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* 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>
* sci-chemistry/dssp: add 4.4.4.1Pacho Ramos2023-10-262-0/+55
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: Fix compilation with gcc-13Pacho Ramos2023-10-202-0/+13
| | | | | Closes: https://bugs.gentoo.org/915694 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/msms-bin: Fix download locationPacho Ramos2023-10-191-2/+2
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/MDAnalysis: add 2.6.1, drop 2.4.3Alexey Shvetsov2023-10-142-1/+1
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* Rename dev-python/{pytables → tables}Michał Górny2023-10-051-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/molequeue: fix VariableShadowedArthur Zamarin2023-09-191-7/+5
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/tinker: update EAPI 6 -> 8Volkmar W. Pogatzki2023-09-172-14/+19
| | | | | | | | | Inherits java-pkg-2 instead of java-pkg-opt-2 Closes: https://bugs.gentoo.org/905682 Signed-off-by: Volkmar W. Pogatzki <gentoo@pogatzki.net> Closes: https://github.com/gentoo/gentoo/pull/32797 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/chemex: drop 2022.3.4Pacho Ramos2023-09-172-43/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2022.3.6Pacho Ramos2023-09-172-0/+44
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/GromacsWrapper: drop 0.8.2Pacho Ramos2023-09-172-41/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/GromacsWrapper: add 0.8.5Pacho Ramos2023-09-172-0/+41
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/autodock: update EAPI 7 -> 8, update HOMEPAGE, SRC_URIBrahmajit Das2023-09-142-0/+112
| | | | | | | | | Fix C++17 does not allow register storage class Closes: https://bugs.gentoo.org/898130 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/31489 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/cluster: Fix error: ISO C++17 does not allow register storage ↵Brahmajit Das2023-09-112-0/+54
| | | | | | | | | class Closes: https://bugs.gentoo.org/898132 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/31488 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/gelemental: remove unused patch(es)Michael Mair-Keimberger2023-08-141-18/+0
| | | | | | Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Closes: https://github.com/gentoo/gentoo/pull/32283 Signed-off-by: Conrad Kostecki <conikost@gentoo.org>
* sci-chemistry/mdtraj: depend on <cython-3Sam James2023-08-131-1/+2
| | | | | Bug: https://bugs.gentoo.org/911646 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gelemental: drop 2.0.1Matthias Maier2023-07-302-49/+0
| | | | Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-chemistry/gelemental: add 2.0.2Matthias Maier2023-07-302-0/+48
| | | | Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-chemistry/dssp: drop 4.4.0Pacho Ramos2023-07-212-40/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.1Pacho Ramos2023-07-212-0/+55
| | | | | Closes: https://bugs.gentoo.org/910585 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Fix install on prefixPacho Ramos2023-07-201-1/+1
| | | | | | Thanks-to: hsk17 Bug: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: drop 4.2.2.1Pacho Ramos2023-07-202-32/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.0Pacho Ramos2023-07-202-0/+40
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Use PEP517 buildPacho Ramos2023-07-202-0/+123
| | | | | Closes: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: drop 2.5.0-r2Pacho Ramos2023-07-191-98/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Fix distutils-r1 usagePacho Ramos2023-07-191-7/+9
| | | | | | Thanks-to: Sam James Closes: https://bugs.gentoo.org/851588 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: add 2023.2Alexey Shvetsov2023-07-132-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2022.6Alexey Shvetsov2023-07-132-0/+336
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Stabilize 2021.7-r1 amd64, #906679Sam James2023-07-101-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: drop 2022.4, 2023Pacho Ramos2023-07-093-674/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: Needs to be rebuilt with cuda subslot changesPacho Ramos2023-07-099-9/+9
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>