cd5f66464d59dd25327b1cffec809af492586be4b56793448f94f9375c16e8a4c4969f7b8f2591049cc5fc -EBUILD avogadro2-1.93.0.ebuild 1224 BLAKE2B 13b6f9bb19f20fb638cae69b4dd556563b749935a79735a4ad55fdcafe0b590320c6040bf8d147cfa657b7c79560fcb40c13993343bf54ecd750da707c23f142 SHA512 c27577dce2314671c15c47d9dfd4b1c0288503d418cb43b22dfa6c240e70c17f21d99f91915a6d6bd1d529426f7f99843954b69d24f08c42e90ecf6fec9b1846 +EBUILD avogadro2-1.93.0.ebuild 1225 BLAKE2B 7dd01683f6f875b7e66457c6debd02f40ba7860f44e1ac1744088496524074944356518ffcac04603b7b86b09f9172268d1f0b67d4afdcf78f0fc9faeaedca0a SHA512 726f46a48c7087a34eed8fe7ad6ce7a9f4b0bb001850a2915ad6a2b47c0e17d4a082cc10bc4317fa4fe64ba44bc8e132e55ae1a389745d2751fa7bd43602bce7 MISC metadata.xml 513 BLAKE2B a8b5cff44b4c27be87ea699d76379063c1ccf26ce04ca2052a08a6a5042e915e24cce853300ecffe9594aa23e9c8370b658ce0bd9595e6b231bc3c6fd6e725a8 SHA512 96e91d4b1243015e2e225ef21d261b09d41d67edf52db85a3059ad7d543d4c592d2a7fdd3ed716c4d633446d13151f2e2fef84ea8bfe5a19fa9e9d8fb8132d9b diff --git a/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild index b4a2a037987e..82feebc5aff7 100644 --- a/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild +++ b/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -23,7 +23,7 @@ RDEPEND=" sci-libs/hdf5:= rpc? ( sci-chemistry/molequeue ) " -DEPEND="${DEPEND} +DEPEND="${RDEPEND} dev-cpp/eigen:3 test? ( dev-qt/qttest:5 ) " diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest index aff262f69648..9ac28a3886c7 100644 --- a/sci-chemistry/cluster/Manifest +++ b/sci-chemistry/cluster/Manifest @@ -1,5 +1,5 @@ AUX 1.3.081231-includes.patch 245 BLAKE2B 6bbe0621d49bc7af8091a5594ebcd52d29d99cc00567eab523186b24c387f5c9af241c7ee53d235c1b56b6a6ea6759d3aeea814e87dd591d585413243be735e2 SHA512 a1261ed2b3f867fe464e1501fa9bc0b1f2909eaf736475e717da95ddbc34ae2938346c0044f7b6d84264a0d85ea5f7b1214caf1c2b12c544876912ff10e2302a AUX 1.3.081231-ldflags.patch 842 BLAKE2B 67085c3dd9ca5e97b28481fbf06a0f9b6294bd519eb3639c54b10cd9b11a4c44a48dbfa907cdf9ff8ec68761164e82d415c44ad0c3a551842416759c76d4b7a9 SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4 DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac -EBUILD cluster-1.3.081231-r1.ebuild 664 BLAKE2B 1bb02947160c9306e9fbeb3fbc8197327b4e19d0ee585170ec2769f578e781ca092015f05f368923f9aae5887a491d9e8029db0e36731aa033d18c5691e15582 SHA512 2179d4beb99e86945b2afa8b0951da4f2c59ad13a0070429d7c0a24e0d363ee0a7f12a3710655305be332cec4744e3b22167e1c99986fcb1e22dec2fc46e6d59 +EBUILD cluster-1.3.081231-r1.ebuild 661 BLAKE2B 2c4054b677172ab3d6dd2e6decae4841e20ac1596d2a92b2bbd5ee633b4934db454fd8e21bd5dc71269224037eee673327b0a95433c19c7e3a0d699e38b15e92 SHA512 81883b09e3159cc2ee01756e4809265723ce9176c78de7fa0dc3c56477c25dcc45b73161268bd9972d881bfb008d9c9df406abe12fe347415a8ec5ecc60edc20 MISC metadata.xml 661 BLAKE2B 602330745970373b72472999d013a804a343da0ea3c2a1ef948d3fea97dfbb1f1533a0322d1b8295a19ea377725d503c36f37316f5168ea815053afde8388b50 SHA512 449c8965bd2f3039effcf1d6fc15fea1708cf5987aee36a4b8c470f85b59f7b04884a796a353f17fd890aa9d2e4ee7b1c25ed969febabaa54e577f8be31ed889 diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild index 955f546926e2..d274ed0d3787 100644 --- a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild +++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit epatch toolchain-funcs DESCRIPTION="Build lists of collections of interacting items" HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" diff --git a/sci-chemistry/easychem/Manifest b/sci-chemistry/easychem/Manifest index c5c420dd34f7..0286e86d8a92 100644 --- a/sci-chemistry/easychem/Manifest +++ b/sci-chemistry/easychem/Manifest @@ -1,4 +1,4 @@ -AUX 0.6-gentoo.patch 1770 BLAKE2B c355edd4187e4fc4928cc520b4a58a5aaea314342dd66e9448e4bddf2989d233611eb41ebe6576f745725d67c32bdc1faa76432d8c0d15c45cc19bea42d4c575 SHA512 bf641ed0d0f01d895de9ff5892c475bda14b7d14d44898e02126d3f56bfdad59f425b722031e5e983f7b9633308d6463653422fa16323e06cf22cd3f9b88f261 +AUX 0.6-gentoo.patch 1695 BLAKE2B cff09334811f4f7f40c77edcfd9c160885f906d616d1b36d0a0c61b0c4d03982ebab91cbcacd55fab1e7b152dec6de26e8f6584b8436a20a3d9e8f43621888e4 SHA512 02b9880ff2b8d9ec81ddd8d96f64a9e1dc38810789eedd18ad7cacc0c594914334971fccf735a7103878c8d32e0a3765d5ff57016b4a4feb2e572915bd7c3eec DIST easychem-0.6.tar.gz 265458 BLAKE2B 673100e6d01653ea16a70a8384dc8c598c8e113e241851b19882b333c95e6118fc180a1123e770c021245417640310a05a9026e55a57ae589bde59cf9e5b4766 SHA512 83f877d1813287592a460f4dc3769feda88e45d8f77cd728c4055b60521babe253b4432033941ff429c753cfe675a642714052a01736534147398d6972e47051 -EBUILD easychem-0.6-r1.ebuild 807 BLAKE2B 9ae7df3170e694a26e24bf2566e528b0684ffed71efd66a05e1e702792c2afa37413fe4b23eb4b4e6cb65f51b088dc9ba7c29cca6a2f0c50bc590f0592c14e9d SHA512 d725ece334db0466722012c5d045cd8a09cd60dbe8e79a17b855b443cbbe216d8792002afc344bcfffa7bbc068e9ac0e2030e99c8a607eaf8d3912f4a21e5c86 +EBUILD easychem-0.6-r1.ebuild 807 BLAKE2B bbd891d60711b8d4fe68e17fa5f71016479c274bc077d277aa49fd4313046d676fc87514513c5468d3bd52a2408b83bacee0a18cce45cb1951f8d87d48fed644 SHA512 49514e7ac39bea63ea697fade31adb0b7b7dbae28867d7f0e3401d52ef9a5d37a431da0fcd61fb5e2f819cada9794f788f254f0b9c41ba1665946f9bb29887b6 MISC metadata.xml 758 BLAKE2B e03f2d584016eb1bf52a93b6bbcf0d77734e50ee7e1ab4fb15cfd15032bb28437d994698e9f221dec7dbe88ca7f3234734ec5819ffce8e103a03ca639984ee8e SHA512 e07eda8ec2fd7a721628cf0ccc1a50876f6cd8aff0a27903366ca03587d8c9dbb5cd830da9dfcfe2aa5d6b64eb577b36f3b5173b5fa6e39b19c6e97d8764a825 diff --git a/sci-chemistry/easychem/easychem-0.6-r1.ebuild b/sci-chemistry/easychem/easychem-0.6-r1.ebuild index f299712514b9..9fbce1815123 100644 --- a/sci-chemistry/easychem/easychem-0.6-r1.ebuild +++ b/sci-chemistry/easychem/easychem-0.6-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit epatch toolchain-funcs DESCRIPTION="Chemical structure drawing program - focused on presentation" HOMEPAGE="http://easychem.sourceforge.net/" diff --git a/sci-chemistry/easychem/files/0.6-gentoo.patch b/sci-chemistry/easychem/files/0.6-gentoo.patch index 000e4373b3c2..be6070603086 100644 --- a/sci-chemistry/easychem/files/0.6-gentoo.patch +++ b/sci-chemistry/easychem/files/0.6-gentoo.patch @@ -1,5 +1,3 @@ -diff --git a/Makefile.linux b/Makefile.linux -index 6638394..5da56b0 100644 --- a/Makefile.linux +++ b/Makefile.linux @@ -1,5 +1,5 @@ diff --git a/sci-chemistry/gelemental/Manifest b/sci-chemistry/gelemental/Manifest index 5f208c77f299..1534cc18ff8d 100644 --- a/sci-chemistry/gelemental/Manifest +++ b/sci-chemistry/gelemental/Manifest @@ -1,3 +1,3 @@ DIST gelemental-2.0.0.tar.gz 779052 BLAKE2B 86f98a97acaf84c2bd6e03e991e226f19e65ed9c06fc43c809278d5e6d8b93645aa64ac4983166fad6b6b9b3d0ad5bba7a7cbfe2dccbbe2ea093deaaa8bdfabd SHA512 86b0f59a3508560e3882f40b820d7b24b780bb4d1619df94f3410b0832255deec8e55d11c5ad960f96fc3e16d8a624279bf53bf178bf1dacdfe80a72181e48d6 -EBUILD gelemental-2.0.0-r1.ebuild 951 BLAKE2B efa247655c31b23277e45949e48228aa17c3f57904a1467afbfbe01baad056613e87943c31b10e8e885c1a2e113cf05bb65740777a815e2a0a57e1f87d1d7a27 SHA512 3780ff5c3b1efa1e3ea34c0a38313e24fc5cba8b1abb40e628f6ba8b0554fe9cc218a1b9d97979ed97c558d0939b2b05ae5de64b88a9dac195f5deae35fd1350 +EBUILD gelemental-2.0.0-r1.ebuild 770 BLAKE2B c7b578b3da601e3691b14a1bd8715d67a249e0c029a342871cb039a333291d208d9dd23c8b034a6f36f61dc8e68252efdcd7af67bd8f0f0837f1955d9fc032a8 SHA512 987740e122b7d9128120ce1878ae578d6e8a2cfd67ec7b50be91ca8c98a3d9765160b7ff7eb276f6536ef99a66b3325eab546dd5800a6b60ab7791b1b365f777 MISC metadata.xml 455 BLAKE2B 7db9d6b4a8896df6385ae2c8c2b8c771c1a6ae82a1072f6d3f9b27fbd7c4d0f3546a03ced3350331d25f48e5631855fc9653a808d49631803f2d526db75b3ac7 SHA512 815bcad86f574f7cb2dfef3205e2a6398f5fd2512395c0c016733d4cb001f70c0003f494a69bc9bc66d675a9eaa89c203ace13f17f4a9f2c6805a34fcf5125d8 