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authorV3n3RiX <venerix@redcorelinux.org>2021-06-17 17:57:35 +0100
committerV3n3RiX <venerix@redcorelinux.org>2021-06-17 17:57:35 +0100
commit7932d472a02d4c016ff7dff4b7a5479ab9d1883d (patch)
treed07709230f82777cae6ba7dab35aee31896060fb /sci-chemistry/gromacs
parentd18bf1e01b65ee4bf0c804e2843b282d3d4e5d7c (diff)
gentoo resync : 17.06.2021
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r--sci-chemistry/gromacs/Manifest24
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.4.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.5.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.6.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.9999.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.1.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.2.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.9999.ebuild59
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.ebuild59
-rw-r--r--sci-chemistry/gromacs/metadata.xml1
10 files changed, 288 insertions, 209 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 15f4d8cc1d82..70b33b6727dc 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -10,6 +10,12 @@ DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7c
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
+DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed
+DIST manual-2020.5.pdf 11850797 BLAKE2B b605de81cce385177f278b563526725688b4c2b0326f6f2c22bddc9b455c016365ee82731ad0ef2b2c9522e7d140c4a097b7a25f91552be60741d876bcc4c929 SHA512 0fa81494dbb4cb71c274fa1d1b1ef13bc5be8e69be841d429d06d5e9ef5517158b2130c0120ef6de13e73de5cd8af941c7b983ddba1da8af8214272704ce629e
+DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437b82d9a593d333dada3989c2c8a936d62c642e195f98bb474b1673b8142405c467348fc96a74d57fb12106d76 SHA512 be508ebec597b82a2c4056029f8bb731b22cb8902628a45462ed21af54c554d28e07d5381efaaa96565202b7b47d33aea67950206cd9e8936211ae721b21b3e1
+DIST manual-2021.1.pdf 12252366 BLAKE2B c3f104f3a5c8b784b78bdb027ae3bf818977fd86e15b81760877423805d74f468417df6ad57b240d138f4ee4c567c2e7676c0084911ee1400ebfa7bab2673901 SHA512 8d4468da400abb39c307b1f31f5b4b4ae52152df1fb5bc7059a37072cd2a20136858d7280ea6a7138fe6c18e04821386d72f1ac4ee9a303e359e1d52b5250f12
+DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984
+DIST manual-2021.pdf 12251377 BLAKE2B 6b3c80fedf04b3cdc05ec9b52e0dd78c0c7abf2d9819c00ad29e1d7e2dd829cfc0e61c86c899859ac6af6b631f856737810f05f9c903456805b5b9c9c6c85c16 SHA512 1bd61e4d052ebe4ff293be710159f135013d38f1299557d0b0e5edcf60d288d8534694896a1feebe572f52187f85e890e59b7c71644a0c03bd264cfae6d348bc
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
@@ -20,13 +26,13 @@ DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3
DIST regressiontests-2021.tar.gz 48513192 BLAKE2B e27898ef3936495fce111c8debdafbdaafae07cd9b27c8591cc27695f681fddda34f083d427e5b3afd2f318ff41201eabc915025f1fddef61ae29ceb13f37557 SHA512 e33578d32b929d516614592d0bf4aac4e518cc4f18fee4048d5b73b11f4373494c6d8aa43442e4e2be632c12c058657bce1064be82c515787d57b449c1241e48
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-2020.4.ebuild 10102 BLAKE2B a2a35b56f765dfaff9062cd4c4462350ee8981206d36c99b623c8d46e62fbd26ce7da9e66a8515378b4766dc99848716fbb50596046a49a5991ea96833be7957 SHA512 f0899a4b589591e0bc9c7ecbdde1b9199d0eda39e93066701f613ae57be408825cbe6c96a828de883978b54b3ef9a8d0b9453867a58cdb3266ad51bfb0f525fb
+EBUILD gromacs-2020.5.ebuild 10105 BLAKE2B 1f1caecdbae2f5fff63e152d84165129c86a3e79e21c0ce464fad9dc0fecffa61267d8af3377ba7d8ba7b2b8b159fe1a716d05eb5254c04dd4fd745387b73faa SHA512 cd566b5bf64c1b3fb2e506ce84530613b0a82d8dcf1e0b85e7287b7c946fb509a010e0214161a2ef18ec923eb0fb6d04f2d4e1b4daa048a5f6bc2462fc68c52e
+EBUILD gromacs-2020.6.ebuild 10105 BLAKE2B 1f1caecdbae2f5fff63e152d84165129c86a3e79e21c0ce464fad9dc0fecffa61267d8af3377ba7d8ba7b2b8b159fe1a716d05eb5254c04dd4fd745387b73faa SHA512 cd566b5bf64c1b3fb2e506ce84530613b0a82d8dcf1e0b85e7287b7c946fb509a010e0214161a2ef18ec923eb0fb6d04f2d4e1b4daa048a5f6bc2462fc68c52e
