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* sci-chemistry/molmol: Drop unused eclassPacho Ramos2022-11-201-1/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Fix sed usagePacho Ramos2022-11-202-11/+10
| | | | | | | And provide an icon with higher resolution Closes: https://bugs.gentoo.org/710876 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/mdtraj: use HTTPS, fix LICENSEMichael Mair-Keimberger2022-11-192-6/+6
| | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/molequeue: fix UnquotedVariableArthur Zamarin2022-11-101-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/GromacsWrapper: remove unused patch(es)Michael Mair-Keimberger2022-10-301-11/+0
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Closes: https://github.com/gentoo/gentoo/pull/28029 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/GromacsWrapper: add 0.8.2, drop 0.8.0-r1Alexey Shvetsov2022-10-292-7/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/chemex: drop 2021.4.0_p6-r1Pacho Ramos2022-10-252-41/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2022.1.0Pacho Ramos2022-10-252-0/+43
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/wxmacmolplt: align longdescription opening and closing tagsPetr Vaněk2022-10-201-2/+2
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/tm-align: align longdescription opening and closing tagsPetr Vaněk2022-10-201-14/+14
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/suitename: align longdescription opening and closing tagsPetr Vaněk2022-10-201-13/+13
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/pdbmat: align longdescription opening and closing tagsPetr Vaněk2022-10-201-13/+13
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/pdbcat: align longdescription opening and closing tagsPetr Vaněk2022-10-201-15/+15
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/nmrglue: align longdescription opening and closing tagsPetr Vaněk2022-10-201-15/+15
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/cluster: align longdescription opening and closing tagsPetr Vaněk2022-10-201-8/+8
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/clashlist: align longdescription opening and closing tagsPetr Vaněk2022-10-201-7/+7
| | | | | Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/vmd: drop 1.9.4_alpha55Sam James2022-10-162-271/+0
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/cara-bin: depend on glibc (binpkg)Sam James2022-10-081-1/+2
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/nmrglue: add 0.9Andrew Ammerlaan2022-10-052-0/+32
| | | | | | Closes: https://bugs.gentoo.org/846230 Closes: https://bugs.gentoo.org/836861 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/chemex: Use PEP517 buildMichał Górny2022-09-182-19/+7
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/chemex: add 2022.0.1Pacho Ramos2022-09-182-0/+49
| | | | | | | | Readding now that deps are satisfied again. Signed-off-by: Pacho Ramos <pacho@gentoo.org> Bug: https://bugs.gentoo.org/871339 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/chemex: Revert "add 2022.0.1"Michał Górny2022-09-182-49/+0
| | | | | | | | Reverting because of pending dev-python/ deps revert. Reverts: 96ce6a9530fc93af92cad81b30dcb4059bc07063 Bug: https://bugs.gentoo.org/871339 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/chemex: add 2022.0.1Pacho Ramos2022-09-182-0/+49
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: add 2021.6Alexey Shvetsov2022-09-152-0/+358
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2022.3, drop 2022.1Alexey Shvetsov2022-09-152-4/+4
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/avogadro2: add 1.97.0Andrew Ammerlaan2022-09-072-0/+84
| | | | | Bug: https://bugs.gentoo.org/868132 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/dssp: remove stale boost lower boundsDavid Seifert2022-09-042-2/+2
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/dssp: remove boost[threads(+)] usedepDavid Seifert2022-09-044-6/+6
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/autodock_vina: remove boost[threads(+)] usedepDavid Seifert2022-09-041-2/+2
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/molmol: fix MissingUseDepDefaultSam James2022-09-011-5/+8
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/molden: Stabilize 6.9-r1 amd64, #867223Jakov Smolić2022-08-301-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/surf: Stabilize 1.0 amd64, #867223Jakov Smolić2022-08-301-2/+2
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/numbat: treecleanJakov Smolić2022-08-294-118/+0
| | | | | | Closes: https://bugs.gentoo.org/862486 Closes: https://bugs.gentoo.org/583038 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/pymol: add github upstream metadataSam James2022-07-311-10/+11
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/mdtraj: add github upstream metadataSam James2022-07-301-4/+7
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/molsketch: do not rdep on linguist-toolsAndrew Ammerlaan2022-07-211-1/+1
| | | | | Closes: https://bugs.gentoo.org/836644 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/molden: install sci-chemistry/surf instead of bundled onePetr Vaněk2022-07-161-10/+6
| | | | | | | | | | | | | | | | | | | | | | | | sci-chemistry/molden newly installs /bin/surf since 6.9, commit ec853626b72f ("sci-chemistry/molden: add version 6.9"), however, this is bundled version of sci-chemistry/surf which should be used instead. This change solves multiple issues: - unnecessary /bin/surf collision with sci-chemistry/surf and www-client/surf, #834033 #858209 - missing SURF license of bundled surf, which is no longer needed - ex: no python-exec wrapped executable found in /usr/lib/python-exec, #849371 issue, which is triggered by surf/surf target. x11-misc/gccmakedep and app-editors/vim dependencies are no longer needed because they were used in surf/surf target. Closes: https://github.com/gentoo/gentoo/pull/26439 Closes: https://bugs.gentoo.org/822510 Closes: https://bugs.gentoo.org/834033 Closes: https://bugs.gentoo.org/849371 Closes: https://bugs.gentoo.org/858209 Signed-off-by: Petr Vaněk <arkamar@atlas.cz> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/propka: drop 3.2.0Andrew Ammerlaan2022-07-062-41/+0
| | | | | Closes: https://bugs.gentoo.org/741376 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/propka: add 3.4.0Andrew Ammerlaan2022-07-063-0/+30
| | | | | Closes: https://bugs.gentoo.org/832251 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/gromacs: Keyword 2022.2 arm64, #856388Arthur Zamarin2022-07-061-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/dssp: Keyword 3.0.11 arm64, #856388Arthur Zamarin2022-07-061-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/gromacs: Update 9999Alexey Shvetsov2022-07-041-1/+2
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: arm was dropped upstream since 2022.xAlexey Shvetsov2022-07-043-3/+6
| | | | | | Closes: https://bugs.gentoo.org/844100 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: eneble py3.11Alexey Shvetsov2022-07-044-4/+4
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: enable py3.11Alexey Shvetsov2022-07-042-2/+2
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: enable py3.11Alexey Shvetsov2022-07-041-1/+1
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: enable py3.11Alexey Shvetsov2022-07-041-1/+1
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2022Alexey Shvetsov2022-07-042-338/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2022.2Alexey Shvetsov2022-07-042-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/molequeue: enable py3.10, py3.11 and disable py3.7Andrew Ammerlaan2022-06-151-4/+8
| | | | | | | | | | Fix build with USE="doc zeromq", if zeromq is enabled the docs are built into the ..._pythonX_Y BUILD_DIR instead of the cmake BUILD_DIR. Therefore we have to define HTML_DOCS within python_foreach_impl Closes: https://bugs.gentoo.org/846227 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>