diff options
author | V3n3RiX <venerix@koprulu.sector> | 2023-02-24 09:47:15 +0000 |
---|---|---|
committer | V3n3RiX <venerix@koprulu.sector> | 2023-02-24 09:47:15 +0000 |
commit | 4003c614d3c4b320c45ab1f4b817459d4709443b (patch) | |
tree | fcc0c42e92c56abe0ea39b717b2c3b019c335e41 /sci-biology/biopython | |
parent | 58177544118b9a8393d7501ee5e0e35cd32f2ad4 (diff) |
gentoo auto-resync : 24:02:2023 - 09:47:15
Diffstat (limited to 'sci-biology/biopython')
-rw-r--r-- | sci-biology/biopython/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/biopython/biopython-1.81.ebuild | 61 |
2 files changed, 63 insertions, 0 deletions
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 90b839a3e687..4835348132b1 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1,5 @@ DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa +DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed EBUILD biopython-1.79.ebuild 1889 BLAKE2B bd56decca7a0e6233bfd68bdf910ecde89452832517202040bfaa732f43f8817edde6ce8996af4c58e5d1ac329316fd4cae14afbb29078f9105c8cb093dbdb81 SHA512 596d2b3577318af2ac6c4ac0062b0e7d88c058050e4f3206218365962ac0a035477a1f162e04295ce87f46611d2caab8efed545442da5143832e8b4f81a7e86c +EBUILD biopython-1.81.ebuild 1842 BLAKE2B 3037b2bd68de90c8d29911c36c82a9d0444fa4b0de4351d17ef261fbc652eba9f949562184b43556e8b9daf8f31c9e3def2af45f1f5355381bd75365c7a833bc SHA512 400ade4fe5e956a16ea939ba5d0f5bfcf6794cda64faeb181e1d8ca1c6ea99983fd89cc33e2d1998fd92da19083c0b9a8d83721af2cdc9f23950368f61a606e5 MISC metadata.xml 334 BLAKE2B 4d97c23444fdddcca57631fa2ddf4a11cfcef0accf91db65071d520f6601c0626e290e67cbf162abdefe7a74f4b410f8366a23186fc417e1fab7e9ce157d7610 SHA512 a870bd044d0e0d4e2a0c48b50f710845c6269e038790243f1d1de65b1252fd653f0f403fc55b98946df8eb27f24dfae5c84f52fcc38c969afcbdb548ccbb7a59 diff --git a/sci-biology/biopython/biopython-1.81.ebuild b/sci-biology/biopython/biopython-1.81.ebuild new file mode 100644 index 000000000000..8b90d610c6ae --- /dev/null +++ b/sci-biology/biopython/biopython-1.81.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 optfeature pypi + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/pygraphviz[${PYTHON_USEDEP}] + >=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND}" +BDEPEND="sys-devel/flex" + +DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. ) + +python_test() { + distutils_install_for_testing + cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die + + # need to create symlinks for doctests + mkdir -p "${TEST_DIR}"/lib/Bio/Align || die + ln -r -s "${S}"/Bio/Align/substitution_matrices \ + "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die + + cd "${TEST_DIR}"/lib/Tests || die + rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die + "${EPYTHON}" run_tests.py --offline --verbose || die +} + +python_install_all() { + # remove files causing ecompressdir to fail + rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die + + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} + +pkg_postinst() { + optfeature_header "For database support you need to install:" + optfeature "MySQL database support" dev-python/mysqlclient + optfeature "PostgreSQL database support" dev-python/psycopg:2 + + optfeature_header "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +} |