diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2020-01-15 15:51:32 +0000 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2020-01-15 15:51:32 +0000 |
| commit | 21435953e16cda318a82334ddbadb3b5c36d9ea7 (patch) | |
| tree | e1810a4b135afce04b34862ef0fab2bfaeb8aeca /sci-chemistry | |
| parent | 7bc9c63c9da678a7e6fceb095d56c634afd22c56 (diff) | |
gentoo resync : 15.01.2020
Diffstat (limited to 'sci-chemistry')
42 files changed, 361 insertions, 501 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild index 688c26cc3807..e9bde2396c60 100644 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) +PYTHON_COMPAT=( python2_7 python3_{6,7} ) if [[ $PV = *9999* ]]; then scm_eclass=git-r3 diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest index cc8676ae54fd..a404a5fc9601 100644 --- a/sci-chemistry/GromacsWrapper/Manifest +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -1,3 +1,3 @@ DIST GromacsWrapper-0.8.0.tar.gz 1205837 BLAKE2B 3627e56df0dc6ba86caac67795416c7c8c187aaa4fac545600d17dcd799cb153feaab61a0f0632e051c4e9c0b4cd74f8e165156873e36bc53571bec78e5fca61 SHA512 da7215216c9a2b52094bb7e43e04f1b429c4893ba67b4bd850fe68e99f338813392fd9d0aa1b19d3398c694be964bc2badbf1b3623420da929ee4abcef18026f -EBUILD GromacsWrapper-0.8.0.ebuild 817 BLAKE2B 12c186f411c5dff106e04d65c3de4350c29ba5f71e4012196674f00ca0711cfa311cce7c1211128c2808add32c05cf36afdf58be2682455a38ca938d45dc69fc SHA512 1518c5ccc637bcf1a8f89896ca4e9b9f31f0331ab07ba5a4b698d81e0233ec75d318f1699981897148e13013a94dcb62ef87478ddce01756d71e164320f96cc4 +EBUILD GromacsWrapper-0.8.0.ebuild 815 BLAKE2B 4b462d20c936994c801855b55652850d0ce4a34ceaa9d8d007a81ef87473a7921958f8b431ddb09ec103414af6d37ce81bcc4aeb2dd2eae313d8176c218e3cee SHA512 30387145d076d73c3a73b8254b104312d60fad3c0daffc0ff867bde7c03e376490ca166adf8a948d75cbdaf956d7a8362eeb5f6f87ef08a1ccd10c08af8e5ea4 MISC metadata.xml 482 BLAKE2B 2745b575ac325e9f8c53d53026ca0c67201f1519725c572813c0ad281b4a39399cbf93176e816646aa83f829c0981ee4457e3ab2232ed095f76d5a2068840912 SHA512 4f2efb8d263f20e50928e0c6f0913c65da746b5253a14658273c830b7f95ecc15620f92e87db9670adfd92792e96cc352af528ed4fa1e874977a744d2e15c6bf diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild index 0e9af8987fab..00d480b169c3 100644 --- a/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild +++ b/sci-chemistry/MDAnalysis/MDAnalysis-0.18.0-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) +PYTHON_COMPAT=( python3_{6,7} ) inherit distutils-r1 diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest index 5918592720ec..cb8b89ffd481 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 935 BLAKE2B e20982f0b1532c30382a9f3a11fff7fe423dc1e06c8be7cacecc5f9cd6ad3f3249334729f4f1ee790bd97a6af8d5954a9ff80d1fddfcbdd3e7172187a45f2d71 SHA512 545868919c247f71b06264cf3b99d70a6f52d32978bf165c795c58bb544305fe2d50508f8434b52581a3b5cfe47a74dd713dc86fad7944ae984dd8e39db6144e +EBUILD MDAnalysis-0.18.0-r1.ebuild 923 BLAKE2B c8a5b31505859c662c0c9fc6d238d778b5f2d32074fdd5be037311d6f8cfe6110ff08cb55e8d94670ebb132dabd089dde2c7d6d45c8d6e62b4834f328eeb2c61 SHA512 24448a1859e49017dfd28e4e3a0e55c38c3efec7cc9bef4d620813f30c2d9c622eb5d4198ee06e19f604be5046a818c850a9b778090ab2bc1f5d484ea7c3cd8c MISC metadata.xml 496 BLAKE2B 1b6faf13663ab39bbb2c5b123f67cd7688c188459133d77411c857bd901f8133f9791d8c54e8fe7dc84e8150187b6562f297e706d36e167b3c20cf7df6e6a682 SHA512 674265a9bdb74cc5d4b059ce2b33cdba84bee097bb5940b3cc55cfdc6b74de5f28a4cfa34e9f0fd4db5d3c336a6f7b3be39235c2d9697d5adf9c7311e348d8a1 diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 6b2ad67562c0..f582eec3184e 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest index 810d6dc67374..9a3e8ce8b7c7 100644 --- a/sci-chemistry/ParmEd/Manifest +++ b/sci-chemistry/ParmEd/Manifest @@ -1,5 +1,5 @@ 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 827 BLAKE2B 017b1b0fa51c1ce2758e780389fd3f87ed0eb0449a0101e0cdc09b5192bb85c1c14eb1002ef5b72d2e62671981021340b38aec51b1eadb2785af87fa04354f01 SHA512 1b7809f150e2e22c07e4c2c34c8c8f36ddc180ca6621dc4706b41c9e8780726e9efa7113159f05ca6349d5c0febaae1d9abed3b56de477fb225d667551d846fb -EBUILD ParmEd-3.0.3.ebuild 828 BLAKE2B d44aa368223f04e91c50b68ed3525932ea14f79381ecc66dc7d0e3b16fc2f35b7536f98ca6402681bb9fdbb568ac6ec561d2feb40c91a166fd415f42c917b2db SHA512 a6a754e78715cedc5739c5c9d5cd06bb3676d9848a128f9796a09c33bc61a40c93f92617156ea7efd9f0b2a2466c23bbcde0977807adedfc7faa813d07dc9bb6 +EBUILD ParmEd-2.7.3.ebuild 823 BLAKE2B aaa7479f94ba8c99f788b19e60bef2177b6ff07a0b5ae1aaa4587fb3720aac07a5b50940ca267236937850d0c06a7900d47c753ef53137c7a7706e859a71dc15 SHA512 66eed20446dd039ca0ee9f75ff341f6a9cd0cf16a7ca64606bd3cccd24824b0b1b537e48c95926e407d8af2f6602cfca18f4c5097e5089ac77525c6cc208b8fa +EBUILD ParmEd-3.0.3.ebuild 824 BLAKE2B 7c362d79a7a0c467038d667d9f5849b77714725f9dc4feebde1389bb3c9be42651ba970679a8820c58221ed0e93991fad5b80b3da1c234655ef2d633bd3bb9b8 SHA512 974004c5b1186a1c0527a9ffc2a8762eb0b954c609d691b63eed4c139fcd8a0cf51d3c0d3fc695c399b8cea1bc22bdfaa9f4851ab974aad150286a47b510e0d8 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 index 0e3074845a2f..ab581daea0c2 100644 --- a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild +++ b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) +PYTHON_COMPAT=( python{2_7,3_6} ) if [[ $PV = *9999* ]]; then scm_eclass=git-2 diff --git a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild index 002ac5a8c6f9..a2a476a1d5ef 100644 --- a/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild +++ b/sci-chemistry/ParmEd/ParmEd-3.0.3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) +PYTHON_COMPAT=( python{2_7,3_6} ) if [[ $PV = *9999* ]]; then scm_eclass=git-r3 diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest index d02f31d201c4..4f6aba7fa386 100644 --- a/sci-chemistry/freeon/Manifest +++ b/sci-chemistry/freeon/Manifest @@ -2,6 +2,6 @@ AUX freeon-1.0.10-stop.patch 970 BLAKE2B 6c1e5dfe5ad881fbbceb071c53cf3fcaa187ae1 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 649 BLAKE2B 11952531b3b20e712f6cbaaac37a6e0aa856c19b0150d11591f7bace60f45ec0266a8251b9efb017cce0eb79eac1f9641450391ccc594f553c9f4cc61a8e56dd SHA512 52bf70f409b594bc92cd611b05adc972cde0c02e69f38c022055e6de9f509045589a12ee86c36967e5fb9e8adf26e9bd378b7983dab0063099ad0518f5d5d210 +EBUILD freeon-1.0.10.ebuild 642 BLAKE2B c25d6ac3201a4f607022e2d887101f8cd8be2f76054a93f7fd6ef95ab640e6500989393e5ef8dd8b61447fa2ff40894b46cc07bede6480060c76fa061f3078c0 SHA512 56d4d8b356f2e7b55deb3ecdd632b7e00b2a0c907d9e5dc1941ef3695e0da14ded7e025b990df46d9c3a19705123e4a5acde4a838e66a61052c9dd698def6d63 EBUILD freeon-1.0.8-r1.ebuild 626 BLAKE2B 5d5a53bd58c81ff88775f1370d0daf71e94d043b5c3fc825cb2e040cbdb4b3129c1b97b88b5eaaed1a21aaa592c0fa27fb4c7d403cacfdb5d2cfef724c8c72f9 SHA512 8474400965e790a50285e2d5687952535e5d2ee4797086dd64b7f62a990d993937f13d28f92f01057185378944f6baa939427b2a9253749cadb992afd9a72940 MISC metadata.xml 528 BLAKE2B aa64697b42ac5f829fc893ae2c05f0bae6bb9bb16f067539ca9a11b9469a9a9f4b203eb2f0242f9fde744ea6905223da2249e50622a479975548ef552e7286dc SHA512 4eea3876d046b423706f565571cbe20dbe2ff724ecd8de7f92ba0103c83f78d9e1d28789d6c35e62a8f0527f13bdadf6303695c529b7b6622bc2e14cf57044da diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild index 37eff15d2079..8dd980d33176 100644 --- a/sci-chemistry/freeon/freeon-1.0.10.ebuild +++ b/sci-chemistry/freeon/freeon-1.0.10.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) +PYTHON_COMPAT=( python{2_7,3_6} ) inherit autotools fortran-2 python-any-r1 diff --git a/sci-chemistry/gmxapi/Manifest b/sci-chemistry/gmxapi/Manifest index ce2771c016a4..8e7fbb119013 100644 --- a/sci-chemistry/gmxapi/Manifest +++ b/sci-chemistry/gmxapi/Manifest @@ -1,3 +1,3 @@ DIST gmxapi-0.0.7.1.tar.gz 671400 BLAKE2B 5db024bceaed262fc1bd2ef35c0c24a31eff12abde7766ba0eea9d5aabe04c435cdf3c79c04d7932f2110de837a0d06e1f66239f22ba6f313410ed8c9d899788 SHA512 4103d67be3c869907613ec74fc46f14b15242ad93a973fc984dbb25e79bb0bb697d9d2ad9b67a8da2500e5a89b8f78ea1ef1632455af29830e11c2bf1f11bc44 -EBUILD gmxapi-0.0.7.1.ebuild 1239 BLAKE2B d8d75f403f2bc68f98d5e72713de382c91bbbe341a83bb4705dba7aeb70fad389435b0fd46838a0bf23fe158721e290dee9a67421f37cd1a427bba172bf687c7 SHA512 e2a0406f92983e40cabbc40bed27ba44de8218573dbda11c6087141bd5f1ccc0e1b90fdfcebbcbeae12c5bbdbe51b3f9f15a50830fcb50c23b7052b5ef92c195 +EBUILD gmxapi-0.0.7.1.ebuild 1232 BLAKE2B ce5e1d18626a71dc760181efa246d9ca422c2710545d0096faac5f0a5f03237011cf27eae74a4d7102427355893beb5e1f830327c66d8e76dfabf788fac4ed9e SHA512 d01b515af311217f0e27c037c93188f1381937b69b9cd2c51ced1bb73a8b6d03c773faf80932d510da2d33c4fdae4267b7156f52a855b994cbcf5bfb9fb10b9c MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8 diff --git a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild index f27d423c9d24..5bb47665f026 100644 --- a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild +++ b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild @@ -1,11 +1,11 @@ -# Copyright 2019 Gentoo Authors +# Copyright 2019-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 MAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) +PYTHON_COMPAT=( python3_{6,7} ) inherit cmake-utils python-r1 diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 203a5b921471..db87a7f4f9f2 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,23 +1,18 @@ AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e -DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 -DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218 -DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 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Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - https://github.com/gromacs/gromacs.git - https://repo.or.cz/r/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - " -DEPEND="${CDEPEND} - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack )" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake-utils_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - #go from slowest to fastest acceleration - local acce="None" - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex doc) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local cuda=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && \ - cuda=( "-DGMX_GPU=ON" ) - local opencl=( "-DGMX_USE_OPENCL=OFF" ) - use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - "${opencl[@]}" - "${cuda[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON ${cuda} - -DGMX_OPENMM=OFF - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile - # not 100% necessary for rel ebuilds as available from website - if use doc; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install - if use doc; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild index 4db9e9672b08..3e5988a06d24 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" diff --git a/sci-chemistry/gromacs/gromacs-2019.4.ebuild b/sci-chemistry/gromacs/gromacs-2019.5.ebuild index a08d3ecc9027..7775143d0ae9 100644 --- a/sci-chemistry/gromacs/gromacs-2019.