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* sci-chemistry/molmol: Fix pkgcheck warningsPacho Ramos2024-05-181-4/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Fix passing incompatible pointer typeBrahmajit Das2024-05-182-0/+118
| | | | | | | Closes: https://bugs.gentoo.org/923325 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/36093 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Fix EmptyGlobalAssignment warningPacho Ramos2024-05-181-1/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: drop 4.3.1, 4.4.1Pacho Ramos2024-05-183-95/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.7Pacho Ramos2024-05-182-0/+55
| | | | | Closes: https://bugs.gentoo.org/924695 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Fix VariableOrderWrong warningPacho Ramos2024-05-181-1/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: drop 2022.3.5Pacho Ramos2024-05-182-43/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2024.02.16Pacho Ramos2024-05-182-0/+46
| | | | | Closes: https://bugs.gentoo.org/929756 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Update to 3.0.0 and drop oldAlexey Shvetsov2024-05-173-105/+6
| | | | | | | Closes: https://bugs.gentoo.org/862441 Closes: https://bugs.gentoo.org/910511 Closes: https://bugs.gentoo.org/929762 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2024.2Alexey Shvetsov2024-05-172-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/modeller: add 10.5, drop 9.25Alexey Shvetsov2024-05-173-9/+37
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: OFL license has been renamed to OFL-1.0Ulrich Müller2024-05-132-4/+4
| | | | | Bug: https://bugs.gentoo.org/931823 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* */*: inline mirror://sourceforgeLucio Sauer2024-04-307-13/+13
| | | | | | | bump copyright of touched ebuilds to 2024 Signed-off-by: Lucio Sauer <watermanpaint@posteo.net> Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/votca: add subslot dep on sci-libs/hdf5Sam James2024-04-232-4/+4
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/mdtraj: Remove last-rited pkgMichał Górny2024-04-134-78/+0
| | | | | Bug: https://bugs.gentoo.org/911646 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/openbabel: Stabilize 3.1.1_p20210225-r1 amd64, #929186Arthur Zamarin2024-04-111-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/nmrglue: Remove last-rited pkgMichał Górny2024-03-293-61/+0
| | | | | Closes: https://bugs.gentoo.org/878725 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/gromacs: drop 2018.8-r2, 2019.6-r3Andreas Sturmlechner2024-03-264-533/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/autodock_vina: add github upstream metadataAlexey Shvetsov2024-03-261-0/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/autodock_vina: add 1.2.5Alexey Shvetsov2024-03-263-0/+115
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/votca: drop 2022Andreas Sturmlechner2024-03-242-81/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* Move {sci-libs → dev-python}/scikit-learnMichał Górny2024-03-101-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/autodock_vina: Fix build with recent boostAlexey Shvetsov2024-03-031-2/+2
| | | | | | Closes: https://bugs.gentoo.org/913037 Closes: https://bugs.gentoo.org/924622 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2023.4, drop 2023.3Alexey Shvetsov2024-02-292-3/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2022.9999Alexey Shvetsov2024-02-291-333/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2021.6Alexey Shvetsov2024-02-292-355/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2022.5-r1Alexey Shvetsov2024-02-292-336/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2023.1-r1, 2023.2Alexey Shvetsov2024-02-293-676/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2024.1Alexey Shvetsov2024-02-292-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2024, drop 2024_rcAlexey Shvetsov2024-02-012-3/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2023.3Alexey Shvetsov2024-01-252-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: destabilize for ~armMatoro Mahri2024-01-234-6/+6
| | | | | | Closes: https://bugs.gentoo.org/906679 Signed-off-by: Matoro Mahri <matoro_gentoo@matoro.tk> Signed-off-by: Ionen Wolkens <ionen@gentoo.org>
* sci-chemistry/gromacs: add 2024_rc, drop 2024_betaAlexey Shvetsov2024-01-212-3/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* Move {app-doc → app-text}/doxygenMichał Górny2024-01-1220-39/+39
| | | | | | | | Per the category metadata, app-doc/ is reserved for documentation *files* and not software. Move it to app-text/ where it seems a better fit. Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/mpqc: sys-devel/flex -> app-alternatives/lexSam James2024-01-081-2/+2
| | | | | | | | | | All of these will be using app-alternatives/lex anyway as they're not unsetting YACC or LEX, so make the dep reflect reality. (Included both YACC and LEX out of conservatism.) Signed-off-by: Sam James <sam@gentoo.org>
* profiles/use.desc: Make USE=cuda globalMichał Górny2023-12-261-1/+0
| | | | | | | | Add a global USE=cuda. It is used semi-consistently in 39 packages. Signed-off-by: Michał Górny <mgorny@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/34348 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/gelemental: Stabilize 2.0.2 amd64, #920146Arthur Zamarin2023-12-161-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/cluster: Stabilize 1.3.081231-r2 amd64, #920145Arthur Zamarin2023-12-161-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/votca: Stabilize 2022.1 amd64, #920126Arthur Zamarin2023-12-161-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/gromacs: add 2024_beta, 2024.9999Alexey Shvetsov2023-11-253-0/+673
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/wxmacmolplt: add github upstream metadataPacho Ramos2023-11-241-7/+10
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/wxmacmolplt: add 7.7.2Pacho Ramos2023-11-242-0/+48
| | | | | | Closes: https://bugs.gentoo.org/741366 Closes: https://bugs.gentoo.org/862447 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: Works with wxGTK 3.2Pacho Ramos2023-11-242-1/+281
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemtool: Use transfig from fig2devPacho Ramos2023-11-122-0/+56
| | | | | | Also use a better icon for Adamantane and drop useless USE flags. Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: enable py3.12Alexey Shvetsov2023-11-0110-10/+10
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add quotes for ${HOME}Alexey Shvetsov2023-11-0110-20/+20
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: disable py3.9Alexey Shvetsov2023-11-0110-10/+10
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Fix urlsAlexey Shvetsov2023-11-0112-32/+32
| | | | | | | Thanks to Andrey Alekseenko Closes: https://bugs.gentoo.org/910639 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/easychem: revbump for clang-16 fixAndrew Ammerlaan2023-10-271-0/+0
| | | | | See-also: https://github.com/gentoo/gentoo/pull/33525#issuecomment-1782844341 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/easychem: Fix build with clang 16Brahmajit Das2023-10-272-1/+15
| | | | | | | Closes: https://bugs.gentoo.org/886085 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/33525 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>