diff --git a/sci-chemistry/gelemental/gelemental-2.0.0-r1.ebuild b/sci-chemistry/gelemental/gelemental-2.0.0-r1.ebuild index 4affe1b9171e..99ac4cd0e9fb 100644 --- a/sci-chemistry/gelemental/gelemental-2.0.0-r1.ebuild +++ b/sci-chemistry/gelemental/gelemental-2.0.0-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit autotools eutils flag-o-matic xdg-utils +inherit autotools flag-o-matic xdg DESCRIPTION="Periodic table viewer with detailed information on the chemical elements" HOMEPAGE="https://github.com/ginggs/gelemental/" @@ -17,11 +17,13 @@ IUSE="doc" RDEPEND=" dev-cpp/gtkmm:2.4 dev-cpp/glibmm:2" -DEPEND="${RDEPEND} - virtual/pkgconfig - sys-devel/gettext +DEPEND="${RDEPEND}" +BDEPEND=" dev-util/intltool - doc? ( app-doc/doxygen )" + sys-devel/gettext + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" src_prepare() { default @@ -30,19 +32,10 @@ src_prepare() { src_configure() { append-cxxflags -std=c++11 #566450 - local myeconfargs=( $(use_enable doc api-docs) ) - default -} - -pkg_postinst() { - xdg_icon_cache_update - xdg_desktop_database_update - xdg_mimeinfo_database_update -} + local myeconfargs=( + $(use_enable doc api-docs) + ) -pkg_postrm() { - xdg_icon_cache_update - xdg_desktop_database_update - xdg_mimeinfo_database_update + econf "${myeconfargs[@]}" } diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 66aa1e5dc750..bd642f2438f8 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,8 +1,11 @@ -AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e +AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee44b700beecc32b083885727d31904649798e38b824a6cf04ea7f9129dbd40e66bdde6e5a88fa4734db51bdf4cc46 SHA512 2c05e243b0e7bb8f9d25051d7bc86463dffa722502586799f0a8ce53bebd24fd0e367b6840365ac4ebc30595ffb8bbccb10a88d0c81148ae198941966cebddb0 +AUX gromacs-2021-nblib.patch 1860 BLAKE2B 3f9d8e5683fee23434ca7bd0d9264eaed5834c3e4164176006fefea27b74ea50e67b743c4d0fa329486545ac1237d9fb288a0fbe7b6a4c06a37c8e85a22cb255 SHA512 1630eacd632519d5440fcae8aba511615ac031ce9828a059308c8ec2f33588c43dc055ab3d435efd622f23a46afa5caa14a6acad5aacb15bed33b9a9be5009f9 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80 SHA512 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768befbbd08adbd39f92bb715798a7ff8d0559bb3dfc3bf58c282ae687d4946f06b32c5a75544dcc33b83e5a874538712021c8ecbee5a989a6f045d752ab359b SHA512 24363e3136b7c81288798ac01f779cf9c06c32482c0b5acd6d1c5f2a66733ddfdf35de661cedb6a23e1a5de08c012b79e6d2903172aee139a675897e5c72e7d3 diff --git a/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch new file mode 100644 index 000000000000..cc7730afecb9 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch @@ -0,0 +1,35 @@ +From e4e1263776844d660c471e3d1203acf54cdc855f Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxyum@gmail.com> +Date: Fri, 23 Apr 2021 13:21:24 +0300 +Subject: [PATCH 2/2] Allow to build python part without build testing enabled + +Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com> +--- + python_packaging/src/CMakeLists.txt | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt +index c75549fc82..4f983fdd5f 100644 +--- a/python_packaging/src/CMakeLists.txt ++++ b/python_packaging/src/CMakeLists.txt +@@ -1,7 +1,7 @@ + # + # This file is part of the GROMACS molecular simulation package. + # +-# Copyright (c) 2019,2020, by the GROMACS development team, led by ++# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by + # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + # and including many others, as listed in the AUTHORS file in the + # top-level source directory and at http://www.gromacs.org. +@@ -252,5 +252,7 @@ endif() + # to the `check` target. Normal usage is to first install the Python package, + # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation. + if(NOT GMXAPI_MASTER_PROJECT) +- add_subdirectory(test) ++ if (BUILD_TESTING) ++ add_subdirectory(test) ++ endif() + endif() +-- +2.31.1 + diff --git a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch deleted file mode 100644 index 452987f38b96..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN gromacs-2020-beta1/python_packaging/src/CMakeLists.txt gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt ---- gromacs-2020-beta1/python_packaging/src/CMakeLists.txt 2019-09-12 05:48:57.000000000 +0300 -+++ gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt 2019-10-09 17:01:30.845304765 +0300 -@@ -201,5 +201,7 @@ - # to the `check` target. Normal usage is to first install the Python package, - # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation. - if(NOT GMXAPI_MASTER_PROJECT) -- add_subdirectory(test) -+ if (GMX_BUILD_TESTING) -+ add_subdirectory(test) -+ endif() - endif() diff --git a/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch new file mode 100644 index 000000000000..67ea6f6f63c8 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch @@ -0,0 +1,53 @@ +From 5771842a06f483ad52781f4f2cdf5311ddb5cfa1 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxyum@gmail.com> +Date: Fri, 23 Apr 2021 13:15:10 +0300 +Subject: [PATCH 1/2] Allow to build and install nblib without GMX TESTS + enabled + +Without it you'll get error like this: + + CMake Error at api/nblib/CMakeLists.txt:79 (add_dependencies): + Cannot add target-level dependencies to non-existent target "tests". + + The add_dependencies works for top-level logical targets created by the + add_executable, add_library, or add_custom_target commands. If you want to + add file-level dependencies see the DEPENDS option of the add_custom_target + and add_custom_command commands. + +Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com> +--- + api/nblib/CMakeLists.txt | 18 ++++++++++-------- + 1 file changed, 10 insertions(+), 8 deletions(-) + +diff --git a/api/nblib/CMakeLists.txt b/api/nblib/CMakeLists.txt +index a2ce06596e..51211c3d70 100644 +--- a/api/nblib/CMakeLists.txt ++++ b/api/nblib/CMakeLists.txt +@@ -76,14 +76,16 @@ add_custom_target(nblib-tests + ) + # Ensure that "make tests" builds all nblib tests so the top-level + # "make check" will work. +-add_dependencies(tests nblib-tests) +- +-# this allows all nblib tests to be run with "make check-nblib" +-add_custom_target(check-nblib +- COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib +- COMMENT "Running nblib tests" +- USES_TERMINAL VERBATIM) +-add_dependencies(check-nblib nblib-tests) ++if (BUILD_TESTING) ++ add_dependencies(tests nblib-tests) ++ ++ # this allows all nblib tests to be run with "make check-nblib" ++ add_custom_target(check-nblib ++ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib ++ COMMENT "Running nblib tests" ++ USES_TERMINAL VERBATIM) ++ add_dependencies(check-nblib nblib-tests) ++endif() + + set(NBLIB_MAJOR 0) + set(NBLIB_MINOR 1) +-- +2.31.1 + diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild index ee771a89ea31..dfe7923415e4 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild index da2db70a9742..37058195e940 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild @@ -5,7 +5,7 @@ EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild index d8b28c2b0a7b..e8417cf59475 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild index 9b2e7ff39e9a..393fdad3162e 100644 --- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild new file mode 100644 index 000000000000..393fdad3162e --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild @@ -0,0 +1,342 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{7,8,9} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + git://git.gromacs.org/gromacs.