gentoo auto-resync : 24:02:2023 - 09:47:15

12 files changed, 177 insertions, 12 deletions

diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
index 25620147ddb8..b4b7974e60d0 100644
--- a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
+++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
@@ -4,7 +4,7 @@
 EAPI=8
 
 DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1 flag-o-matic
 
@@ -23,8 +23,6 @@ fi
 
 LICENSE="GPL-3+"
 SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 25620147ddb8..b4b7974e60d0 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -4,7 +4,7 @@
 EAPI=8
 
 DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1 flag-o-matic
 
@@ -23,8 +23,6 @@ fi
 
 LICENSE="GPL-3+"
 SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index 5d2f4f537f72..052df8b8e9b4 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1,4 +1,4 @@
 DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d
-EBUILD HTSeq-2.0.2.ebuild 1569 BLAKE2B 70b1e6ad30c3e2e668dc6e87d6c5ab05890ff370768c8f039e4b8a664c6bf775028b2fb315b5f4884fcd5cbf0889976eef87e9022b8d90cd30a147e6b20b8f94 SHA512 cd0d45310ee60a192b76fb218b7f5b67c28e3a9f8b8ea1277095ebd67c3e2acc69b5ba9fe8375c94b8e69784c6809bb20237261c184cf35d54c017d4fa7f207e
-EBUILD HTSeq-9999.ebuild 1569 BLAKE2B 70b1e6ad30c3e2e668dc6e87d6c5ab05890ff370768c8f039e4b8a664c6bf775028b2fb315b5f4884fcd5cbf0889976eef87e9022b8d90cd30a147e6b20b8f94 SHA512 cd0d45310ee60a192b76fb218b7f5b67c28e3a9f8b8ea1277095ebd67c3e2acc69b5ba9fe8375c94b8e69784c6809bb20237261c184cf35d54c017d4fa7f207e
-MISC metadata.xml 330 BLAKE2B 0710ed510732fd584ecbee4d193bf2cccf72af692cc5ce7243ab7864f00ba23d22fca0c4b06213d7e40697c0e469c29f36d988c7fa0d8ab6ea985f8df7255388 SHA512 481004c3e6ba51f4e983e265b7a3f9e4281e27c95ea894eb7f166a339059507cb947eddba1d8642d952289936c8145fc20fa26ed11522535d4c097cc6a3cb018
+EBUILD HTSeq-2.0.2.ebuild 1530 BLAKE2B 1a6bcac47e4f7b92e627e8982664061f6eea9961ea4bb9f3610a5d10ab75bfa87292314fdc92e7bfbc81897aea5567af7e49d27be61c7a575995bdbb35b4ac04 SHA512 4ea3d3733f87952b0c46449f95d740ed5be7abdf92f951f6c2773173d319508552baf744c9619d6859eb84aa730f0e265f7a0c15be095063adec2e41ca685a37
+EBUILD HTSeq-9999.ebuild 1530 BLAKE2B 1a6bcac47e4f7b92e627e8982664061f6eea9961ea4bb9f3610a5d10ab75bfa87292314fdc92e7bfbc81897aea5567af7e49d27be61c7a575995bdbb35b4ac04 SHA512 4ea3d3733f87952b0c46449f95d740ed5be7abdf92f951f6c2773173d319508552baf744c9619d6859eb84aa730f0e265f7a0c15be095063adec2e41ca685a37
+MISC metadata.xml 381 BLAKE2B 3f734f3608731ea9d4e893965a96d3abceddbdff04309350ede193ef721eb8faec3e6050850fb4410557536058d9852ae5b02e0d99b9eb79f4b2091b58bcb6f2 SHA512 227191a1fd9fc0e5cbf9091a48eb51baa5bfe97637b5fc27c419b2b2225c03759ca98bc84b7974338bd2b52db5dbf848b084c2b2f1f300b70b94fb209528fe91
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
index 649077f8337e..6ada1a530737 100644
--- a/sci-biology/HTSeq/metadata.xml
+++ b/sci-biology/HTSeq/metadata.xml
@@ -7,5 +7,6 @@
 	</maintainer>
 	<upstream>
 		<remote-id type="pypi">HTSeq</remote-id>