+EBUILD gromacs-2020.9999.ebuild 10105 BLAKE2B 1f1caecdbae2f5fff63e152d84165129c86a3e79e21c0ce464fad9dc0fecffa61267d8af3377ba7d8ba7b2b8b159fe1a716d05eb5254c04dd4fd745387b73faa SHA512 cd566b5bf64c1b3fb2e506ce84530613b0a82d8dcf1e0b85e7287b7c946fb509a010e0214161a2ef18ec923eb0fb6d04f2d4e1b4daa048a5f6bc2462fc68c52e
+EBUILD gromacs-2021.1.ebuild 10317 BLAKE2B 578f747981f9857b00543b0fda21189f43ede3e771b5017994cebfd51a7dd807361761adb56bca08b6b3e297e38712ce70e3b327373e8d52cc6e0ce062166287 SHA512 0d2d2e5a0cc0cb7932cbbe7ce091857340432cd864dc4a830959630a34dc46ef8361815854f10c585d2f862e11088cc2c335c5e70419610b64d81055e7654e9c
+EBUILD gromacs-2021.2.ebuild 10327 BLAKE2B 935f1635adb43e43f8f9d159826b43028a3c70bf70e26af5c5754a77401a177f2ed39834ce9cf6425d82a01ccf7193f4fe612ddfb3b728f079cd1a9cd882fd5f SHA512 47f930b93eb292d9194f8dedca487b3fda6ebbab2e5c3f320f9569d244deec8bff4fef27934cd21ec162f021571e48f6e9abded8719479a1220e18488a457360
+EBUILD gromacs-2021.9999.ebuild 10237 BLAKE2B 346372007800569bdf4517f9b710c71d7b5717e6dba1e7ea992027fb743c42ff94638eac40ae28fe4b51ff1fae27f89d320f7c44186d3ef01f8798d3533e8091 SHA512 d123afdfcc7a13a56babf650e2476e003790b705a9e59aa67cf98fd4a690a1969bb0b60e9b1ee5615edacbe49a880be722c4870c89b43f9ba814e716455dc8ba
+EBUILD gromacs-2021.ebuild 10278 BLAKE2B c17da5a50ddd0b6e4b93779d59185fbe57d4b3bfec80a52a857eb53f86d2fcb6a1b7f63782d558e4a3eb8f3c7a54d75f73c4bd0036472272109fe1d6d6781c30 SHA512 80745295416d0e8e8c739da20aaff54bf2dca88d7b5dc8a800c1d334b7579ef7b85421388c0121acf2e0b3a43bed16545e65b8fc30f4618b5cfc18d8c81e4c7d
EBUILD gromacs-9999.ebuild 9932 BLAKE2B 45040b96ec2454338a1085048ef3b9c22a18b20167993de547b0f0226124bdb4be9b8b6acc19a998373d8438ea10a4e1e364c46f10def7e84b2d0542807b7e30 SHA512 a926a895411c07f18262f8f4a785028551ad5d1b1644429b112be5c1d9f14a830f07de7a0acff11582093fb0ee33c4122b67ce96e568736f76d11f20f7b6665a
-MISC metadata.xml 1149 BLAKE2B c2a231776a6e0e3b62c8ca9e05ee0012b5c90ff3d752034ff1f32e46c0cb5240f1a45a78ad0d8cf62c46ddcdd689aa50f9bbe955547f800baf7c037872295e98 SHA512 0799ce85673f6c8161fe18eeb6303844a0de41ea6c164c6bf16c42e7619c248c8d840dcffd55785699dbfd433d0b086c8982fc36a2414b3fdb687578602b6c83
+MISC metadata.xml 1223 BLAKE2B 9e48794b267cdb031dcc680ecce38c0d9727c2706d95a0a52d3502d4aa73d245db419a77823d10c5022d65628390b2fd476e489ec764cdd1721c9dd8295a8232 SHA512 d9320e5896bd32e892a9be573da92943236d0cf912f3417b823a415c5470ad9e37a934eafcede6ab7487197854c515ef81270e44c8503540b14dc13356beb3de
diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
index d04309a01fc7..266941a81e30 100644
--- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -133,28 +136,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -208,7 +212,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -282,7 +286,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -308,9 +312,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
index 59a156235552..41ac7771497c 100644
--- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -133,28 +136,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -208,7 +212,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -282,7 +286,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -308,9 +312,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
index 59a156235552..41ac7771497c 100644
--- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -133,28 +136,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -208,7 +212,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -282,7 +286,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -308,9 +312,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index 59a156235552..41ac7771497c 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -133,28 +136,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -208,7 +212,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -282,7 +286,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -308,9 +312,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
