diff options
Diffstat (limited to 'sci-chemistry')
26 files changed, 380 insertions, 314 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 214c4b6c36b5..a53aabe15254 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 796f237d7b12..15f4d8cc1d82 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -6,6 +6,7 @@ DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9 DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80 SHA512 fe38fda36d31aef5ce01a3dbc29c9f50d3cc05b20bb34a9a8f10fda5aecde4f93ca8a3f85433139e1bb88fc23d77916a4aff5a292abaa528bd0e6138e84cba18 DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea DIST gromacs-2021.1.tar.gz 37971732 BLAKE2B 722a3c21afd9d5ad432b601c99a2d5ebb85012479851d52517559bc113d75424e7509f417fb74f5f935ae6614e01a31e7361e7e673c966964fd73f08621c8415 SHA512 7f9104a3df8aa808940fd380653e43ae716167df717687717d67ddd556a29acc6ba7c2e78ff9b920b145eb521998645bee0b3816438b1398374b6b7a1831513e +DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 DIST gromacs-2021.tar.gz 35061679 BLAKE2B a7d8bd728480455e5c069392e3921a4f788802ec164ee24241cac9bc7c555cee07ef26853efa61e40a787fa87e6d20af35d56b98ac6a3757ef07fc4176679e19 SHA512 10d9d64b3c2329613a18d861589428841f55bede45e1800aec25246258209be1385aabaa0d5b52425c0ac21804c38b401db76448bb539ff3cf25f8b94e09575c DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb @@ -15,15 +16,17 @@ DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2d DIST regressiontests-2020.5.tar.gz 48541167 BLAKE2B 81f0505090203c970178ca4eba8dfd54d942a20970525cad954833481cd79141fa33fc97e8940ca83cee104ef6b017bc0f7bbed9eddc620a86c818760b3fc261 SHA512 aba67542ed00145cae8de040e4a9074a8a359a529135180e6083b2330934962302349d382d6626bddc6971ae6d44e09c8ea44d5df55ca5fcd038055a1c3e5cc3 DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2 DIST regressiontests-2021.1.tar.gz 48516304 BLAKE2B 61e49e7a3ce0856cd22a6adc360f476bd4978650e21ad64074d3cd8db1d6109fb86cb91bcb161d00d1e912cf3fa40dd83c07e5cc873dc2177a11d7fb304e7ecc SHA512 c1158b7890e2ff94c6600e531fdceee439f19ee2d18093b8be68fbd18064aae4b035c697ebda4e9b74d61c68d905c26515a41c34a2ac9f8dd8a29c5348ecbab1 +DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec DIST regressiontests-2021.tar.gz 48513192 BLAKE2B e27898ef3936495fce111c8debdafbdaafae07cd9b27c8591cc27695f681fddda34f083d427e5b3afd2f318ff41201eabc915025f1fddef61ae29ceb13f37557 SHA512 e33578d32b929d516614592d0bf4aac4e518cc4f18fee4048d5b73b11f4373494c6d8aa43442e4e2be632c12c058657bce1064be82c515787d57b449c1241e48 -EBUILD gromacs-2018.8.ebuild 6944 BLAKE2B a91190e99ed188eeff085d164dee6d65a886906cc4555bbbd61f195e345cb276b5ccfc67e4e356253b11ff2af60af61783be70425292220c5aa5172ece1a21d3 SHA512 5df8545501f57f44a88406da75185fa107fb44446cdbd26bb0ed79086484e9933e0d147de39d7b7797bd6d18f8b2fcdbbe5acda3fc2c39ca29490452d4776082 -EBUILD gromacs-2019.6.ebuild 7265 BLAKE2B 70135e4b38335ccbf51d99a22572dd07bb25df895b4dd50da0297ed7852884bb102e40d94216c04b9503e58473579e8b001f4c94fe8cc164a4d6277b52384f59 SHA512 b95fdca7d93c3817ff820d5e2692b9c396a0fae46e7a700c2aab3e3fcfe29c76099222f61213a7c1e1279fc61dba74dcdb22127b6ada4ee870e813c1d0407e68 -EBUILD gromacs-2020.4.ebuild 9798 BLAKE2B 1b5f2c4d9f095e656c64c5478141dcfca3906640b25aabedf8582e707c6ae3862368b67c4dc79e9244caf5161573fd548169fcd3dbd2129a7d19e54602202d85 SHA512 74ec944c55091fc2ce6923b532e3c9a32a2b73de5329edbbe34f9b4de34efb32d19b85698b7a5fa98053b1ce646ae8c7213386a525abf60ee655313a905b0a34 -EBUILD gromacs-2020.5.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f -EBUILD gromacs-2020.6.