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + !sci-chemistry/gmxapi + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_MULTI_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + if use custom-cflags; then + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${opencl[@]}" + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + "${opencl[@]}" + "${cuda[@]}" + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild index 9b2e7ff39e9a..393fdad3162e 100644 --- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild new file mode 100644 index 000000000000..2a4610540b55 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild @@ -0,0 +1,349 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{7,8,9} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + git://git.gromacs.org/gromacs.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + !sci-chemistry/gmxapi + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_MULTI_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +PATCHES=( + "${FILESDIR}/${PN}-2020-pytest.patch" + "${FILESDIR}/${PN}-2021-nblib.patch" +) + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + if use custom-cflags; then + #go from slowest to fastest acceleration + local acce="None" + if (use amd64 || use x86); then + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + use cpu_flags_x86_avx512f && acce="AVX_512" + elif (use arm); then + use cpu_flags_arm_neon && acce="ARM_NEON" + elif (use arm64); then + use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" + fi + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local gpu=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${gpu[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + "${opencl[@]}" + "${cuda[@]}" + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index a1ba0b4d74a3..dbeed6f4fec5 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) - pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild index a1ba0b4d74a3..069792626140 100644 --- a/sci-chemistry/gromacs/gromacs-2021.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index a1ba0b4d74a3..dbeed6f4fec5 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -9,14 +9,14 @@ PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 -inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils -if [[ $PV = *9999* ]]; then +if [[ ${PV} = *9999* ]]; then EGIT_REPO_URI=" https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git git://git.gromacs.org/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) - pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index d514defea079..8ab95b157670 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 3851 BLAKE2B 0eb8c97adb3944b57d226ac4fcbbc2fa4e38b496d301ce2080dd6aaa1a6ae90783cbb70868dd7ca645eec64c9de7566b3d6506519e5663c12df66c5e61756fbc SHA512 838037687a6c277239837caa0538e3ae3ce1c9301f83b7fc0ac85f8195de5dfd8d645415cb789d6359c43b5fbdd0c9a73ffc0fb84c73178efd09ee56433a9811 +EBUILD modeller-9.25.ebuild 3844 BLAKE2B 6190491bec7c4ca0bbca56675b6a5dd36ffe4381ebb779ae9fdb4760e71a04a503ff452e1d45ee297f8474152eb0e91dc10de74184e4bee8c48dac22191a81b3 SHA512 9e44ef9659c7cc6ce5d3c21a4c3706e9fffe38872312c3da1443d6200c6dcf879827537b0e131409f54268658ff9774176580babb3c4506fa216ec51f89b7cd7 MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8 diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild index 468f241f377f..7dd6a1001545 100644 --- a/sci-chemistry/modeller/modeller-9.25.ebuild +++ b/sci-chemistry/modeller/modeller-9.25.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,7 +6,7 @@ EAPI=7 PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_USE_SETUPTOOLS=no -inherit distutils-r1 eutils multilib +inherit distutils-r1 multilib DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" HOMEPAGE="https://salilab.org/modeller/" diff --git a/sci-chemistry/molscript/Manifest b/sci-chemistry/molscript/Manifest index c4d12f363599..b2d92abfac12 100644 --- a/sci-chemistry/molscript/Manifest +++ b/sci-chemistry/molscript/Manifest @@ -4,5 +4,5 @@ AUX 2.1.2-prll.patch 409 BLAKE2B 83eefcd062c9904a06a69ccafa9da14578f102af96ad1b3 AUX fix-makefile-shared.patch 2051 BLAKE2B 145edf9dc11ee0f59325fcc3e2f981de03aeaa582bea06ca80406cc88ce38971590b687aa9dd40b37fb8edd07c9b30a0f81aa20ab38dcdb02378a407ba068878 SHA512 0c12bd5aea0a6175b7647ed61ae139113329058c42cfb56105ee35af35bdab9f61adfe635a1c3322dbff00ddfcee06383bbd6bd048cc7ded1961f3997a527358 AUX glutbitmap.h 845 BLAKE2B e5c5a6fed84021a35e132301c06efa9b877fc475a1230a58c93e9e24fb0b220cea1bcb68d411ed17897877dd3b9c4e3d6a1646906b0f09819449e6321e8f108a SHA512 a11e8c23472ed8950c8b56fdfd57ddd9c6539f427437ab26a2d3561ad388ca24a36029dee9ff6b8af759eeadf89fbd45dd10279d8089e6978eec07858624c7da DIST molscript-2.1.2.tar.gz 412497 BLAKE2B ca28cf90cfbd1314351abd0c32e4a4012f2f6f178537e12918942f3c5e21e6875d045d46d76e645b4e9982d6d0784029b3d26eb17bb65aa486ecbea70842d9b4 SHA512 0f82936da3123770c0fdb703094dbb5289cc39e9f9ffd034d8dba563f8d615788f67040d38158ac2f203b480c5838a7d8e71ca07bc5098181c1e3cfea26703a4 -EBUILD molscript-2.1.2-r2.ebuild 1401 BLAKE2B 2c06899f86ce8c75bdc9081866fcf5b81406c2d1aee06284f56157a6a05da03606e98adf12b1ed634945a4da1b5741a6350313ab0a2b366f000abb14262c6b42 SHA512 48ae8900e68d17f886cd1d8ab0f42a154b569cc0368149c223788c6a65423bc963e0631ad90e4ea1e8406badfd1c710d1cb7b6f6d13a4b89cd248062ade0b9b3 +EBUILD molscript-2.1.2-r2.ebuild 1401 BLAKE2B 540ffefe06faf6189bd649131c514066296504ab99b2c1480b2428ef42a84a72e313c29928b7a68d7199916e116796c46126837ea635d82cc791da306293646a SHA512 86f2af9b346e45eeeb096fd6e1a0c46977789307f4acfa5524551f5e6afe08bc19412962da91815c5ba0062a78194b0bd5d8e18eb6dba6cf98e2750c20d71c35 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild index 0628b53b087d..7196e6fbf7f1 100644 --- a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild +++ b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit epatch toolchain-funcs DESCRIPTION="Display 3D molecules (e.g., proteins) in schematic and detailed representations" HOMEPAGE="http://www.avatar.se/molscript/" diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest index 7c13d47c4a56..7fbdd268c336 100644 --- a/sci-chemistry/mustang/Manifest +++ b/sci-chemistry/mustang/Manifest @@ -1,4 +1,4 @@ AUX mustang-3.2.1-gcc-4.7.patch 477 BLAKE2B 1e380b3b4bd96c61e316b7aa150f1e5e290dbb2e9d93876ef31adf6cdb482f5390eb630e34a4a1851bd7f5dfea5d93cadedbb320ad336f48fa87c8a4dbd8be81 SHA512 169e68335093d3400c3294a38246d5e9264f77bbaeab7c047318f8db5934cfed24ae5f0f421f2483e2c9fe8df1db40b8ab48c0dac1c20867f4119011b3e4f52e DIST mustang_v3.2.2.tgz 141940 BLAKE2B b90b42df782bd1dbdb387d0d0ab42430c5212b439da84f56a33ca2c746c8937ae330dfb8d634e7d1c5ffd0f6959cd9e4be0efe8f569c452930a3481894c68ec5 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d -EBUILD mustang-3.2.2.ebuild 1103 BLAKE2B 7320fe67ab0e48489cb59a35f44fa3a692bc15fac876c1db6869413f4f7eac419df28a5fb680008e9bcc978ca060912227c9f0f82f057e488e042ce87f732da0 SHA512 3a6cc607780bb4f2a95005867c06e4e24e84e559f356a25cda0586f3cd504af285f8f0d8b453ee6afa07fae52e0b277844d8f1a7e8312d5a8a747026527dd45b +EBUILD mustang-3.2.2.ebuild 1103 BLAKE2B 0d56516a4ffc44784786ab9b10759dc04bb08ecd906cb281b8174ac4f0af44e67d7f340bfcada2dbf465ee986a3fce0fe9b4cca9fc7dcada3d00d8711649be3e SHA512 9b6e784bd46029c575d68b472693bc98ec788cdc1b415ddc27d492b4a88967af25e2c1d865db3b57307c2ce6a8b863a3a576b178b863646be8aa1c47db9f8263 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild index 82f1f1deadec..c82add5410d0 100644 --- a/sci-chemistry/mustang/mustang-3.2.2.ebuild +++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils toolchain-funcs +inherit epatch toolchain-funcs MY_PN="MUSTANG" SRC_P="${PN}_v${PV}" diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest index 385e3ddc7291..fe6cf97f6233 100644 --- a/sci-chemistry/namd/Manifest +++ b/sci-chemistry/namd/Manifest @@ -1,5 +1,5 @@ AUX namd-2.10-gentoo.patch 4637 BLAKE2B 