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* */*: Switch sci-biology proj to cmake.eclassAndreas Sturmlechner2020-01-052-6/+6
| | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* */*: Clean PYTHON_COMPAT of obsolete implsMichał Górny2020-01-056-12/+12
| | | | | Closes: https://github.com/gentoo/gentoo/pull/14246 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/biopython: Drop python2_7Andreas Sturmlechner2019-12-291-2/+1
| | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-biology/biopython: Remove oldDavid Seifert2019-12-293-114/+0
| | | | | Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/embassy-phylipnew: Change LICENSE to "free-noncomm".Ulrich Müller2019-12-281-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702534 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/phylip: Change LICENSE to "free-noncomm".Ulrich Müller2019-12-281-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702536 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/embassy: Fix LICENSE.Ulrich Müller2019-12-241-2/+2
| | | | | | Closes: https://bugs.gentoo.org/702532 Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/gatk: Drop broken -9999Michał Górny2019-12-151-40/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-run: Drop unmaintained -9999Michał Górny2019-12-151-40/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-network: Drop unmaintained -9999Michał Górny2019-12-151-31/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl-db: Drop unmaintained -9999Michał Górny2019-12-151-37/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioperl: Drop unmaintained -9999Michał Górny2019-12-151-73/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: [QA] Remove redundant `|| die` guardsDavid Seifert2019-12-116-9/+9
| | | | | | | | | | | | * Since all ebuilds in the tree are EAPI>=4, `|| die` on builtin commands is redundant and dead code. Closes: https://github.com/gentoo/gentoo/pull/13940 Reviewed-by: Ulrich Müller <ulm@gentoo.org> Reviewed-by: Michał Górny <mgorny@gentoo.org> Reviewed-by: Andreas K. Hüttel <dilfridge@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/shrimp: Remove oldDavid Seifert2019-12-112-55/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/velvet: Port to EAPI 7David Seifert2019-12-113-126/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/augustus: Port to EAPI 7David Seifert2019-12-111-9/+10
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/tree-puzzle: Port to EAPI 7David Seifert2019-12-111-21/+18
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/mrbayes: Remove oldDavid Seifert2019-12-111-51/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/plink: Remove oldDavid Seifert2019-12-115-164/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/last: Remove oldDavid Seifert2019-12-112-40/+0
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/gibbs: Port to EAPI 7David Seifert2019-12-112-18/+27
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/glimmerhmm: Port to EAPI 7David Seifert2019-12-112-17/+34
| | | | | Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: [QA] Fix trivial cases of MissingTestRestrictMichał Górny2019-12-1113-11/+24
| | | | | | | | | | | | | | | | | | The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/mcl: drop old EAPIAaron Bauman2019-11-233-74/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/psipred: drop old EAPIAaron Bauman2019-11-233-107/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/ariadne: drop last-rited packageAaron Bauman2019-11-205-100/+0
| | | | Signed-off-by: Aaron Bauman <bman@gentoo.org>
* sci-biology/bamtools: Remove USE="static-libs"David Seifert2019-11-132-60/+6
| | | | | Package-Manager: Portage-2.3.78, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/goby-cpp: Remove last-rited pkgMichał Górny2019-10-145-104/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Remove mirror://gentoo rename hackMichał Górny2019-10-051-1/+1
| | | | | | | | Replace 'mirror://gentoo/X -> Y' with plain 'mirror://gentoo/Y'. Since actual filenames are used on the mirrors, the latter is valid for all packages already. Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/ApE: Add bindist restrictionMichał Górny2019-09-191-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* Make a bunch of metadata.xml files uniformMatt Turner2019-09-151-1/+1
| | | | | | When put into a squashfs image, these files are deduplicated. Signed-off-by: Matt Turner <mattst88@gentoo.org>
* sci-biology/goby: Remove last-rited pkgMichał Górny2019-09-144-127/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bioruby: amd64 stable wrt bug #690048Agostino Sarubbo2019-09-081-1/+1
| | | | | | Package-Manager: Portage-2.3.69, Repoman-2.3.16 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/bioruby: x86 stable (bug #690048)Thomas Deutschmann2019-09-071-1/+1
| | | | | Package-Manager: Portage-2.3.75, Repoman-2.3.17 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org>
* sci-biology/stride: Port to EAPI 7David Seifert2019-08-173-25/+31
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/stride: [QA] Version the distfileDavid Seifert2019-08-172-3/+3
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/sim4: [QA] Version the distfileDavid Seifert2019-08-172-4/+4
| | | | | Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vaal: remove last rited packageMikle Kolyada2019-07-224-72/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* sci-biology/allpathslg: remove last rited packageMikle Kolyada2019-07-224-69/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* */*: Add maintainer-needed comment to all unmaintained packagesMichał Górny2019-07-171-0/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/vcftools: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/poa: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/bedtools: Sort KEYWORDSMichał Górny2019-07-151-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/foldingathome: Permit dev-libs/openssl-compatMichał Górny2019-06-141-1/+4
| | | | | Signed-off-by: Michał Górny <mgorny@gentoo.org> Signed-off-by: Thomas Deutschmann <whissi@gentoo.org>
* sci-biology/{blossoc,snpfile}: Remove last-rited pkgsDavid Seifert2019-05-1912-974/+0
| | | | | Closes: https://bugs.gentoo.org/683762 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/cufflinks: Remove last-rited pkgDavid Seifert2019-05-1910-314/+0
| | | | | Closes: https://bugs.gentoo.org/671432 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/arb: remove last rited packageMikle Kolyada2019-05-026-281/+0
| | | | Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
* sci-biology/biopython: Bump to version 1.73David Seifert2019-04-212-0/+59
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: David Seifert <soap@gentoo.org>
* */*: Remove python3_4 PYTHON_COMPAT correctlyMichał Górny2019-04-176-12/+12
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* */*: Drop python3_4 from PYTHON_COMPATMichał Górny2019-04-161-1/+1
| | | | | Closes: https://github.com/gentoo/gentoo/pull/11706 Signed-off-by: Michał Górny <mgorny@gentoo.org>