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -19,7 +19,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" @@ -93,7 +93,7 @@ src_unpack() { if use test; then EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests" \ git-r3_src_unpack fi fi diff --git a/sci-chemistry/gromacs/gromacs-2020_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild index a47062613711..f40242167fd7 100644 --- a/sci-chemistry/gromacs/gromacs-2020_beta1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -1,11 +1,13 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python3_{5,6,7} ) +PYTHON_COMPAT=( python3_{6,7} ) + +DISTUTILS_SINGLE_IMPL=1 inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils @@ -50,6 +52,7 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} + !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig @@ -79,7 +82,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${P}-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" @@ -87,6 +90,10 @@ pkg_pretend() { die "Please switch to an openmp compatible compiler" } +pkg_setup() { + python-single-r1_pkg_setup +} + src_unpack() { if [[ ${PV} != *9999 ]]; then default @@ -229,6 +236,7 @@ src_configure() { "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure [[ ${CHOST} != *-darwin* ]] || \ @@ -253,11 +261,6 @@ src_configure() { [[ ${CHOST} != *-darwin* ]] || \ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die done - if use python; then - cd python_packaging - distutils-r1_src_configure - cd .. - fi } src_compile() { @@ -265,6 +268,12 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ @@ -275,11 +284,6 @@ src_compile() { BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ cmake-utils_src_compile done - if use python; then - cd python_packaging - distutils-r1_src_compile - cd .. - fi } src_test() { @@ -287,17 +291,16 @@ src_test() { BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_make check done - if use python; then - cd python_packaging - distutils-r1_src_test - cd .. - fi } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install ${GMX_PYTHON_INSTALL} + cmake-utils_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install python_packaging/install + fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi @@ -310,17 +313,12 @@ src_install() { insinto /usr/include/tng doins src/external/tng_io/include/tng/*h fi - if use python; then - cd python_packaging - distutils-r1_src_install - cd .. - fi # drop unneeded stuff rm "${ED}"/usr/bin/GMXRC* || die for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do local n=${x##*/gmx-completion-} n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die newbashcomp "${T}"/"${n}" "${n}" done rm "${ED}"/usr/bin/gmx-completion*.bash || die diff --git a/sci-chemistry/gromacs/gromacs-2019.3.ebuild b/sci-chemistry/gromacs/gromacs-2020.ebuild index 5254b1f3f38b..f40242167fd7 100644 --- a/sci-chemistry/gromacs/gromacs-2019.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.ebuild @@ -1,13 +1,15 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python3_{6,7} ) -inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -32,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -50,8 +52,9 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} + !sci-chemistry/gmxapi " -DEPEND="${CDEPEND} +BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen @@ -79,12 +82,18 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi +PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) + pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ die "Please switch to an openmp compatible compiler" } +pkg_setup() { + python-single-r1_pkg_setup +} + src_unpack() { if [[ ${PV} != *9999 ]]; then default @@ -221,11 +230,13 @@ src_configure() { -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure [[ ${CHOST} != *-darwin* ]] || \ @@ -257,6 +268,12 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ @@ -280,6 +297,10 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install python_packaging/install + fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi @@ -293,14 +314,14 @@ src_install() { doins src/external/tng_io/include/tng/*h fi # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do local n=${x##*/gmx-completion-} n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die newbashcomp "${T}"/"${n}" "${n}" done - rm "${ED}"usr/bin/gmx-completion*.bash || die + rm "${ED}"/usr/bin/gmx-completion*.bash || die readme.gentoo_create_doc } diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index f9d980d7c0f3..aa6382b595a9 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -1,11 +1,15 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +PYTHON_COMPAT=( python3_{6,7} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -30,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -47,13 +51,16 @@ CDEPEND=" lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + !sci-chemistry/gmxapi " -DEPEND="${CDEPEND} +BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen - dev-python/sphinx + dev-python/sphinx[${PYTHON_USEDEP}] media-gfx/mscgen + media-gfx/graphviz dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -64,7 +71,8 @@ REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack )" + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" DOCS=( AUTHORS README ) @@ -74,12 +82,18 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi +PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) + pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ die "Please switch to an openmp compatible compiler" } +pkg_setup() { + python-single-r1_pkg_setup +} + src_unpack() { if [[ ${PV} != *9999 ]]; then default @@ -116,6 +130,28 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF } src_configure() { @@ -172,6 +208,7 @@ src_configure() { -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" ${extra} ) @@ -193,11 +230,13 @@ src_configure() { -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure [[ ${CHOST} != *-darwin* ]] || \ @@ -207,9 +246,11 @@ src_configure() { mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON ${cuda} + -DGMX_MPI=ON -DGMX_OPENMM=OFF -DGMXAPI=OFF + "${opencl[@]}" + "${cuda[@]}" -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF @@ -227,6 +268,12 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ @@ -250,6 +297,10 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install python_packaging/install + fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi @@ -263,14 +314,14 @@ src_install() { doins src/external/tng_io/include/tng/*h fi # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do local n=${x##*/gmx-completion-} n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die newbashcomp "${T}"/"${n}" "${n}" done - rm "${ED}"usr/bin/gmx-completion*.bash || die + rm "${ED}"/usr/bin/gmx-completion*.bash || die readme.gentoo_create_doc } diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest index ed5b2ebbe93c..9d178ddd5bc2 100644 --- a/sci-chemistry/mdtraj/Manifest +++ b/sci-chemistry/mdtraj/Manifest @@ -1,3 +1,3 @@ DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76 -EBUILD mdtraj-1.9.1.ebuild 913 BLAKE2B 219e598b0f693590a70c7221fb247587d17eb0214838e45517a099fcbcd936d342735a02da84ca81c74c6ab11ece7fe31cfc74d5610e728d79437867a2d12f9a SHA512 e169ea7efef0a9531657ee793a1bba5e020f3d5d013b8ffed5e6198d2057d98e0961fc734edfefe0b9592d60d22fd6d67c631c071073ce75d1359ea5dbfd774e +EBUILD mdtraj-1.9.1.ebuild 902 BLAKE2B 2bbbf367b06fd0ae53c134d1ab214350e26675ae52f71c633f0a5102e36515976ba16e726e648c2b4ccddc4330f5eb1498f20441d034e5aa16f60a32223c07d9 SHA512 258e368468af7347ae1e27e1167aae3fe656c085533082ffe2cb3dc5e6e0538148602ccf45bda4fdb7d25f4a0b9bf8816f421b83dcaa84815a90cf06a727927b 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 889d5e8e0b26..761ab50155c8 100644 --- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild +++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild @@ -1,10 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) - +PYTHON_COMPAT=( python3_6 ) inherit distutils-r1 DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code" diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest index 6b1e2c080a55..5c2bb9440789 100644 --- a/sci-chemistry/nmrglue/Manifest +++ b/sci-chemistry/nmrglue/Manifest @@ -1,4 +1,4 @@ AUX nmrglue-0.5-nohyper.patch 1408 BLAKE2B 8e91e270183ce8f4c361fd3577dc4942b2afab81ee8f59df5c8dd9056dbf639653d2e84f9dc04026636dda98e28a244586ba5bc2cd4ed5c43c8a31d0c0cab4d1 SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd DIST nmrglue-0.5.tar.gz 142604 BLAKE2B 9a018a73bea46176fc06042013cb23b3eeb962df8a595388da536d17f1d2d4d550065c5492df28de860ea1290314d2fa1110af349be0c2a8b1b31677b3e4afbc SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 -EBUILD nmrglue-0.5-r1.ebuild 753 BLAKE2B 37b2d1f011c7cf4f44fbf4468154384173d40310c519b9a10c49cd684291c912add9abc9ea1b19254302a520a1dc3b204b80ad23056f78bc59d0f993c99fe3a4 SHA512 6242503f01772bf425bd6665b51f2a00288f1c352ac7b9f1ecc154a9c5ed99e19c58ddf09dd4e0a9cf9f5991fcdbe208b06300290c968ebd2d16f2894487562d +EBUILD nmrglue-0.5-r1.ebuild 749 BLAKE2B fb7edbcd7e664e3ddb3f51d4c569abe49080262805ba1d9c32ee2ea61f64af26e4fe8405118e7fd5d37147f90aab955566b991a439cde3e2bbc5ed5a8b941003 SHA512 b62d23ba30bd96b65760947010bfb1d519057777bfb4bcc2b8a53bb6625dada73a2d20f16a8c4e2e9d93c1eb341d6fc9318db69972f889c788c0c5a10d5876be 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 97ddc5611088..49d670980a09 100644 --- a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild +++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit distutils-r1 diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest index decaeb88f1c3..ed04c0eac855 100644 --- a/sci-chemistry/openbabel-python/Manifest +++ b/sci-chemistry/openbabel-python/Manifest @@ -1,4 +1,4 @@ AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 -EBUILD openbabel-python-2.4.1-r1.ebuild 2170 BLAKE2B ff6345bd83a8bb97071710f9215e83516aab062ab5e40f30adfddf7e5883b702503f94ab6d2c177589958b127a3fc2422893e5c4f4e9ca4cbc700f3c36ef53bc SHA512 a993e4c10c36e51af247d6065c0f823f593f47f37cae1b9aafdf95cd9ee99264a71fe440497217bde42ec6a0945e2282ae40a3dee1b4658ff97c05cb15ec6b55 +EBUILD openbabel-python-2.4.1-r1.ebuild 2166 BLAKE2B 45ed425ebe47014c04d8f71661d0e29259d7b3d598695de0c7f0c7027b1488e70855ab4acb74b3d901f706bd58a8cb43ef7f4b1d5f927f8a16220f0cf7ffba41 SHA512 03bfaad27c45362252ebd719d7b526e977b1330e02251e8c82e0568c9f8a8759a5796dd2a22f22419d0f3465fe325d45c4f41a40b9a85edb14cd0a8ad4bed1b7 MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e 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 index 92382447cd1a..270018c23410 100644 --- a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild +++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 python3_{5,6} ) +PYTHON_COMPAT=( python2_7 python3_6 ) inherit cmake-utils python-r1 diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest index c6ed1f7d6178..351e29ce5d76 100644 --- a/sci-chemistry/pdb-tools/Manifest +++ b/sci-chemistry/pdb-tools/Manifest @@ -1,4 +1,4 @@ DIST pdbTools_0.2.1.tar.gz 103835 BLAKE2B ad4b5c8d6eb000c79a6d2797519b99027350fa34f6d543f6302f1a9edbe3497afe1a7b5c5c0e7243081cc709d9f1c37da5fc31605a0a225413851ce7288f64c9 SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 -EBUILD pdb-tools-0.2.1-r1.ebuild 1669 BLAKE2B 6fb471e4908d4aed5efb4b5129ca4a54f2f45d6b8d0c1cc716bba8a8ce20cb9ecc64cd91223cf5b2a39714e3c2e2d0a8d7d5baafb8c1fb8ac1be485f651ae457 SHA512 806c9517f124a674bf4772d6f3e6379da075760a4b6cd60d00676410d3419306d73d367fbf95462fa9515589cdef94f1b4fae6e69249955d1dfe2bf0a89123ac +EBUILD