0439e424f3d2a73378c68052f9d9dd69dc9590b9f83fa4062d4abc156b3b682f0e8a2cffd8a1e1f751f8dfd71d067c0234ba56946773ca9139e73c57e775c631 SHA512 35afda71ad7567d1b2c4c1f4073792d5977edc997ba7a43cf71c8ed32308062edc5cb4923202d599d59ade2f98602a0fac21138ba205a3bf6b681c86a61411f8 AUX namd-2.7-iml-dec.patch 520 BLAKE2B c16430d1161b9d7e3faf22257d84ff1090eccf906a296f91d4ec0731fa89d23334d5c39c7988f8ac6d5f5020d403d4491dadbe34b1e9800ada81ad18b2448b7d SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37 DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 -EBUILD namd-2.10.ebuild 2651 BLAKE2B 49f86253643a8d54f844c3edf47d53ac0ece857d47fead5b12b93885f68d671ec74b0ddb0d3eb998c4806dd41550edbc9950edf658ca83eece5069392bb87a70 SHA512 643d3300a3256dd28c04e2070aaff6bd5720473b7d69f16ac5a641a76ff2c6d98be4e467220b6f4ef00243eeb2198b1d7b8a9a50b781c0281caac9bca7a995ff +EBUILD namd-2.10.ebuild 2644 BLAKE2B 6d91c9f7f90f2b304c18bb176e7fdfcfff98a077bf8d6ed720b24ee186b5dece164fde49cee6db3f3dff217a53bba76d6d1c00b45ca7633ab1d9fb2a0b53ef46 SHA512 816bc445d23cc15fcf7d17bacb11b7ae4566a7bf135a88f80b7587d9630db0650e0f8b54b828bbbe8454008b6967fc276fbfc347cda351ec4b9e370d08671e08 MISC metadata.xml 376 BLAKE2B 04d5215096c154f2414dc0475c6510a66b6978bd85169311d4b17303bafea893f8e3c2afb83080d72492c5dc82a62b2522ca079e300c917c00e439da932fee68 SHA512 578a3221496eb1470d9fcac9e784f62bb39591448a35a24e1881b5be69473689770bbc928c5779b76bed8c657b1e44d929093e6a39812d135199e37a0e8938e2 diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild index 96b58d22a0aa..76a34c5a0a19 100644 --- a/sci-chemistry/namd/namd-2.10.ebuild +++ b/sci-chemistry/namd/namd-2.10.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 MY_PN="NAMD" -inherit eutils multilib toolchain-funcs flag-o-matic +inherit multilib toolchain-funcs flag-o-matic DESCRIPTION="A powerful and highly parallelized molecular dynamics code" HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest index 9363cbaa95a8..31c9db303cf6 100644 --- a/sci-chemistry/numbat/Manifest +++ b/sci-chemistry/numbat/Manifest @@ -1,4 +1,4 @@ AUX numbat-0.999-gnuplot.patch 2048 BLAKE2B 662ff2337d8a56ba21d1037911dab787ce3faead57a692310e694be4435875c1c7b66a6b756b28c2a2bd8ee29c29b845b794c6f70720c9f7b31810cd8296a083 SHA512 dd646e8f6652a63cb4e1c97830a755629e45d20fa13431f628b66fe8a5062b7bd7ebacddb3dbcca5aeeac3ae0d89f59c61036c1a3639d25fe0426ada77a888bb DIST Numbat-0.999.tar.gz 1791471 BLAKE2B 7f6536533fdf6bc3860dc1a7c03ade4896e782c5ecadf1c6a7d70896f4c6ef9f0571796c171012497d7b47b3342c215a5302ed210d7dde3ecdbef170c3f55dbc SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c -EBUILD numbat-0.999-r1.ebuild 1075 BLAKE2B e9ef3bf4ab2b0c751809a4f412e2f44514637a88c0c03cdbb7c47bb554c1d3ac6f6ae1468c0e304db5743dd83239cc300779e5d8c286d54432562cc40ab0c4ef SHA512 28df0153d08c7656c59212ced742ab2d6c8e3eaefaa96c5f62d44beb2e56e39cc60d51a8dc284187e90b3eb57322f7352137908294508b53b13e79e7e0719a30 +EBUILD numbat-0.999-r1.ebuild 1005 BLAKE2B 7f2925f5d97e688fb8e31768523aa6d0c0e4529f9e5b0cf0acc639b5dd96b79d81e65445f79dc63086142192d9aeeab83dc30fb459338803a903cb54379dd041 SHA512 a4e95f3f0d5df19c46ec0a8c2f647258c0a70fba9447f2f669fe86c3437a2026196c1076adce22c6b41fb445c36bdcc382e3801373460e1ca6ce1992f8c6eb63 MISC metadata.xml 852 BLAKE2B 623b64ec229e39a4def8e03c4b69e6268abb2a42f7d2337e71d17da183a0ac99b953e820c2875703dfb5a599229ec94cea9f40a4386563acadb5082a835ff186 SHA512 64e5552a677fc7370f68f7f811734ac17144fcb95e23503c962b678a1678dccf22a2d19991eb69dcdf8d4c1c97448d35d7f34654245ebe3fee8b30a0a8fa586c diff --git a/sci-chemistry/numbat/numbat-0.999-r1.ebuild b/sci-chemistry/numbat/numbat-0.999-r1.ebuild index 66f5b2ae0652..766c64b1b9cd 100644 --- a/sci-chemistry/numbat/numbat-0.999-r1.ebuild +++ b/sci-chemistry/numbat/numbat-0.999-r1.ebuild @@ -1,52 +1,56 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils +inherit autotools MY_PN="Numbat" MY_P="${MY_PN}-${PV}" -DESCRIPTION="new user-friendly method built for automatic dX-tensor determination" +DESCRIPTION="New user-friendly method built for automatic dX-tensor determination" HOMEPAGE="http://www.nmr.chem.uu.nl/~christophe/numbat.html" SRC_URI="http://comp-bio.anu.edu.au/private/downloads/Numbat/${MY_P}.tar.gz" +S="${WORKDIR}"/${MY_P} SLOT="0" LICENSE="GPL-3" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" -CDEPEND=" +DEPEND=" gnome-base/libglade:2.0 sci-libs/gsl - x11-libs/gtk+:2" -DEPEND="${CDEPEND} - virtual/pkgconfig" -RDEPEND="${CDEPEND} + x11-libs/gtk+:2 +" +RDEPEND=" + ${DEPEND} sci-chemistry/molmol sci-chemistry/pymol - sci-visualization/gnuplot" - -S="${WORKDIR}"/${MY_P} + sci-visualization/gnuplot +" +BDEPEND="virtual/pkgconfig" PATCHES=( # "${FILESDIR}"/${P}-glade.patch - "${FILESDIR}"/${P}-gnuplot.patch ) + "${FILESDIR}"/${P}-gnuplot.patch +) src_prepare() { + default + sed \ -e '/COPYING/d' \ -e "s:doc/numbat:share/doc/${PF}:g" \ -i Makefile.am src/common.h || die - rm missing + + rm missing || die + emake distclean - autotools-utils_src_prepare + eautoreconf } src_install() { docompress -x /usr/share/doc/${PF} - autotools-utils_src_install + + default } diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest index 782bf7a5fc8f..c030e3c66b6c 100644 --- a/sci-chemistry/openbabel/Manifest +++ b/sci-chemistry/openbabel/Manifest @@ -1,6 +1,8 @@ AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 AUX openbabel-2.4.1-gcc-8.patch 707 BLAKE2B 2b40d3e573664d036ef961e0298d34e093370485a07790ec2bb9628b02928f3977c70381ba1337e1394601300c2b7b1f05306476302ef0b894ebfadcd01322d9 SHA512 c23fc09ea9cc72c84782a95cfcc59cba5270bbeb24bc50e8aa5349bb22d691c59684c9ca8fdc870733432429e3d9e0a5c660317ee19fa7e8f3fb62c9ebc2dbbd +AUX openbabel-2.4.1-gcc10.patch 2317 BLAKE2B a76a4ef8b7502f8a80ebb807d2874d77f2ef5f532fa7b71a398245b737d1d55387121f4c24fc7dda7df47ddac4ad16e9cd12076787bedf0f63872708e9516d99 SHA512 ea37e5c53360728455be3d819c29fc27aa10556451a437e05c71c6a5e2bd5e1cfb4c229ff0e67e6c8ae7554f08b7bb16ad4be9ace36991c9c9f2417574b373f2 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70 EBUILD openbabel-2.4.1-r1.ebuild 2226 BLAKE2B 1342b61d567112528a5d574e0529837d96b53e98ca96a71b05336079f2caf7489b74cf98a83d15d884f19ed24090f1284313cd1b5df552f6482fe6dfa045a40d SHA512 1566ba69f27e97acfbb2950b65844987dc9a21410f42d540e0e3a6c732c151395b80cc6fa371b70414ffcc5b61c445efb6f893653b2b5d353579c73f6804f247 +EBUILD openbabel-2.4.1-r2.ebuild 2178 BLAKE2B fd0d324a28dac54a6b67359b9250ab4331195eeb32c10de46d9d5d4e5c4bce44298eb0953eb06006823b7c6bdc5ab0b7f22b0b3334800e2f06d080a3e24fe311 SHA512 494acf7a358eb01a8bc77713da9135195013833c8bc993adad25221715238e53309719c0e42bdcd8ee076d35b26228946cfad5e08aab3259119db741c27ae5bd MISC metadata.xml 665 BLAKE2B 4657b85c826c006b6d69e06240dd908a72397a32cb0c0512810e22d1b02478eaa3ab460535b300eba653a334a79c81a102007da1a901d6d1dbd04fc5e795df73 SHA512 0555e7c7401dfd5fbeee339302f8eb7a104ad6538db2839d8e89c20ac5ad2184070335677671a58eb91be2780ae485467d33302f3a14d0caab4ae8c0148f03bb diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch new file mode 100644 index 000000000000..88d8c2add64a --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch @@ -0,0 +1,62 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 2e66dd1..ef4f16b 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1,16 +1,11 @@ + # Please ensure that any changes remain compliant with 2.4.8. + if(NOT EMBED_OPENBABEL) +- cmake_minimum_required(VERSION 2.4.8) ++ cmake_minimum_required(VERSION 2.4.10) + endif() + + project(openbabel) + set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules) + +-# Allow loose loop constructs, i.e. no matching in if/else/endif or loops. +-# Note that this is true by default in CMake 2.6.0, but we currently only +-# require CMake 2.4.8 - remove this when the CMake requirement is