diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/Manifest.gz | bin | 17558 -> 17560 bytes | |||
| -rw-r--r-- | sci-chemistry/ghemical/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/ghemical/metadata.xml | 1 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 12 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2016.5.ebuild | 2 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2018.3.ebuild | 2 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2019.9999.ebuild | 29 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2019_rc1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2019_beta1.ebuild) | 43 | ||||
| -rw-r--r-- | sci-chemistry/votca-csg/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild | 2 |
10 files changed, 71 insertions, 24 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 06e29e04f82c..6831f51f192f 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest index d96c08f98719..b7a28786abd5 100644 --- a/sci-chemistry/ghemical/Manifest +++ b/sci-chemistry/ghemical/Manifest @@ -1,4 +1,4 @@ AUX 2.99.2-docs.patch 785 BLAKE2B c731e7366ad44dde7c8754dc6e450e26436f69f4dda5547c61e73d4aa2da69be66cf46204481b1726a7ca746712f0a35c3e689f9da99d4376bc62097512958ec SHA512 0d8754b31eeec184a0d3becb75d3c69c2e922abbe00c175c8cb23d7ea96838896db2da90de45653a7612a041975975f062d289d7d362f6f1abae1d916dbc4b89 DIST ghemical-3.0.0.tar.gz 2196716 BLAKE2B 62008667c58cb058beb8eb3946bb96fb03aceff7cc93f64aecc697a7648946936208063b419aca57f740d5760a90d923d81f8cc8d80fb68bdf924b23cd2061b3 SHA512 d4dd0b063a4dea33fa7430e77a2da253c74079fd8b5f21e8c2b5da1383f3689b93305417e1bf0d4908b87c91afb33c3266dd6bd6fbcd768cc98614a3f730ee94 EBUILD ghemical-3.0.0.ebuild 1353 BLAKE2B 5037472809fb5ff199c6683d4db73bd2c86ebd1764f4c2263bbcb5fb0910c12d768692451f7a8a27dc5307023f5a710b1cac933da16f211705d5744db8129028 SHA512 790b807c3e9e33230a752187cb362336de8f2f953e5bc6cbe834c53a85cd74509449c4e20e1fd0cc22f9e092c44bb4f24c57cf2a96ec38cb7059188a68f5237e -MISC metadata.xml 775 BLAKE2B c41e23e584e920e6ec68591abedaf69d746279e5c0cf45d65eb3afd150a2c4c747a2bdcc15386e85309300200877d2013fdd6d5aaf8b09bcfa8b45cfa32084c3 SHA512 59e27f59b90d5f7436855509a6de0c0b296cd9ae1ccaec02570a5055482e033c12df040430f466a1ba2c004b555fdd89617ad65b608590a40fe27790888940fe +MISC metadata.xml 851 BLAKE2B 119f8bdb334c7e1391c821aa99b59e9433ea1856a79e5216d1d35fa1349b36dff1288a3fb816af9547d451a95d8266889df7e6a79cf73748094fce7876125074 SHA512 bde362ad42f9648cd8e5f32e1c9b9e10159bf9b850a86e80012f067530d6e5912bfc54eb22c170a8eeb0a8ba705db4ecc3c0559b431eaee8ea474d4f9c82de93 diff --git a/sci-chemistry/ghemical/metadata.xml b/sci-chemistry/ghemical/metadata.xml index 05b56d91546f..90f25b17693e 100644 --- a/sci-chemistry/ghemical/metadata.xml +++ b/sci-chemistry/ghemical/metadata.xml @@ -15,5 +15,6 @@ visualization tools are currently available. <use> <flag name="openbabel">Use <pkg>sci-chemistry/openbabel</pkg> for file conversions</flag> + <flag name="seamonkey">Add support for the Seamonkey web-browser</flag> </use> </pkgmetadata> diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index a366fac0307d..a1937a84ebf0 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -2,25 +2,25 @@ DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060da DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955 -DIST gromacs-2019-beta1.tar.gz 33549950 BLAKE2B 667246f9a7cb136efca3fbda21aabe5ab0a759aa42896f8a9ddc86fafbfb1906e31fe46688c98477a5841e8fe5708b960c2a26abe754b8d793046734cd509377 SHA512 9f8bec3671f6f7421dc45cab1b5edb8ba8f2ebc34cd19ebd3d5d534be1f84135a112f49733a3f8c79e93ffc2b09c5053ae0dea31e95832a2b98acaee47f7d1af +DIST gromacs-2019-rc1.tar.gz 33426863 BLAKE2B 8de7eeee128389652922dafe2a6f73fadfeb463a9a1ffea898ac34cfe056500113a12c795aa9ba1304d6e4a737dcfa7bd537bab2f1d49c0951f8b68714c13458 SHA512 ade6e9df653f1212540ca969d0b70b046fe30de866ca899ecb463d2c96e6dd70ac8a5ff08df801728332357abefee2d73cd3e77cae4b2b586a827c69e0257654 DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe -DIST regressiontests-2019-beta1.tar.gz 67604794 BLAKE2B 163046e54206d3406d39e6bd9552dcce5a9a05a73e14249bf371d2432d902a3e336c0caa3e0c83353ac4566d91f4f805724f8eb996a831f8d3b712f65b1d1c42 SHA512 eef7eaacf56ba9358bfb0a3e34da4bc00d2a65564da81d144f57ee8a732081882b8e1c96f7006b966455105b834271715273e7590d3d4310209ee0324e7fa585 +DIST regressiontests-2019-rc1.tar.gz 67606596 BLAKE2B e614b21fdf73e205c6ad870e19998f9fdb52cb0c54f878a0ab924772f8a710b7ac3d68faf8b77a043f03f3302f829de61e729e69d04abb38de761022dcb7aa7c SHA512 7521bc03a410d2532ee8681a0a3544f3a33f1aaff83513765ed1a28a756f24812955a44c0d8ae88988e23c347c4df455dd4bd3db7b9bb6d3d7d0bf0cc57bbebb DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81 -EBUILD gromacs-2016.5.ebuild 7972 BLAKE2B ef58c4b3b1a455d077485806cca50cdb7346f1be3b5eacb640c572b86b96978ebfcba74c31f1b708bbaf700e2bc9b8bbb1d255087810d9cd8b1b67bf1486f9c0 SHA512 6951728e27609b26d5fc1c21fa40a98b5d83ce25385d4d6ca889682da0a2335df98861a409bd40105809486f1442f97fea404b5b8f518faf46eb7d65e488864f +EBUILD gromacs-2016.5.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81 EBUILD gromacs-2016.9999.ebuild 7974 BLAKE2B 5568ed9513fd44da7382370e418ffe456db73076c0000101c96bba4e704e6eece7ef6131379ddbe95c42e9fa4b082346db2ee4f6bb15a25d8c6afd9209db2e5c SHA512 911a5f71d9dde20d11a13cff416db12d6722cf9fb9609895a3d3bd2381c36a875f80f1617f6960deae2ceaa951f60a14738dfe5065f41560cfeecf7ad26b7c70 EBUILD gromacs-2018.3-r1.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5 -EBUILD gromacs-2018.3.ebuild 7823 BLAKE2B 9a741bdeade19ed1da85e090c2afdc87bb9678545b64edafcd5865de91b889e3543ef80b5ef41c149d3fd0260c3fc0522fedd0f4ab135fed6dacc76c7bd70063 SHA512 1a31a9da7cfcd1379ce1654a1935f9afd86c127981220e61a016671fed82e9e7a492b69b1f25e3a0a4933d2700b7a6529603bac00b6be420bf7dfb5857ad7de6 +EBUILD gromacs-2018.3.ebuild 7822 BLAKE2B af732727b7050314a4d4d38f5d4b753f96f26b3f506aba2be6ad61381fc41988d969251e82bd0c00e690e803c1a1aeddbe5db4e92109b86f128d83b2a02fb9bf SHA512 5dd227aa588940f42e4a05610bbd74e4c5d36daffc37817ccab66b8dde612400a945d48f7087266d85a41629f21496e4f50277ac7aa4eff40f8496158ffacb69 EBUILD gromacs-2018.4.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5 EBUILD gromacs-2018.9999.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5 -EBUILD gromacs-2019.9999.ebuild 8228 BLAKE2B 65de6a319ba40e78d72b33b9c0566fde5fd8dbd642b7a54f147f7575fc70aae41496d7010c073264a0ab5737dc6aade8bd5208d60c3043ad309bf5ef4fa41238 SHA512 c95821d7c2c8b5add4472bac614a9cf784b1c849bcef25a57714c4a37324f5209e49dc3911001764d198aeb6c5b0df5353ae46a39d0e99c56b97bb923d228148 -EBUILD gromacs-2019_beta1.ebuild 8099 BLAKE2B 3df16a2b8f90b3a75221ca9d7faa97d5286c929287a0426ac26d42c924c45fd70643d95f30d1e666c0e87c3a56ae601e8d26c34d9f4d96d6b2dca14f8a55d8b1 SHA512 c23895ca932fb0217c283ccc32ef86b74af6c205d330edb5690e0b9753c30cdc304050d06e811072a424f43ffd767b8d3fc9bd27ed0640c36c4fb2ea30f8317f +EBUILD gromacs-2019.9999.