pdb-tools-0.2.1-r1.ebuild 1661 BLAKE2B c4e0dde9acb97813824bb8992c747fd850c47e6cd346d921e37cd39a4e1c0e18ee883ecdd90edec1eb8aa5e81afa90ad3d5719b4038a652244ed678e20a267fc SHA512 744eaff99bf693c803b20546a6a9d4b8a1083d7278fa363ba50ae709d6ab1c6e9bd3100ad992b3bce419ef5dd16036e6397465fb6b2a413764e73f10d2818721 EBUILD pdb-tools-0.2.1-r2.ebuild 1734 BLAKE2B f1b28c6b9c60c5573c9bf6ab092c32f3e4aa6df7bc484dca74aeda8c12f78dafcd94db9f1976932264be4be24c01f29a38750cfe1081058fe0e964345bfe9565 SHA512 dd9a534af4c275a3fba95ce88e4a9e22e5f182c63210717fb66ab62afd67e179541e58d6d1a3af03a550f5718166f9d0974f7d2f47b401adf670b27376f73cf8 MISC metadata.xml 413 BLAKE2B f3fc199d95acf174f2d5cf9e0ea9c645e3b49e7241122bde730db90a095a0ef0f763dd3dcbcd5f14c1da520630c58bf9e7fe40828d267cb5a2ad5c796b72993e SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2 diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild index 8dc55d31e546..090b7c041dfe 100644 --- a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.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=5 -PYTHON_COMPAT=( python2_7 pypy ) +PYTHON_COMPAT=( python2_7 ) inherit fortran-2 python-single-r1 toolchain-funcs diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index 53ff74f8d77e..9f630322ba87 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -2,17 +2,21 @@ DIST votca-csg-1.4.1.tar.gz 347702 BLAKE2B 8c98804bafd75148fa72a9e119d4448ab9b04 DIST votca-csg-1.4.tar.gz 346527 BLAKE2B 8f0a41f9aa9fd865e2e544d5fd587d93d631edc2dabab8edfc3461582da2e0401a266a42be1c0f1e6647502cdcccee55b5bba891aa156394012b8b5e1b06f7e8 SHA512 26318644c7af2dfa1b81242b27ffac98f2180c3a1f05581bc50a00f644cec4b19ffbaf41c9d941a4714171b56ae93fe41f1a663cd0593ae2b0be2da379119d9b DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 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f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7 DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c DIST votca-csg-tutorials-1.5.tar.gz 5947774 BLAKE2B d497f1e9282c4cacc070d09d901ad8f5d3042ab3a279aa4d1c3bcd3184dc22231d1f2a75ba0ffe245e6f6300fb740e562b24c8039594ec01307491a6068b55f6 SHA512 00447380fa887178ad02cc4e1425a04fc2fd2babdd4790d387fcd4aa2734dc14dacf4b4444d420937aa0a5b53e90741b44f9a4bca31bdcdae10fbfb8323e9848 +DIST votca-csg-tutorials-1.6_rc1.tar.gz 5946622 BLAKE2B 7bf0c7083ca7b148d16f7b77b9f785c11b16a8124a5435522e8c065859f4c2ae560c622f04021918b2683c9955d5a1b674c84fad179319f5fedb86616bbe24e7 SHA512 1c89f95944f8277a995d9d6d7dacfae2ae1be54a9a7b19c53d3464a4bdf5da0556e862033ba0a5f442b1ee5bd79bafd478655856fe266f4285c98e14512ce259 EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d EBUILD votca-csg-1.4.ebuild 3200 BLAKE2B 041deefd8fc208525c636d00665f7ea70d0efafb78fa98a3437823fb550e6c39a29d33e94860c3d8f01dbbdb050dd568c63dc1099d4da620f9044545850f40d1 SHA512 939608311d071b6abf8cc26dd73c9713c41476772bb37b41fc77fb3a02672989664b8a06e5465b2825285c3365ad3d70879e5c24a1c698cbb3c8ab6d2341fe31 -EBUILD votca-csg-1.5.1.ebuild 2546 BLAKE2B ef9552a84560fa785dab1752939be518dd310967077263f45334dfa942b5d2e8c0ad6d184e8721ba7e9ea1bf4465dbf6fe4a5745e4c90475dc71926a5ea960aa SHA512 be9245c6359e241944619366574bafe5216ee2ca096ee69fcf190caff4b8ff9ff7433f2961b166a25bc1c05ef7c76c59ebe32447ab10d75a10398498c507d964 -EBUILD votca-csg-1.5.ebuild 2544 BLAKE2B e76bd6372f66745230d307d6214e031367f83ddf673e3f3a3e8e5263053de49e102c415baed7c6e709f164d6b994363540d4152f5202660c4b87894b8837cf37 SHA512 66a240156d31a389a91cd8a8e9f5e65236005683fef5d01657386297fb812706bcd43933cbf0d7d6fa9fa8456fe216e45ae651ebb52309ed845cd9dde076f02c -EBUILD votca-csg-9999.ebuild 2540 BLAKE2B 7391ae1af857c92b688fab507417c875189725d8f121296aaefccecc903501cc6c50561b0a7a4f834d5713f2bdd75b2325594fbbc32e6d0a0d814cf5c7ca7b14 SHA512 fc36ac2de479e2766722b3eb64d8f4eb43233c9625c67124d2ec583e21e22f1c77d6bee2a71d9c3b35451eeb0c6ddc729f4726e8b56f7e45b2c64a9f45fd94ae +EBUILD votca-csg-1.5.1.ebuild 2552 BLAKE2B a64b31b3b6a9297b6ead93e9f5605ace929fecf98ee377eff17a0b529b9176fe5d251e9efb5dada1c7d29b144b7e89dcd95ff3c6921b7584f225f842bc93f94b SHA512 3d96fac05c344f0986597ec6ce50f07a19327113d3b02238df60ce28ab2788f91a224f9c70ecdaaf6cfe6206f00f8e86e4ad2dde1c68c5c0a32f5d20eee658cd +EBUILD votca-csg-1.5.ebuild 2550 BLAKE2B 7fb2a4280fca23370169fbf04c3b9251065f06d56d7df29a26f3bbaf642e3296e400a23cc3c7524a830cee0dd881e598569c82bbcfacbec35198dd564d379828 SHA512 9516699dbfab66505053d701a31440ce0ca16484b6b0f60b072f6d5a54740449c90ea96461e08d598933dd7f7803278dbc4e19df381f5b57c541b9d3de90c9d5 +EBUILD votca-csg-1.6_rc1.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac +EBUILD votca-csg-9999.ebuild 2358 BLAKE2B 5124239dade6f735c1f1da0071e30bf245728431a46f4361271d1eea9962249ff1bcc621db193f69ae04b61343aaafa01c64cfb4a131c6ce83b9135c5a7f39c5 SHA512 a8f2298c212299689a96d4a15e73b851725f45c6ad9fc20610a155625c5d58d1d462ba7c01fdd206fba8b43fe032b65f992ee58107e1245565cb482f8507d6ac MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 diff --git a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild index 8ae77aec9f51..8f8ca82c0667 100644 --- a/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-1.5.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -31,7 +31,7 @@ SLOT="0" RDEPEND=" ~sci-libs/votca-tools-${PV} >=dev-cpp/eigen-3.3 - gromacs? ( sci-chemistry/gromacs:= ) + gromacs? ( <sci-chemistry/gromacs-2020:= ) hdf5? ( sci-libs/hdf5 ) dev-lang/perl app-shells/bash:*" diff --git a/sci-chemistry/votca-csg/votca-csg-1.5.ebuild b/sci-chemistry/votca-csg/votca-csg-1.5.ebuild index 1999a051a01a..879db65b2de9 100644 --- a/sci-chemistry/votca-csg/votca-csg-1.5.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-1.