bumped. +-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1) +- + if(COMMAND cmake_policy) + cmake_policy(SET CMP0003 NEW) + cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW +@@ -20,7 +15,6 @@ if(COMMAND cmake_policy) + endif() + + include (CheckCXXCompilerFlag) +-include (MacroEnsureVersion) + + # Version numbering - should be bumped for each release + # Note that for "beta" releases, we should start at x.90.0 -- we've +@@ -238,16 +232,21 @@ check_type_size(clock_t CLOCK_T) + + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) +- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") +- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the +- # patch level, handle this here: +- if (NOT _gcc_version) +- string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" _gcc_version "${_gcc_version_info}") +- endif () +- macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0) +- macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1) +- macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2) ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0)) ++ set(GCC_IS_NEWER_THAN_4_0 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_0 FALSE) ++ endif() ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0)) ++ set(GCC_IS_NEWER_THAN_4_1 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_1 FALSE) ++ endif() ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0)) ++ set(GCC_IS_NEWER_THAN_4_2 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_2 FALSE) ++ endif() + endif() + + if(UNIX) diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild new file mode 100644 index 000000000000..95161d26d6d6 --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +WX_GTK_VER="3.0-gtk3" + +inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="http://openbabel.org/wiki/Main_Page" +SRC_URI=" + mirror://sourceforge/openbabel/${P}.tar.gz + https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png +" + +# See src/CMakeLists.txt for LIBRARY_VERSION +SLOT="0/5.0.0" +LICENSE="GPL-2" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc openmp test wxwidgets" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sci-libs/inchi + sys-libs/zlib + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] ) +" +DEPEND="${RDEPEND}" +BDEPEND=" + >=dev-util/cmake-2.4.10 + doc? ( app-doc/doxygen ) +" + +DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} ) + +PATCHES=( + "${FILESDIR}"/${P}-gcc10.patch +) + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi +} + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + cmake-utils_src_prepare +} + +src_configure() { + use wxwidgets && setup-wxwidgets + local mycmakeargs=( + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DENABLE_OPENMP=$(usex openmp) + -DBUILD_GUI=$(usex wxwidgets) + ) + + cmake-utils_src_configure +} + +src_install() { + docinto html + dodoc doc/{*.html,*.png} + if use doc ; then + docinto html/API + dodoc -r doc/API/html/* + fi + + make_desktop_entry obgui "Open Babel" "${PN}" + doicon "${DISTDIR}/${PN}.png" + + cmake-utils_src_install +} + +src_test() { + local mycmakeargs=( + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DPYTHON_EXECUTABLE=false + -DOPENMP=$(usex openmp) + -DBUILD_GUI=$(usex wxwidgets) + -DTESTS=$(usex test) + ) + + cmake-utils_src_configure + cmake-utils_src_compile + cmake-utils_src_test -E py +} + +pkg_postinst() { + optfeature "perl support" sci-chemistry/openbabel-perl + optfeature "python support" sci-chemistry/openbabel-python +} diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest index 02b58a98d2f0..8f4bc1240300 100644 --- a/sci-chemistry/povscript+/Manifest +++ b/sci-chemistry/povscript+/Manifest @@ -1,4 +1,4 @@ AUX povscript+-2.1.2.2.19-libpng15.patch 542 BLAKE2B 1fcc229fd3e90a1c567ea42bd87b4b9de281b4976016a0c990f3a66ba2d9d3d8b7eacb80c1caf31326a4c35ff33863d9495b857163ee86bf7060e44debbe19f6 SHA512 5f795238f95adfa0712c92afda669d461cc292b358aa51907ceea1c2d5e5e470d1817d75f461a46efb962ffefafa2606400d32c1f681192f8e161d6e23ee5224 DIST molscript-2.1.2pov2.20.tar.gz 822930 BLAKE2B da050db5124d04e7c0e2c06b0e666d631f214b4519b41ac4b4775dbdbf5be2608f5417f13fad45c36f796d486a8d9211d2fd3d9403afa1b6d27e52b4f0a7f248 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2 -EBUILD povscript+-2.1.2.2.20.ebuild 1263 BLAKE2B 11784b37663618506624aa8f3f9b034ee01c387dbb286c226b01c35fcbf6075bb355ed96d7663f8c46feb9da08d2c92ef06521f1b64d0e9a50ffb3453957d2bb SHA512 54cebb95ef03430d1071a894b2a47f118ae0e952bcacc0f80f3d727aa18912d4701a116c97469bf2a37b28e01fa5fe51cf7aa02fe2fb69134bf98465210d4770 +EBUILD povscript+-2.1.2.2.20.ebuild 1260 BLAKE2B e87e2245fe685e882b8c4d794933a89fbcfb7a2d276f6153f89344e7cc79a240df6a76a27d27e02bea9408f1c88afc2ae79bf980a36f63d6e74a25641dd13e26 SHA512 e47e4402bcf2debf0b539db25971b068a7ca9253adebfdf84788d2aa0e0a12b44afa94e3dcff5559c906c480f98216c0ec211f59dcd0873382ac49ac0c2737b7 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild index 905006c1d66c..a2caada48ed1 100644 --- a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild +++ b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils versionator +inherit epatch versionator V1=$(get_version_component_range 1 ${PV}) V2=$(get_version_component_range 2 ${PV}) diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest index b2c751807965..1578aefbece1 100644 --- a/sci-chemistry/rasmol/Manifest +++ b/sci-chemistry/rasmol/Manifest @@ -3,5 +3,5 @@ AUX rasmol-2.7.5.2-format-security.patch 1617 BLAKE2B d9a083ae6c72724359274da5b6 AUX rasmol-2.7.5.2-glib.h.patch 770 BLAKE2B 1c83587711540a9e2b91b53ffd0836cde27f040c593b7d771eb185edf8e72b50f09d1c38ef0b2510effee95649bbaf3adf7d0340f49a38381bd15200fd94e749 SHA512 d743b89817d0ed2aa551f3a6529e5bcc50c811d79c0deddd50d07a59614cb0c2d71500452ff9aec4b4b84e4985d9851f61aafa30196356aa1724212b5159375e AUX rasmol-2.7.5.2-longlong.patch 396 BLAKE2B 68ce4bff3584bbc6331ad5e27171d23e443be2d24b60bbd45dd02d4f04b5531cfd7fdb18904471c85ef107875fb23574f6b3212b78706746cc73c39d09cda801 SHA512 4c3ce01ade36fe8a9512bdac62bcd47268bcc5a0448f4af69b26d8add9cc8495d376bac33a8ae5aeae42fa114a1cba980ce86559bf2d52334257f2e001c011d3 DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 BLAKE2B dcc9bfe9381ebab6bbf5a12e233490f076ead2388a22e3186421e3489bedde987813b1f65ce7b17ef168389c33d03bd7d4a8162635c0a79b3dc704eade23715d SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f -EBUILD rasmol-2.7.5.2-r2.ebuild 2273 BLAKE2B 44264c14a7f44c7577d4624daad6f6e813d621bc26ab1fbbfa848e8f899fdf5db97c74a2c94ac28252573be824696b1586686123a2cf065df4616ec24b0ab874 SHA512 2a5bd8b137e9490415926cd9d7b29f092703d8ae1d9b4f4aeea958eacfead072086e85ce5741ff644c587c6e7c99d7afb375f66f6bfc3330d936b13d9d611f4b +EBUILD rasmol-2.7.5.2-r2.ebuild 2335 BLAKE2B 3eb46ccf0799da8a5514e963193593ee4319cda48f474c616bb09191e59163c49d922f1c865b43fc5e49abc4e146c0725a66a95527e8ae55aff79368d9ee3ebc SHA512 c67480fea952676dbaee686ca6e6a5c4a7b0750b72ab45247f469c8643ec8a4a46b5d60c89aab531c84666560a3414fc0ccd176dab0ea17094cc7c7db3ff9bc8 MISC metadata.xml 355 BLAKE2B 71f9b1537eea00556419ae1c9920458d86992e3c0b01083d55ca02f162c420f82e8f52ee8af224573912e2b988497901702962ed3b54342991f22e1eec37ce2e SHA512 98822367149551ef6af6d75e4bd0b9104f1a625a5a17e1a2dad32e7ed83345870dc45392525cfe7e49514eae29f986e8ac2ed253ec22fec94d6152f96620b916 diff --git a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild index 6c8eb7c7eea0..534cffb9bba5 100644 --- a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild +++ b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -inherit eutils fortran-2 multilib prefix toolchain-funcs +inherit epatch fortran-2 multilib prefix toolchain-funcs MY_P="RasMol_${PV}" VERS="13May11" @@ -33,7 +33,7 @@ RDEPEND=" DEPEND="${RDEPEND} app-text/rman