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f -EBUILD gromacs-2020.9999.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f -EBUILD gromacs-2021.1.ebuild 10013 BLAKE2B 84d8df2311c84183cdc2e9766048b86eaf664ef40016632b3beffac251596e50c52ebe7cc4add2289ab092323895ef5b419ffa09114e614acc7dd3ca8b9db128 SHA512 0bc4811c4f5e54ff4df13415bdb6b3aaee3c37de5e839f39acf5cd21ded8b1b427470145c1cdae99d891757fa6060af15a29001427bc30018b4a72adf626a71d -EBUILD gromacs-2021.9999.ebuild 9923 BLAKE2B 29847a40e8a7bc586d04dedbef998eff22388f91459cf364dcea0ff07bd5328e9dc2226237fbd608f96f5511f23d6de067804342c8c2faf95cc0e681403143a5 SHA512 b2ca0e12587d64b0482e026134d43530951b8b8c1df4f082bb85ffda51bc7b347617acf5f002f26e3a4607b29e2d974475fab573ea9d98dea7cf2028673647fc -EBUILD gromacs-2021.ebuild 9974 BLAKE2B cfb46e429458b38c130ee731af60515ecca1660606ae7ec941dd2da0c5f2e84e8437c141126b859a9dc783c1ffe0b00376faa7535a65ea017a81febb57cb3ea6 SHA512 4c7ee67248e529af4f3f377c8da72e728954a62297b446fc0bc0fe84c3a75bc1ab8d9fdf5ab5e4205471519245a0a2d9f611b940ef641258523b479e3049f0ab -EBUILD gromacs-9999.ebuild 9923 BLAKE2B 29847a40e8a7bc586d04dedbef998eff22388f91459cf364dcea0ff07bd5328e9dc2226237fbd608f96f5511f23d6de067804342c8c2faf95cc0e681403143a5 SHA512 b2ca0e12587d64b0482e026134d43530951b8b8c1df4f082bb85ffda51bc7b347617acf5f002f26e3a4607b29e2d974475fab573ea9d98dea7cf2028673647fc +EBUILD gromacs-2018.8.ebuild 6943 BLAKE2B bd0a58000cf2c669bc4871f2f68d06b4ef7b4e40ef4a35ce306854fd1ebcdf99baed53199bc803b4fda40124226a1093168bf6fe262e27b9086bede6004db0ce SHA512 df2193024fec30dff1a9e87774267f93f46c1636893a4eb65d50ebe7314cf6cc39eee94c9b252247b40508cea2cbcbc6749681ce16c3ce461f0b2545e0418926 +EBUILD gromacs-2019.6.ebuild 7264 BLAKE2B 6196f750a81562c82f1004ba3e4be05193aa9100de0d5a917df242c1287989e83992a5574812f332639c95fc009b860fcfd4b563b5e5148dfa650ce82e861f5b SHA512 ac84483eeb66765b7ae0e5489d5c3b8d293dca6108b79dfcdc35674e033af1a487d0db0bcfc7ad1158fd3ae3aedef236a6549f8ade85483ef6dfb8309cccb05a +EBUILD gromacs-2020.4.ebuild 9797 BLAKE2B 870bdddbca955a5433b82b76a47ab61fd56d679c04d46c22e57581a3326c5c82afada94aca5cfbff0ee03e48d7f50064d43c33427eabb27bf9f03182f3b7f231 SHA512 6355decbfea4f70b7729f3a64a66174354fed048c6ed4d0e326ef974a2681471c3c207dbe4d11b773cdda29f43ea4a73f71292d44bd4728e35c2c22f4af50786 +EBUILD gromacs-2020.5.ebuild 9800 BLAKE2B 334e9b961d3d704f95dd9aba5caa1c323e95aa4e79ff1e9c95dda998dd54e0cbda632feef930a57187f9e16a9260765eb4341aa33c8d3f7224522eb4168ae3b7 SHA512 954bad1826b6706af821e497bb0a4abbcd4013e3056e74ee74e9efe6ac1820e287b696621d66a53381fb21f3f49a629d17321b2c719ef48b347a8058d826fa36 +EBUILD gromacs-2020.6.ebuild 9800 BLAKE2B 334e9b961d3d704f95dd9aba5caa1c323e95aa4e79ff1e9c95dda998dd54e0cbda632feef930a57187f9e16a9260765eb4341aa33c8d3f7224522eb4168ae3b7 SHA512 954bad1826b6706af821e497bb0a4abbcd4013e3056e74ee74e9efe6ac1820e287b696621d66a53381fb21f3f49a629d17321b2c719ef48b347a8058d826fa36 +EBUILD gromacs-2020.9999.ebuild 9800 BLAKE2B 334e9b961d3d704f95dd9aba5caa1c323e95aa4e79ff1e9c95dda998dd54e0cbda632feef930a57187f9e16a9260765eb4341aa33c8d3f7224522eb4168ae3b7 SHA512 954bad1826b6706af821e497bb0a4abbcd4013e3056e74ee74e9efe6ac1820e287b696621d66a53381fb21f3f49a629d17321b2c719ef48b347a8058d826fa36 +EBUILD gromacs-2021.1.ebuild 10012 BLAKE2B 31de6cde38931315e9316a315f868d9571314d50b208e9ca8b46931fcfa17cbd2391ee0e0d635777f9ad2599161e15983bdf23419be83b810462984a0705156b SHA512 fce1e83a45c280085358d666f62c1eb1180129ce5a19c2f1bc61d63801195622774e453b7511e55e432dfd7d1c6d4a0e8f4dc0de6314a4a63b20a6eaa159914a +EBUILD gromacs-2021.2.ebuild 10022 BLAKE2B 90dc43e1aafe220870c86471e8a13564f2022e2a5ec8df0c9abc8e029da1f78e037d7e61a3d25dcefe8484945a6595c2a8ade0622651c2a71e0ee5a159b3a47d SHA512 e5c8f7e14ae5cfdf7845d592e48df7355a5faa38521d24ec16e815140442749f4429e5cb781ba4e54aede3c28b24cb886b52ac2422f12258abac07a321513d75 +EBUILD gromacs-2021.9999.ebuild 9932 BLAKE2B 45040b96ec2454338a1085048ef3b9c22a18b20167993de547b0f0226124bdb4be9b8b6acc19a998373d8438ea10a4e1e364c46f10def7e84b2d0542807b7e30 SHA512 a926a895411c07f18262f8f4a785028551ad5d1b1644429b112be5c1d9f14a830f07de7a0acff11582093fb0ee33c4122b67ce96e568736f76d11f20f7b6665a +EBUILD gromacs-2021.ebuild 9973 BLAKE2B 7c2db369fb2bf900cc30a2f4b8b35d3c193581a1db0885a46a43f81414c9abf057e3a3f9b88560ee51a903188ce1d4e90c9418dcc3692092a17d55596f5a09ad SHA512 79512ad0e28e079e0b76e14f0a01e9f54daf3516d0b51a5ee8e9406362e8c6099d90439bdf8a1aab1313e4e57889c568e7608acbc779de47abc314160e692928 +EBUILD gromacs-9999.ebuild 9932 BLAKE2B 45040b96ec2454338a1085048ef3b9c22a18b20167993de547b0f0226124bdb4be9b8b6acc19a998373d8438ea10a4e1e364c46f10def7e84b2d0542807b7e30 SHA512 a926a895411c07f18262f8f4a785028551ad5d1b1644429b112be5c1d9f14a830f07de7a0acff11582093fb0ee33c4122b67ce96e568736f76d11f20f7b6665a MISC metadata.xml 1149 BLAKE2B c2a231776a6e0e3b62c8ca9e05ee0012b5c90ff3d752034ff1f32e46c0cb5240f1a45a78ad0d8cf62c46ddcdd689aa50f9bbe955547f800baf7c037872295e98 SHA512 0799ce85673f6c8161fe18eeb6303844a0de41ea6c164c6bf16c42e7619c248c8d840dcffd55785699dbfd433d0b086c8982fc36a2414b3fdb687578602b6c83 diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild index 7c0c24d883f4..88cd8246d14d 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild @@ -23,7 +23,7 @@ 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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild index 5ba8f9df146a..b93b01a654e2 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild @@ -23,7 +23,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${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 +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild index 3c700bbb99a6..d04309a01fc7 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild index ff5aa7c43fdc..59a156235552 100644 --- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild index ff5aa7c43fdc..59a156235552 100644 --- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild index ff5aa7c43fdc..59a156235552 100644 --- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild index 75d52731734e..16a2bffe6a33 100644 --- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-2021.2.ebuild b/sci-chemistry/gromacs/gromacs-2021.2.ebuild new file mode 100644 index 000000000000..e8cbb127fefd --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2021.2.ebuild @@ -0,0 +1,349 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{7,8,9} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + git://git.gromacs.org/gromacs.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + !sci-chemistry/gmxapi + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_MULTI_USEDEP}] + ') + media-gfx/mscgen + media-gfx/graphviz + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +PATCHES=( + "${FILESDIR}/${PN}-2020-pytest.patch" + "${FILESDIR}/${PN}-2021-nblib.patch" +) + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + if use custom-cflags; then + #go from slowest to fastest acceleration + local acce="None" + if (use amd64 || use x86); then + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + use cpu_flags_x86_avx512f && acce="AVX_512" + elif (use arm); then + use cpu_flags_arm_neon && acce="ARM_NEON" + elif (use arm64); then + use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" + fi + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local gpu=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${gpu[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + "${opencl[@]}" + "${cuda[@]}" + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"/usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index 82fafe89e639..19c3097b599b 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -44,7 +44,7 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) hwloc? ( sys-apps/hwloc ) diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild index b5e91e41ba15..ea5d7cd93dc2 100644 --- a/sci-chemistry/gromacs/gromacs-2021.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 82fafe89e639..19c3097b599b 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -35,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -44,7 +44,7 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) hwloc? ( sys-apps/hwloc ) diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest index 31c9db303cf6..5d9c9b80e2eb 100644 --- a/sci-chemistry/numbat/Manifest +++ b/sci-chemistry/numbat/Manifest @@ -1,4 +1,4 @@ AUX numbat-0.999-gnuplot.patch 2048 BLAKE2B 662ff2337d8a56ba21d1037911dab787ce3faead57a692310e694be4435875c1c7b66a6b756b28c2a2bd8ee29c29b845b794c6f70720c9f7b31810cd8296a083 SHA512 dd646e8f6652a63cb4e1c97830a755629e45d20fa13431f628b66fe8a5062b7bd7ebacddb3dbcca5aeeac3ae0d89f59c61036c1a3639d25fe0426ada77a888bb DIST Numbat-0.999.tar.gz 1791471 BLAKE2B 7f6536533fdf6bc3860dc1a7c03ade4896e782c5ecadf1c6a7d70896f4c6ef9f0571796c171012497d7b47b3342c215a5302ed210d7dde3ecdbef170c3f55dbc SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c -EBUILD numbat-0.999-r1.ebuild 1005 BLAKE2B 7f2925f5d97e688fb8e31768523aa6d0c0e4529f9e5b0cf0acc639b5dd96b79d81e65445f79dc63086142192d9aeeab83dc30fb459338803a903cb54379dd041 SHA512 a4e95f3f0d5df19c46ec0a8c2f647258c0a70fba9447f2f669fe86c3437a2026196c1076adce22c6b41fb445c36bdcc382e3801373460e1ca6ce1992f8c6eb63 +EBUILD numbat-0.999-r2.ebuild 1007 BLAKE2B e65d5f9eb640f0f9f87a928b63b61e21f1944f7f57799dd98459749fe503ec5812a8190bed700f2747325220f3a54d935f16200adf5177180ceb11eab5c971a2 SHA512 f9f92be8144897cc537d218a944b88a98c240933153b7d1e2a5ba16e8657fe3cdc8b4dac2eaf33b411c8849e0dfbe6036898b59dc4fc81544041062bd0a29cde MISC metadata.xml 852 BLAKE2B 623b64ec229e39a4def8e03c4b69e6268abb2a42f7d2337e71d17da183a0ac99b953e820c2875703dfb5a599229ec94cea9f40a4386563acadb5082a835ff186 SHA512 64e5552a677fc7370f68f7f811734ac17144fcb95e23503c962b678a1678dccf22a2d19991eb69dcdf8d4c1c97448d35d7f34654245ebe3fee8b30a0a8fa586c diff --git a/sci-chemistry/numbat/numbat-0.999-r1.ebuild b/sci-chemistry/numbat/numbat-0.999-r2.ebuild index 766c64b1b9cd..ddfec41ed12b 100644 --- a/sci-chemistry/numbat/numbat-0.999-r1.ebuild +++ b/sci-chemistry/numbat/numbat-0.999-r2.ebuild @@ -19,7 +19,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" DEPEND=" gnome-base/libglade:2.0 - sci-libs/gsl + sci-libs/gsl:= x11-libs/gtk+:2 " RDEPEND=" diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest deleted file mode 100644 index 1578aefbece1..000000000000 --- a/sci-chemistry/rasmol/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX 2.7.5-bundled-lib.patch 2513 BLAKE2B d913fb8572abb58ffcb6a48f2f855432e33ef74168b6461d3b2d18bba9c0fedb33a975a5d754ac9ffc56644d9256bf428694afbf0b3a078421ab372c6c84570d SHA512 