index 16a2bffe6a33..e8ea613693f0 100644
--- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -136,28 +139,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -218,7 +222,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -289,7 +293,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -315,9 +319,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2021.2.ebuild b/sci-chemistry/gromacs/gromacs-2021.2.ebuild
index e8cbb127fefd..7b257ee4f40f 100644
--- a/sci-chemistry/gromacs/gromacs-2021.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.2.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -136,28 +139,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -218,7 +222,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -289,7 +293,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -315,9 +319,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index 19c3097b599b..16825937690a 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -131,28 +134,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -213,7 +217,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -284,7 +288,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -310,9 +314,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild
index ea5d7cd93dc2..a4fdab0dfaf7 100644
--- a/sci-chemistry/gromacs/gromacs-2021.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.ebuild
@@ -7,6 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
DISTUTILS_SINGLE_IMPL=1
inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
@@ -21,6 +22,7 @@ if [[ ${PV} = *9999* ]]; then
else
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi
@@ -35,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${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 build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -57,7 +59,7 @@ CDEPEND="
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
+ build-manual? (
app-doc/doxygen
$(python_gen_cond_dep '
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
@@ -72,6 +74,7 @@ RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
+ || ( doc build-manual )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
@@ -133,28 +136,29 @@ 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
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write" pattern="PS" />
- <policy domain="coder" rights="read | write" pattern="PS2" />
- <policy domain="coder" rights="read | write" pattern="PS3" />
- <policy domain="coder" rights="read | write" pattern="EPS" />
- <policy domain="coder" rights="read | write" pattern="PDF" />
- <policy domain="coder" rights="read | write" pattern="XPS" />
- </policymap>
- EOF
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
}
src_configure() {
@@ -215,7 +219,7 @@ src_configure() {
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
@@ -286,7 +290,7 @@ src_compile() {
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
- if use doc; then
+ if use build-manual; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile manual
fi
@@ -312,9 +316,14 @@ src_install() {
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install python_packaging/install
fi
- if use doc; then
+ if use build-manual; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
+
+ if use doc; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 4235f32ded67..44134f443625 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -10,6 +10,7 @@
<name>Gentoo Chemistry Project</name>
</maintainer>
<use>
+ <flag name="build-manual">Build manual instead of downloading it</flag>
<flag name="cuda">Enable cuda non-bonded kernels</flag>
<flag name="double-precision">More precise calculations at the expense of speed</flag>
<flag name="gmxapi">Add support for gmxapi library</flag>