+		<remote-id type="github">htseq/htseq</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 58f4d20c7165..73acfdc415db 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest
index 5d803512b7ab..0b5bde56bed0 100644
--- a/sci-biology/biopandas/Manifest
+++ b/sci-biology/biopandas/Manifest
@@ -1,3 +1,5 @@
 DIST biopandas-0.2.7.tar.gz 255846 BLAKE2B b8c6a66f51a00266bc1a271ecfe00b4cfddd24b9766e63e2ad4187048ddd8f985d70eb8083b1be3887a0fd9b666c97553029ecd90c7b73ae882e5347bbc54d2e SHA512 cf4f12601b7f63ca3d5e9a17c6628e4975968f722c9db72e32c00e80ec335c5bf6a928a5f887b16ecd316c49b298d77634cbe1c4ef1ca505379b1de5335e2569
+DIST biopandas-0.4.1.gh.tar.gz 5330292 BLAKE2B 78b783ed77bbd8e6efd115a108f99c502fd71ef4c231746575599828699dac1de85125273df1af74d0bd51e092751113474ef2baf312a184e23b3057cd21222a SHA512 e08694fad927a5ac096b2cd78f641a2af262ebfc7351fc4dc37e5df39e98a6e984ccab26718109f18eed988a4a4af5b29d19c5cf3e8e2d794246b1410a9b5440
 EBUILD biopandas-0.2.7.ebuild 1030 BLAKE2B 9e6532e22646eb0d8f5d4f916490d6d08218db61feab06d4778ae6a1fdff916531aea5ca05d4405da109ef02c9068d43ad696714fccc2b4b6ff2db641b91b4eb SHA512 179f13e3c0599965f6179dbae0be86f7da3f8f87dcd066be03ea9ae506c5f121fc4d2378c53a52d28800827e9a790f1f395397211e15cec5c458bd01edfa53a4
-MISC metadata.xml 537 BLAKE2B 3a84070766aa469d204a25e3dec6864db46db27a681327124b208f64b782b598d3b46b4495e08c3e9fd0484980ce1966b498cfd74d81f8d20849f6e531e0bc3e SHA512 13055720124f4586a2949140068976090fe90d997035a8426ee0833c0df9eb082abe838312d44df78c2b28ab16a9cd48df181a2082496278243e4b0e5f8fd25a
+EBUILD biopandas-0.4.1.ebuild 669 BLAKE2B c8169a146ac2a23317152e374df3a72545399c4dd162a6b9c0394c40e83eb296cf09ddc35a02237b0894bede3573247467376240ee50abe5558bf183a7e65486 SHA512 47eb4221c05e2819deff8598c6f3e67d53c6cd7de40ada5a6d1b97b206c6bdaa9240cd1f2c4f3b1ad2aab66ff62c02a9179667353f9bd4e412ac3b703074493d
+MISC metadata.xml 541 BLAKE2B 45092856329b54575afe8a96a334b0face2c980cea240f57135c5a631088f114944a3c80ffde509af7e3a14c3a17652c8df4828919474e6b9961b93b51c8abbf SHA512 aafea3a1194d6cebddcf3b3d42a7c26a510c360259ffcf49c16f2de8742f1d24097cfeccd2e33a1d8d30a3c63fb5ca0a21469bac3c30aad6a4d41136f87cc4df
diff --git a/sci-biology/biopandas/biopandas-0.4.1.ebuild b/sci-biology/biopandas/biopandas-0.4.1.ebuild
new file mode 100644
index 000000000000..50fe601ed514
--- /dev/null
+++ b/sci-biology/biopandas/biopandas-0.4.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Molecular Structures in Pandas DataFrames"
+HOMEPAGE="
+	https://rasbt.github.io/biopandas/
+	https://github.com/BioPandas/biopandas
+	https://pypi.org/project/biopandas/
+"
+SRC_URI="https://github.com/BioPandas/biopandas/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests nose
diff --git a/sci-biology/biopandas/metadata.xml b/sci-biology/biopandas/metadata.xml
index 1b4a0fc84ad0..5133b4eff6ab 100644
--- a/sci-biology/biopandas/metadata.xml
+++ b/sci-biology/biopandas/metadata.xml
@@ -6,11 +6,11 @@
     <name>Gentoo Biology Project</name>
   </maintainer>
   <upstream>
-    <remote-id type="pypi">BioPandas</remote-id>