940e85bbe35ed6055d8deb1d761e925aec3b60d63c3e91bcc3c08596f1b8269efd4c8a257ff9efdbe32888e987852e85ed19cba5566d8d610e8d625a23b0994a -AUX rasmol-2.7.5.2-format-security.patch 1617 BLAKE2B d9a083ae6c72724359274da5b61683b615ca1daf8e0dd8763e999ee7cfbe7ec23cdefffd4d5fda94c9d5366c812f51fef663578d9c39805b6a6eaa8f9e3c569a SHA512 cab29465d5830e669eca152880ae60c403f90668ee5bf97e3694b6e754e2e23086a520717c2df990c74fcfbafc761a460bea111d868a57ae63f13bce1603f074 -AUX rasmol-2.7.5.2-glib.h.patch 770 BLAKE2B 1c83587711540a9e2b91b53ffd0836cde27f040c593b7d771eb185edf8e72b50f09d1c38ef0b2510effee95649bbaf3adf7d0340f49a38381bd15200fd94e749 SHA512 d743b89817d0ed2aa551f3a6529e5bcc50c811d79c0deddd50d07a59614cb0c2d71500452ff9aec4b4b84e4985d9851f61aafa30196356aa1724212b5159375e -AUX rasmol-2.7.5.2-longlong.patch 396 BLAKE2B 68ce4bff3584bbc6331ad5e27171d23e443be2d24b60bbd45dd02d4f04b5531cfd7fdb18904471c85ef107875fb23574f6b3212b78706746cc73c39d09cda801 SHA512 4c3ce01ade36fe8a9512bdac62bcd47268bcc5a0448f4af69b26d8add9cc8495d376bac33a8ae5aeae42fa114a1cba980ce86559bf2d52334257f2e001c011d3 -DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 BLAKE2B dcc9bfe9381ebab6bbf5a12e233490f076ead2388a22e3186421e3489bedde987813b1f65ce7b17ef168389c33d03bd7d4a8162635c0a79b3dc704eade23715d SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f -EBUILD rasmol-2.7.5.2-r2.ebuild 2335 BLAKE2B 3eb46ccf0799da8a5514e963193593ee4319cda48f474c616bb09191e59163c49d922f1c865b43fc5e49abc4e146c0725a66a95527e8ae55aff79368d9ee3ebc SHA512 c67480fea952676dbaee686ca6e6a5c4a7b0750b72ab45247f469c8643ec8a4a46b5d60c89aab531c84666560a3414fc0ccd176dab0ea17094cc7c7db3ff9bc8 -MISC metadata.xml 355 BLAKE2B 71f9b1537eea00556419ae1c9920458d86992e3c0b01083d55ca02f162c420f82e8f52ee8af224573912e2b988497901702962ed3b54342991f22e1eec37ce2e SHA512 98822367149551ef6af6d75e4bd0b9104f1a625a5a17e1a2dad32e7ed83345870dc45392525cfe7e49514eae29f986e8ac2ed253ec22fec94d6152f96620b916 diff --git a/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch deleted file mode 100644 index 10705165ad47..000000000000 --- a/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch +++ /dev/null @@ -1,80 +0,0 @@ -diff --git a/src/Imakefile b/src/Imakefile -index 03be00e..a0c68f9 100755 ---- a/src/Imakefile -+++ b/src/Imakefile -@@ -176,7 +176,7 @@ XFORMSLIB_DIR = /usr/local - #endif - endif - XFORMSLIB_INCLUDE_DIR = $(XFORMSLIB_DIR)/include --XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib -lforms -+XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib - #endif - #endif - #endif -@@ -281,17 +281,10 @@ RASMOLDIR = $(USRLIBDIR)/rasmol/ - - #ifndef USE_XFORMSLIB - DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ -- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ -- -I$(CQRLIB_INCLUDE_DIR) \ -- -I$(CVECTOR_INCLUDE_DIR) \ -- -I$(NEARTREE_INCLUDE_DIR) -+ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib - #else - DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ -- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ -- -I$(CQRLIB_INCLUDE_DIR) \ -- -I$(CVECTOR_INCLUDE_DIR) \ -- -I$(NEARTREE_INCLUDE_DIR) \ -- -I$(XFORMSLIB_INCLUDE_DIR) -+ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib - #endif - - -@@ -317,11 +310,11 @@ OBJS = rasmol.o molecule.o abstree.o cmndline.o command.o transfor.o \ - # Additional RS6000 AIX MITSHM Library - # LDLIBS = -lm -lXi -lXextSam $(XLIB) - --LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(XFORMSLIB) $(GTKLIBS) \ -- $(CBFLIB_LDLIB) \ -- $(CQRLIB_LDLIB) \ -- $(CVECTOR_LDLIB) \ -- $(NEARTREE_LDLIB) $(XFORMSLIB_LDLIB) -+LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(GTKLIBS) \ -+ -lcbf \ -+ -lCQRlib \ -+ -lCVector \ -+ -lCNearTree -lgfortran - - - # -@@ -425,11 +418,11 @@ $(NEARTREE_DIR): - $(NEARTREE_DIR)/CNearTree.c: $(NEARTREE_DIR) - #endif - --$(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ -- $(CQRLIB_OBJDEP) \ -- $(CVECTOR_OBJDEP) \ -- $(NEARTREE_OBJDEP) \ -- $(XFORMSLIB_OBJDEP) -+# $(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ -+# $(CQRLIB_OBJDEP) \ -+# $(CVECTOR_OBJDEP) \ -+# $(NEARTREE_OBJDEP) \ -+# $(XFORMSLIB_OBJDEP) - - - gtkwin.c: gtkui.h -diff --git a/src/Makefile.in b/src/Makefile.in -index fc6d0af..bad90fc 100755 ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -165,7 +165,7 @@ $(CBFLIBDIR)/lib/libcbf.a: $(CBFLIBDIR) - - all: postdownload rasmol rastxt - --rasmol: postdownload $(X11OBJS) $(CBFLIBDIR)/lib/libcbf.a -+rasmol: postdownload $(X11OBJS) - $(CC) -o rasmol $(LFLAGS) $(X11OBJS) $(X11LIBS) - chmod 755 rasmol - diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch deleted file mode 100644 index 22eb229d8a3d..000000000000 --- a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -urp RasMol-2.7.5.2/src/command.c RasMol-2.7.5.2_sprintf/src/command.c ---- RasMol-2.7.5.2/src/command.c 2011-05-15 01:23:49.000000000 +0700 -+++ RasMol-2.7.5.2_sprintf/src/command.c 2014-02-12 18:02:24.633489549 +0700 -@@ -1286,7 +1286,7 @@ void ShowRecordCommand( void ) { - if (record_on[1]) WriteString("record appearance on\n"); - else WriteString("record apperance off\n"); - if (RecordMaxMS == 1.) { -- sprintf(param,RecordTemplate); -+ sprintf(param, "%s", RecordTemplate); - } else{ - sprintf(param,RecordTemplate,millisec<0?0:millisec); - } -@@ -1381,7 +1381,7 @@ void ShowPlayCommand( void ) { - WriteString(param); - } - if (PlayMaxMS == 1.) { -- sprintf(param,PlayTemplate); -+ sprintf(param, "%s", PlayTemplate); - } else{ - sprintf(param,PlayTemplate,millisec<0?0:millisec); - } -@@ -1469,7 +1469,7 @@ void WriteMovieFrame( void ) { - RecordPause = True; - } else { - if (RecordMaxMS == 1.) { -- sprintf(param,RecordTemplate); -+ sprintf(param, "%s", RecordTemplate); - } else{ - sprintf(param,RecordTemplate,millisec); - } -@@ -1505,7 +1505,7 @@ static int PlayMovieFrame( void ) { - for (play_frame[1] = 0;play_frame[1]<=millisec; play_frame[1]++) - { - if (RecordMaxMS == 1.) { -- sprintf(param,PlayTemplate); -+ sprintf(param, "%s", PlayTemplate); - } else{ - sprintf(param,PlayTemplate,millisec-play_frame[1]); - } diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch deleted file mode 100644 index 69c19dae5e8d..000000000000 --- a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch +++ /dev/null @@ -1,31 +0,0 @@ - src/egg-macros.h | 3 ++- - src/eggfileformatchooser.c | 2 ++ - 2 files changed, 4 insertions(+), 1 deletions(-) - -diff --git a/src/egg-macros.h b/src/egg-macros.h -index 9a7caad..1a6bce0 100644 ---- a/src/egg-macros.h -+++ b/src/egg-macros.h -@@ -9,7 +9,8 @@ - #ifndef _EGG_MACROS_H_ - #define _EGG_MACROS_H_ - --#include <glib/gmacros.h> -+#include <glib.h> -+#include <glib/gprintf.h> - - G_BEGIN_DECLS - -diff --git a/src/eggfileformatchooser.c b/src/eggfileformatchooser.c -index 32ce2ab..febfc2e 100644 ---- a/src/eggfileformatchooser.c -+++ b/src/eggfileformatchooser.c -@@ -19,6 +19,8 @@ - #include "eggfileformatchooser.h" - #include "egg-macros.h" - -+#include <glib.h> -+#include <glib/gprintf.h> - #include <glib/gi18n.h> - #include <gtk/gtk.h> - #include <string.h> diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch deleted file mode 100644 index 3cff0fa2f98f..000000000000 --- a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urp rasmol-2.7.5-23Jul09/src/rasmol.h rasmol-2.7.5-23Jul09-64b/src/rasmol.h ---- rasmol-2.7.5-23Jul09/src/rasmol.h 2009-07-20 21:08:43.000000000 +0700 -+++ rasmol-2.7.5-23Jul09-64b/src/rasmol.h 2013-02-22 14:40:00.378574163 +0700 -@@ -125,6 +125,8 @@ - #define VECTOR_FAR - #endif - -+#define _LONGLONG -+ - /*========================*/ - /* Default User Options! */ - /*========================*/ diff --git a/sci-chemistry/rasmol/metadata.xml b/sci-chemistry/rasmol/metadata.xml deleted file mode 100644 index 59ea086025a2..000000000000 --- a/sci-chemistry/rasmol/metadata.xml +++ /dev/null @@ -1,11 +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> - <upstream> - <remote-id type="sourceforge">openrasmol</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild deleted file mode 100644 index 534cffb9bba5..000000000000 --- a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild +++ /dev/null @@ -1,106 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch fortran-2 multilib prefix toolchain-funcs - -MY_P="RasMol_${PV}" -VERS="13May11" - -DESCRIPTION="Molecular Graphics Visualisation Tool" -HOMEPAGE="http://www.openrasmol.org/" -#SRC_URI="http://www.rasmol.org/software/${MY_P}.tar.gz" -SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/${P}-${VERS}.tar.gz" -#SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/RasMol.tar.gz" - -LICENSE="|| ( GPL-2 RASLIC )" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - dev-libs/cvector - dev-util/gtk-builder-convert - >=sci-libs/cbflib-0.9.2 - >=sci-libs/cqrlib-1.1.2 - >=sci-libs/neartree-3.1.1 - x11-libs/cairo - x11-libs/gtk+:2 - x11-libs/libXext - x11-libs/libXi - x11-libs/vte:0" -DEPEND="${RDEPEND} - app-text/rman - x11-base/xorg-proto - >=x11-misc/imake-1.0.8-r1" - -#S="${WORKDIR}/${PN}-2.7.5-${VERS}" -S="${WORKDIR}/RasMol-${PV}" - -src_prepare() { - cd src || die - - epatch \ - "${FILESDIR}"/${P}-glib.h.patch \ - "${FILESDIR}"/${P}-format-security.patch \ - "${FILESDIR}"/${P}-longlong.patch - - if use amd64 || use amd64-linux; then - mv rasmol.h rasmol_amd64_save.h && \ - echo "#define _LONGLONG"|cat - rasmol_amd64_save.h > rasmol.h - fi - - sed \ - -e 's:-traditional::g' \ - -i Makefile* || die - - cat > Imakefile <<- EOF - #define PIXELDEPTH 32 - #define GTKWIN - EOF - - cat Imakefile_base >> Imakefile || die - epatch "${FILESDIR}"/2.7.5-bundled-lib.patch - - eprefixify Imakefile - - sed \ - -e 's:vector.c:v_ector.c:g' \ - -e 's:vector.o:v_ector.o:g' \ - -e 's:vector.h:v_ector.h:g' \ - -i *akefile* || die - - sed \ - -e 's:vector.h:v_ector.h:g' \ - -i *.c *.h || die - - mv vector.c v_ector.c || die - mv vector.h v_ector.h || die - - CC="$(tc-getBUILD_CC)" LD="$(tc-getLD)" \ - IMAKECPP="${IMAKECPP:-$(tc-getCPP)}" xmkmf -DGTKWIN || die -} - -src_compile() { - emake -C src clean - emake \ - -C src \ - DEPTHDEF=-DTHIRTYTWOBIT \ - CC="$(tc-getCC)" \ - CDEBUGFLAGS="${CFLAGS}" \ - EXTRA_LDOPTIONS="${LDFLAGS}" -} - -src_install() { - libdir=$(get_libdir) - insinto /usr/${libdir}/${PN} - doins doc/rasmol.hlp - dobin src/rasmol - dodoc PROJECTS {README,TODO}.txt doc/*.