x11-base/xorg-proto - x11-misc/imake" + >=x11-misc/imake-1.0.8-r1" #S="${WORKDIR}/${PN}-2.7.5-${VERS}" S="${WORKDIR}/RasMol-${PV}" @@ -78,7 +78,8 @@ src_prepare() { mv vector.c v_ector.c || die mv vector.h v_ector.h || die - xmkmf -DGTKWIN || die "xmkmf failed with ${myconf}" + CC="$(tc-getBUILD_CC)" LD="$(tc-getLD)" \ + IMAKECPP="${IMAKECPP:-$(tc-getCPP)}" xmkmf -DGTKWIN || die } src_compile() { diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest index 742af600c3fc..cb9f38fd30e8 100644 --- a/sci-chemistry/theseus/Manifest +++ b/sci-chemistry/theseus/Manifest @@ -1,3 +1,3 @@ DIST theseus_3.3.0.tar.gz 22548124 BLAKE2B 0ad49f768e1584bf40e90ff6fd0d884b6b27ee59ad31ce75050293b817a3747969ab0c4b4ff982aadbdc5301c1c56522540b78aab045e841c099a80dd546c8e9 SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2 -EBUILD theseus-3.3.0.ebuild 1499 BLAKE2B 23e60b603438314d0a5068651cfbbe6a9eeec9569a276ca9695eb4a24a5969ee798265085023c734038aabea515f5c9f6b49876569428da10ad08a62ac5a6327 SHA512 edbe86d80416fa9256b26ee95ae77e3973b2cd171e3a6ab02976127b8dfaa7541a1f35f1500afcc7200140a54bc22309bcbeaaa341b5032e6549fb5e85bfdfda +EBUILD theseus-3.3.0.ebuild 1508 BLAKE2B 26711e23e5c2709dc9addd289c80cd74a877674ebab6bc128d48249cd64cdd7daee2f00e78633e02fb55cc667041dfda3ada6f9354643043be3feacec2d095b6 SHA512 6b2d63c2d988534cb7b0f00e9b5eb20a63c8ad814c38bef94f41fc33d6f2dce826632191ed48952b447995af21958366ad56bef6b9f8b63fafe3085f588fd736 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/theseus/theseus-3.3.0.ebuild b/sci-chemistry/theseus/theseus-3.3.0.ebuild index 583bdf1e28c5..dd9c0b802edc 100644 --- a/sci-chemistry/theseus/theseus-3.3.0.ebuild +++ b/sci-chemistry/theseus/theseus-3.3.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -35,7 +35,7 @@ src_prepare() { ARCHFLAGS = -rvs RANLIB = $(tc-getRANLIB) LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) - SYSLIBS = $(pkg-config --libs gsl) -lpthread + SYSLIBS = $($(tc-getPKG_CONFIG) --libs gsl) -lpthread LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus LIBDIR = -L./lib INSTALLDIR = "${ED}"/usr/bin diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest index cf7d425fd094..58eab1647163 100644 --- a/sci-chemistry/tinker/Manifest +++ b/sci-chemistry/tinker/Manifest @@ -1,4 +1,4 @@ AUX 8.2.1-openmp.patch 559 BLAKE2B 254a7b5d5d40bec938420527ad77e4ec96b9cee50392137eab3370df35a00a00b9488b5cd95c4e3c52d4904a6093216a782f52c82c2141cd913c6cf10f2fbcc7 SHA512 799b488ddba95ec75c2f5f97bdba10e297cad12d23239354b7d66af47b4e9ef1496e8f6b8a7446f85827a8303105af7552616bc865a4e8114b89d3e6e3302ed6 DIST tinker-8.2.1.tar.gz 33015410 BLAKE2B 0b7c94662248761459cf9d681056f5cf9c4d669a790a522f23f800bf355235f6a9f392e008b13d14cf1e17d9725abb6512077c24ff7772108d69c9cf35b43e6e SHA512 5039078781d1ce226456882dd95ad15715f1e91829d26efcdb29ceedc213973883699eb6710b0a162a74208809305b7fee734b175139e6df63d0460fe5751ae7 -EBUILD tinker-8.2.1.ebuild 2247 BLAKE2B ae2b50605eb32edd748884e731dffad61b56c3c4e620cb6db071b032045591cf40ac9ce086e5be8c275f26f863760505edd4cf095233d944a3abb5963aa55e6c SHA512 276d8152b83db1709590fc7be373da5732c81413945f61cccff8135025ff367985f238ae4569a561556a91b748826a3b910ca47cc2d011863bcd5002de514a79 +EBUILD tinker-8.2.1.ebuild 2257 BLAKE2B 3464309efba4ec65effc9fa9c8fbab167116844f51f0101a22b9b964c610458f5daa5324d21affd93880bdd9c00a2b805bc09b1de80cff5dc2f17f45181ebd51 SHA512 51d5cd018b4146e6b68540dc7ec50a5f84c3f4ee2fa71c23417fc0a5005a847cd347d3d2223cdd6366e0a058a03a43ea5d2d1d12dacd7156c3f9f5ea93b01d37 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/tinker/tinker-8.2.1.ebuild b/sci-chemistry/tinker/tinker-8.2.1.ebuild index 5dfafe90e1f4..d181dee95c44 100644 --- a/sci-chemistry/tinker/tinker-8.2.1.ebuild +++ b/sci-chemistry/tinker/tinker-8.2.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs +inherit flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" HOMEPAGE="http://dasher.wustl.edu/tinker/" @@ -15,14 +15,16 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="examples" DEPEND=" - >=virtual/jdk-1.6" - + >=virtual/jdk-1.6 + virtual/pkgconfig +" RDEPEND=" >=sci-libs/fftw-3.2.2-r1[fortran,threads] dev-libs/maloc !sys-apps/bar !dev-util/diffuse - >=virtual/jre-1.6" + >=virtual/jre-1.6 +" RESTRICT="mirror" diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index d45414d9fe6a..ddc5a5ef1eaf 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -1,17 +1,13 @@ DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c DIST votca-csg-1.6.4.tar.gz 537966 BLAKE2B c9ccc3aa28bdc4a2a2c080104b70602d8cf4be19a71e7d0b4a1c03d11f54b645984103d1662823a9308a4e4c4baedef731de06ff314b168f89e7326c0d3c8ee9 SHA512 4cdbf6c0a593720675f48f574ff9a93d038a48037543c1e09a4559d3eb262a2d8bf83d5f5dab85b4820a541e0c57f7cca78315d5b3382763e8acd8cc0fcb65ac -DIST votca-csg-1.6.tar.gz 464175 BLAKE2B 1871c7edc4b4e848a06049a7c687e906f166312777bdbf5c65be8efe8d5032582fdca9dc7eca453b7013901f409326b0583c79731c68fa2b4e6366f021958b0b SHA512 76cda93023d46a66ae31edcec0ece709ddc70a9be9d098721b945006c197ed3b6cbd1e643158797be518c4fe66f7b23d3e8d8735cbd9e155db3db0d79929cfbe DIST votca-csg-2021.tar.gz 4300573 BLAKE2B ba589c97f22888b8a1a12c71314133c08c89e44c201bafa6e5f1d74dfe90c87dd84a5d1c2883b26402858b6aa990d37add57bdfb9db6836a7c287f0685a40a59 SHA512 8eacf4045ddc13d33e853cd35a67d03dfb63da60c3e879ea4f16e63f27a92aa13cbf4e367d9258778c9c09462443e4bb2b937c247c6246377ceeecf56bc6fc12 DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642 DIST votca-csg-manual-1.6.4.pdf 1242124 BLAKE2B 003a255d2869c8185f9e03038f646a80b682be3daceb18757c791f5d52101379402aee20c5dcb65ef8ce651bd6f6590ad5249e835e53ce92e04eb33214017a9e SHA512 36956acd24a21cb0a1dd26d6640b41b7473132948327c05856191b4f9531b4d1d5f98be68a9d1a847935d47633d483e87c2300634233a6e617a010c1fb563690 -DIST votca-csg-manual-1.6.pdf 1248178 BLAKE2B 5213d55787041db81fe8563febbf130db6aed9233e569039b66d69cfb173131353d45bef824640ee7b0a3fed7821ede4d5a6ce6ffc14d1548499317afdc0248a SHA512 e91d4b8397b67808c9671b9adbaad41fd9a0ede90066e220839d86f21a9bbcd4e433534faf1dfbca106d55af5a6cce0425a5bdfa3eb30ebe14469594da0129ca DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c DIST votca-csg-tutorials-1.6.4.tar.gz 5944389 BLAKE2B 66f1d4947bb28ec602250226ad2c08cc02278a90776acbcadca2df3078361435fb2353ee0fa299d0d19697d36682f20aab709d45539d5ac7e7070942601ebc3f SHA512 7e40037f2e70c861fd7f5c63806c17ad56672a340a8795fa745414940c55f593bef32b9f6b9050400131ed9e66aa927149e9d324a1c264364d8504baf1921e28 -DIST votca-csg-tutorials-1.6.tar.gz 5946764 BLAKE2B 018bd00c86c0a85baf35afd2ea4206c96dee8f948dcbf331b53e6f685b69bf2c909731b15ba3261c86cee9e1960ec5cfa7b2ee0c6dcfabbbbc110789840184ad SHA512 36d3a66c19d230f2002170851345da7063aeef1f29841945b8a182f73922617823815dde5d7289fb0f80e771ac03780adacdf95af4814235edbf69a4772b3696 DIST votca-csg-tutorials-2021.tar.gz 5942031 BLAKE2B 60ef492c98bf07b5169c6f1be2298b6dac76003ef9981064463de9fdae649c215d469424e253d06b63637bb3eee9383c587a98322ab987995f8b4861bb0002e1 SHA512 844706407cb91d507c6b0433e23f4b27756dd4c882f6cef79d51f2b2acae6cd0114ccd91d626d090d0f61c58a57cc3c1eda0a0d10d6f4bfa522eda7ee8de21b3 EBUILD votca-csg-1.5.1.ebuild 2522 BLAKE2B 0fe2b373307c76ebab320169b5ae837c463a734b029af1a328a87c2428b19484f138c75e7bb1e4ad91d0c099aa24c97c411c2f00308ebad051a81d0275e797be SHA512 2c6018212ae244e7387a2f63e186e970dd18825d77994f862c283131796ac93c6bb25a5233a41e306d8090ee75c82759025b74c3d1e0a0211adf67e0b3964449 -EBUILD votca-csg-1.6.4.ebuild 2292 BLAKE2B 09218b100241e4025010215d975195b7d6f17343f4dce8d4a0e1c18b8c2c99d7fba8f0a8e8372ea8a543cd13b96514e2c2e3bec61ba23ce99031c107f30600fb SHA512 68d528d8b8496c65ec30ec8552baf9bd8b74d75ecafb3972c19e3b1d13214dc93215f5f50c96cd7ef0e86cdfce53d1a9da83514c5babc673dd6763a1657464b5 -EBUILD votca-csg-1.6.ebuild 2332 BLAKE2B 