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -31,7 +31,7 @@ SLOT="0" RDEPEND=" ~sci-libs/votca-tools-${PV} >=dev-cpp/eigen-3.3 - gromacs? ( sci-chemistry/gromacs:= ) + gromacs? ( <sci-chemistry/gromacs-2020:= ) hdf5? ( sci-libs/hdf5 ) dev-lang/perl app-shells/bash:*" diff --git a/sci-chemistry/votca-csg/votca-csg-1.6_rc1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.6_rc1.ebuild new file mode 100644 index 000000000000..0e02baa215a8 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.6_rc1.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs hdf5" +PDEPEND="extras? ( ~sci-chemistry/${PN}apps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) + examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" + PDEPEND="${PDEPEND} doc? ( ~app-doc/${PN}-manual-${PV} )" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV} + >=dev-cpp/eigen-3.3 + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex '!hdf5') + -DWITH_RC_FILES=OFF + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild index 7aad54413e78..0e02baa215a8 100644 --- a/sci-chemistry/votca-csg/votca-csg-9999.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" @@ -37,12 +37,6 @@ RDEPEND=" app-shells/bash:*" DEPEND="${RDEPEND} - doc? ( - app-doc/doxygen[dot] - dev-texlive/texlive-latexextra - virtual/latex-base - dev-tex/pgf - ) >=app-text/txt2tags-2.5 virtual/pkgconfig" @@ -73,15 +67,13 @@ src_configure() { src_install() { cmake-utils_src_install - newbashcomp scripts/csg-completion.bash csg_call + newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call for i in "${ED}"/usr/bin/csg_*; do [[ ${i} = *csg_call ]] && continue bashcomp_alias csg_call "${i##*/}" done if use doc; then [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" - cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html - dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html fi if use examples; then insinto "/usr/share/doc/${PF}/tutorials" diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest index 13065a99df56..8c0e2b6f1316 100644 --- a/sci-chemistry/votca-csgapps/Manifest +++ b/sci-chemistry/votca-csgapps/Manifest @@ -2,9 +2,11 @@ DIST votca-csgapps-1.4.1.tar.gz 21066 BLAKE2B 8e1d25957b7c62d2182872de4d0c50c90f DIST votca-csgapps-1.4.tar.gz 21072 BLAKE2B 30c2f6692544741bfbec09efea2f68ae48cd4716e61e40d3da12a17ad941f2947cc6a8477229b80e420e217a95adff4152a07215e2e913e71736b61ba1ac226a SHA512 325c99606f17d7bb00e2cc3b1545f31dd4cf1fbc0d216f2da2c48e06b2011c9f99096643a6c6efd794a169de056f803f791c156afec4a73e41c58bc4ca1055f9 DIST votca-csgapps-1.5.1.tar.gz 26006 BLAKE2B 8651978c15087fc7332fe229cfc33d8c4257faf46d72f7ac5fbaaf5f31133c4df3d97cae2b18730b5700e742c27e3db39696fdfe910ed884952ba0f832220c3d SHA512 4f83a46f16eb0a4cb9acc6c0d9523fa746dcf670107355c95fc02daa6ca91fb4f8d5e48bc920d8c13a9445390a25415f7217979903ea86f890df1d4704944c28 DIST votca-csgapps-1.5.tar.gz 25975 BLAKE2B 185e759d658c6f763da2d26770766ec8ee05017b4c6a67e13915de04fbf2ecf268f2f800c5e18ef0f38c615340b0db163e886dc98a9395a69359f94dc8773f60 SHA512 20dda9d07ef2f33c9decff2766ece8f24cf2562993b4dfb7dd637d84325b835a6ecd30d34c5cfb9c428dbf72c2b5dfe9fd49d266182704b981db151c3c4ea2e4 +DIST votca-csgapps-1.6_rc1.tar.gz 20138 BLAKE2B 9374911f761fd78f01721e8e10f3b9c14f2ba894735735e4d09f5e29eb1d1b69f4fa081699d7a93abfad2ebe55d6439edbb6db547618e6d2cfbaf7bbc8a79ca8 SHA512 153bd6e537175c9908739c60ce80830ebf57c0686f11b21fc541995cb5355d4a3f7f7ee7d1707bb85f5fc859bf260a3a167450175ffe8feb92044e8018be996b EBUILD votca-csgapps-1.4.1.ebuild 653 BLAKE2B 208ae3538fcf42296a4a1077d222a9d6f752648834dc8f74941546fa2bdffb6fd9ea60ad31d124b8de52c3f59c089f48d4395b5166989fec19191076570e1bf0 SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2 EBUILD votca-csgapps-1.4.ebuild 649 BLAKE2B 4b219583f5d5a1f7f4ed7635b4fedce2619d6a0b13bcab7bde2f88cf177a9478fefcb71974deacc09eded4f278ae27c95bd2aa387c79ad4ae2268c2ff0f40a94 SHA512 b6400f2a28ce0c2953495c00aeaab0bfd15c52df28a5e6575b0f568c9a777678495b591cbce58fa61e1d54149fa3f684c6f9f99aaa82127e2eedcc67f6259ed8 EBUILD votca-csgapps-1.5.1.ebuild 668 BLAKE2B c1a715dcf42281b13819c20b51fc0c16f0435059e4f1dcfe83babd15eda4dc179d50ffe4a6252cd3155aec9545f2e5fc3bba728e2a6f739097422f5c6d94f247 SHA512 23d3ed6be1ea715a367f6203c9431598068ec7b1494865e594a67bfc55bc0f65e86914ad04cff7eff5a9e83fb79cae46fb4abd7997752a1a72dd90a68e173f97 EBUILD votca-csgapps-1.5.ebuild 666 BLAKE2B de904c4c69f9b223466bc97f646a861a5e1ff64d061389a1a1ac845e7351f9626226354c7c080d7a52ef5db2eddf397b2bf48ce042e168a881cb12da14338333 SHA512 e768e56d45d9e8b4ce2c01358b9de4b876a7a4149947445d388a4a1cffb6ac6882b17cdd794b17eee7abdb75d34c4e108f399c28fbca5ae0b11bbe5d57e07202 -EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 23030fd2ba47629a9285fc8c9b436bb45614ba3ca8198592aea4189e5d2ae005d88b96a745e6de4db8f913e37e73e07f33a15ec0ef5dda9932a99159286711d4 SHA512 a72ac9569a69e4d94180fd45daf1d06496ea8e253f97a4ec877eb66db62bb7b600ab122909994504b5f677d3424a79e9e663dfa8f5c8d5a5b1388bee325aa524 +EBUILD votca-csgapps-1.6_rc1.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7 +EBUILD votca-csgapps-9999.ebuild 665 BLAKE2B 893814bcc1e8413a5c6454c32092aa51e3633f2917aedf47bc928c603554acf064a299208e9a1c8cf58437cebdee00f6d07fd30424540081ef3d0c7f2636d8d0 SHA512 a32d204985dd20ef8389cbfd44f6e45d44542480d0593ddaa17d5976e193db687f26d1e818251325c939552c7e9a1c1f95ec20ca952834cc4a4ca6c4836ea2b7 MISC metadata.xml 457 BLAKE2B 9d392be6c061ebd3d975308065fcdec4ee061268f4b8b79e122b183d2e4f7259fdb9e165b8b3f030f1edbbc4f112757b1de7a50929ac112d5633143f9585699a SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563 diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.6_rc1.