+    <remote-id type="pypi">biopandas</remote-id>
     <maintainer status="unknown">
       <email>mail@sebastianraschka.com</email>
       <name>Sebastian Raschka</name>
     </maintainer>
-    <remote-id type="github">rasbt/biopandas</remote-id>
+    <remote-id type="github">BioPandas/biopandas</remote-id>
   </upstream>
 </pkgmetadata>
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
+}
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 9160409c20e7..182f6a8c17fd 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,3 +1,5 @@
 DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
+DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
 EBUILD bowtie-2.4.4.ebuild 1207 BLAKE2B 4e89cd7884065637cba84784321100b90a0c0e561dca1519f843be418b33737f31d7db9cc74810a67b1211b9e69e0ac5e7b45548b5b8b0999d42a36a317e9491 SHA512 28473ddcd136172f0b35625cc2a79c4a9a5801c65df28aa0800ed6ea9552f2cf381377ef81504279764fecc7fc2e3c0566c1f7dbc98e2e578ef0452bc2c33653
+EBUILD bowtie-2.5.1.ebuild 1528 BLAKE2B eec523c39c69b9b0862696b0579441c79c028eb2465fdb3c5c153cd1dcaf403e43eb6596bbb64e41f2e7b1fbf27fa832d019720f6c31361d047d4d341e987a6a SHA512 1f7b179a376d0f6a89c223cdf8bc5804b13bef4b9cba3cf4364c109f4d622beba51c2b79f238f92ffb44922711530fbf199af1db36e93d7236b6ce23312e124c
 MISC metadata.xml 342 BLAKE2B 7f98f1707e3f53e7c2e532427d6935c692cdcf45304701d28d245ba13b62e752d14d5c3a96925fdf5bceb87a9c291edad0ce715339a5bf92ca6de7ee839adced SHA512 b7f0359b22f70ab25737565bda08e500f6a79bf33052d39fe2013b085c3f636122d0f373430ce3f0b56f95051db9571cb6c79b6f58e30658f45ef752ec708df6
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
new file mode 100644
index 000000000000..353362fd6026
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 2021-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit python-single-r1 toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/"
+SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
+S="${WORKDIR}/${PN}2-${PV}"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="test cpu_flags_x86_sse2 examples"
+# Test script missing from tarball
+# ./scripts/sim/run.sh: No such file or directory
+RESTRICT="test"
+REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/perl
+	sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-arch/unzip
+	test? (
+		dev-perl/App-cpanminus
+		dev-perl/B-COW
+		dev-perl/Clone
+		dev-perl/Config-General
+		dev-perl/File-Which
+		dev-perl/local-lib
+		dev-perl/Math-Random
+		dev-perl/Test-Deep
+		dev-perl/Text-Template
+	)
+"
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		CXXFLAGS="" \
+		CPPFLAGS="${CPPFLAGS}" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS} -msse2"
+}
+
+src_install() {
+	dobin bowtie2 bowtie2-*
+
+	exeinto /usr/libexec/bowtie2
+	doexe scripts/*
+
+	HTML_DOCS=( doc/{manual.html,style.css} )
+	einstalldocs
+	dodoc TUTORIAL
+	newman MANUAL bowtie2.1
+
+	python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
+
+	if use examples; then
+		docinto examples
+		dodoc -r example/.
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}