4241ebb2ab2c45fdd192eee0fc1ff111ddfa025ac5c1ff0fb98e551ff842ec91b3c299e8e662dedfbc5783707c107ac94df79d18747dba2f7a5e5853e7d4b38e SHA512 e821e4a31d4811abaa8fd05e225ab090c2d67d7bc2e3c399d544ae22fb14a4f6bb2e4f9ce94ecabd11b5c3fe0623523efc2d93fde3428bb6b5d492b366803216 +EBUILD votca-csg-1.6.4.ebuild 2290 BLAKE2B 1fa3398fce620103e69529a1b36f1b21fac4ff633ed602f218a61f8c41471376842c7e51e428bf6da165f225be8c54a6c76107fee7fd691c3cbf2a7fdcfcb6c8 SHA512 b794120a45fc6616873b31989e3d7df64c545673305ef714c189dce6f2725ab2f93e2e5625f38bf34fe6711583088e947ef3407e902ec0be5b5babac72316458 EBUILD votca-csg-2021.ebuild 2033 BLAKE2B 77fc10474aff5882c3d99133175f67ee51704dd1a32e101a42afb5e4417f3c478b4311f9ed619d62c1eab13328b130cfb1e500ff1e890c518adc0b1fcf167c6c SHA512 de1e8c1d9cb22e75ebc8dc7c043aafb04dce6eaf3d7173f1e745a6578b7236e9f71ce3b75fa5698333eca7c5c74a41337eba3fb4cd5c037e8bf3172bf78296eb EBUILD votca-csg-9999.ebuild 2072 BLAKE2B 1b13ee8b2bd47a7bd17fbddf1cc46f3ac38a21ba4c2d6d5a453ef3c55e2894b31c20c0f32d2b335b76d76ca56df6838b2ed6a616ee96e9dcb6fb7981f2f10346 SHA512 561f20660a4db6bca57c3bcf10c69aab2834b0a054c2ce95245a52536a1064c1481840001594cf2bcc4c060e3c407078d9d0b67497bd861d3f0a1df6b0ba3678 MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 diff --git a/sci-chemistry/votca-csg/votca-csg-1.6.4.ebuild b/sci-chemistry/votca-csg/votca-csg-1.6.4.ebuild index 4a22a2fb7665..12ea52d3312e 100644 --- a/sci-chemistry/votca-csg/votca-csg-1.6.4.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-1.6.4.ebuild @@ -13,7 +13,7 @@ else SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" - KEYWORDS="~amd64 ~x86 ~amd64-linux" + KEYWORDS="amd64 x86 ~amd64-linux" S="${WORKDIR}/${P#votca-}" PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" fi diff --git a/sci-chemistry/votca-csg/votca-csg-1.6.ebuild b/sci-chemistry/votca-csg/votca-csg-1.6.ebuild deleted file mode 100644 index 6af82c74dd7b..000000000000 --- a/sci-chemistry/votca-csg/votca-csg-1.6.ebuild +++ /dev/null @@ -1,91 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils multilib - -IUSE="doc examples extras +gromacs hdf5" -PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" -if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz - doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) - examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" - KEYWORDS="amd64 x86 ~amd64-linux" - S="${WORKDIR}/${P#votca-}" -else - inherit git-r3 - EGIT_REPO_URI="https://github.com/${PN/-//}.git" - PDEPEND="${PDEPEND} doc? ( ~app-doc/${PN}-manual-${PV} )" -fi - -DESCRIPTION="Votca coarse-graining engine" -HOMEPAGE="http://www.votca.org" - -LICENSE="Apache-2.0" -SLOT="0" - -RDEPEND=" - ~sci-libs/votca-tools-${PV} - >=dev-cpp/eigen-3.3 - gromacs? ( sci-chemistry/gromacs:= ) - hdf5? ( sci-libs/hdf5 ) - dev-lang/perl - app-shells/bash:*" - -DEPEND="${RDEPEND} - >=app-text/txt2tags-2.5 - virtual/pkgconfig" - -DOCS=( README.md NOTICE CHANGELOG.md ) - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use examples; then - EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" - EGIT_BRANCH="master" - EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ - git-r3_src_unpack - fi - fi -} - -src_configure() { - mycmakeargs=( - -DWITH_GMX=$(usex gromacs) - -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5') - -DWITH_RC_FILES=OFF - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call - for i in "${ED}"/usr/bin/csg_*; do - [[ ${i} = *csg_call ]] && continue - bashcomp_alias csg_call "${i##*/}" - done - if use doc; then - [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" - fi - if use examples; then - insinto "/usr/share/doc/${PF}/tutorials" - docompress -x "/usr/share/doc/${PF}/tutorials" - rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* - doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* - fi -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " - einfo "https://dx.doi.org/10.1021/ct900369w" - einfo -} diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest index d265f8690db9..3dee00de8140 100644 --- a/sci-chemistry/votca-csgapps/Manifest +++ b/sci-chemistry/votca-csgapps/Manifest @@ -1,7 +1,5 @@ DIST votca-csgapps-1.5.1.tar.gz 26006 BLAKE2B 8651978c15087fc7332fe229cfc33d8c4257faf46d72f7ac5fbaaf5f31133c4df3d97cae2b18730b5700e742c27e3db39696fdfe910ed884952ba0f832220c3d SHA512 4f83a46f16eb0a4cb9acc6c0d9523fa746dcf670107355c95fc02daa6ca91fb4f8d5e48bc920d8c13a9445390a25415f7217979903ea86f890df1d4704944c28 DIST votca-csgapps-1.6.4.tar.gz 19589 BLAKE2B 90a20c3acef3254b412697dbb543c216d4546241c2f98d8b1e6c7fbd2de5dc5268965f1035843c6832579158843069c610ebbf3363d2e604a1c7c3dc82e3d8d2 SHA512 89ea658092e979c90b9f3d75a8dd9f8ec95278c26fafb30c31a23581dcd7a65e52c8c7696ef14da5821e283d16ab96880041b7b20c9097f99b2fc1eac4a38184 -DIST votca-csgapps-1.6.tar.gz 20130 BLAKE2B 0c34fba42a70f756043aae89f51b94cc0a9c9a85680ed78c56b4c05f834d94c74aff59e4adf6155e5fab81d057da58ec420d843532af57beeaa6e81f82432d92 SHA512 5a85abaf6b09a225604f33f2e0cfb774525159e9bce89efd7ebfc0c9c37342e472503ff51c3065be2a4b87e95671f55164c630477f404f94b0510a83e262352f EBUILD votca-csgapps-1.5.1.ebuild 638 BLAKE2B 4aab8967b46b38c2202ff567618f8903ae07784d413d3204e5951febfee11bef58b66915f7d441e91a185267b61b72ef77c4c9d476274ec48bf1be9007c49896 SHA512 c2c959e0e9f551807d4cc395346159529669b4ad87b6550a20d281c4a27e93dd98d6288869b9bd9548e2f228fe451ed4327351faa6340518c6be3e074c1f0bc7 -EBUILD votca-csgapps-1.6.4.ebuild 602 BLAKE2B 971f950ceae2c75e048cd710be75d5bc6d35b77e4d6944ef03fa8d812705017f094c94119910b376a75afe3cf41805759293edc441d98cfdc46e389f6df43835 SHA512 b577565d5d5b8d38643c6e4b3e0c5159bb3c2d96e97f232fbe776790d5785ba1e1c5046fce2e940ce3ff2910d236ffb02cf2984c0e44e50e33a447dbad9da8e0 -EBUILD votca-csgapps-1.6.ebuild 639 BLAKE2B e13211e82d52b68a1e8b734b79b0c3541e4c356749ece251750f0ae4bce7d05aeaf0116061a185e4a69aff487e9fa21922d498b802363aa69f70feee064ebcc1 SHA512 c17fee9eb368026bd7ab2cc242ae1df456d68439ed13b4d8feaa54a26c70a1472effa2dac773f0d5d6ab78110622a94cb30cd54bea765760acd8b352f41c6897 +EBUILD votca-csgapps-1.6.4.ebuild 600 BLAKE2B 1c09b68b2bf4497dd45335823296fbc3ec9e11c12588ed1d7d1ba261bc61d14b7260c2618922cfa09f7303525ed3fec4c1d744fb855f05ae29001c53ef2d9a4d SHA512 5203f67e3ac3c96f807ba42d7ce6b9daccdf71fb51422e204908092e44a5ddb89eb33a5c44ea6dbf571cf7ad2b5f3c826d01ce90a51f64514c61ae41473dd1f2 MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563 diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.4.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.4.ebuild index bc3c61b39c2a..132c6fce4013 100644 --- a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.4.ebuild +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.4.ebuild @@ -10,7 +10,7 @@ if [[ ${PV} == *9999 ]]; then EGIT_REPO_URI="https://github.com/${PN/-//}.git" else SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux" + KEYWORDS="amd64 x86 ~amd64-linux" S="${WORKDIR}/${P#votca-}" fi diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.6.ebuild deleted file mode 100644 index c3d00dcd7af6..000000000000 --- a/sci-chemistry/votca-csgapps/votca-csgapps-1.6.