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7 +EBUILD gromacs-2019_rc1.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7 EBUILD gromacs-4.6.9999.ebuild 8094 BLAKE2B b5d89654043667e88e275270bc3d79fa5b6168cb76450cecc6e143a19d606ddfadeb7cb2d97a3a623e5069159151017afa0ced6080264ecd09de9afb4652457e SHA512 0701afb0d0ccb977aad8cf69209299db91babdcbc3d8b1abc2f727637956e2d86cbb7c36f38be35f793a8abd684f51bc68ab8f107006f02e0975a2b05f317c58 EBUILD gromacs-5.0.4.ebuild 8413 BLAKE2B 3e78b8d41d4499293ec54c3442d6412e9c1c6fd33f5830d2a4dbf7a369f896f0be2f9407eb3c2a444a29677e261cdf14589e8a80c8b64f5beeaa24800a4e1cce SHA512 b5ed004538c3fdfc4a265ccdc0771f5cd49e21d84d0af916e7dfeb6e32a083c2fe2d93d83c14bc1e657abfafe7204e7a2f337bb639b727eafc71c6525abe9626 EBUILD gromacs-5.0.9999.ebuild 8423 BLAKE2B c3b636e32170f00ce77260e7d58bc2a36a6fcc1e2220045a51f151fff9cf3aac617a755fbfd647b262bf6cd44ef4201ac8716b942f71a868679eef6498e29229 SHA512 7cee51a8d1809f2c111acfda77525dd02b853735c0af31d5439c80943dddc2d8a50b5c00999c1808c2eb8daa6f158003048e6348d683b5c9d93fd3c383c73423 diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild index a2b7857286d7..15acf0b2cf75 100644 --- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2016.5.ebuild @@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild index 5a0ffcb03beb..45a172545346 100644 --- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.3.ebuild @@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" diff --git a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild index 4c507ba350aa..c090fc6b03ef 100644 --- a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild @@ -7,7 +7,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja" PYTHON_COMPAT=( python2_7 ) -inherit bash-completion-r1 cmake-utils cuda eutils multilib python-any-r1 readme.gentoo-r1 toolchain-funcs xdg-utils +inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -54,8 +54,7 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen - ${PYTHON_DEPS} - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') + dev-python/sphinx[${PYTHON_USEDEP}] media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra @@ -117,6 +116,28 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF } src_configure() { @@ -167,13 +188,13 @@ src_configure() { -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex doc) - -DPYTHON_EXECUTABLE="${PYTHON}" -DGMX_HWLOC=$(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} ) diff --git a/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2019_rc1.ebuild index 85a14370a8ea..c090fc6b03ef 100644 --- a/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019_rc1.ebuild @@ -5,7 +5,9 @@ EAPI=6 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +PYTHON_COMPAT=( python2_7 ) + +inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -52,7 +54,7 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen - dev-python/sphinx + dev-python/sphinx[${PYTHON_USEDEP}] media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra @@ -114,6 +116,28 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF } src_configure() { @@ -170,6 +194,7 @@ src_configure() { -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" ${extra} ) @@ -226,10 +251,10 @@ src_compile() { BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile # not 100% necessary for rel ebuilds as available from website - #if use doc; then - # BUILD_DIR="${WORKDIR}/${P}_${x}"\ - # cmake-utils_src_compile manual - #fi + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ @@ -248,9 +273,9 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install - #if use doc; then - # newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - #fi + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ cmake-utils_src_install diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest index c9dfe8ebe96a..2c8806e1dad9 100644 --- a/sci-chemistry/votca-csg/Manifest +++ b/sci-chemistry/votca-csg/Manifest @@ -4,7 +4,7 @@ DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d546b509366863f593776a62dd3064662535d4fd525f1063f5ccaf47446822f13fefd7f66aa9d68cd1a4a7c99d66a790 SHA512 2e1f4a4375d83df9bd357d4d17e79d26a3a31c9177f008de86721427ffc6f43a5000ec840691108b52a8aecf962321ba6363cd975c7445d7230ee5b0b151b3fa DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90 DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d6e031ea8cd55ebe3f4d246c0876e272e6e6dd535c8dd2f24f7593cb1ef31fbc18111269d29cb69120368ddef7b1b7d25825c SHA512 f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7 -EBUILD votca-csg-1.4.1.ebuild 3198 BLAKE2B 47ee7941de81e6de211b945ddb95f27c7d9cd7509e84784a57222e4acbca1f15181042d74ebec9198a1074e1eae553438ea073f10385e8c016b947ed6618d332 SHA512 093ae1b82f6498df6befbd24ae3146c275257ec20dd9d466bc5dd93d5ca5a4e48650b2a16d0e7d750b82bd5e3d5bce85fe8ac7ad428f91a1376a0be4b3e8b3de +EBUILD votca-csg-1.4.1.ebuild 3204 BLAKE2B e447a6859d7ee4d722701f96634667529bd183f10dd4affeb2713023edfe52ab73988df7ef912963bd154b893bd2d401d2fd110a729040a2a2c52ec5fd44985c SHA512 df94c127269df2a2eaa9643005eeeae6925b458fbb0cb4d1661757a49e5ab4926a613c532e4df4475b34768e904d2388270c868c9ad675cd110e2b1737153e3d EBUILD votca-csg-1.4.ebuild 3191 BLAKE2B 93981bf3302b4c0feaaf1e45005df343ab5e12011a461e0f9729a9e6d50f1268fb016ce2bbe397a2b673fb0172a9971bc9e67fb806fa9a56fb7ab4e05235bd56 SHA512 ddeed3f96f097e73ad3593daebab448ae992a3f0d4ba9d46b9027c79c9654457ba3611af51049741f8ff04c0f8425eb097a6115f75d1ec7704f48c46a71ea088 EBUILD votca-csg-9999.ebuild 2540 BLAKE2B 605ea77ddd320c1e0af4c93468261e3a44ef49fa1073568d64521a1557f5cdbd18fbf66e82be235b2e221adddacbc731fde63233d2ecb05e37528d0ce16be79c SHA512 932e5be7cf66118e246a56fa4420d4a5df07fc1ebb82ce6a5331b3ca71eace4ac79a7a84bc5186515e7bbd6856de6c604bc8b1351020146d466f4bd229f7446c MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 diff --git a/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild index 47c989751bff..80e7fca62425 100644 --- a/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild +++ b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild @@ -29,7 +29,7 @@ SLOT="0" RDEPEND=" ~sci-libs/votca-tools-${PV} - gromacs? ( <sci-chemistry/gromacs-2019:= ) + gromacs? ( <sci-chemistry/gromacs-2019_beta1:= ) hdf5? ( sci-libs/hdf5 ) dev-lang/perl app-shells/bash:*" |