diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2020-09-23 10:22:15 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2020-09-23 10:22:15 +0100 |
| commit | 8b4ace9c50842c5b83401ea7b179dcab940387e1 (patch) | |
| tree | 230f3135ceaace633cf93e9838b185c4a6664c2e /sci-chemistry | |
| parent | 9ee6d97c2883d42f204a533a8bc1f4562df778fb (diff) | |
gentoo resync : 23.09.2020
Diffstat (limited to 'sci-chemistry')
60 files changed, 435 insertions, 1736 deletions
diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild index 00d480b169c3..688fa93d394c 100644 --- a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild +++ b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild @@ -18,7 +18,7 @@ IUSE="test" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] sci-biology/biopython[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] dev-python/GridDataFormats[${PYTHON_USEDEP}] diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest index cb8b89ffd481..a9f769d9da07 100644 --- a/sci-chemistry/MDAnalysis/Manifest +++ b/sci-chemistry/MDAnalysis/Manifest @@ -1,3 +1,3 @@ DIST MDAnalysis-0.18.0.tar.gz 11085390 BLAKE2B 70b5530a0800370fbee2805d8c4cb495f2e339b29c13c0a2442e3310c1b941ccf459a19d0a490c47a28b77ffeeaca581100ef06b7196cb9fcdb1b71d5d0c871f SHA512 b235471c04ab2e117fe25e972d88a6245b1641f96d30eafd2f68949c8af8c1360eed49b1ec9960d8c386c0bbca8b3749cec322eb19f9975f15225983af0f5819 -EBUILD MDAnalysis-0.18.0-r1.ebuild 923 BLAKE2B c8a5b31505859c662c0c9fc6d238d778b5f2d32074fdd5be037311d6f8cfe6110ff08cb55e8d94670ebb132dabd089dde2c7d6d45c8d6e62b4834f328eeb2c61 SHA512 24448a1859e49017dfd28e4e3a0e55c38c3efec7cc9bef4d620813f30c2d9c622eb5d4198ee06e19f604be5046a818c850a9b778090ab2bc1f5d484ea7c3cd8c +EBUILD MDAnalysis-0.18.0-r1.ebuild 925 BLAKE2B 013879930fd02094967db072867f5d38b481ccd8112f787590be32d1e73b8cfa1726d58d3bbf206d5341285316283865779023cfd71c8d9cce7e634b2b4cddfd SHA512 9ed907cce72e7b9a416a2eae4d2bd7219f582c37278c49d4523d79aa151718a2af19f406a99f03fa1a44a58396de80e61d309c8294e198721a9d7dcc98f84667 MISC metadata.xml 496 BLAKE2B 1b6faf13663ab39bbb2c5b123f67cd7688c188459133d77411c857bd901f8133f9791d8c54e8fe7dc84e8150187b6562f297e706d36e167b3c20cf7df6e6a682 SHA512 674265a9bdb74cc5d4b059ce2b33cdba84bee097bb5940b3cc55cfdc6b74de5f28a4cfa34e9f0fd4db5d3c336a6f7b3be39235c2d9697d5adf9c7311e348d8a1 diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 01116e7b4fff..fe2ae16e7a21 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest deleted file mode 100644 index 40f5ac7b64e8..000000000000 --- a/sci-chemistry/ParmEd/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -DIST ParmEd-2.7.3.tar.gz 34494858 BLAKE2B 8e3ac8776f30ac73b06fd2241e5d73ba54517805ffcef7cb2f71281248df4f8afdaa05c2186ff50ba0df45df313ebdecd69a4482c8339d41baf804c37069affe SHA512 a3444f915e188bcc924f28b6b4235246e2c063ae98881c48f6e13ebc685d085d6a1bcb61b29509a343cbe58369bc6233acc20ee620c6f1d42da2033772a12e07 -DIST ParmEd-3.0.3.tar.gz 35159355 BLAKE2B 76b4655905276fe498f38c6a3bd483e89e95d3a339fbcd9ceb90d16f68d417b62e0aacaf18143d0b57167ee7acdc726c44324c844462af4d2385872210daef2a SHA512 60b8ee100a301fbddec8323a3dba550c96ffa09624f41e457d4b3941a4e4a15e903c3da6de24a5183731406f19f9e6436a2111d654bc902c0f06ac8b643acf09 -EBUILD ParmEd-2.7.3.ebuild 817 BLAKE2B 11ac051d0c48b5f1a495b5d51762ba7abe352802e26a62ca66dd8a503fb4ffcb2cd95cfd64ac8e3d9010a9ca6ea76ca307541faeba69ced29534858725ef40dd SHA512 16a9979dbbb21e724655a3e536b7ac3edf73a6f85c607ca96d708b49dd73822056e263e77b9bbe049aa5273f9b0b9b05e1bf5d27fc14a2bffa8d475c8829ecee -EBUILD ParmEd-3.0.3.ebuild 818 BLAKE2B ef854aea1fe59b8724a62311e22442313a7ce1002a86f02410f3c7c9788eae80954ce23f8c2c5ad0902842cf3310864e83a79fa55908b5dbf1bea06ae67d3422 SHA512 ff1b52ffb0e74fa8941bd78bce65b2fd2bca2e3eb1d63bd26c2ecc64c9a9d8c004d4e9bc6b6bca3c34a8495d20ed30814526b78d101f23cb643c263ae19466df -MISC metadata.xml 468 BLAKE2B 2e3781c6ebea297fb8480c2d54be22da0e8d6906607513e3b78fe89a926cf691048fb90576cadde7321d964e8269950437f48bb54270c9a1bd487bfe3ce30b84 SHA512 47e3516aabe02112a52e851ac9294a0096001373d546462f9185754356c72dd37a0a8efa3b40311e43e27e2953ea5879c1141488649f3faef0aa43a692205499 diff --git a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild deleted file mode 100644 index b7a964b81652..000000000000 --- a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -if [[ $PV = *9999* ]]; then - scm_eclass=git-2 - EGIT_REPO_URI="https://github.com/${PN}/${PN}.git" - SRC_URI="" - KEYWORDS="" -else - scm_eclass=vcs-snapshot - SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -inherit eutils distutils-r1 ${scm_eclass} - -DESCRIPTION="Parameter/topology editor and molecular simulator" -HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html" - -LICENSE="LGPL-2" -SLOT="0" -IUSE="" - -DEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" - -RDEPEND="${DEPEND}" - -src_prepare() { - sed \ - -e "/delfile/d" \ - -e "/deldir/d" \ - -i setup.py || die - distutils-r1_src_prepare -} diff --git a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild deleted file mode 100644 index 37f959acdc6e..000000000000 --- a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -if [[ $PV = *9999* ]]; then - scm_eclass=git-r3 - EGIT_REPO_URI="https://github.com/${PN}/${PN}.git" - SRC_URI="" - KEYWORDS="" -else - scm_eclass=vcs-snapshot - SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -inherit eutils distutils-r1 ${scm_eclass} - -DESCRIPTION="Parameter/topology editor and molecular simulator" -HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html" - -LICENSE="LGPL-2" -SLOT="0" -IUSE="" - -DEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" - -RDEPEND="${DEPEND}" - -src_prepare() { - sed \ - -e "/delfile/d" \ - -e "/deldir/d" \ - -i setup.py || die - distutils-r1_src_prepare -} diff --git a/sci-chemistry/ParmEd/metadata.xml b/sci-chemistry/ParmEd/metadata.xml deleted file mode 100644 index 6272f2698a54..000000000000 --- a/sci-chemistry/ParmEd/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="github">ParmEd/ParmEd</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index 446ce0b434b9..82d5059b60d1 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,6 +1,6 @@ AUX chemex-2018.10.2-tests-package.patch 418 BLAKE2B 7547e44f73bba8f48dda46e1867cff75a4343b26732b59b011470a7a8143bc0b17c7a7f87d97672239b679406fc54662d68f04e2b1548adddd723ecced954205 SHA512 5e3c58ab4ba271672381308177c462e0813a2e43ced602090b527d99be3e3f38f53f822cfe62ed8f841a16f4c04a933f4ed08d2e71c04777745298e3354bfb4a DIST chemex-2018.10.2.tar.gz 546575 BLAKE2B c36ae3bc152459844633276ab286b6f750ed5b2538c4289ceb75de9a081ad74fe346a79357fd6fc2f8972722b3520473262c4d623e46d6a4b30395962164a51f SHA512 f8ed017c0881ea9188e150456827e2c6302bdfe546c8058bd0261e43d941fbd1ac9e6abf1621d82107a4f6bd4e9aa4bc70c46e42dc98eabf2dba45a4fa78f77e DIST chemex-2018.10.3.tar.gz 546696 BLAKE2B d283cfb94118686f1974780249641e0ea6f86cdb854c4a256897e361a300a94506813a5035ee2f300fca13263e8452b77e7a0817436cbd620ba16d801a541af7 SHA512 784bd03b354724d6aa52d663c6f661f865d4ef7ca345573bc8aae9ef63e5dbb3e65abba364de3ff441b78adfa588344c718809c5880b3fc70d8ed24be06a0826 -EBUILD chemex-2018.10.2.ebuild 1155 BLAKE2B caf445596bf98c1b0fccaf1c894c23937fb2087d149254ff07bf1cd4d4c47acd4526f733f6c86739cb6206a73bf98b9b8f34fc074ed9d7d3f5ddb0551c34d8bc SHA512 c330644a70739efd68293d0cb9295bd3bae0635747fd402ab1b9ebd1d18e239f88eeadd95209e2cd660c0d1151e31c7d4bbfea9ed3493888360fcec57f287724 -EBUILD chemex-2018.10.3.ebuild 1051 BLAKE2B b021e1ccff297a6cee7aa940e45c64b8067c109ac2f9c2d03825ee9ce86a7f4d215111ad0c8a66877d13f224cd6bba7bb781caf86903d7dab27e6df3f8dce048 SHA512 7eb418b6d8443cada7146755fe011862d90e0c5d2085ed6b565dea1fba530bcff6464261e8e73eeeb5e09d354b84e41e717c40a81d84a18c7fa84fcd01a1a0e3 +EBUILD chemex-2018.10.2.ebuild 1157 BLAKE2B 53801ad283382f7d1edb55611c0d8696c1c40e2cf2c6074f5a3feb2bc4c7b378cd567a4a8cd458143f7ecba2decb1c50818ec3b0a36e998805b411da20979708 SHA512 d214a52e33a8b47a16c2f43b228855d96f8bcf62fa66dc0956a13e4498e64aa338b1c623d28b329599026b913a598ed3353f31bc51f1d46b526d213600a406a7 +EBUILD chemex-2018.10.3.ebuild 1053 BLAKE2B 4f4e380c52f45f435168c506e77a02404c385c0ead97b281583a440d8c2f7e0791698ffb47acda20e8d97f6bd2aeb1f098f94afb8ecc39f08f8ab9f3a59b4202 SHA512 9edf9f46e4fa5fd2ced2cbbea6f92c64da9bd24f94369d54359a6e72d13e590918f7506cd2ddd03c53e28ba45161ef6e0f825befb4bbdc90252b2cface229d42 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6 diff --git a/sci-chemistry/chemex/chemex-2018.10.2.ebuild b/sci-chemistry/chemex/chemex-2018.10.2.ebuild index 99f888adb024..b73bd7a2fa61 100644 --- a/sci-chemistry/chemex/chemex-2018.10.2.ebuild +++ b/sci-chemistry/chemex/chemex-2018.10.2.ebuild @@ -25,7 +25,7 @@ RDEPEND=" >=dev-python/matplotlib-1.1[${PYTHON_MULTI_USEDEP}] dev-python/numpy[${PYTHON_MULTI_USEDEP}] dev-python/setuptools_scm[${PYTHON_MULTI_USEDEP}] - >=sci-libs/scipy-0.11[${PYTHON_MULTI_USEDEP}] + >=dev-python/scipy-0.11[${PYTHON_MULTI_USEDEP}] ') " DEPEND="${RDEPEND}" diff --git a/sci-chemistry/chemex/chemex-2018.10.3.ebuild b/sci-chemistry/chemex/chemex-2018.10.3.ebuild index d0634c88451f..4e6e2d717f91 100644 --- a/sci-chemistry/chemex/chemex-2018.10.3.ebuild +++ b/sci-chemistry/chemex/chemex-2018.10.3.ebuild @@ -25,7 +25,7 @@ RDEPEND=" >=dev-python/matplotlib-1.1[${PYTHON_MULTI_USEDEP}] dev-python/numpy[${PYTHON_MULTI_USEDEP}] dev-python/setuptools_scm[${PYTHON_MULTI_USEDEP}] - >=sci-libs/scipy-0.11[${PYTHON_MULTI_USEDEP}] + >=dev-python/scipy-0.11[${PYTHON_MULTI_USEDEP}] ') " DEPEND="${RDEPEND}" diff --git a/sci-chemistry/clashlist/Manifest b/sci-chemistry/clashlist/Manifest index 0f7ec0929c75..e02c80211ba7 100644 --- a/sci-chemistry/clashlist/Manifest +++ b/sci-chemistry/clashlist/Manifest @@ -1,3 +1,3 @@ DIST molprobity-3.17.tgz 26429898 BLAKE2B f2ed8f71c4f71c19aac6278eed40cba0db53e88dc1be7ccb6e3e831d4202456822efe93ded2cc8ca3226efb9ef10999895b191e8b5d5188d577b78c9fa5a8c66 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f -EBUILD clashlist-3.17-r1.ebuild 652 BLAKE2B aae73ca5458b0aa1d2cb95ca43c70ed48902909947b8da5f817c711fb3a0fd920afe65090b2d92f203d06b6fa06b2cb20e2e0553b1c522f9c7b1aee673afac74 SHA512 600b5dca240537ca83fb374c72e73f205bb2ce320cbccd03b5c922f5163b43a059dc2f6fab481f0b54d066d3ed1a7f06c125b95ba7f05a2065b62395193961c9 +EBUILD clashlist-3.17-r1.ebuild 650 BLAKE2B 157db4a2b157a5da8046925420e7b1f0ed5e2dbc3fae07df137e676dadfb89d0710229e4562fca87a97348ba002a5daed25f435f246d03aeab267eebaf1b905e SHA512 96c83e6ea78acec35cb235722600f2bdbf3492e4b99f3dff9582ea05fe92fcc981ce0669bd729d1dd97f0d891a3a12f92d46b05f3b6274f835568d4af6d15a33 MISC metadata.xml 723 BLAKE2B 80e17900042e416acc6a990161dcfa3b968e5331cd96945c8a12bb516de7b486fe2fc9fd3b6cbf72f818ef9cf34853a01fadf843161dd2bb02fe796eb1f30586 SHA512 7da0ab5c03d802eac05b84e5f47fecdaf990ace2789f0f88c69e730155c9a9637ce23d5ede6633c6e6f7cf9c2cdf3e7b7c82de169caa291bd8facab327577e16 diff --git a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild index 7028015f5835..096a8047939e 100644 --- a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild +++ b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild @@ -1,16 +1,15 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 DESCRIPTION="Build lists of van der Waals clashes from an input PDB file" HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" SRC_URI="mirror://gentoo/molprobity-${PV}.tgz" -SLOT="0" LICENSE="richardson" +SLOT="0" KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND=" >=sci-chemistry/cluster-1.3.081231-r1 @@ -20,6 +19,7 @@ DEPEND="${RDEPEND}" S="${WORKDIR}" src_prepare() { + default sed \ -e 's: cluster : molprobity-cluster :g' \ -i molprobity3/bin/clashlist || die diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest deleted file mode 100644 index 728938a13a88..000000000000 --- a/sci-chemistry/freeon/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX freeon-1.0.10-stop.patch 970 BLAKE2B 6c1e5dfe5ad881fbbceb071c53cf3fcaa187ae1f19ad9f342ca004e66d6c15ea6fe923303b2c81dfd43367c59871bbf2480802a9fdefc01c8456307fc4b03b94 SHA512 b0ba7adaf23a7b91650790cad77e0f06e75a42183c0443dbb5c8f569c77fda2dae2702729236275bc148759247675be5bef4080bba4b9532c22e21160ea62ce7 -AUX freeon-1.0.8-blas.patch 5076 BLAKE2B 198f65079462b8c7af860b98894526bdc98172035c3d0b5ccd0cfd8bca14e36790c9e20771b7ec8ce5ca4d47f2d5dc7f768c7cf1a4b4868bb48285ef518851fd SHA512 89012c6f8583a8736344a7bfa74a64bbe1af793443b7255ccb1fd73366d44527ed40c6dc3124caff1af02f4e662227c66aeced8d8526dbd26bb7a50e294b5da3 -DIST freeon-1.0.10.tar.bz2 5872019 BLAKE2B c3fde00a9ed67550bb5820ac78ff32d9f6d011db9291c45c0b7e62cacb62b48e7506d7bf1aa86e176577d18e679e859435f0d3b63289bc08e502a35f86c036d3 SHA512 5bae89d6421600792bf986f6fb7504d321d5d51782587237ecba35191e54c1ec6c5ea1fdc50ed2d339551c527e4efcc5421048ccce0404c4b06875cbd0800862 -DIST freeon-1.0.8.tar.bz2 5957707 BLAKE2B b76ae0ca17cc8407b37fac243523d2f8db63382a6f39d24380d2f01356ac78fbe2fb905bb525d979c9832b820623bffa7a0930d312c36f29138defb0d8bce106 SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd -EBUILD freeon-1.0.10.ebuild 636 BLAKE2B 79e5034c4ba6fe4e5a862d4c18566504b73cea81e16b75f2b871ec44b0e0c0f95fc4f44a53bf0d016a872efdc276359583e66947e6cce2d33daecf6986e9dd1e SHA512 d6ab2836564776cbe004f1fd4121188e625810e1a37aae24af30becb056b4e66a9d5a53923505533d9d7fd3191595d5b013413896ba9bd00d5b6a0d68f935376 -EBUILD freeon-1.0.8-r1.ebuild 626 BLAKE2B 5d5a53bd58c81ff88775f1370d0daf71e94d043b5c3fc825cb2e040cbdb4b3129c1b97b88b5eaaed1a21aaa592c0fa27fb4c7d403cacfdb5d2cfef724c8c72f9 SHA512 8474400965e790a50285e2d5687952535e5d2ee4797086dd64b7f62a990d993937f13d28f92f01057185378944f6baa939427b2a9253749cadb992afd9a72940 -MISC metadata.xml 376 BLAKE2B 04d5215096c154f2414dc0475c6510a66b6978bd85169311d4b17303bafea893f8e3c2afb83080d72492c5dc82a62b2522ca079e300c917c00e439da932fee68 SHA512 578a3221496eb1470d9fcac9e784f62bb39591448a35a24e1881b5be69473689770bbc928c5779b76bed8c657b1e44d929093e6a39812d135199e37a0e8938e2 diff --git a/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch b/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch deleted file mode 100644 index a20d520e553c..000000000000 --- a/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch +++ /dev/null @@ -1,36 +0,0 @@ -From 882b51fb718c2eed98ef3e8f3be0c5b7320024e1 Mon Sep 17 00:00:00 2001 -From: Justin Lecher <jlec@gentoo.org> -Date: Mon, 2 Jan 2017 07:56:11 +0000 -Subject: [PATCH] Add missing blank after STOP - -The STOP statement requires preceding blank. Newer gcc -will fail with - - CASE DEFAULT; STOP'Err:WghtMtrx' - 1 -Error: Blank required in STOP statement near (1) - -See: -https://bugs.gentoo.org/show_bug.cgi?id=604138 - -Signed-off-by: Justin Lecher <jlec@gentoo.org> ---- - FreeON/Optimizer.F90 | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/FreeON/Optimizer.F90 b/FreeON/Optimizer.F90 -index 0ef22269..0bbd9008 100644 ---- a/FreeON/Optimizer.F90 -+++ b/FreeON/Optimizer.F90 -@@ -3055,7 +3055,7 @@ CONTAINS - SELECT CASE(FromTo) - CASE('CToWC');IFromTo=0 - CASE('WCToC');IFromTo=1 -- CASE DEFAULT; STOP'Err:WghtMtrx' -+ CASE DEFAULT; STOP 'Err:WghtMtrx' - END SELECT - DO AtB=1,NAtoms - IF(IFromTo.EQ.0) THEN --- -2.11.0 - diff --git a/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch b/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch deleted file mode 100644 index 46fca7fa2a52..000000000000 --- a/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch +++ /dev/null @@ -1,165 +0,0 @@ - FreeON/Makefile.am | 2 +- - HiCu/Makefile.am | 2 +- - ONX/Makefile.am | 1 + - OneE/Makefile.am | 2 +- - QCTC/Makefile.am | 2 +- - SCFeqs/Makefile.am | 2 +- - configure.ac | 12 ++++++++---- - make.inc | 2 +- - tests/Makefile.am | 8 ++++---- - tools/Makefile.am | 2 +- - 10 files changed, 20 insertions(+), 15 deletions(-) - -diff --git a/FreeON/Makefile.am b/FreeON/Makefile.am -index 18e0283..12db056 100644 ---- a/FreeON/Makefile.am -+++ b/FreeON/Makefile.am -@@ -50,7 +50,7 @@ FreeON_DEPENDENCIES = $(LIBRARY_DEPENDENCY_FILES) - - SOURCES_DEPCHECK = $(FreeON_SOURCES) - --FreeON_LDADD = $(LDADD_MODULES) -+FreeON_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - AM_CPPFLAGS += \ - -DFREEON_BASISSETS=\"$(datadir)/$(PACKAGE)/BasisSets\" \ -diff --git a/HiCu/Makefile.am b/HiCu/Makefile.am -index 1847354..cc4ebef 100644 ---- a/HiCu/Makefile.am -+++ b/HiCu/Makefile.am -@@ -27,7 +27,7 @@ EXTRA_DIST = \ - MMA/CubeRules/RuleD.Inc \ - MMA/CubeRules/RuleE.Inc - --LDADD = $(LDADD_MODULES) -+LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - EXTRA_INCLUDES = -I$(top_srcdir)/Modules/MMA/Functionals - AM_CPPFLAGS += -DRULE7 -DEXPLICIT_SOURCE -diff --git a/ONX/Makefile.am b/ONX/Makefile.am -index 4d25029..b27b149 100644 ---- a/ONX/Makefile.am -+++ b/ONX/Makefile.am -@@ -61,6 +61,7 @@ EXTRA_INCLUDES = \ - - LDADD = \ - $(LDADD_MODULES) \ -+ $(LAPACK_LIBS) \ - $(builddir)/../TwoE/libfreeonTwoE.la - - # In case we have ctags installed, make the necessary tags files. -diff --git a/OneE/Makefile.am b/OneE/Makefile.am -index 784bede..ea86ae7 100644 ---- a/OneE/Makefile.am -+++ b/OneE/Makefile.am -@@ -46,7 +46,7 @@ EXTRA_DIST = \ - MMA/QQuad32.Inc \ - MMA/QQuad64.Inc - --LDADD = $(LDADD_MODULES) -+LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - EXTRA_INCLUDES = -I$(srcdir)/MMA - -diff --git a/QCTC/Makefile.am b/QCTC/Makefile.am -index 3ec39f0..53c358c 100644 ---- a/QCTC/Makefile.am -+++ b/QCTC/Makefile.am -@@ -105,7 +105,7 @@ EXTRA_DIST = \ - PBCTensor/Majik_Kubic_WS2.Inc - - EXTRA_INCLUDES = -I$(top_builddir)/OneE -I$(top_srcdir)/Modules/MMA/LookUpTables_800_6x --LDADD = $(LDADD_MODULES) libktrax.la -+LDADD = $(LDADD_MODULES) libktrax.la $(LAPACK_LIBS) - - # In case we have ctags installed, make the necessary tags files. - .PHONY : tags -diff --git a/SCFeqs/Makefile.am b/SCFeqs/Makefile.am -index 2ee640f..709f220 100644 ---- a/SCFeqs/Makefile.am -+++ b/SCFeqs/Makefile.am -@@ -57,7 +57,7 @@ SOURCES_DEPCHECK = \ - $(P2Use_SOURCES) \ - $(DIIS_SOURCES) - --LDADD = $(LDADD_MODULES) -+LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - # In case we have ctags installed, make the necessary tags files. - .PHONY : tags -diff --git a/configure.ac b/configure.ac -index e0c6a77..726c880 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -784,12 +784,16 @@ END PROGRAM test_compiler - you use a version >= 4.2.0])]) - - # Check for BLAS. --AC_SEARCH_LIBS([dgemm], [blas], [], -- [AC_MSG_FAILURE([specify the location of dgemm()])]) -+PKG_CHECK_MODULES([BLAS],[blas],[], -+ AC_SEARCH_LIBS([dgemm], [blas], [], -+ [AC_MSG_FAILURE([specify the location of dgemm()])]) -+ ) - - # Check for LAPACK. --AC_SEARCH_LIBS([dsyev], [lapack], [], -- [AC_MSG_FAILURE([specify the library that contains dsyev()])]) -+PKG_CHECK_MODULES([LAPACK],[lapack],[], -+ AC_SEARCH_LIBS([dsyev], [lapack], [], -+ [AC_MSG_FAILURE([specify the library that contains dsyev()])]) -+ ) - - AC_ARG_VAR([H5CC], [h5cc compiler wrapper command]) - -diff --git a/make.inc b/make.inc -index cf35e40..5766ff9 100644 ---- a/make.inc -+++ b/make.inc -@@ -9,7 +9,7 @@ AM_CPPFLAGS = @AM_CPPFLAGS@ - # Fix for bug in autoconf-2.59 - builddir = . - --LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la -+LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_MODULES) - - # On filesystems which are case-insensitive (which really means HFS+ on OS X) - # we can not preprocess into a filename that differs by the case only, i.e. .C -diff --git a/tests/Makefile.am b/tests/Makefile.am -index 6bd89f2..ae9da60 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -7,16 +7,16 @@ noinst_PROGRAMS = \ - sendReceive_HGRho - - sleeper_SOURCES = sleeper.F90 --sleeper_LDADD = $(LDADD_MODULES) -+sleeper_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - lock_SOURCES = lock.F90 --lock_LDADD = $(LDADD_MODULES) -+lock_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - sendReceive_DBL_RNK2_SOURCES = sendReceive_DBL_RNK2.F90 --sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) -+sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - sendReceive_HGRho_SOURCES = sendReceive_HGRho.F90 --sendReceive_HGRho_LDADD = $(LDADD_MODULES) -+sendReceive_HGRho_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) - - if HAVE_MPIRUN - MPI_TESTS = locktest -diff --git a/tools/Makefile.am b/tools/Makefile.am -index e0baaff..a6b18b2 100644 ---- a/tools/Makefile.am -+++ b/tools/Makefile.am -@@ -19,7 +19,7 @@ python_PYTHON = \ - bin_PROGRAMS = printBCSR convertBCSR - - printBCSR_SOURCES = printBCSR.F90 --printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la -+printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_LIBS) - - convertBCSR_SOURCES = \ - convertBCSR.cc \ diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild deleted file mode 100644 index f17708da523a..000000000000 --- a/sci-chemistry/freeon/freeon-1.0.10.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python3_6 ) - -inherit autotools fortran-2 python-any-r1 - -DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" -HOMEPAGE="http://www.freeon.org" -SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - sci-libs/hdf5 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND} - ${PYTHON_DEPS}" - -PATCHES=( - "${FILESDIR}"/${P}-stop.patch -) - -src_prepare() { - default - eautoreconf -} diff --git a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild deleted file mode 100644 index 59b2b4ec6ffd..000000000000 --- a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=1 -FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python2_7 ) - -inherit autotools-utils fortran-2 python-any-r1 - -DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" -HOMEPAGE="http://www.freeon.org" -SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - sci-libs/hdf5 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND} - ${PYTHON_DEPS}" - -PATCHES=( "${FILESDIR}"/${P}-blas.patch ) diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml deleted file mode 100644 index 2fe5325ae7fa..000000000000 --- a/sci-chemistry/freeon/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>nicolasbock@gentoo.org</email> - <name>Nicolas Bock</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest index 29e85fc38b85..9d6e4c3e7bc1 100644 --- a/sci-chemistry/ksdssp/Manifest +++ b/sci-chemistry/ksdssp/Manifest @@ -1,3 +1,3 @@ DIST ksdssp-040728.shar 104347 BLAKE2B f77ba1fd83e9dd959dabf49818c541605eb8fba895880dbd8324cd02a0528d7961ced200de4b64c18c897a18e9f78474293a9f95fee9beace36f5faba61fcaa2 SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689 -EBUILD ksdssp-040728-r1.ebuild 916 BLAKE2B 7d2461015ee5646fc30b2ce61f52c63b01340b32a8b79e70eff1c3762cf7e82967063abee0b12195e4ff2db6afd4f13b501faec4116a464de10fb63e376e0318 SHA512 90eeb66be6665ca20bbe2dfdf1515d4ff44480dba23c47511501750749f903c2a1f80394e7c026b0ed99f4e545dcf3d70c64bcf8f21b49d945ed6e99878b5d30 +EBUILD ksdssp-040728-r1.ebuild 905 BLAKE2B 59721748af82ddd4fb21c7de46b4902f6af95656b5cc97685189500117a9e80ded0fb91944d5503347ddcb792037076621f61946b54e495098b8fe417a2cb9d3 SHA512 97bc00690752386c5048f5c87d5f926eb68275b449439e82186371124feb534c0e27ce67ca1c8d1521ce42935a3c125f53981ac07e75482622f620483595837d MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild index b5e9e772743f..118f15c3c2d6 100644 --- a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild +++ b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 inherit toolchain-funcs @@ -9,19 +9,18 @@ DESCRIPTION="An open source implementation of sci-chemistry/dssp" HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" SRC_URI="mirror://gentoo/${P}.shar" -SLOT="0" LICENSE="BSD" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" RDEPEND="sci-libs/libpdb++" -DEPEND="${RDEPEND} - app-arch/sharutils" +DEPEND="${RDEPEND}" +BDEPEND="app-arch/sharutils" -S="${WORKDIR}"/${PN} +S="${WORKDIR}/${PN}" src_unpack() { - "${EPREFIX}/usr/bin/unshar" "${DISTDIR}"/${A} || die + unshar "${DISTDIR}"/${A} || die } src_compile() { @@ -39,8 +38,10 @@ src_compile() { } src_install() { - dobin ${PN}{,.csh} - dodoc README - dohtml ${PN}.html - doman ${PN}.1 + dobin ksdssp{,.csh} + + HTML_DOCS=( ksdssp.html ) + einstalldocs + + doman ksdssp.1 } diff --git a/sci-chemistry/mars/Manifest b/sci-chemistry/mars/Manifest index 8c837657ac68..0c0842b31d72 100644 --- a/sci-chemistry/mars/Manifest +++ b/sci-chemistry/mars/Manifest @@ -1,3 +1,3 @@ DIST mars-1.2_linux.tar.gz 2058733 BLAKE2B 3ca8c636e619313c5462b4deda1f1c34b64574d869bd285c2a07cf7a1e36103a38d2a3401a29ef50f1e97478f1d8a5a3eab01a70aa410fd953a8d6261d14595a SHA512 ba7ec4e94cf5918d22405022c75feabf3e5b345d96075eabf50eb24857101575bb41d15e5686822c2b2f25ba554aa7d7a2b65122dd47304939234a4a884ae4d2 -EBUILD mars-1.2.ebuild 905 BLAKE2B 725c629326bb3b87900a17b253b60df7ff63cf73b0282ae133074c328e4adb837070907768ae0025662acb25ad9f6370030e3c498e166932b60e8b81ac0791a3 SHA512 c2abf892fa6fcbbafafe2dd6446679cd577dc85e744734ec36ebac42259e2e1de41704228ba99eef6da9eb465c3e2f65e0ea26a906da61290a97aa5c9a040ca9 +EBUILD mars-1.2.ebuild 901 BLAKE2B 197ac1220f0aca771ac5bac15aa6fe53f370cbbd36c4179a3ef5e48631ded5459a3b30b2cc4d3cf2153b0bc6c595471134749ed55be30279216fb2ca1b3fba05 SHA512 7ca5f05418a5aa9f78aff5b0cbe353b5ecad9b45d46ad9be31a1cae83636457c7c3d3417d552de3288acff662838b8115d9b5ec9004c8f6f515dadaf80ae3f27 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/mars/mars-1.2.ebuild b/sci-chemistry/mars/mars-1.2.ebuild index 5fd849dc4cb1..58667bc6dd8e 100644 --- a/sci-chemistry/mars/mars-1.2.ebuild +++ b/sci-chemistry/mars/mars-1.2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 MY_P="${P}_linux" @@ -9,17 +9,15 @@ DESCRIPTION="Robust automatic backbone assignment of proteins" HOMEPAGE="http://www.