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit cmake-utils - -if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="amd64 x86 ~amd64-linux" - S="${WORKDIR}/${P#votca-}" -else - inherit git-r3 - EGIT_REPO_URI="https://github.com/${PN/-//}.git" -fi - -DESCRIPTION="Extra applications for votca-csg" -HOMEPAGE="http://www.votca.org" - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="" - -RDEPEND=" - >=dev-cpp/eigen-3.3 - ~sci-chemistry/${PN%apps}-${PV}" - -DEPEND="${RDEPEND}" - -DOCS=( README.md ) diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest index 41b68fe052cd..a720c673de91 100644 --- a/sci-chemistry/votca-xtp/Manifest +++ b/sci-chemistry/votca-xtp/Manifest @@ -1,8 +1,6 @@ DIST votca-xtp-1.6.4.tar.gz 1405299 BLAKE2B 9d4e9d3f87e0c6be886df77bf52f9d8c0b4010fb1d77621a51b739986f3f5d70c85637c0d7b4d6a8a06d7dfc7e70ff5491bdc833a1b9da6fe1e8a9742a82d220 SHA512 f35e9605f4ac92547c801b254de792b5c3bf40200e8636869467997412357251df08f88ad851bc76cb0ba15428f06f28dbd4f64043a7612273468c8d653e52af -DIST votca-xtp-1.6.tar.gz 1404955 BLAKE2B 1599281ea1cd6b5a93b1d91f69a793af7bb9cd2fbf70157e5d40a5bfc72f973f3d97338f92157c2c482ad041f8afda298282b1f83dda66d0bb189bdc07bb5a23 SHA512 cb99c31fe7f1af53b8ccf50cc9cc304ed5c5b5d1a165e1a72a456c0bbf5ac8bb9263c9eff829acc74be348192afbf80fd4d80a2c20d1dd5d7f909b1b50368670 DIST votca-xtp-2021.tar.gz 2192166 BLAKE2B bcacdfe92b8c9fbbe2fe949d7096c09928ef7ece3cc4e40adbf58f2894036588762f9905bce1a1595bea99d1dfb8bcd99f395bed2ce7b94eeaf51b1c33719558 SHA512 1444fd0a64a684fd2b1327a9c3af067ea812190fa95cab5f3bfcc7aae932cc7469d07fc219871ca594496fbfe74e277d3b6ccfbd7d5c24c162623515ee2fef0b -EBUILD votca-xtp-1.6.4.ebuild 918 BLAKE2B 5ed068af82c39ebe9a67e34157f4382a0b79048110305660eeac7d714d21376768ad63c6311f218d7c58c757201472190c69b6bbdc570fcd28d34291f9f20568 SHA512 370253c1fe351fe528502b221cd7c7f1cd05331313fbbfd974ef0ba2c85f8247fbe9d2fbe14ca180954b04e52c33458c636f4a1c41eda78ed689fc26723e117a -EBUILD votca-xtp-1.6.ebuild 955 BLAKE2B 02248b9fd6aff495ba7362e836e78540c489696c8035b2dc36494d2574a4eabdb9e89e41f277ca59e1b6b0fc0929ed2e1ed5d4fb7a302b7f3ee4c02199006004 SHA512 c7094ef6df89b323ab69f7dc369bbf88758c35803dcfa8bf2acc9390b34fc556aef3917c1167b8303870c85b507940798a4286460483ecb8a7016baa762728c5 +EBUILD votca-xtp-1.6.4.ebuild 916 BLAKE2B 3f322407b39ca300186e1e283a6a85749b79518cbd7355577992fc4eeb7931c419e018a384a29d1e84becc5a7c94f7905c96d26cf6a750a9b0124ea35a40bd7a SHA512 65a479d3292c7296cbfb6543fe47e54f2824705dcbc2b2e75f6f2f4fda9f827ce15904aacff59c927061547a45c940eebef4f4fa3e3bcb226f401a6817dd74fc EBUILD votca-xtp-2021.ebuild 943 BLAKE2B a0596dab1f69c3c8e9afb3699b44ab0e49cd4e8f5ef6a397eed39ed051e13f0b457ca0b0e225329dcf73bc58799d4e3fc217805784f936d9e1ee09c3586bd998 SHA512 9c4688a19b3a4ef75c79a0500f253aaa1a99d38ed4e56948e4743ea03e734e613be845b56d084c67d783a8e76cd4ebc2888b94bfe3c6e67a9799bc22af6ff19b EBUILD votca-xtp-9999.ebuild 1073 BLAKE2B a9c1b41b9c84fdc31a6203714b183bb5d119e14e4a7e7c439d854c8f484bfab1e7f7f547b47ca059a080d667db36acf1311f406c83bcae3cfadd99c2262b8c39 SHA512 158015f6f79d215ab8a443cec0b104992e3ccea07356ea7a1c24790d8f0ee67eacff1f238fac30a5f9f522b131a599d6ea9fc6ed943c9889203826c7a9ea8849 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6.4.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6.4.ebuild index d9f436b0316c..6a0bba5928b3 100644 --- a/sci-chemistry/votca-xtp/votca-xtp-1.6.4.ebuild +++ b/sci-chemistry/votca-xtp/votca-xtp-1.6.4.ebuild @@ -10,7 +10,7 @@ if [[ ${PV} == *9999 ]]; then EGIT_REPO_URI="https://github.com/${PN/-//}.git" else SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux" + KEYWORDS="amd64 x86 ~amd64-linux" S="${WORKDIR}/${P#votca-}" fi diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6.ebuild deleted file mode 100644 index f05d152ddbf8..000000000000 --- a/sci-chemistry/votca-xtp/votca-xtp-1.6.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils multilib - -IUSE="" -if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="amd64 x86 ~amd64-linux" - S="${WORKDIR}/${P#votca-}" -else - inherit git-r3 - EGIT_REPO_URI="https://github.com/${PN/-//}.git" -fi - -DESCRIPTION="Votca excitation and charge properties module" -HOMEPAGE="http://www.votca.org" - -LICENSE="Apache-2.0" -SLOT="0" - -RDEPEND=" - ~sci-libs/votca-tools-${PV} - >=dev-cpp/eigen-3.3 - sci-libs/hdf5[cxx] - ~sci-chemistry/votca-csg-${PV} - sci-libs/libxc" - -DEPEND="${RDEPEND} - virtual/pkgconfig" - -DOCS=( README.md NOTICE CHANGELOG.md ) - -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 -} diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest index 4debb3518814..bfd3f0f96752 100644 --- a/sci-chemistry/wxmacmolplt/Manifest +++ b/sci-chemistry/wxmacmolplt/Manifest @@ -1,4 +1,4 @@ -AUX wxmacmolplt-7.5-glew.patch 415 BLAKE2B 733398664fae6fa3a6d11026a085010381998c68b2032958e3c7aa6516eb8578d08656b0ff5fcd2742c52f8b20053241a140b207ca08509396dd7177ed5247b4 SHA512 4d15247fbb5c2d9a60e7427b2c2f91d8a8f82cc457c681687f3046eda8e913125a0e041fd5d28744e0b12fe96b71280432b27bcdea5b7a8af7718b2f2d820d9e +AUX wxmacmolplt-7.5-glew.patch 232 BLAKE2B 9e0bd2849cc20664ca4a6b6678d2d78a723ae3e730225355dd70db0cac56d501c14aaa34d86d2ff87932feb950178a7245a943b763bde728f64a07a49ed4ba29 SHA512 cf1f77f9a86224b866f55154316a044314fda47a82de9b5be4ee58ed4ea8f4a07f9540e7060f477249b773e147739f15f43df293110045bdbca9567c60fbd5dc DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0 -EBUILD wxmacmolplt-7.5-r1.ebuild 930 BLAKE2B 5eedb7b7ba03b601a466ab9058fb0e2c1bea1d6da37ec0641fa15be58bbe616f358b5683cb21531c1b66b64d66ac0d9ce7ed5235d010dbab177da4ae1f25c95c SHA512 4306d954b510e242a4ede6bdf56c53ea5b2e73e9d8ddcfc9fd8ffe52e8bcceae7b3e9b7d327f87e8005c919b3c061d501838001cf7f2b935db9ef359be7946d8 +EBUILD wxmacmolplt-7.5-r1.ebuild 986 BLAKE2B 67cccea1d2e7886ee67f78ac54548047c2fe889dedfef45956a4614149d5597fd0376f0f01fd59085c9f925faa2284c2c22d4bae2d8ee98f2eca3be6b06e96ed SHA512 6e1d9051621a36deb7aeb997aa93a0b5becea1b3f7512fc56d2ee97788b5a9bedace25fb40a7a7b4e77a76830e7f8aa61ad0c32ea3e1afdb66b744197d50daf0 MISC metadata.xml 635 BLAKE2B 16b84b540cfe7fd49b9087c530ee49e035fc930a392dfaaef798338b3361c2b1d11626020d56de871066998f0e88ab39c3a6fac0633b3f8b07864a9c3424d0ae SHA512 d9bddd02379c3a39633028fbc6d0645ea9c46c344781e2c754539afa35577967a02e5c44278ec0fa015d0b9ba7f8fdeb0c9ad14d72d6abcaba85d0021c426f76 diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch index 08986db5bff2..809d7723cbb0 100644 --- a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch +++ b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch @@ -1,12 +1,11 @@ -diff -urN wxmacmolplt-7.4.2.orig/configure.ac wxmacmolplt-7.4.2/configure.ac ---- wxmacmolplt-7.4.2.orig/configure.ac 2010-12-05 02:48:29.000000000 +0300 -+++ wxmacmolplt-7.4.2/configure.ac 2010-12-06 19:30:24.000000000 +0300 +--- a/configure.ac ++++ b/configure.ac @@ -20,7 +20,7 @@ ;; *) HOST=LINUX - LIBGL="-lGL -lGLU" -+ LIBGL=`pkg-config --libs glu glew` ++ LIBGL=`${PKG_CONFIG} --libs glu glew` ;; esac AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW]) diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild index b102cd19a244..d100dad51cbc 100644 --- a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild +++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild @@ -1,31 +1,30 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 WX_GTK_VER=3.0 - -inherit autotools eutils wxwidgets +inherit autotools desktop toolchain-funcs wxwidgets DESCRIPTION="Chemical 3D graphics program with GAMESS input builder" HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/" SRC_URI="https://wxmacmolplt.googlecode.com/files/${P}.tar.gz" LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" SLOT="0" -IUSE="" +KEYWORDS="~amd64 ~x86" RDEPEND=" media-libs/glew:0= media-libs/mesa[X(+)] x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]" -DEPEND="${RDEPEND} - virtual/pkgconfig" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-glew.patch ) src_prepare() { - need-wxwidgets unicode - epatch "${FILESDIR}"/${P}-glew.patch + default sed \ -e "/^dist_doc_DATA/d" \ -i Makefile.am || die "Failed to disable installation of LICENSE file" @@ -33,6 +32,9 @@ src_prepare() { } src_configure() { + tc-export PKG_CONFIG + + setup-wxwidgets unicode econf \ --with-glew \ --without-ming @@ -40,6 +42,7 @@ src_configure() { src_install() { default + doicon resources/${PN}.png make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;" } |