{ps,pdf}.gz doc/rasmol.txt.gz - doman doc/rasmol.1 - insinto /usr/${libdir}/${PN}/databases - doins data/* - - dohtml -r *html doc/*.html html_graphics -} diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest index cb9f38fd30e8..66b55599c691 100644 --- a/sci-chemistry/theseus/Manifest +++ b/sci-chemistry/theseus/Manifest @@ -1,3 +1,3 @@ DIST theseus_3.3.0.tar.gz 22548124 BLAKE2B 0ad49f768e1584bf40e90ff6fd0d884b6b27ee59ad31ce75050293b817a3747969ab0c4b4ff982aadbdc5301c1c56522540b78aab045e841c099a80dd546c8e9 SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2 -EBUILD theseus-3.3.0.ebuild 1508 BLAKE2B 26711e23e5c2709dc9addd289c80cd74a877674ebab6bc128d48249cd64cdd7daee2f00e78633e02fb55cc667041dfda3ada6f9354643043be3feacec2d095b6 SHA512 6b2d63c2d988534cb7b0f00e9b5eb20a63c8ad814c38bef94f41fc33d6f2dce826632191ed48952b447995af21958366ad56bef6b9f8b63fafe3085f588fd736 +EBUILD theseus-3.3.0-r1.ebuild 1510 BLAKE2B 8527637cfbeb666aa84112bf01867ba14d34e819ccb8f372bfc032315eb8e00645af56588262d0a088db1976d439531f96ffaee8af5a42e99fe8eebb60dd6e5d SHA512 ce61c47d06d624ef6b8c70dba821715e7fe8ef2a82ccacfd16c53bd2e76b77343299ead01a78267dd7d7c4fb9b8894d0fa58bd86234ce011011e99dcb1229116 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/theseus/theseus-3.3.0.ebuild b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild index dd9c0b802edc..f9e62b3916d7 100644 --- a/sci-chemistry/theseus/theseus-3.3.0.ebuild +++ b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild @@ -15,7 +15,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="examples" RDEPEND=" - sci-libs/gsl + sci-libs/gsl:= || ( sci-biology/muscle sci-biology/probcons diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest index 49547d1bbcb4..b0a68a069235 100644 --- a/sci-chemistry/votca-ctp/Manifest +++ b/sci-chemistry/votca-ctp/Manifest @@ -1,4 +1,4 @@ DIST votca-ctp-1.5.1.tar.gz 1345994 BLAKE2B 6e927c5d57abfff335412bdac085c9dd81696503310e58a89bf2207b07f9d9900d11d20176a11fbde6d6cdfa97f50faa5e877889e35201ad9ed5dd93dbc158cb SHA512 686d7193cdd6a763197dd4f332554c9c6c2022c539191d0a243e70450aa2a4c7048fff3c06636aee09525516fb3717fe49934d5daf2dfcdcbc08be416cc4b6c0 DIST votca-ctp-manual-1.5.1.pdf 948647 BLAKE2B 4afec48d0e6bb29dc86d4d22fce74a8d2197d6b7a1ed35a5b09af84c5bbc0fc49b91e045c85e5b5ab79beb5a7de1db78a15e395a1a5faf4c11cc1b58c1ffca97 SHA512 b4ae79b2da0037cc325fdff3b0fd8d142d6bfdad5bc11991cee314f40f105bcdcb1189d17679a84eb37da7a9bb686d0c5ee57c7796a0c6b787b70d53222dbc17 -EBUILD votca-ctp-1.5.1.ebuild 1513 BLAKE2B 4fd8750c2d7e507205addab5c7250dac6f14ae56f770ea4bdd1da6f74082baeb2b47e0a0acc76190102cfc298145b729495570a370ef7f0b1f5bd2b672a805a7 SHA512 8f236eadba99d0f89cb3750a2c1727acc29f2cab1bcd5686236d1eca1d9f0392fe23b51bbb82a98fac0bd0f709d65d04841d0184be87e338dd6ce55855151dc2 +EBUILD votca-ctp-1.5.1-r1.ebuild 1515 BLAKE2B 634ed349161b15dfc152ffbfe0ad3a24f0544c470c597f30fcf8c1ed4a198e4db4f95c41aa71db0db1bd3faecb71ad8fc437b4ec9793d2e8def8dc12489ecd11 SHA512 f2e0cbf730a44aabd0fe5d34626781dc43977023e6a1d7a98604563430f28a18e79214b1dda818f8b5c25827db8ca4dafac587c064f75d4278916af6668791a2 MISC metadata.xml 453 BLAKE2B a61c365529a1c877e5bad44f6e2f0a24a8797956e9e3a5b3d4649c58c27df9301b50c84bb5767ca52a151e2b509f46a92cd3f17c1020fb7bedf7fb2fe708b48d SHA512 53ace87a281559ae8881b8b010c76801696521de930dcfaf12a5e320456cb4a21a55a7873d173bdb5cc740f3cdbccf1daf62bc83579342f4f23329df7dbd2dba diff --git a/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild b/sci-chemistry/votca-ctp/votca-ctp-1.5.1-r1.ebuild index 779c83919b3e..ace4787f199b 100644 --- a/sci-chemistry/votca-ctp/votca-ctp-1.5.1.ebuild +++ b/sci-chemistry/votca-ctp/votca-ctp-1.5.1-r1.ebuild @@ -27,7 +27,7 @@ SLOT="0" RDEPEND=" ~sci-libs/votca-tools-${PV}[sqlite] >=dev-cpp/eigen-3.3 - sci-libs/gsl + sci-libs/gsl:= ~sci-chemistry/votca-csg-${PV}" DEPEND="${RDEPEND} |