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.6_rc1.ebuild new file mode 100644 index 000000000000..463cba8e0e38 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.6_rc1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND=" + >=dev-cpp/eigen-3.3 + ~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README.md ) diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild index f229849683d2..463cba8e0e38 100644 --- a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild +++ b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" @@ -30,4 +30,4 @@ RDEPEND=" DEPEND="${RDEPEND}" -DOCS=( README ) +DOCS=( README.md ) diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest index 4aa7aa917476..1f193d348910 100644 --- a/sci-chemistry/votca-ctp/Manifest +++ b/sci-chemistry/votca-ctp/Manifest @@ -4,5 +4,4 @@ DIST votca-ctp-manual-1.5.1.pdf 948647 BLAKE2B 4afec48d0e6bb29dc86d4d22fce74a8d2 DIST votca-ctp-manual-1.5.pdf 970539 BLAKE2B 8646215a4c2cd7be6d4c03820f00b8067e15c27f51fb6678540026cff1af0e28dffa528423ad47a4047a8f84fc1078d503a56a4a235e004735f0276ec1a6a33e SHA512 a315c1b4b37461f4f0d30ead1fec2ca33ff23d81c9d5e4d888ef7d7dd722f68f9596826f828f8a76841d6dde6889f623b73d9fe0f8a6c5a7cec1c16a83cf9030 EBUILD votca-ctp-1.5.1.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 EBUILD votca-ctp-1.5.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 -EBUILD votca-ctp-9999.ebuild 1537 BLAKE2B 352a11fec91618444983028294c92cdb878396135f00ddecf0d316772f39d1c33e7be370b12efc59ae720b834eb47b8463eefdbb06c60f18d5ec732bcf789938 SHA512 c6685c4aa7e2fd14e15233cdd3671a4c39230901ef061d2af291bf74c39208457c17724588befd115cb491771409514597d06e5ec48915a3fcb3a840a185df84 MISC metadata.xml 453 BLAKE2B a61c365529a1c877e5bad44f6e2f0a24a8797956e9e3a5b3d4649c58c27df9301b50c84bb5767ca52a151e2b509f46a92cd3f17c1020fb7bedf7fb2fe708b48d SHA512 53ace87a281559ae8881b8b010c76801696521de930dcfaf12a5e320456cb4a21a55a7873d173bdb5cc740f3cdbccf1daf62bc83579342f4f23329df7dbd2dba diff --git a/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild b/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild deleted file mode 100644 index 892997f7af3e..000000000000 --- a/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit cmake-utils multilib - -IUSE="doc" -if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz - doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" - S="${WORKDIR}/${P#votca-}" -else - inherit git-r3 - EGIT_REPO_URI="https://github.com/${PN/-//}.git" - KEYWORDS="" -fi - -DESCRIPTION="Votca charge transport module" -HOMEPAGE="http://www.votca.org" - -LICENSE="Apache-2.0" -SLOT="0" - -RDEPEND=" - ~sci-libs/votca-tools-${PV}[sqlite] - >=dev-cpp/eigen-3.3 - sci-libs/gsl - ~sci-chemistry/votca-csg-${PV}" - -DEPEND="${RDEPEND} - virtual/pkgconfig" - -if [ "${PV}" != "9999" ]; then - DEPEND="${DEPEND} - doc? ( - app-doc/doxygen[dot] - dev-texlive/texlive-latexextra - virtual/latex-base - dev-tex/pgf - )" -fi - -DOCS=( README.md NOTICE CHANGELOG.md ) - -src_configure() { - [[ ${PV} = *9999* ]] && mycmakeargs=( - -DBUILD_XTP_MANUAL=$(usex doc) - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - if use doc; then - [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" - cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html - dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html - fi -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" - einfo "https://dx.doi.org/10.1021/ct200388s" - einfo -} diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest index 8f2cf4195de6..34950fb4ccb2 100644 --- a/sci-chemistry/votca-xtp/Manifest +++ b/sci-chemistry/votca-xtp/Manifest @@ -2,6 +2,7 @@ DIST votca-xtp-1.4.1.tar.gz 15214413 BLAKE2B 0f6e67179e2ee1fa8ab79ca0c2d810f9867 DIST votca-xtp-1.4.tar.gz 15214266 BLAKE2B 435ba1603495d904ccce20b4fa665d3a1c62fc04005ea89cf83b431240fb78f8a44f09ad619af331802e43ca3d05b20a4c6bbbb0c75360940d4f786c0030fd7a SHA512 ffc32260331862393e199f7ab643b1008ee4f800cd017f175550a079afaa20e5c929cb8599bc0c2a2328253051895de7b979f5fec044243abc680a0dc87a69b9 DIST votca-xtp-1.5.1.tar.gz 14634849 BLAKE2B 84ee9fc531a530ba276a6fd3eccc78dd25c27346db76871f33fe307dde451956bf091b636dd5594bf3b8b24a727fe7e5a730fb85cd2cbb0e5605705996e69bd2 SHA512 8fb6891e84d4d685e26287344554b705c607e7cb9f497c00ac9cd8328e50210c56706abdb7004b83d4addbfbc7b35c3526b4feabf75f681362b3b7a39c54b668 DIST votca-xtp-1.5.tar.gz 14637712 BLAKE2B af04de706f0d100968928459a03b6a94a94a211b3f5bd056d123756d40760fb0ada70add429ed5b86e211dbdd3b91aa4cf12e51a260638766d04158e7b5a1201 SHA512 693f34004749edfbabcd0a19dc23b3de3c09858c7c0dfe1e420b92632397971e3687489c1074a489d4d2fd337ddc5749c419869db104c65736e7c01bf12cd140 +DIST votca-xtp-1.6_rc1.tar.gz 13586771 BLAKE2B d5b72a7389b77df0570eac0021870bba3fa66a89b3a2df1e08632b1c1827884d101ef8d972762dae35e44e53e7a9fe9278d3204eec09c35d091ab3427b055be4 SHA512 0b54eddcf944967b1d41f75f4887eba9edc3be18b94d319e93e795a24f58a2877d7f60afd806290eacb41d329d1b1206ebaab83874d6be2d5b026f06dbc19dfd DIST votca-xtp-manual-1.4.1.pdf 1066873 BLAKE2B 8cbd4b55b013794a19a8b5867b929b8e2d9084e6780d777b2a2bbaea23006f4f4ec5b26bd4a07c59e1c6726f23471eb1756b668636e0c4e656a0807e64197586 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f DIST votca-xtp-manual-1.4.pdf 1064006 BLAKE2B e4f0c20c6d40a5f58b863258cc122e5a7cf376b7138927c0a6bdd400841c330fc013287513258f6f68609e39f0bf39b965fd099171594c5e2730fba82a2488d4 SHA512 96d7f59dbcc3a6efdc297237025217d5a56d2c81e491d90680786ea4769a5ebbea379df3b06c4847307ee30accd7415e316dee4730361262f5aff73d2f5d387e DIST votca-xtp-manual-1.5.1.pdf 912290 BLAKE2B 4511885f5506f542d639b5c7d2bb2e6f4f24df8d7929959ff707ae9c28c357346ebc7cde072f742309f3ef8a6b00a51d0873071cdc4cbcd291670fca788f46a7 