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm" SRC_URI="http://www.mpibpc.mpg.de/groups/zweckstetter/_software_files/_${PN}/${MY_P}.tar.gz" +LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="all-rights-reserved" IUSE="examples" +RESTRICT=mirror RDEPEND="sci-biology/psipred" -DEPEND="" -RESTRICT=mirror - -S="${WORKDIR}"/${MY_P} +S="${WORKDIR}/${MY_P}" QA_PREBUILT="opt/mars/*" @@ -28,15 +26,17 @@ src_install() { exeinto /opt/${PN}/ doexe bin/{${PN},calcJC-S2,runmars*,*.awk} *.awk + insinto /opt/${PN}/ doins bin/*.{tab,txt} + if use examples; then insinto /usr/share/${PN}/ doins -r examples fi - cat >> "${T}"/23mars <<- EOF - MARSHOME="${EPREFIX}/opt/${PN}" + cat >> "${T}"/23mars <<- EOF || die + MARSHOME="${EPREFIX}/opt/${PN}" EOF doenvd "${T}"/23mars diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest index 2380c38512ec..d42ea0a16668 100644 --- a/sci-chemistry/mdtraj/Manifest +++ b/sci-chemistry/mdtraj/Manifest @@ -1,5 +1,5 @@ DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76 DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38 -EBUILD mdtraj-1.9.1.ebuild 902 BLAKE2B 2bbbf367b06fd0ae53c134d1ab214350e26675ae52f71c633f0a5102e36515976ba16e726e648c2b4ccddc4330f5eb1498f20441d034e5aa16f60a32223c07d9 SHA512 258e368468af7347ae1e27e1167aae3fe656c085533082ffe2cb3dc5e6e0538148602ccf45bda4fdb7d25f4a0b9bf8816f421b83dcaa84815a90cf06a727927b -EBUILD mdtraj-1.9.4.ebuild 1069 BLAKE2B ab4010ead403045d3e29f48e862565475c7c6e648d59d2c7bf5d53d58fbb5444a5da73b10b5012d37062a1b08c7dbcd47475f3009573518c847b95437661d5e5 SHA512 859df401866e75f7c0d9500d97c6587cac20bd9cf57690cfbcd2226dbf3fdcd6c3d6b21e29269a9d992e8a5e1a4416d61b74c97f6a1f2b3b26e5ed962c4da282 +EBUILD mdtraj-1.9.1.ebuild 904 BLAKE2B f9d83a07faa64fd2d2cfc842683f77bcd9763cbe74e8b0a3981ede65be15bcc61e0d32bd950fec69c6fa39b06919d9c572d24679e84ea6d7f0c0ecadd4069c9a SHA512 9b67d016fa023bdd12b224559a86456b969b033b8f2c9ada250494e6b30e123fd91ae1f448b8891d77be0bb37652f8b450f9e48452a3abf0fa8b0ecbd0aff530 +EBUILD mdtraj-1.9.4.ebuild 1071 BLAKE2B 85fc5d891ac4e6b05c43102928a241d40391656b1a805e282e57034a2bd8b1fc0da5a4225bdfd2d37155d2023dae7e1b1d59a6a236de7cc5657f317cfa7df686 SHA512 66bb3f8324063a7fe6190970b00350effc18d77d551e6c5bd2a977c709540c5cf3c59583f6c96d62f5706e249e015b63899a42ba396f5beca85ef8eb9fe2ca3c MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild index 761ab50155c8..cdf5b949625f 100644 --- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild +++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild @@ -19,7 +19,7 @@ RESTRICT="!test? ( test )" RDEPEND=" dev-python/setuptools[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] dev-python/pytables[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild index 5537daa6a536..fba1fb10eed2 100644 --- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild +++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild @@ -22,7 +22,7 @@ RDEPEND=" dev-python/pandas[${PYTHON_USEDEP}] dev-python/pytables[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] " DEPEND="${RDEPEND} test? ( diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest index 6ab473c01cc1..8774ffcf18f3 100644 --- a/sci-chemistry/moldy/Manifest +++ b/sci-chemistry/moldy/Manifest @@ -1,4 +1,4 @@ AUX 2.16e-as-needed.patch 3226 BLAKE2B 777b34d43da82b036e401c398d0f59a5f268905a399f38277be73ba6bdaefd6f1de2ec748302edfc68c6389acb22fa50d72b465522b1f2d5bbd14eca289d7595 SHA512 b32461bb052c908106f0f8d74be4eba52daa41ba592a7ba6083edc2a54c4a14003cf33560572e57f2b370ad5ea1f703e388855e8e7fa67ccec40e3015a8f5803 DIST moldy-2.16e.tar.gz 488410 BLAKE2B 44ff1dacc66922ba11297ca54c645f209b782b8cde50e427d54d1d249a93b718eeb865357ea47b820801fdbca325d5f0d6027fe11ce6e0a842e77d1970a0467c SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877 -EBUILD moldy-2.16e-r2.ebuild 1804 BLAKE2B 3c4865ada8baec131c5bb92e6856e3526a4aea05cb754423bf7cb896992c6e2732ad42b31808059c602549de7fd5054de780cfbe85218056c975f7c4c5fbda90 SHA512 5b8b76efa8f2132b50abd4ce3f0a137a8ed433c4e88b5b60df7043df00d5c78696c08dcfaade590842625429fa67656fa2d4537b158bedfb54da1eb79224bdcf +EBUILD moldy-2.16e-r2.ebuild 1747 BLAKE2B 961cd390e657e578d9873bc7a15634333c3f451591610cf44936b94360e644118fca4254e88c62a020fbaaa169cce2b2d970335b550571e9bf75780bba0cc2b4 SHA512 c8458f6d37289c6ecb147c1a0b53d7888a58207d1bf1a6de891bcd9c8ce463355f3b350f744bbc3a299c1b1c10b3b237352572c95245d629f62bb8bbbc317733 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild index 0d3399860306..81b2d5bf314b 100644 --- a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild +++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Molecular dynamics simulations platform" HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html" @@ -12,15 +12,16 @@ SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc examples" +IUSE="doc" -DEPEND="doc? ( virtual/latex-base )" -RDEPEND="" +BDEPEND="doc? ( virtual/latex-base )" S="${WORKDIR}" +PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) + src_prepare() { - epatch "${FILESDIR}"/${PV}-as-needed.patch + default sed \ -e 's:-O2::g' \ -e 's:-ffast-math::g' \ @@ -47,6 +48,7 @@ src_configure() { src_compile() { emake + # To prevent sandbox violations by metafont if use doc; then VARTEXFONTS="${T}"/fonts emake moldy.pdf @@ -58,13 +60,12 @@ src_install() { emake prefix="${ED}"/usr install dodoc BENCHMARK READ.ME RELNOTES - if use examples; then - rm Makefile.in configure.in config.h.in - insinto /usr/share/${PN}/examples/ - doins *.in *.out control.* - fi + rm Makefile.in configure.in config.h.in || die + insinto /usr/share/${PN}/examples/ + doins *.in *.out control.* + if use doc; then - insinto /usr/share/doc/${PF}/pdf - newins moldy.pdf moldy-manual.pdf + docinto pdf + newdoc moldy.pdf moldy-manual.pdf fi } diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest index 05e55b4e65bc..dbc96c65f761 100644 --- a/sci-chemistry/molequeue/Manifest +++ b/sci-chemistry/molequeue/Manifest @@ -1,5 +1,3 @@ -AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335 EBUILD molequeue-0.9.0-r1.ebuild 1959 BLAKE2B e395842e8456fb5a9d8d1ac8bf560105d3a04a93041ce478cd3b59890fcee337a1892bda3e07802102a2ea62608b86157f990527c464f386a77119669fde9c99 SHA512 b95e16f135d040508952a46c6064a21c64d0bddb6e472c305f372cda582395088fd6622fb3b96da50d93b58aebe9e197550e5fe867cdbd2d6e9d1a998ed3c92e -EBUILD molequeue-0.9.0.ebuild 1506 BLAKE2B e1e8a1a55cbe1da01199049ff97ca9e1950c5eb258a07e65e3d8e9eb3f5260e809c96a0abc96d1986f1fd822abc94a8a561538d8560195b8237284556e888edd SHA512 9fc628c00e53d86a4a0c9fc94bc4fc9f30375adb1ab9b89b64369770fb464544b2d49c2a8b62029f1319794d1dffcde0fdff4b6b99a3788ac5bb6d5f7792be12 MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058 diff --git a/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch b/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch deleted file mode 100644 index 0e04e22f7434..000000000000 --- a/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch +++ /dev/null @@ -1,154 +0,0 @@ -From 844c6a7ee7f4ad00bc8225549d26c6bde8b683ab Mon Sep 17 00:00:00 2001 -From: Andreas Sturmlechner <asturm@gentoo.org> -Date: Tue, 17 Apr 2018 10:50:36 +0200 -Subject: [PATCH] Fix build with Qt 5.11_beta3 (dropping qt5_use_modules) - ---- - molequeue/app/CMakeLists.txt | 14 +++++--------- - molequeue/app/testing/CMakeLists.txt | 6 ++---- - molequeue/app/testing/clienttestsrc/CMakeLists.txt | 3 +-- - molequeue/client/CMakeLists.txt | 2 +- - molequeue/plugins/localsocketserver/CMakeLists.txt | 3 +-- - molequeue/servercore/CMakeLists.txt | 2 +- - molequeue/zeromq/CMakeLists.txt | 3 +-- - 7 files changed, 12 insertions(+), 21 deletions(-) - -diff --git a/molequeue/app/CMakeLists.txt b/molequeue/app/CMakeLists.txt -index d40fce5..b6e72f8 100644 ---- a/molequeue/app/CMakeLists.txt -+++ b/molequeue/app/CMakeLists.txt -@@ -1,11 +1,9 @@ --set(qt_components Core Widgets Network) -+find_package(Qt5 REQUIRED COMPONENTS Core Widgets Network) - - if(MoleQueue_USE_EZHPC_UIT) -- list(APPEND qt_components XmlPatterns) -+ find_package(Qt5XmlPatterns REQUIRED) - endif() - --find_package(Qt5 COMPONENTS ${qt_components} REQUIRED) -- - # Provide some simple API to find the plugins, scripts, etc. - if(APPLE) - # It is a special case, the app bundle logic breaks the relative pathing. -@@ -170,12 +168,11 @@ qt5_wrap_ui(ui_srcs ${ui_files}) - qt5_add_resources(rcc_srcs queuetray.qrc) - - add_library(molequeue_static STATIC ${mq_srcs} ${ui_srcs}) --qt5_use_modules(molequeue_static ${qt_components}) - set_target_properties(molequeue_static PROPERTIES AUTOMOC TRUE) --target_link_libraries(molequeue_static MoleQueueServerCore) -+target_link_libraries(molequeue_static MoleQueueServerCore Qt5::Core Qt5::Widgets Qt5::Network) - - if(MoleQueue_USE_EZHPC_UIT) -- target_link_libraries(molequeue_static KDSoap::kdsoap) -+ target_link_libraries(molequeue_static KDSoap::kdsoap Qt5::XmlPatterns) - endif() - - if(MoleQueue_BUILD_CLIENT) -@@ -195,8 +192,7 @@ elseif(WIN32) - endif() - - add_executable(molequeue WIN32 MACOSX_BUNDLE ${sources} ${rcc_srcs}) --qt5_use_modules(molequeue ${qt_components}) --target_link_libraries(molequeue molequeue_static) -+target_link_libraries(molequeue molequeue_static Qt5::Core Qt5::Widgets Qt5::Network) - if(WIN32) - target_link_libraries(molequeue Qt5::WinMain) - endif() -diff --git a/molequeue/app/testing/CMakeLists.txt b/molequeue/app/testing/CMakeLists.txt -index 5b88038..f79a17a 100644 ---- a/molequeue/app/testing/CMakeLists.txt -+++ b/molequeue/app/testing/CMakeLists.txt -@@ -31,8 +31,7 @@ set(testutils_SRCS - - add_library(testutils STATIC ${testutils_SRCS}) - set_target_properties(testutils PROPERTIES AUTOMOC TRUE) --qt5_use_modules(testutils Test) --target_link_libraries(testutils molequeue_static) -+target_link_libraries(testutils molequeue_static Qt5::Test) - - set(MyTests - filespecification -@@ -71,9 +70,8 @@ endif() - - foreach(test ${MyTests}) - add_executable(${test}test MACOSX_BUNDLE ${test}test.cpp) -- qt5_use_modules(${test}test Test) - set_target_properties(${test}test PROPERTIES AUTOMOC TRUE) -- target_link_libraries(${test}test testutils) -+ target_link_libraries(${test}test testutils Qt5::Test) - add_test(NAME molequeue-${test} COMMAND ${test}test) - endforeach() - -diff --git a/molequeue/app/testing/clienttestsrc/CMakeLists.txt b/molequeue/app/testing/clienttestsrc/CMakeLists.txt -index d506010..7377e3c 100644 ---- a/molequeue/app/testing/clienttestsrc/CMakeLists.txt -+++ b/molequeue/app/testing/clienttestsrc/CMakeLists.txt -@@ -9,6 +9,5 @@ set(srcs sendRpcKill) - foreach(source ${srcs}) - add_executable(${source} ${source}.cpp) - set_target_properties(${source} PROPERTIES AUTOMOC TRUE) -- qt5_use_modules(${source} Core) -- target_link_libraries(${source} MoleQueueClient) -+ target_link_libraries(${source} MoleQueueClient Qt5::Core) - endforeach() -diff --git a/molequeue/client/CMakeLists.txt b/molequeue/client/CMakeLists.txt -index 8cb131a..c614aea 100644 ---- a/molequeue/client/CMakeLists.txt -+++ b/molequeue/client/CMakeLists.txt -@@ -15,7 +15,7 @@ set(headers - include_directories(${CMAKE_CURRENT_BINARY_DIR}) - - add_library(MoleQueueClient ${sources}) --qt5_use_modules(MoleQueueClient Network) -+target_link_libraries(MoleQueueClient Qt5::Network) - set_target_properties(MoleQueueClient PROPERTIES AUTOMOC TRUE) - include(GenerateExportHeader) - generate_export_header(MoleQueueClient EXPORT_FILE_NAME molequeueclientexport.h) -diff --git a/molequeue/plugins/localsocketserver/CMakeLists.txt b/molequeue/plugins/localsocketserver/CMakeLists.txt -index fd030f9..80018c3 100644 ---- a/molequeue/plugins/localsocketserver/CMakeLists.txt -+++ b/molequeue/plugins/localsocketserver/CMakeLists.txt -@@ -2,9 +2,8 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY - ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/../lib/molequeue/plugins) - - add_library(LocalSocketServer MODULE localsocketconnectionlistenerfactory.cpp) --qt5_use_modules(LocalSocketServer Network) - set_target_properties(LocalSocketServer PROPERTIES AUTOMOC TRUE PREFIX "") --target_link_libraries(LocalSocketServer MoleQueueServerCore) -+target_link_libraries(LocalSocketServer MoleQueueServerCore Qt5::Network) - - set_property(GLOBAL APPEND PROPERTY MoleQueue_PLUGINS LocalSocketServer) - -diff --git a/molequeue/servercore/CMakeLists.txt b/molequeue/servercore/CMakeLists.txt -index aab0bec..eee1bfd 100644 ---- a/molequeue/servercore/CMakeLists.txt -+++ b/molequeue/servercore/CMakeLists.txt -@@ -12,7 +12,7 @@ add_library(MoleQueueServerCore - messageidmanager_p.cpp - ) - --qt5_use_modules(MoleQueueServerCore Network) -+target_link_libraries(MoleQueueServerCore Qt5::Network) - set_target_properties(MoleQueueServerCore PROPERTIES AUTOMOC TRUE) - #target_link_libraries(MoleQueueServerCore) - -diff --git a/molequeue/zeromq/CMakeLists.txt b/molequeue/zeromq/CMakeLists.txt -index 188f437..451c0ec 100644 ---- a/molequeue/zeromq/CMakeLists.txt -+++ b/molequeue/zeromq/CMakeLists.txt -@@ -13,9 +13,8 @@ set(sources - ) - - add_library(MoleQueueZeroMq ${sources}) --qt5_use_modules(MoleQueueZeroMq Network) - set_target_properties(MoleQueueZeroMq PROPERTIES AUTOMOC TRUE) --target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES}) -+target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES} Qt5::Network) - - generate_export_header(MoleQueueZeroMq - EXPORT_FILE_NAME molequeuezeromqexport.h) --- -2.17.0 - diff --git a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild deleted file mode 100644 index 0a2c4acc3e53..000000000000 --- a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 virtualx - -DESCRIPTION="Abstract, manage and coordinate execution of tasks" -HOMEPAGE="https://www.openchemistry.org/projects/molequeue/" -SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+client doc server test +zeromq" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} - server? ( client ) - test? ( server )" - -BDEPEND=" - doc? ( app-doc/doxygen )" -RDEPEND="${PYTHON_DEPS} - dev-qt/qtcore:5 - dev-qt/qtgui:5 - dev-qt/qtnetwork:5 - dev-qt/qtwidgets:5 - zeromq? ( net-libs/cppzmq:0= )" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}"/${P}-qt-5.11b3.patch ) - -src_configure() { - local mycmakeargs=( - -DMoleQueue_USE_EZHPC_UIT=OFF - -DBUILD_DOCUMENTATION=$(usex doc) - -DMoleQueue_BUILD_CLIENT=$(usex client) - -DMoleQueue_BUILD_APPLICATION=$(usex server) - -DENABLE_TESTING=$(usex test) - -DUSE_ZERO_MQ=$(usex zeromq) - -DINSTALL_LIBRARY_DIR=$(get_libdir) - ) - use zeromq && \ - mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" ) - - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile all $(usex doc documentation "") -} - -src_test() { - VIRTUALX_COMMAND=cmake-utils_src_test - virtualmake -} - -src_install() { - use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) - cmake-utils_src_install -} diff --git a/sci-chemistry/msms-bin/Manifest b/sci-chemistry/msms-bin/Manifest index c3d88f6df9a9..f4893956b9dd 100644 --- a/sci-chemistry/msms-bin/Manifest +++ b/sci-chemistry/msms-bin/Manifest @@ -1,4 +1,4 @@ DIST msms_i86Linux2_2.6.1.tar.gz 112762 BLAKE2B 8ceb55eef29234b38d631ea4aa63c7f11e4a606b8f14526412ed64d2ac9174604fd6ecb8c11c8e7629fd570b2298ee81d4f364c75ee64a41b1bc9fd9c661277b SHA512 814a5b5fa760b57c773f6900d42cacc5b68a2bf16d8792aa63cfa779aeabdab4e05064b86de6fb2551194543db925d83e07cf4ef74be8c08935ef5ecc8dcfe73 DIST msms_i86_64Linux2_2.6.1.tar.gz 593147 BLAKE2B b66430303f732bc66c62577950671a947c2a81efa139857a255522fa5dc73f042b571e7756e76246aaeac30cb8cf3ac7383645b35a70bb08a15572de1c5fb2af SHA512 630da1ae57b2d8d072247b650636a71e5ef6f07a245c8c4d07b26e20618d9c5dbaffcff563d0504b9b899ca263ba5f3458447f0e649bbfb895aea34305c1c8f8 -EBUILD msms-bin-2.6.1-r1.ebuild 1075 BLAKE2B f324e286a4a567c34a7c4b1b6887eda3bcb53cc06b74c00bead500a4552cd367458d56d09e67cbdb84f2770486a531ea3a95d68536188995dd5ffd6fd427251c SHA512 be2c1c95d2a63c3471f47e6aac6bb086eb01fd4c23c98c53ada2ae5dbbd1db39fe0728a5439172b1a0163c1c20320ac48dda6feca22ce047a7571f08fae2a41d +EBUILD msms-bin-2.6.1-r1.ebuild 991 BLAKE2B 14f67e7f92cfaedd3bfcba2063527d482645355393014fc25d3db791d8aaf1069aaf073333f4dec7a72e17af2d03cd5456d6bdc4b46fec9722553f75fc9d3782 SHA512 4041d972a774eddc85932c34a3bad7766d1778ec4ad59690683be2ec2e1fa51f3b7c6d2f7c80182c56275b4798fe392310d73cd4c054c0b720f7aed918d85c3c MISC metadata.xml 342 BLAKE2B e5edc8e8d81d013be77e02718bb4fe50564226ec1c028daad92c3c5b882b2eb840be28ce78dfc83ab3a58e1a428b55caed99971b9b84a8bec23349952496eea1 SHA512 2dbd8b2bdf37d4a2d4127cb373db2c6ff8fc4de6bf294e4518f1d424115860c0b083d538935a8b1a54543b396b968985e46a7ca293367ee1a0b462d11639b7ab diff --git a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild index 13eebfcdc23e..6f6335e72bf8 100644 --- a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild +++ b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild @@ -1,25 +1,22 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 DESCRIPTION="MSMS very efficiently computes triangulations of Solvent Excluded Surfaces" HOMEPAGE="http://mgl.scripps.edu/people/sanner/html/msms_home.html" SRC_URI=" - amd64? ( msms_i86_64Linux2_2.6.1.tar.gz ) - x86? ( msms_i86Linux2_2.6.1.tar.gz ) -" + amd64? ( msms_i86_64Linux2_2.6.1.tar.gz ) + x86? ( msms_i86Linux2_2.6.1.tar.gz )" LICENSE="MSMS" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - RESTRICT="fetch" S="${WORKDIR}" -QA_PREBUILT="${EROOT#/}opt/bin/.*" +QA_PREBUILT="opt/bin/*" pkg_nofetch() { einfo "Please download ${A} from http://mgltools.scripps.edu/downloads#msms and" @@ -27,19 +24,18 @@ pkg_nofetch() { } src_install() { - doman msms.1 - dodoc README msms.html ReleaseNotes + dobin pdb_to_xyz* + exeinto /opt/bin - if use amd64; then - newexe ${PN%-bin}.x86_64Linux2.${PV} msms - elif use x86; then - newexe ${PN%-bin}.i86Linux2.${PV} msms - fi + newexe ${PN%-bin}.$(usex amd64 x86_64Linux2 i86Linux2).${PV} msms + + dodoc README msms.html ReleaseNotes + doman msms.1 + insinto /usr/share/${PN}/ doins atmtypenumbers sed \ -e 's:nawk:awk:g' \ -e "s:./atmtypenumbers:${EPREFIX}/usr/share/${PN}/atmtypenumbers:g" \ -i pdb_to_xyz* || die - dobin pdb_to_xyz* } diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest index ef6f4e0129d0..e06d5701afbc 100644 --- a/sci-chemistry/nmrglue/Manifest +++ b/sci-chemistry/nmrglue/Manifest @@ -1,6 +1,6 @@ AUX nmrglue-0.5-nohyper.patch 1408 BLAKE2B 8e91e270183ce8f4c361fd3577dc4942b2afab81ee8f59df5c8dd9056dbf639653d2e84f9dc04026636dda98e28a244586ba5bc2cd4ed5c43c8a31d0c0cab4d1 SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd DIST nmrglue-0.5.tar.gz 142604 BLAKE2B 9a018a73bea46176fc06042013cb23b3eeb962df8a595388da536d17f1d2d4d550065c5492df28de860ea1290314d2fa1110af349be0c2a8b1b31677b3e4afbc SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 DIST nmrglue-0.7.tar.gz 166596 BLAKE2B 769dbe1330a2b610393cea07edcb7c997d219038ead0330e442b491b84a51f3d1ac0dd22a9399b1af2f97fbfbf0d24316bd834d71804b4607209c5d11f24939e SHA512 4d9959d151954f38efc7ea4f93539970bc75098403b0b5575f0c4ff6c2c25c1f08e207d2dee281109ffb2bdea53f2e7beb04e251cec1f638712dfe38430c23d5 -EBUILD nmrglue-0.5-r1.ebuild 740 BLAKE2B 1659c4d8ee0d0dd8c049aff32953694669d02259587443dabc59fd34d1616b84195f621647789e0f05e397121b6f03c2b859ab248b5c2aa8510fbbb18b7b2ae5 SHA512 295058d83b37c64df02011be40d1841714c6870306b08f8852c00e95ca1c182f1690d29c2b2b72acfefd1c10bc257f6182876c8729cabc8e9cf95ed1ade5e807 -EBUILD nmrglue-0.7.ebuild 594 BLAKE2B 5171f7324bc0416d0e1fb570f943b576c305b4efd55b903af3ab7492a2d1fed06325081012db75d5d4bac5a950769ee2c09c1c329fae94ed300484b49722b71b SHA512 1e511634315ff5af81b02d959a85d67f8c1edd76edf7f12425c6ee4ae92cd8bad1ccaee9d19147d5e5962787b4000d8f3f81f23b8b252259cfaf4549b44c2e8b +EBUILD nmrglue-0.5-r1.ebuild 742 BLAKE2B bf7fb9d26c723d6d255f00ad68765927af0465cbe56bef317538292a44d790ab5a9e6730d3be53fef44e905295177eb283150269a5aedfa0ecaf3385040089d2 SHA512 09b9caccff10a98fbb88e2dee52ec800f2a2643827d565cf6c1737d54d1c8bdfcd10f757242ba1b7ed64b1c2947277c56d49a6c175424ab2a83c8170625ccc1a +EBUILD nmrglue-0.7.ebuild 596 BLAKE2B b9ea11afa6fa1ca2f9cb29cb7cb462ff8ddaf48396573b21fcd0030cc5d165eedddf104c4b040267b4b4a1fa2351efe757f34b29a7bf5a03ed5dfcbe634ef010 SHA512 bb7b9a52ae16986cd01ca4f2a34ac9bcdbf9a50d4ea5c4db74c5a3b9735d0c6aced2272aa6aaee96be541c99a3b9d599e8342d365af5f967ae65599b675a44d5 MISC metadata.xml 1338 BLAKE2B 480651ef6112e93e3c70e734f4ca7d7b24653109f503fab6a340c9dc246b881b5ab103b90f8ffbc92a6d5352b399c15a33072292e549b4ffcc2689f049996cfd SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild index 78539bfaf771..3a767944a130 100644 --- a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild +++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild @@ -20,7 +20,7 @@ RESTRICT="!test? ( test )" RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}]" + dev-python/scipy[${PYTHON_USEDEP}]" DEPEND=" test? ( ${RDEPEND} diff --git a/sci-chemistry/nmrglue/nmrglue-0.7.ebuild b/sci-chemistry/nmrglue/nmrglue-0.7.ebuild index 7772d64fc7d3..8b3a7eac6041 100644 --- a/sci-chemistry/nmrglue/nmrglue-0.7.ebuild +++ b/sci-chemistry/nmrglue/nmrglue-0.7.ebuild @@ -18,7 +18,7 @@ IUSE="" RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] " DEPEND="${RDEPEND}" diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest deleted file mode 100644 index cc936a87477e..000000000000 --- a/sci-chemistry/openbabel-python/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 637 BLAKE2B e913c1d1bc93fd8443faa20fc9d7b28b89b276f7561d4208a42abd379111d19ff26179b2fbdca946a9df38e42d31f32b68423be073611e79615dcd6ae20d8f0d SHA512 0108f7bc83e046e29b2ae0b822787f58c6930de775dc94df89ba741f41cb3873a3bd2b677c11ccad4c32172e486b8331c25492127c83e4ab8d066bd129aa5538 -DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 -EBUILD openbabel-python-2.4.1-r1.ebuild 2156 BLAKE2B 5d6def900a348c7d090e2caa177ca7b4a5c2dc08ed6e77bec76801b36d3bdc092a0fa31bc4ae18d4152c6391feaf35e8856cda50e4889d5c0643e25528fd53ed SHA512 df4c7d34a91ab093a39d99b342b36c9c9984e8bc9e7e18f31641873da86baef4f1141bef20cb2493287bd38e1099b48b6b212fae2e0d21eaf5b04a30943cf281 -MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch deleted file mode 100644 index 1624262e6982..000000000000 --- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 0ee545cf..7f4b944e 100755 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -239,7 +239,7 @@ 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}") -+ string(REGEX MATCH "[3456789]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") - # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the - # patch level, handle this here: - if (NOT _gcc_version) diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml deleted file mode 100644 index 06fa4d2398d3..000000000000 --- a/sci-chemistry/openbabel-python/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> -OpenBabel is a chemical toolbox designed to speak the many languages of -chemical data. It's an open, collaborative project allowing anyone to -search, convert, analyze, or store data from molecular modeling, chemistry, -solid-state materials, biochemistry, or related areas. This package enables -to access OpenBabel library from Python programs. -</longdescription> - <upstream> - <remote-id type="sourceforge">openbabel</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild deleted file mode 100644 index fe6933bd9868..000000000000 --- a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild +++ /dev/null @@ -1,91 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_6 ) - -inherit cmake-utils python-r1 - -DESCRIPTION="Python bindings for OpenBabel (including Pybel)" -HOMEPAGE="http://openbabel.sourceforge.net/" -SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" - -KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" -SLOT="0/5" -LICENSE="GPL-2" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - ~sci-chemistry/openbabel-${PV} - sys-libs/zlib" -DEPEND="${RDEPEND} - >=dev-lang/swig-2" - -S="${WORKDIR}"/openbabel-${PV} - -PATCHES=( - "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch - ) - -src_prepare() { - cmake-utils_src_prepare - sed \ - -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ - -i test/testbabel.py || die - swig -python -c++ -small -O -templatereduce -naturalvar \ - -I"${EPREFIX}/usr/include/openbabel-2.0" \ - -o scripts/python/openbabel-python.cpp \ - -DHAVE_EIGEN \ - -outdir scripts/python \ - scripts/openbabel-python.i \ - || die "Regeneration of openbabel-python.cpp failed" - sed \ - -e '/__GNUC__/s:== 4:>= 4:g' \ - -i include/openbabel/shared_ptr.h || die -} - -src_configure() { - my_impl_src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_RPATH= - -DBINDINGS_ONLY=ON - -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" - -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" - -DLIB_INSTALL_DIR="${D}$(python_get_sitedir)" - -DPYTHON_BINDINGS=ON - -DPYTHON_EXECUTABLE=${PYTHON} - -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" - -DPYTHON_INCLUDE_PATH="$(python_get_includedir)" - -DPYTHON_LIBRARY="$(python_get_library_path)" - -DENABLE_TESTS=ON - -DCMAKE_INSTALL_PREFIX="${ED%/}/usr" - ) - - cmake-utils_src_configure - } - - python_foreach_impl my_impl_src_configure -} - -src_compile() { - python_foreach_impl cmake-utils_src_make bindings_python -} - -src_test() { - python_foreach_impl cmake-utils_src_test -R py -} - -src_install() { - my_impl_src_install() { - cd "${BUILD_DIR}" || die - - cmake -DCOMPONENT=bindings_python -P cmake_install.cmake - - python_optimize - } - - python_foreach_impl my_impl_src_install -} diff --git a/sci-chemistry/pdbcns/Manifest b/sci-chemistry/pdbcns/Manifest index 5cee99b1b10c..859d0c72ffb0 100644 --- a/sci-chemistry/pdbcns/Manifest +++ b/sci-chemistry/pdbcns/Manifest @@ -1,3 +1,3 @@ DIST pdbcns.2.0.010504.perl.tgz 6806 BLAKE2B a7501b818c7b32f9116a3407234f2ceb39602032a47338772dc7bdf146f4b829091da4caba40045118f52e562f5b62fc270525fc880f80bf0bee50cd7ad4fe88 SHA512 5174cb51dbe3ead405fa1005d81a7ee063bf4be4268b0e728f1ca0aa3e6cbc005fb0bac3e21e06f872c6f4d42c23f50b6e6130391e3b825260c890070e6f766b -EBUILD pdbcns-2.0.010504.ebuild 668 BLAKE2B e85485f753dc383e8f477eda221069436dc4049807e25c05d4ceb55405ecacad828296906a0bdb8abc56e89e6f4ec8889194c6d2cd1270dd1c6f1f99320f9b46 SHA512 6426d86b45e7af51fe2a0baad95d378d3ceb16a729ed6469a3b00ecd44aed368b942498fd1c53f0b62060f2170ce6191a9dca04fd23f3de2d58911614cd552c0 +EBUILD pdbcns-2.0.010504.ebuild 650 BLAKE2B f830c0f90504a009d3123845003e567b05a2ad151b24f01216464cc0cc4740fdc64bdf23c3583c9c55090c74e0e892134c56917d1a6774e350ee6a0165a0c1f8 SHA512 376da16e7be6a668e9230e1e8e79bd2b4f7452b5d5f47e6038ee4efb499902d31ed3b3ad9daf280828ffe4f01a4359059421f2cf3d5b51b47829ccdc5083c154 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild index b0b57ed0d51f..cd155ac0f067 100644 --- a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild +++ b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild @@ -1,25 +1,24 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 DESCRIPTION="Convert atom names for amino acids/nucleic acid bases between PDB and CNS format" HOMEPAGE="http://www.mybiosoftware.com/3d-molecular-model/314/" #SRC_URI="http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/software/scripts/${PN}.${PV}.perl.tgz" SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${PN}.${PV}.perl.tgz" +LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="BSD" -IUSE="" -DEPEND="" -RDEPEND="${DEPEND} - dev-lang/perl" +RDEPEND="dev-lang/perl" S="${WORKDIR}"/${PN} src_install() { newbin ${PN}*.pl ${PN} - dohtml *html + + docinto html + dodoc *html } diff --git a/sci-chemistry/probe/Manifest b/sci-chemistry/probe/Manifest index 8765128226d6..9d8bfc8574ea 100644 --- a/sci-chemistry/probe/Manifest +++ b/sci-chemistry/probe/Manifest @@ -1,5 +1,5 @@ AUX as-needed.patch 594 BLAKE2B dc558fa12441780347e1d751ed7a32a8030d5c3cfcc8b7c96c2e918d43e4dea334248e88807db9dab42178e75aa80341267c9c79f6ea71330cdabaf1a62e995a SHA512 6478862bc967614e8fc57abaa03b92f62943508ae77710b179bb71ae96d21c289b4f2836d76236297ba66ed97954997f4e6c8874f369af03200bf13e5226f8c9 AUX probe-2.13.110909-as-needed.patch 634 BLAKE2B 91848bcef2330e1f394c7c21388db1b761facefe73cbd0e244636e5b899f032463b9e643f2a48d84d028973695f1ef9359137aae8e65290a9f3bbe24f6dae204 SHA512 24b291cffbc00588626ac9da3e38e9bbb9a9ba121a3ae74fa5e91c94cd30489d61a559351d5a4b89ebb4c1564be30144d1eec295032ed612fa6e80d47d9ba8a6 DIST probe.2.13.110909.src.zip 131063 BLAKE2B da2cc9f43c96043b4cba0c628856e32aa7d5d9ca49d58d4e3f02c8d3aa106955d562c6212240d3d977940fc7301ce2bd27c86915517d5e5a313e5a7e459479ca SHA512 5efa066873d0e139da66bf8edb541fe42df94e99cab171ad8d06a8a6f5caada982ef5b18481e748b224dbed86f63c99237d04ecd107c82855b44de91fb6d2b16 -EBUILD probe-2.13.110909.ebuild 705 BLAKE2B ecaaeb8b1a3dc980c39dad241bb49ee5e08eb0a92edfeda62c22909f1d75af3713ad7a3a3c0096c509968013e1bb8b839f0f6b70aa288a7d35b0c88d48a7c86e SHA512 525ecf8ed9db9b5c99f618c3186bd54f1b99d3c97f6c05c48d51a8a8e672b41d548c62d9468f05c95794bb71fbd9f49f24e9c21686dc48414211600b1f5256ce +EBUILD probe-2.13.110909.ebuild 657 BLAKE2B dfdea26113059369a2e9a9dde47954751d1dbdb47291ea459cdf190dfcdefd807579b1da39255463594f473c09bfcf4b6e85dc7290861f6fd7ffaa66dc546b8d SHA512 06ae1a63ac0651d98f10fb1f6681eefff22be193aa893aaefa96a72c7257b85063634b9946a2d0f588d4bb972600b8075ed758996333124ee16cfbf3d20941b8 MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a diff --git a/sci-chemistry/probe/probe-2.13.110909.ebuild b/sci-chemistry/probe/probe-2.13.110909.ebuild index 66b1ac8c56da..628e2654bd30 100644 --- a/sci-chemistry/probe/probe-2.13.110909.ebuild +++ b/sci-chemistry/probe/probe-2.13.110909.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs MY_P="${PN}.${PV}" @@ -11,23 +11,21 @@ DESCRIPTION="Evaluates atomic packing within or between molecules" HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php" SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip" -SLOT="0" LICENSE="richardson" +SLOT="0" KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="" -RDEPEND="" -DEPEND="${RDEPEND} - app-arch/unzip" +BDEPEND="app-arch/unzip" + +S="${WORKDIR}/${MY_P}.src" -S="${WORKDIR}"/${MY_P}.src +PATCHES=( "${FILESDIR}"/${P}-as-needed.patch ) -src_prepare() { - epatch "${FILESDIR}"/${P}-as-needed.patch +src_configure() { tc-export CC } src_install() { - dobin "${S}"/probe - dodoc "${S}"/README* + dobin probe + einstalldocs } diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest index 20d6841c24e5..16451dfe6c2f 100644 --- a/sci-chemistry/raster3d/Manifest +++ b/sci-chemistry/raster3d/Manifest @@ -1,7 +1,5 @@ AUX 3.0.2-as-needed.patch 1579 BLAKE2B a9a8290e1d58da904835a3badd11eec07d4a968f81016e30641df917b14edf178c85e4410607b29cf2255fea4b770502a3544729ed6973a53d7470e1de20f8b1 SHA512 2898b55dca4e8d8d353922c36f44a9bb1dece19fa4c1de3f13ea5a09202004c10fbab6c2df2a39b71a65de3f30c19cd2724703b22b7ef978f366c69894761ce9 AUX 3.0.2-gentoo-prefix.patch 738 BLAKE2B 1d2b11034bf058d45d0c55391b8f297774f2ef09278275f77625a51f965de336ae23009f5f614447483be7aa63f951cb8f435fba9e739a6f9f2d9e4a289bee92 SHA512 5cb22fdff116c6a84a9f570af99062c08463d391cb0460d06e64990eaab2c945e86f0b3f5a378144c49014c0c41dc70cafb102c5feba500c43c8555ce41612a0 -DIST Raster3D_3.0-2.tar 1743034 BLAKE2B 3331d971696f2d95d1b2afe09995a8b5ce5ce7041725f1dd8a5ea27645d1e824956019a1466b60395ac0406d8c055a5052e0a483564777435d7fafda15cad6bb SHA512 f8f73cc91eae521839a9db8ee1a7a9d8727ed510cb574116d89e918480700d844691a6fc3c4a28cb54312b0133cc610422e55d99716803cf3e8bb5d9d934e37f -DIST Raster3D_3.0-3.tar 1729356 BLAKE2B be933cfb2c4bdc500d2cd221b8d71a01f1f4fab9cc0c70e0f5538363fa53714b6198a78e7cf7dd111dd0242e8537f2fcc38e54a12fc71588250e6ecfc561c0bc SHA512 bd372c4ba8d40db38e19f520883ca71ab7c5ef7a451b67150894e229b45167dfe00b77c19e118afc6abdb9ac07800cc16de5d2dc82c3ef9baa751200490e40fa -EBUILD raster3d-3.0.2.ebuild 2465 BLAKE2B b451cd2b8590bc6efb717f823183737eebe1bd108fbb2b313a7752a762f213775602182f3ac6878567840083796c7681c900bf4e5d1ec9a0c360f74553a6d683 SHA512 4e8a30469d18f14da0b8258622adaa17c8ac6ff06229dfa59efdf1ec4ba5386c23a594317d059a53d21160d229c17b2fb0db8b8cfc02c36d257230ec641ba9db -EBUILD raster3d-3.0.3.ebuild 2468 BLAKE2B e336eae62daef4a89526bb9d3f28f3aa040d26ff4f6c7f22b41d2a5601c7ecd314abfaf377a69eedb25c466e267e1f4141a0d4a0af6388b85ce459322f198078 SHA512 3cb278b220520dec632ed9c15c33df8774e4c99b327cd0e895307f9b61c427a8da31d321e27df04985b780957470b739d5202d4d8544c8864ebaeaa50dd0df38 +DIST Raster3D_3.0-6.tar 1729698 BLAKE2B d51b752c189ef720306e78a97e75a8b30c4286b1e75bfa20dd6d8c6e02e3a57d49508faaa1324d8b1f8311049ab3a9b18847bdcb73e7237e3bc91c34fb1ea55b SHA512 656bc19fdef882713c540598173e7f46246b4245f7983edc906fe9fdab7393c47c1687c6e9366987e8af7627d4bfe56a996ff0003aa19872d79724b3e555fdda +EBUILD raster3d-3.0.6.ebuild 2352 BLAKE2B 873821af6c3823f9ecc459526e5b1933a6147ad4d440f89c2f9c91499fdcaab4da8d766b0f98a4a8304f885ef57e20f709ea9390cbd70650f2263ef2ed6789c6 SHA512 6f8e78b35b631588679429b7495ab3ba1e0c128b1e8d76349cb8604c9fd8ffe6d437761e3936ddd9322b8274f605a2e903464cdba00d293bc7959dad55c8706d MISC metadata.xml 459 BLAKE2B c04c6562ba9f56e65d106bcab29b29f5d3000d9ea6270777df8b6d6d90f80c35464d9d1958b991bd23b2f4d946bac4f4486baf74b2b533bd1b43fd131efae52f SHA512 fe5bb2f873ea63f4c7185601842757cb0f791cecd8651fb4e15ea4992898ae60508e4a4c7bc161bddcfa3cf4125577da029b04cf06c900d6269af3f5b63bd916 diff --git a/sci-chemistry/raster3d/raster3d-3.0.2.ebuild b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild deleted file mode 100644 index a83e43ba57cf..000000000000 --- a/sci-chemistry/raster3d/raster3d-3.0.2.ebuild +++ /dev/null @@ -1,106 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix - -MY_PN="Raster3D" -MY_PV=$(replace_version_separator 2 -) -MY_P="${MY_PN}_${MY_PV}" - -DESCRIPTION="Generation high quality raster images of proteins or other molecules" -HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html" -SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar" - -LICENSE="Artistic-2" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="gd tiff" - -RDEPEND=" - tiff? ( media-libs/tiff:0 ) - gd? ( media-libs/gd[jpeg,png] )" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-as-needed.patch \ - "${FILESDIR}"/${PV}-gentoo-prefix.patch - - sed \ - -e "s:MYPF:${PF}:" \ - -e "s:MYLIB:$(get_libdir):g" \ - -i Makefile.template || \ - die "Failed to patch makefile.template" - - if ! use gd; then - sed \ - -e "/GDLIBS/s:^:#:g" \ - -e "/GDDEFS/s:^:#:g" \ - -i Makefile.template || die - fi - - if ! use tiff; then - sed \ - -e "/TLIBS/s:^:#:g" \ - -e "/TDEFS/s:^:#:g" \ - -i Makefile.template || die - fi - - if [[ $(tc-getFC) =~ gfortran ]]; then - append-cflags -Dgfortran - fi - - append-fflags -ffixed-line-length-132 - - eprefixify Makefile.template - cp Makefile.template Makefile.incl || die -} - -src_compile() { - local target - local i - - if [[ $(tc-getFC) =~ gfortran ]]; then - target="linux" - else - target="linux-$(tc-getFC)" - fi - - for i in render.o ${target} all; do - emake \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - FFLAGS="${FFLAGS}" \ - CC="$(tc-getCC)"\ - FC="$(tc-getFC)" \ - INCDIRS="-I${EPREFIX}/usr/include" \ - LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \ - ${i} - done -} - -src_install() { - emake prefix="${ED}"/usr \ - bindir="${ED}"/usr/bin \ - datadir="${ED}"/usr/share/Raster3D/materials \ - mandir="${ED}"/usr/share/man/man1 \ - htmldir="${ED}"/usr/share/doc/${PF}/html \ - examdir="${ED}"/usr/share/Raster3D/examples \ - install - - dodir /etc/env.d - echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ - "${ED}"/etc/env.d/10raster3d || \ - die "Failed to install env file." -} - -pkg_postinst() { - elog "Add following line:" - elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />" - elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml" - elog "to make imagemagick use raster3d for .r3d files" -} diff --git a/sci-chemistry/raster3d/raster3d-3.0.3.ebuild b/sci-chemistry/raster3d/raster3d-3.0.6.ebuild index 309e0dfc1ba5..eb03d6182a84 100644 --- a/sci-chemistry/raster3d/raster3d-3.0.3.ebuild +++ b/sci-chemistry/raster3d/raster3d-3.0.6.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix +inherit fortran-2 flag-o-matic prefix toolchain-funcs MY_PN="Raster3D" -MY_PV=$(replace_version_separator 2 -) +MY_PV=$(ver_rs 2 -) MY_P="${MY_PN}_${MY_PV}" DESCRIPTION="Generation high quality raster images of proteins or other molecules" @@ -19,16 +19,19 @@ KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" IUSE="gd tiff" RDEPEND=" - tiff? ( media-libs/tiff:0 ) - gd? ( media-libs/gd[jpeg,png] )" + gd? ( media-libs/gd[jpeg,png] ) + tiff? ( media-libs/tiff:0 )" DEPEND="${RDEPEND}" S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/3.0.2-as-needed.patch + "${FILESDIR}"/3.0.2-gentoo-prefix.patch +) + src_prepare() { - epatch \ - "${FILESDIR}"/3.0.2-as-needed.patch \ - "${FILESDIR}"/3.0.2-gentoo-prefix.patch + default sed \ -e "s:MYPF:${PF}:" \ @@ -62,14 +65,13 @@ src_prepare() { src_compile() { local target - local i - if [[ $(tc-getFC) =~ gfortran ]]; then target="linux" else target="linux-$(tc-getFC)" fi + local i for i in render.o ${target} all; do emake \ CFLAGS="${CFLAGS}" \ @@ -85,17 +87,16 @@ src_compile() { src_install() { emake prefix="${ED}"/usr \ - bindir="${ED}"/usr/bin \ - datadir="${ED}"/usr/share/Raster3D/materials \ - mandir="${ED}"/usr/share/man/man1 \ - htmldir="${ED}"/usr/share/doc/${PF}/html \ - examdir="${ED}"/usr/share/Raster3D/examples \ - install - - dodir /etc/env.d - echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ - "${ED}"/etc/env.d/10raster3d || \ - die "Failed to install env file." + bindir="${ED}"/usr/bin \ + datadir="${ED}"/usr/share/Raster3D/materials \ + mandir="${ED}"/usr/share/man/man1 \ + htmldir="${ED}"/usr/share/doc/${PF}/html \ + examdir="${ED}"/usr/share/Raster3D/examples \ + install + + newenvd - 10raster3d <<-EOF + R3D_LIB="${EPREFIX}/usr/share/${NAME}/materials" + EOF } pkg_postinst() { diff --git a/sci-chemistry/suitename/Manifest b/sci-chemistry/suitename/Manifest index b56c5a057c2e..016fd00ac953 100644 --- a/sci-chemistry/suitename/Manifest +++ b/sci-chemistry/suitename/Manifest @@ -1,3 +1,5 @@ +AUX suitename-0.3.070628-Wimplicit-function-declaration.patch 806 BLAKE2B a27bf0a9c1b650c51df72ee8135ddb63c9a2f10626349fd5235696590552b4f11770b8f7c10085bd1c9759029ae3fa67c556dedbfad71efbf33857a0429845f2 SHA512 ceb59844aefa50c2d4f4be605e93e01d6349def97bcb7d69768d38d23b86f1c002412e78f86b5cdf2edd17e2787e50ad05c8e04efa2a3ca84ec239f02011cd28 +AUX suitename-0.3.070628-makefile.patch 718 BLAKE2B 099d1628ca9207f04936a48a89d99303ed948e0778e32e0f89ad462136c5b37d13ed6c9e97bb0ecf91f03ebcd44477b85466872b26117815555f17f52a3acd46 SHA512 c659afd83584a02995559e1452aa7c7e3aa2db439283aa0af10e07451bf44843a5884add46d30076c387d37bd117656d6f6b3dfa1d89c52013ea29676873e1d3 DIST suitename.0.3.070628.src.tgz 29914 BLAKE2B 9633ca34c882dccb285aa98e3d9eee3663b15cffc649ec227ca78758511e5a9d3a3716c77eabf18825e3793af6d115db2ab4b0cd672d8af26eeb294340f525c8 SHA512 27811e2511da760c3c35d0a44aa798a35610a0e80a72d8aa58b78cb780156508f96e1890f558b1aa43bc3469d433352b29e53dca79f3a876ae2b7073f8e73088 -EBUILD suitename-0.3.070628.ebuild 726 BLAKE2B ab5cc3123c164466949a49ae93935e9909329edc592eec3ee824dea0cd1089f86662574cbe303f19ee685a4db5737c57f88b8f354d84b6dda26a630d98289097 SHA512 508b64119cf3c2ae72e5e321d7364401c33939490595bb2febae866df6ce2a00d506d78425d4de644fbe49191dc9163283e60835dd1ccb3bc428c9b9d1f4f079 +EBUILD suitename-0.3.070628.ebuild 710 BLAKE2B dc0e238a485a5b3585d01e5c326bf02ebbd65be71ba9b4c2f4c898d992a5eab3bc4591dfc3dd85d883e884c815d6e1fe7fcec9947ba437046d29794c13317e9d SHA512 b8aa083a08c1230618da91a61de2ae6c1a149d77e4608384558f1a0bf660f182386a164009c3067102189b9e455146707302a2733045ae13a463de6f3723948d MISC metadata.xml 1118 BLAKE2B f10c14e983382b489ea47eec41a17e39df81660cc56ea001ddfc9b6c67f8e96f65f52cb5e8c24d5d5211dfbf5fa17293f3dac1d2924a77e3b517d1b3796f7892 SHA512 7b2b6baa9bbc3e4ff3e2b2c0ba15dce0af04b06133c96872bbbb3626566a025d1b7d5472fc159e879e7be0cf50b5c27ebbcbd8def5cb182fc3654b893d88f2f2 diff --git a/sci-chemistry/suitename/files/suitename-0.3.070628-Wimplicit-function-declaration.patch b/sci-chemistry/suitename/files/suitename-0.3.070628-Wimplicit-function-declaration.patch new file mode 100644 index 000000000000..762715abdd46 --- /dev/null +++ b/sci-chemistry/suitename/files/suitename-0.3.070628-Wimplicit-function-declaration.patch @@ -0,0 +1,33 @@ +--- a/suitename.c ++++ b/suitename.c +@@ -25,7 +25,7 @@ + /*0.2.070628 triage reports zeta-1, epsilon-1, delta-1,... Ltriage codes */ + + /****main()*******************************************************************/ +-main(int argc, char** argv) ++int main(int argc, char** argv) + { + int LOK=1,ibin=0,jclst=0; + char sour[32]; +--- a/suiteninit.c ++++ b/suiteninit.c +@@ -9,6 +9,8 @@ + #include "suiteninpt.h" + #include "suitenout.h" + ++#include <ctype.h> ++ + /****initializations()********************************************************/ + int initializations(void) + { +--- a/suitenutil.c ++++ b/suitenutil.c +@@ -6,6 +6,8 @@ + + #include "suiteninit.h" + ++#include <ctype.h> ++ + /****vector7ab()**************************************************************/ + void vector7ab(float* atob, float* a, float* b) + { diff --git a/sci-chemistry/suitename/files/suitename-0.3.070628-makefile.patch b/sci-chemistry/suitename/files/suitename-0.3.070628-makefile.patch new file mode 100644 index 000000000000..b4766d4238d4 --- /dev/null +++ b/sci-chemistry/suitename/files/suitename-0.3.070628-makefile.patch @@ -0,0 +1,29 @@ +--- a/Makefile.linux ++++ b/Makefile.linux +@@ -1,24 +1,14 @@ + # suitename + +-ifeq ($(MAKECMDGOALS),debug) +-CFLAGS = -g +-else +-CFLAGS = +-endif +- +-LIBS = -lm ++LDLIBS = -lm + + # --------------------------------------------------------------------- + +-OBJS = suitename.o suitenscrt.o suiteninit.o suiteninpt.o suitenout.o suitenutil.o ++OBJS = suitenscrt.o suiteninit.o suiteninpt.o suitenout.o suitenutil.o + + # --------------------------------------------------------------------- + HEADERS = suitename.h suitenscrt.h suitenutil.h suiteninit.h suiteninpt.h suitenout.h + suitename: $(OBJS) +- cc -o suitename $(CFLAGS) $(OBJS) $(LIBS) +- +-debug: $(OBJS) +- cc -o suitename $(CFLAGS) $(OBJS) $(LIBS) + + clean: + rm -f *.o diff --git a/sci-chemistry/suitename/suitename-0.3.070628.ebuild b/sci-chemistry/suitename/suitename-0.3.070628.ebuild index 8441770df5ca..2243ccf61e55 100644 --- a/sci-chemistry/suitename/suitename-0.3.070628.ebuild +++ b/sci-chemistry/suitename/suitename-0.3.070628.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=4 +EAPI=7 inherit toolchain-funcs @@ -11,26 +11,25 @@ DESCRIPTION="The ROC RNA Ontology nomenclature and conformer-list development" HOMEPAGE="http://kinemage.biochem.duke.edu/software/suitename.php" SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" +LICENSE="richardson" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="richardson" -IUSE="" -S="${WORKDIR}"/${MY_P} +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-Wimplicit-function-declaration.patch +) -src_prepare() { +src_configure() { tc-export CC - cp Makefile.linux Makefile || die - sed \ - -e 's:cc:${CC}:g' \ - -e "s:-o:${LDFLAGS} -o:g" \ - -i Makefile || die } src_compile() { - emake CFLAGS="${CFLAGS}" + emake -f Makefile.linux } src_install() { - dobin ${PN} + dobin suitename } diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest index 5a66f3575403..701e9493a5d0 100644 --- a/sci-chemistry/surf/Manifest +++ b/sci-chemistry/surf/Manifest @@ -1,3 +1,5 @@ +AUX surf-1.0-Wreturn-type.patch 3022 BLAKE2B b97dea56225fd9018a39ef9db9d385fdc1ff143b7b595e15143ce3f38d195409ace81211d7e6b77eaab0165b3675a7c9cce02b29a0052bfcf15cbd82d2e8c3ef SHA512 17bab124975525ad0959bfa05e22926fc4849dc2e19bf7262b2ad79e857434641dc378a6cc57edbcfda1772efe138ea860424ad6e31b45495ad1f75579f5921f +AUX surf-1.0-makefile.patch 4592 BLAKE2B b402f39c180ae2a7f11f32c21dd7d5c3ef6c46204283e0f2bb76c2d260ec4f65b77ba3a351cabae850705b40a5a52fdfee8a58ea8d280ac7b6762eb7ae70f157 SHA512 618e2a8b98d004fb4730387dc1b064feab504abffc1066c17b79022f4033749bcd7173255029fe3aad2c480d3a91294d225615d6d44e79949beca1a66c9aee23 DIST surf-1.0.tar.Z 74347 BLAKE2B 543696838470f8b263d3841e177bb9054eb24a1ff0978fa09d9617e32a3a3e6b0662b37c1faa83fa449321276c8b3dd4aed80e978ea3c8315ed5b11f37196a73 SHA512 55b0e771f880931e43d677498ef4cdd92e5f57980d90b686b13c7ae612c8d695353a6f3b5ad0dab184d44e67d8cc5244e7b3f45b4f067c4174ed4399c184d435 -EBUILD surf-1.0.ebuild 796 BLAKE2B 3e66904e8e7fd63a6577a64c011ced32e73031807a7470c9895c172743759133e7423404a4107c5f99d127124d2bb14457ff882627ace6e524257200b67bcef2 SHA512 774ac12030accc1959b6eb22bd52ddd32b3a4b53ade020a5e36d58d160c0b5c3beed3c49eb8ae13b02d68dc95a21675063eb4b9c4262f804bf60a700c0d0b31b +EBUILD surf-1.0.ebuild 597 BLAKE2B 2a7c1ca764d287a8cae7b488aa6c093f9bf39d9f0f5eeb95e40bf266ecbfb2a6626e26b5ec35b703e24444db0ae9e34b9543e860e84cdffc3903c59f0a4333ce SHA512 000baae1d0e630b52382ef2a122dd0653f4bfb39d9811fabda931c9721e2c5ff448771b914e3d2aca88323d7c72e87085ee1df46edf85274590e9665e67b8a6c MISC metadata.xml 261 BLAKE2B 509ce9958149f9cd522a2c68dd0d23ed851d19d02494611456592897093378d180a6006cddf1575fd60106119e72726255c49db2e10fde1b370bdf2f3cf8c94a SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 diff --git a/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch b/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch new file mode 100644 index 000000000000..9ad6cf31593d --- /dev/null +++ b/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch @@ -0,0 +1,108 @@ +--- a/compute.c ++++ b/compute.c +@@ -210,7 +210,7 @@ + + Current_atom = atom_id; + +- if (!compute_neighbors(atom_id, &num_constraints)) return; ++ if (!compute_neighbors(atom_id, &num_constraints)) return -1; + + compute_planes(atom_id, num_constraints,constraints); + +@@ -597,7 +597,7 @@ + */ + if (all_verts_in_sphere(rvertices, rvertices_count, sq_radius)) + { /* printf("atom_id %d all_in = TRUE \n", atom_id); */ +- return; ++ return -1; + } + + for(i = 0; i < rfaces_count; i++) /* for each face */ +@@ -647,7 +647,7 @@ + if (DOTPROD3(diff, diff) < 1e-10) + /* atom center lies in the feasible region, and so can be also + taken to be the tes_origin - no more computations required */ +- return; ++ return -1; + + /* try computing the tes_origin as the average of all int_pts */ + VEC3_ZERO(temp_origin); count = 0; +--- a/tessel_concave.c ++++ b/tessel_concave.c +@@ -178,7 +178,7 @@ + if ((sq_side_len[0] < EPS) && + (sq_side_len[1] < EPS) && + (sq_side_len[2] < EPS)) +- { return; ++ { return -1; + } + + /* evaluate which side of the plane the points lie wrt the probe center */ +@@ -195,14 +195,14 @@ + max_len = FMAX((FMAX(sq_side_len[0], sq_side_len[1])), sq_side_len[2]); + max_side = (max_len==sq_side_len[0])?0:((max_len==sq_side_len[1])? 1 : 2); + +- if (num_fine_points == 0) return; /* all points are on the wrong side */ ++ if (num_fine_points == 0) return -1; /* all points are on the wrong side */ + + if (max_len <= Max_Tess_Len_Sq) + { /* sufficiently small so display but first check to see whether it + intersects the plane or not and if so, clip it accordingly */ + if (num_fine_points == 3) + { gen_tris(points[0], points[1], points[2]); +- return; ++ return -1; + } + else if (num_fine_points == 1) /* two points are on the wrong side */ + i = (itemp[0] == 1)? 0 : ((itemp[1] == 1)? 1: 2); +@@ -305,7 +305,7 @@ + (sq_side_len[1] < EPS) && + (sq_side_len[2] < EPS)) + { +- return; ++ return -1; + } + + if (max_len > Max_Tess_Len_Sq) +--- a/tessel_convex.c ++++ b/tessel_convex.c +@@ -74,7 +74,7 @@ + atoms[atom_id].center[Y], atoms[atom_id].center[Z], atoms[atom_id].radius); + fflush(stderr); + free(sph_side); +- return; ++ return -1; + } + + +--- a/tessel_torus.c ++++ b/tessel_torus.c +@@ -191,7 +191,7 @@ + + if (j > n) + { printf("gen_torus(): Too many torus verts %d (limit %d)\n",j, n); +- return ; ++ return -1; + } + old_j = j; + +@@ -202,7 +202,7 @@ + gen_linear_recurse(tor_pts[0][i],tor_pts[1][i],r[k],&j,fcenter,fradius,0); + if (j > n) + { printf("gen_torus(): Too many torus verts %d (limit %d)\n",j, n); +- return ; ++ return -1; + } + + for(m = 0; m < j-1; m++) +--- a/utils.c ++++ b/utils.c +@@ -91,7 +91,7 @@ + disc = radius*radius - DOTPROD3(EO, EO); + if (FP_EQ_EPS(disc, 0, GP_EPS*GP_EPS)) + { VEC3_ASN_OP(int_point, =, ray_pt); +- return; ++ return -1; + } + + one_by_sq_dir_mag = 1.0/DOTPROD3(ray_dir, ray_dir); diff --git a/sci-chemistry/surf/files/surf-1.0-makefile.patch b/sci-chemistry/surf/files/surf-1.0-makefile.patch new file mode 100644 index 000000000000..ae5177ffb501 --- /dev/null +++ b/sci-chemistry/surf/files/surf-1.0-makefile.patch @@ -0,0 +1,112 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,24 +1,19 @@ + # Compilation flags + #CC = cc +-CC = cc +-INCLUDE = -I. ++CPPFLAGS += -I. + #LINCLUDE = -lcurses -ltermcap -lm +-LINCLUDE = -lm +-OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE) +-#CFLAGS = -g $(FLAGS) $(INCLUDE) +-CFLAGS = -O2 $(FLAGS) $(INCLUDE) ++LDLIBS = -lm + + # These are the user object files in the application + SRCS = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \ + tessel_patches.c tessel_convex.c tessel_concave.c tessel_torus.c + + # obj files for sequential execution +-OBJS = surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \ ++OBJS = io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \ + tessel_patches.o tessel_convex.o tessel_concave.o tessel_torus.o + + # make objects +-surf: $(OBJS) Makefile +- $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) ++surf: $(OBJS) + + lint: + lint $(INCLUDE) $(SRCS) +@@ -29,80 +24,3 @@ + release: + tar -cvf surf.tar README *.