SHA512 b410ddad0566933a2c9ad386fb6f4df0e71b316a84bce8c841e94df8f438959f0967ade63d1146549d453c2ecdb48e3d8b1fd147e53888e1717c6db3d07ba061 @@ -10,5 +11,6 @@ EBUILD votca-xtp-1.4.1.ebuild 1622 BLAKE2B 1358e16a21b653584fefdf8eb673744f18ba7 EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34ccb229c63d9de14086055684ee9440102b0c9a5bf807ddad69d22ee1b680120f493f18891e8719211509a418f SHA512 affe412a6c4cb8139530d559ae4c12d519eb6b9190075743ed7806c2975a4647f48282893d71b4bef3477b0d35ee07815e416c33095be819967d235c9623a48a EBUILD votca-xtp-1.5.1.ebuild 1628 BLAKE2B a89ea389a31edce013d2e41eca4a0a818fd3f0b359aa9e770ecf3e04089b99063106d8b20562b36ad83fdc318c6cc6ffc119a589d995db08175e704ff7ce53f1 SHA512 a90fd6523ef6d42af25b99509718511cf0303bef2e0b083b6e4e8cbb5160bf1cc802b0e60a682c7bd1301f5b17cbaf78c2d2e593d2528f9c24b5f6c3c1aa984f EBUILD votca-xtp-1.5.ebuild 1626 BLAKE2B 15b3e63d11348ac376e15769b6106c98144a0ce88bbc7149fcf98bede2f7a29ee4ea066cea67fadf14e60e6dbc6745de4bffa4cf11d6ce6f08d5631fad0af347 SHA512 ac39f8f262a40683ff267dd13ea17cdfb9bd3ba62d698e8e20c98ee1adce53bd002a10dd7805a4ba419ca80a4a3ffd0b3b5c8f9e4b040182eaa6ffd069df114e -EBUILD votca-xtp-9999.ebuild 1622 BLAKE2B 0c99db3dbba224f0485838e5fddb8b857fd13d5e5d798bbaa4b64f89ffcbb1bbbb55a626ff601efd583bf32270c4a8be21a4f8357e6a67e1d8f3feac7c2eccdc SHA512 31a8520c2438ecd0407748b65d363c5ebf2027b71b19fd90810f75b25cf5ea90ed7eedde354fb17dbd0f087963b0b23923f29a9d028d899668fd90eda0806231 +EBUILD votca-xtp-1.6_rc1.ebuild 961 BLAKE2B daa3640486b6405ae8542d99aacb9c3db9c0e30ba69fba949047fd85be8d47748fb363a5ef3790d647468e851bdbf88a3b8dc4cceb89b3ea1cb4962cbc138e7c SHA512 d23d65d51e1a585d42cd42d75bf96a8fa90db1c6977a76712cc372177cd5c9715053e4ea0873d2df2c24446766212032ee6e47f9b0dfc4ef8a37081e3ee97e88 +EBUILD votca-xtp-9999.ebuild 961 BLAKE2B daa3640486b6405ae8542d99aacb9c3db9c0e30ba69fba949047fd85be8d47748fb363a5ef3790d647468e851bdbf88a3b8dc4cceb89b3ea1cb4962cbc138e7c SHA512 d23d65d51e1a585d42cd42d75bf96a8fa90db1c6977a76712cc372177cd5c9715053e4ea0873d2df2c24446766212032ee6e47f9b0dfc4ef8a37081e3ee97e88 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild new file mode 100644 index 000000000000..4de1f7f7474f --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + ~sci-libs/votca-tools-${PV} + >=dev-cpp/eigen-3.3 + ~sci-chemistry/votca-csg-${PV} + sci-libs/libxc" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)" + einfo "https://doi.org/10.1021/acs.jctc.8b00617" + einfo +} diff --git a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild index 15a8759ad217..4de1f7f7474f 100644 --- a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild +++ b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild @@ -1,16 +1,15 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake-utils multilib -IUSE="doc" +IUSE="" if [ "${PV}" != "9999" ]; then - SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz - doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" S="${WORKDIR}/${P#votca-}" else @@ -26,44 +25,16 @@ LICENSE="Apache-2.0" SLOT="0" RDEPEND=" - ~sci-libs/votca-tools-${PV}[sqlite] + ~sci-libs/votca-tools-${PV} >=dev-cpp/eigen-3.3 ~sci-chemistry/votca-csg-${PV} - sci-libs/ceres-solver sci-libs/libxc" DEPEND="${RDEPEND} - >=app-text/txt2tags-2.5 virtual/pkgconfig" -if [ "${PV}" != "9999" ]; then - DEPEND="${DEPEND} - doc? ( - app-doc/doxygen[dot] - dev-texlive/texlive-latexextra - virtual/latex-base - dev-tex/pgf - )" -fi - DOCS=( README.md NOTICE CHANGELOG.md ) -src_configure() { - [[ ${PV} = *9999* ]] && mycmakeargs=( - -DBUILD_XTP_MANUAL=$(usex doc) - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - if use doc; then - [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" - cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html - dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html - fi -} - pkg_postinst() { einfo einfo "Please read and cite:" diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest index c4f95ff331e1..964712af25b5 100644 --- a/sci-chemistry/xyza2pipe/Manifest +++ b/sci-chemistry/xyza2pipe/Manifest @@ -1,4 +1,4 @@ AUX xyza2pipe-20121001-gentoo.patch 3974 BLAKE2B cf3f4b58c6348a6295b7874ca20d7d88f6477e1174b54bac7089898ff7509fbf07d8d34aab2d333059c67f7ccc9d1b99e4e40c9bfd8a327f600fc4578a2f1a06 SHA512 7b8be1fd799d65e9a600766afb21e95a4722eff8a657f88d0adaf5aaf11ed369f6d8a27f3e003337570837abc45cfa9e758d1219af275773f79b81d1c1c322c4 DIST xyza2pipe-20121001.tgz 61002 BLAKE2B 648e65b63cc0b363dd0087b7ef64a1e287654a165baaf7d967821f11cffb70dd7f0da864dfa3b915553546c8cbbc83fda411d9b979551d3d72334db6580e5d64 SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855 -EBUILD xyza2pipe-20121001.ebuild 686 BLAKE2B bf487f605d1a120df8788fa5b55a1581e244a248d793c0fd28a07f13d42d15859bb789baf8b6db778d7c658caf45628a330403a1a29b82b0b68fa7cc8a9da79f SHA512 407fcfd20d9bc7c4ed85b6a8838996ec014d5c631f355be88d67f3cd42376617716286f43ecb01d1acba866f49d232ddf8c1d7e3b44975b1d552baaaa9fc9fe2 +EBUILD xyza2pipe-20121001.ebuild 682 BLAKE2B a1cbd50a946dc37ab1e55f998b2ad6631e53fd6138f886009ef28e4a121721c5a8e6ffcdd0d79c4b387e2016b456c14d9b3db039f95bd6d6c85f774d8fff71b2 SHA512 4253c166e0a2101b3a5b91aed25193107d588cfbc3db07b66f64ab98bb2888a5e3342d093db15c9686be6519d3ad3372cd6b53f52a4091ee35a458d210c428e6 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild index 033619474de5..e6ba5c19332f 100644 --- a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild +++ b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -21,7 +21,7 @@ PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) src_prepare() { default tc-export CC - mkdir bin || die + mkdir bin || die } src_install() { |