[hc] Makefile + compress surf.tar +- +-.c.o: +- $(CC) $(CFLAGS) -c $*.c +- +- +-# make depend makes the proper include file dependencies. You _could_ run +-# it on a sun4, but there's a bug in the SunOS version of sed that causes +-# the all-important "cat makedep | sed -e 's/\.o/.d4o/p'" etc. line to +-# not print the results to the stdout (but to keep pumping it through the +-# edits. The 'p' flag effectively does nothing). To avoid this I have +-# replaced the 'p' flag by the 'w file' flag in sed. +- +-DEPEND = $(SRCS) +- +-depend: $(DEPEND) +- @ echo making dependencies... +- @ echo ' ' > makedep +- @ makedepend $(INCLUDE) -f makedep $(DEPEND) +- @ echo '/^# DO NOT DELETE THIS LINE/+2,$$d' >eddep +- @ echo '$$r makedep' >>eddep +- @ echo 'w' >>eddep +- @ cp Makefile Makefile.bak +- @ ed - Makefile < eddep +- @ rm eddep makedep +- @ echo ' ' >> Makefile +- @ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile +- @ echo '# IF YOU PUT STUFF HERE IT WILL GO AWAY' >> Makefile +- @ echo '# see make depend above' >> Makefile +- @ echo 'done.' +- @ echo ' ' >> Makefile +- +-# DO NOT DELETE THIS LINE -- make depend depends on it. +- +- +-# DO NOT DELETE THIS LINE -- make depend depends on it. +- +-surf.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-surf.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-surf.o: linalg.h +-io.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-io.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-io.o: linalg.h +-compute.o: surf.h /usr/include/stdio.h /usr/include/math.h +-compute.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-compute.o: /usr/include/sys/time.h linalg.h chull.h dual.h +-dual.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-dual.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-dual.o: linalg.h dual.h chull.h +-utils.o: surf.h /usr/include/stdio.h /usr/include/math.h +-utils.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-utils.o: /usr/include/sys/time.h linalg.h +-lp.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-lp.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-lp.o: linalg.h +-chull.o: surf.h /usr/include/stdio.h /usr/include/math.h +-chull.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-chull.o: /usr/include/sys/time.h linalg.h chull.h +-tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_cases.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_cases.o: /usr/include/string.h /usr/include/sys/time.h linalg.h dual.h +-tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_patches.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_patches.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_convex.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_convex.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_concave.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_concave.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_torus.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_torus.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +- +-# DEPENDENCIES MUST END AT END OF FILE +-# IF YOU PUT STUFF HERE IT WILL GO AWAY +-# see make depend above +- diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild index 5b6ff83975fd..16adc336a34d 100644 --- a/sci-chemistry/surf/surf-1.0.ebuild +++ b/sci-chemistry/surf/surf-1.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI="4" +EAPI=7 inherit toolchain-funcs @@ -12,31 +12,21 @@ SRC_URI="http://www.ks.uiuc.edu/Research/vmd/extsrcs/surf.tar.Z -> ${P}.tar.Z" LICENSE="SURF" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="" -DEPEND=" - !www-client/surf - sys-apps/ed - x11-misc/makedepend" -RDEPEND="" +RDEPEND="!www-client/surf" -S=${WORKDIR} +S="${WORKDIR}" -src_prepare() { - sed \ - -e 's:$(CC) $(CFLAGS) $(OBJS):$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS):g' \ - -i Makefile || die -} +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-Wreturn-type.patch +) -src_compile() { - emake depend \ - && emake \ - CC="$(tc-getCC)" \ - OPT_CFLAGS="${CFLAGS} \$(INCLUDE)" \ - CFLAGS="${CFLAGS} \$(INCLUDE)" +src_configure() { + tc-export CC } src_install() { - dobin ${PN} - dodoc README + dobin surf + einstalldocs } diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index d305a69e14e2..d9163127f214 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,11 +1,6 @@ -AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00 -AUX vmd-1.9.3-cuda.patch 15569 BLAKE2B a26ce893fd2808b7ce1ad36f6d2d690be482d24805f44030434fd3aadaa9f9a834ae8b73d7f1c759161e20041c2372181b90ae17f71eab50c94e6b38e3b133a3 SHA512 ba6f435601a53d5ed26ceab9ab86a9734e6a3b60f9cb61be5c9f59676a5145a4c64a538ddadf446e82608ade5a3d86ec6b8cb7257d9c402e245f845371feb571 -AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4 AUX vmd-1.9.4-gentoo-paths.patch 11523 BLAKE2B 3e02c73b49a3686ce00deb44f4bca0809c527a53d7fb13315c5799c5e9fe1d8ada9664452e41f49ad084abed96d2e5a6d01b000e49393e97eeb5fb2378af888f SHA512 da8e723d12ca7728d67dffcd0bf2e9c856764917d3f3ef07756febbc981bae20b061e0ead3fa617de18b94918d855c09f68c24a979c6f9f0cdea12b343a22756 AUX vmd-1.9.4-tmpdir.patch 398 BLAKE2B cf61240688f111d4763f458f0e10319a8154c5427172ba99d4bcfc7a9d8fd559fe7777c1ff703f81b68b2f10ec2a8c4af5cf61fd91d147aec2f4fafcf6753c82 SHA512 c5f96b3ef880ccdcf86d3927308c85aeaf3260ed0e54d60cbf186a0d63f6a88da16e49b14d6815d97bfd1ff4500bf9ce99d183d26ee78b67fed388e2217a7f10 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 -DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0 -EBUILD vmd-1.9.3-r5.ebuild 7822 BLAKE2B 2a3933c1008dcde65b37846ae5cfc993036d387a9a62a4cb207865187a22e8cf41401000171d083e059abc17c43adf773490aafcfbc576480b241fd359f6fb88 SHA512 9abc8facc673387ee0fcc77b27e4f421f2c7cb590b451b5d8ce4165a66be27ad1b69a45d9c939718a4359f1c76591855219bdb5956947aa2408d61f338eb78ca -EBUILD vmd-1.9.4_alpha43.ebuild 7539 BLAKE2B ea95aabc508d753de691e2986b1c36b03d9edf56d9b3843e564977fceb9974519219710c311efc677bcfb941c0aed49247980146678911e7a7a5c52202aff59e SHA512 4fa5a8681a76272f524901fe8a1e1b9b222227d48e86def3edd112b543f5c1f9feb0c046f050715ef7a4d66a7d31096a6d62609691944e778e71204a15b61819 +EBUILD vmd-1.9.4_alpha43.ebuild 7643 BLAKE2B 298be7052331709d194263c557558bbf0ca66936f460dcb1ac7aeb59add81519a856bdc61d61ab1ad216f5da199435eefb515a14cab59378a052bf8ae4bf6bce SHA512 4b504629e6d784d1da6ccf7db9f5a14da4b00869705851f3842c7d6f07cd0ac4ee45125c779b91862cceea54836eb06e84773098d3113a0d0b856fbb775ff07e MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9 diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch deleted file mode 100644 index b71cd97210a8..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/configure.old 2019-05-16 17:26:05.347560700 +0200 -+++ b/configure 2019-05-16 17:30:25.478455770 +0200 -@@ -1105,8 +1105,8 @@ - # This may be commented out if not required. - $libtachyon_defines = "-DVMDLIBTACHYON"; - $libtachyon_dir = "$vmd_library_dir/tachyon"; --$libtachyon_include = "-I$libtachyon_dir/include"; --$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; -+$libtachyon_include = "-Igentoo-libtachyon-include"; -+$libtachyon_library = "-Lgentoo-libtachyon-libs"; - $libtachyon_libs = "-ltachyon"; - @libtachyon_cc = (); - @libtachyon_cu = (); diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch deleted file mode 100644 index 258efb777caf..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch +++ /dev/null @@ -1,426 +0,0 @@ ---- a/src/CUDAMarchingCubes.cu 2018-03-30 18:52:25.467189457 +0300 -+++ b/src/CUDAMarchingCubes.cu 2018-03-30 18:52:02.387136244 +0300 -@@ -10,7 +10,7 @@ - * - * $RCSfile: CUDAMarchingCubes.cu,v $ - * $Author: johns $ $Locker: $ $State: Exp $ -- * $Revision: 1.30 $ $Date: 2016/11/28 03:04:58 $ -+ * $Revision: 1.32 $ $Date: 2018/02/15 05:15:02 $ - * - *************************************************************************** - * DESCRIPTION: -@@ -25,14 +25,17 @@ - // - // Description: This class computes an isosurface for a given density grid - // using a CUDA Marching Cubes (MC) alorithm. --// The implementation is based on the MC demo from the --// Nvidia GPU Computing SDK, but has been improved --// and extended. This implementation achieves higher --// performance by reducing the number of temporary memory --// buffers, reduces the number of scan calls by using vector --// integer types, and allows extraction of per-vertex normals --// optionally computes per-vertex colors if provided with a --// volumetric texture map. -+// -+// The implementation is loosely based on the MC demo from -+// the Nvidia GPU Computing SDK, but the design has been -+// improved and extended in several ways. -+// -+// This implementation achieves higher performance -+// by reducing the number of temporary memory -+// buffers, reduces the number of scan calls by using -+// vector integer types, and allows extraction of -+// per-vertex normals and optionally computes -+// per-vertex colors if a volumetric texture map is provided. - // - // Author: Michael Krone <michael.krone@visus.uni-stuttgart.de> - // John Stone <johns@ks.uiuc.edu> -@@ -48,7 +51,7 @@ - #include <thrust/functional.h> - - // --// Restrict macro to make it easy to do perf tuning tess -+// Restrict macro to make it easy to do perf tuning tests - // - #if 0 - #define RESTRICT __restrict__ -@@ -171,6 +174,11 @@ - texture<float, 3, cudaReadModeElementType> volumeTex; - - // sample volume data set at a point p, p CAN NEVER BE OUT OF BOUNDS -+// XXX The sampleVolume() call underperforms vs. peak memory bandwidth -+// because we don't strictly enforce coalescing requirements in the -+// layout of the input volume presently. If we forced X/Y dims to be -+// warp-multiple it would become possible to use wider fetches and -+// a few other tricks to improve global memory bandwidth - __device__ float sampleVolume(const float * RESTRICT data, - uint3 p, uint3 gridSize) { - return data[(p.z*gridSize.x*gridSize.y) + (p.y*gridSize.x) + p.x]; -@@ -592,6 +600,30 @@ - cudaBindTextureToArray(volumeTex, d_vol, desc); - } - -+#if CUDART_VERSION >= 9000 -+// -+// XXX CUDA 9.0RC breaks the usability of Thrust scan() prefix sums when -+// used with the built-in uint2 vector integer types. To workaround -+// the problem we have to define our own type and associated conversion -+// routines etc. -+// -+ -+// XXX workaround for uint2 breakage in CUDA 9.0RC -+struct myuint2 : uint2 { -+ __host__ __device__ myuint2() : uint2(make_uint2(0, 0)) {} -+ __host__ __device__ myuint2(int val) : uint2(make_uint2(val, val)) {} -+ __host__ __device__ myuint2(uint2 val) : uint2(make_uint2(val.x, val.y)) {} -+}; -+ -+void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) { -+ const uint2 zero = make_uint2(0, 0); -+ thrust::exclusive_scan(thrust::device_ptr<myuint2>((myuint2*)input), -+ thrust::device_ptr<myuint2>((myuint2*)input + numElements), -+ thrust::device_ptr<myuint2>((myuint2*)output), -+ (myuint2) zero); -+} -+ -+#else - - void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) { - const uint2 zero = make_uint2(0, 0); -@@ -601,6 +633,7 @@ - zero); - } - -+#endif - - void ThrustScanWrapperArea(float* output, float* input, unsigned int numElements) { - thrust::inclusive_scan(thrust::device_ptr<float>(input), -@@ -639,11 +672,9 @@ - } - - --/////////////////////////////////////////////////////////////////////////////// - // - // class CUDAMarchingCubes - // --/////////////////////////////////////////////////////////////////////////////// - - CUDAMarchingCubes::CUDAMarchingCubes() { - // initialize values -@@ -713,9 +744,6 @@ - } - - --//////////////////////////////////////////////////////////////////////////////// --//! Run the Cuda part of the computation --//////////////////////////////////////////////////////////////////////////////// - void CUDAMarchingCubes::computeIsosurfaceVerts(float3* vertOut, unsigned int maxverts, dim3 & grid3) { - // check if data is available - if (!this->setdata) - ---- a/src/CUDAMDFF.cu 2016-12-01 10:11:56.000000000 +0300 -+++ b/src/CUDAMDFF.cu 2018-03-30 18:56:44.352937599 +0300 -@@ -11,7 +11,7 @@ - * - * $RCSfile: CUDAMDFF.cu,v $ - * $Author: johns $ $Locker: $ $State: Exp $ -- * $Revision: 1.75 $ $Date: 2015/04/07 20:41:26 $ -+ * $Revision: 1.78 $ $Date: 2018/02/19 07:10:37 $ - * - *************************************************************************** - * DESCRIPTION: -@@ -28,12 +28,16 @@ - #include <stdlib.h> - #include <string.h> - #include <cuda.h> --#include <float.h> // FLT_MAX etc -- -+#if CUDART_VERSION >= 9000 -+#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0 -+#endif - #if CUDART_VERSION < 4000 - #error The VMD MDFF feature requires CUDA 4.0 or later - #endif - -+#include <float.h> // FLT_MAX etc -+ -+ - #include "Inform.h" - #include "utilities.h" - #include "WKFThreads.h" -@@ -588,6 +592,43 @@ - } - - -+ -+// #define VMDUSESHUFFLE 1 -+#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000 -+// New warp shuffle-based CC sum reduction for Kepler and later GPUs. -+inline __device__ void cc_sumreduction(int tid, int totaltb, -+ float4 &total_cc_sums, -+ float &total_lcc, -+ int &total_lsize, -+ float4 *tb_cc_sums, -+ float *tb_lcc, -+ int *tb_lsize) { -+ total_cc_sums = make_float4(0.0f, 0.0f, 0.0f, 0.0f); -+ total_lcc = 0.0f; -+ total_lsize = 0; -+ -+ // use precisely one warp to do the final reduction -+ if (tid < warpSize) { -+ for (int i=tid; i<totaltb; i+=warpSize) { -+ total_cc_sums += tb_cc_sums[i]; -+ total_lcc += tb_lcc[i]; -+ total_lsize += tb_lsize[i]; -+ } -+ -+ // perform intra-warp parallel reduction... -+ // general loop version of parallel sum-reduction -+ for (int mask=warpSize/2; mask>0; mask>>=1) { -+ total_cc_sums.x += __shfl_xor_sync(0xffffffff, total_cc_sums.x, mask); -+ total_cc_sums.y += __shfl_xor_sync(0xffffffff, total_cc_sums.y, mask); -+ total_cc_sums.z += __shfl_xor_sync(0xffffffff, total_cc_sums.z, mask); -+ total_cc_sums.w += __shfl_xor_sync(0xffffffff, total_cc_sums.w, mask); -+ total_lcc += __shfl_xor_sync(0xffffffff, total_lcc, mask); -+ total_lsize += __shfl_xor_sync(0xffffffff, total_lsize, mask); -+ } -+ } -+} -+#else -+// shared memory based CC sum reduction - inline __device__ void cc_sumreduction(int tid, int totaltb, - float4 &total_cc_sums, - float &total_lcc, -@@ -629,6 +670,7 @@ - total_lcc = tb_lcc[0]; - total_lsize = tb_lsize[0]; - } -+#endif - - - inline __device__ void thread_cc_sum(float ref, float density, -@@ -750,6 +792,92 @@ - } - - -+#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000 -+ // all threads write their local sums to shared memory... -+ __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ]; -+ __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ]; -+ __shared__ float tb_lcc_s[TOTALBLOCKSZ]; -+ __shared__ int tb_lsize_s[TOTALBLOCKSZ]; -+ -+ tb_cc_means_s[tid] = thread_cc_means; -+ tb_cc_squares_s[tid] = thread_cc_squares; -+ tb_lcc_s[tid] = thread_lcc; -+ tb_lsize_s[tid] = thread_lsize; -+ __syncthreads(); // all threads must hit syncthreads call... -+ -+ // use precisely one warp to do the thread-block-wide reduction -+ if (tid < warpSize) { -+ float2 tmp_cc_means = make_float2(0.0f, 0.0f); -+ float2 tmp_cc_squares = make_float2(0.0f, 0.0f); -+ float tmp_lcc = 0.0f; -+ int tmp_lsize = 0; -+ for (int i=tid; i<TOTALBLOCKSZ; i+=warpSize) { -+ tmp_cc_means += tb_cc_means_s[i]; -+ tmp_cc_squares += tb_cc_squares_s[i]; -+ tmp_lcc += tb_lcc_s[i]; -+ tmp_lsize += tb_lsize_s[i]; -+ } -+ -+ // perform intra-warp parallel reduction... -+ // general loop version of parallel sum-reduction -+ for (int mask=warpSize/2; mask>0; mask>>=1) { -+ tmp_cc_means.x += __shfl_xor_sync(0xffffffff, tmp_cc_means.x, mask); -+ tmp_cc_means.y += __shfl_xor_sync(0xffffffff, tmp_cc_means.y, mask); -+ tmp_cc_squares.x += __shfl_xor_sync(0xffffffff, tmp_cc_squares.x, mask); -+ tmp_cc_squares.y += __shfl_xor_sync(0xffffffff, tmp_cc_squares.y, mask); -+ tmp_lcc += __shfl_xor_sync(0xffffffff, tmp_lcc, mask); -+ tmp_lsize += __shfl_xor_sync(0xffffffff, tmp_lsize, mask); -+ } -+ -+ // write per-thread-block partial sums to global memory, -+ // if a per-thread-block CC output array is provided, write the -+ // local CC for this thread block out, and finally, check if we -+ // are the last thread block to finish, and finalize the overall -+ // CC results for the entire grid of thread blocks. -+ if (tid == 0) { -+ unsigned int bid = blockIdx.z * gridDim.x * gridDim.y + -+ blockIdx.y * gridDim.x + blockIdx.x; -+ -+ tb_cc_sums[bid] = make_float4(tmp_cc_means.x, tmp_cc_means.y, -+ tmp_cc_squares.x, tmp_cc_squares.y); -+ tb_lcc[bid] = tmp_lcc; -+ tb_lsize[bid] = tmp_lsize; -+ -+ if (tb_CC != NULL) { -+ float cc = calc_cc(tb_cc_means_s[0].x, tb_cc_means_s[0].y, -+ tb_cc_squares_s[0].x, tb_cc_squares_s[0].y, -+ tb_lsize_s[0], tb_lcc_s[0]); -+ -+ // write local per-thread-block CC to global memory -+ tb_CC[bid] = cc; -+ } -+ -+ __threadfence(); -+ -+ unsigned int value = atomicInc(&tbcatomic[0], totaltb); -+ isLastBlockDone = (value == (totaltb - 1)); -+ } -+ } -+ __syncthreads(); -+ -+ if (isLastBlockDone) { -+ float4 total_cc_sums; -+ float total_lcc; -+ int total_lsize; -+ cc_sumreduction(tid, totaltb, total_cc_sums, total_lcc, total_lsize, -+ tb_cc_sums, tb_lcc, tb_lsize); -+ -+ if (tid == 0) { -+ tb_cc_sums[totaltb] = total_cc_sums; -+ tb_lcc[totaltb] = total_lcc; -+ tb_lsize[totaltb] = total_lsize; -+ } -+ -+ reset_atomic_counter(&tbcatomic[0]); -+ } -+ -+#else -+ - // all threads write their local sums to shared memory... - __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ]; - __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ]; -@@ -794,6 +922,7 @@ - } - __syncthreads(); // all threads must hit syncthreads call... - } -+//#endif - - // write per-thread-block partial sums to global memory, - // if a per-thread-block CC output array is provided, write the -@@ -847,6 +976,7 @@ - } - #endif - } -+#endif - } - - - ---- a/src/CUDAQuickSurf.cu 2016-12-01 10:11:56.000000000 +0300 -+++ b/src/CUDAQuickSurf.cu 2018-03-30 19:01:38.777196233 +0300 -@@ -11,7 +11,7 @@ - * - * $RCSfile: CUDAQuickSurf.cu,v $ - * $Author: johns $ $Locker: $ $State: Exp $ -- * $Revision: 1.81 $ $Date: 2016/04/20 04:57:46 $ -+ * $Revision: 1.84 $ $Date: 2018/02/15 04:59:15 $ - * - *************************************************************************** - * DESCRIPTION: -@@ -22,6 +22,9 @@ - #include <stdlib.h> - #include <string.h> - #include <cuda.h> -+#if CUDART_VERSION >= 9000 -+#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0 -+#endif - - #if CUDART_VERSION < 4000 - #error The VMD QuickSurf feature requires CUDA 4.0 or later -@@ -130,14 +133,14 @@ - #define GUNROLL 1 - #endif - --#if __CUDA_ARCH__ >= 300 - #define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ ) --#define MINBLOCKDENS 1 -+#if __CUDA_ARCH__ >= 600 -+#define MINBLOCKDENS 16 -+#elif __CUDA_ARCH__ >= 300 -+#define MINBLOCKDENS 16 - #elif __CUDA_ARCH__ >= 200 --#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ ) - #define MINBLOCKDENS 1 - #else --#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ ) - #define MINBLOCKDENS 1 - #endif - -@@ -150,7 +153,7 @@ - // - template<class DENSITY, class VOLTEX> - __global__ static void --// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS ) -+__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS ) - gaussdensity_fast_tex_norm(int natoms, - const float4 * RESTRICT sorted_xyzr, - const float4 * RESTRICT sorted_color, -@@ -217,6 +220,8 @@ - for (yab=yabmin; yab<=yabmax; yab++) { - for (xab=xabmin; xab<=xabmax; xab++) { - int abcellidx = zab * acplanesz + yab * acncells.x + xab; -+ // this biggest latency hotspot in the kernel, if we could improve -+ // packing of the grid cell map, we'd likely improve performance - uint2 atomstartend = cellStartEnd[abcellidx]; - if (atomstartend.x != GRID_CELL_EMPTY) { - unsigned int atomid; -@@ -296,7 +301,7 @@ - - - __global__ static void --// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS ) -+__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS ) - gaussdensity_fast_tex3f(int natoms, - const float4 * RESTRICT sorted_xyzr, - const float4 * RESTRICT sorted_color, -@@ -363,6 +368,8 @@ - for (yab=yabmin; yab<=yabmax; yab++) { - for (xab=xabmin; xab<=xabmax; xab++) { - int abcellidx = zab * acplanesz + yab * acncells.x + xab; -+ // this biggest latency hotspot in the kernel, if we could improve -+ // packing of the grid cell map, we'd likely improve performance - uint2 atomstartend = cellStartEnd[abcellidx]; - if (atomstartend.x != GRID_CELL_EMPTY) { - unsigned int atomid; -@@ -550,7 +557,6 @@ - - // per-GPU handle with various memory buffer pointers, etc. - typedef struct { -- /// max grid sizes and attributes the current allocations will support - int verbose; - long int natoms; - int colorperatom; -@@ -561,18 +567,18 @@ - int gy; - int gz; - -- CUDAMarchingCubes *mc; ///< Marching cubes class used to extract surface -+ CUDAMarchingCubes *mc; - -- float *devdensity; ///< density map stored in GPU memory -- void *devvoltexmap; ///< volumetric texture map -- float4 *xyzr_d; ///< atom coords and radii -- float4 *sorted_xyzr_d; ///< cell-sorted coords and radii -- float4 *color_d; ///< colors -- float4 *sorted_color_d; ///< cell-sorted colors -- -- unsigned int *atomIndex_d; ///< cell index for each atom -- unsigned int *atomHash_d; ///< -- uint2 *cellStartEnd_d; ///< cell start/end indices -+ float *devdensity; -+ void *devvoltexmap; -+ float4 *xyzr_d; -+ float4 *sorted_xyzr_d; -+ float4 *color_d; -+ float4 *sorted_color_d; -+ -+ unsigned int *atomIndex_d; -+ unsigned int *atomHash_d; -+ uint2 *cellStartEnd_d; - - void *safety; - float3 *v3f_d; diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch deleted file mode 100644 index 22712abf30b8..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- a/scripts/vmd/vmdinit.tcl~ 2016-10-27 05:46:34.000000000 +0200 -+++ b/scripts/vmd/vmdinit.tcl 2019-12-03 16:29:01.894002827 +0100 -@@ -197,7 +197,7 @@ - set env(TMPDIR) /tmp - } - default { -- set env(TMPDIR) /usr/tmp -+ set env(TMPDIR) /tmp - } - } - } ---- a/scripts/vmd/chemical2vmd~ 2000-07-03 19:30:23.000000000 +0200 -+++ b/scripts/vmd/chemical2vmd 2019-12-03 16:28:49.316861178 +0100 -@@ -61,7 +61,7 @@ - - - # Make a temp. file to store the load command --$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'}; -+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'}; - sub tmpfile { - local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$; - local ($i); diff --git a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild deleted file mode 100644 index a4e0e6db49b0..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild +++ /dev/null @@ -1,272 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar -" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/chemical-mime-data - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" - elog - elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" - elog "file may get downloaded as a compressed tarball or not. In that case" - elog "you will need to ensure you uncompress the file and rename it" - elog "as ${P}.src.tar" -} - -src_prepare() { - xdg_src_prepare - - use cuda && cuda_sanitize - - # Compat with newer CUDA versions (from Arch) - eapply "${FILESDIR}"/${P}-cuda.patch - - cd "${WORKDIR}"/plugins || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch - eapply "${FILESDIR}"/${P}-configure-libtachyon.patch - eapply "${FILESDIR}"/${P}-tmpdir.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - # Open PDB files with VMD - echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild index 6ff1210c5426..8ffb5a090074 100644 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild @@ -78,11 +78,15 @@ pkg_nofetch() { } src_prepare() { + # Apply user patches from ${WORKDIR} to allow patching on patches + # subdir too + cd "${WORKDIR}" xdg_src_prepare use cuda && cuda_sanitize - cd "${WORKDIR}"/plugins || die + # Prepare plugins + cd plugins || die sed '/^.SILENT/d' -i $(find -name Makefile) |