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* sci-chemistry/psi: update EAPI 7 -> 8David Seifert2024-11-032-3/+25
| | | | | Closes: https://bugs.gentoo.org/886127 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gromacs: Re-enable man-pagesAlexey Shvetsov2024-10-251-0/+2
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop upstreamed patchAlexey Shvetsov2024-10-252-42/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Sync patch with upstreamed oneAlexey Shvetsov2024-10-202-2/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Correct depend when openmp is enabledAlexey Shvetsov2024-10-198-0/+32
| | | | | Closes: https://bugs.gentoo.org/927990 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Update live versionAlexey Shvetsov2024-10-193-3/+55
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/mopac7: treecleanArthur Zamarin2024-10-184-113/+0
| | | | | | Closes: https://bugs.gentoo.org/877105 (pkgremoved) Closes: https://bugs.gentoo.org/927389 (pkgremoved) Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/gromacs: drop 2024.1, 2024.2Alexey Shvetsov2024-10-183-676/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2024.3Alexey Shvetsov2024-10-182-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop 2023.4Alexey Shvetsov2024-10-182-338/+0
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2023.5Alexey Shvetsov2024-10-182-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/molmol: drop 2k_p2-r8Pacho Ramos2024-10-171-102/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Really disable parallel buildPacho Ramos2024-10-171-1/+7
| | | | | | | | | Enforce the disabling of parallel build, this also allows to drop the ugly upstream delays to make it build. Closes: https://bugs.gentoo.org/880621 Closes: https://bugs.gentoo.org/941488 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.10Pacho Ramos2024-10-172-0/+56
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: drop 4.4.4.1Pacho Ramos2024-10-172-55/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.8Pacho Ramos2024-10-172-0/+56
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Multiple bugfixesPacho Ramos2024-09-287-0/+485
| | | | | | | | | | | | | | | | | Upstream fixes for multiple bugs, also fixing python 3.12 and numpy2 compat, and fixing LTO building. Format-security patch looks to not be needed anymore (at least I couldn't reproduce the problem). If the problem reappears, please report the bug to upstream to follow its progress properly. Use icon from the pymol tarball and update desktop file. Update ebuild to try to run the tests, but keep them restricted for now as they keep failing. Bug: https://bugs.gentoo.org/932127 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemical-mime-data: drop 0.1.94-r4 and it's patchesFilip Kobierski2024-09-257-198/+0
| | | | | | Signed-off-by: Filip Kobierski <fkobi@pm.me> Closes: https://github.com/gentoo/gentoo/pull/37842 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/GromacsWrapper: remove empty variablesFilip Kobierski2024-09-251-3/+1
| | | | | Signed-off-by: Filip Kobierski <fkobi@pm.me> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/GromacsWrapper: drop 0.8.4Filip Kobierski2024-09-252-41/+0
| | | | | Signed-off-by: Filip Kobierski <fkobi@pm.me> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/chemical-mime-data: fix pkgcheck issuesFilip Kobierski2024-09-251-4/+2
| | | | | Signed-off-by: Filip Kobierski <fkobi@pm.me> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/mopac7: mark as LTO-unsafeEli Schwartz2024-09-091-1/+7
| | | | | | | Unmaintained, treecleaning candidate. Still, it is unsafe so say so. Closes: https://bugs.gentoo.org/927389 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/pymol: mark as LTO-unsafeEli Schwartz2024-09-051-0/+5
| | | | | Closes: https://bugs.gentoo.org/933235 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/pymol: drop a bunch of dependencies to runtime-onlyEli Schwartz2024-09-051-6/+7
| | | | | | | | | | | | They aren't needed to run setup.py (whether via gpep517 or otherwise). They are only used by the runtime code. The distinction between dependency types is sometimes seen as a bit academic, but it matters for --buildpkgonly. This is especially useful as one of the runtime-only dependencies will, in turn, depend on python[tk], and moving it out of DEPEND means the package can be test-compiled with --buildpkgonly, without rebuilding and reinstalling python. Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/tinker: mark as LTO-unsafeEli Schwartz2024-08-051-1/+6
| | | | | | | | At least, the tests fail if you use LTO. So it is apparently unsafe, though unsafe here means the results you get are wrong! Closes: https://bugs.gentoo.org/878059 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/votca: sync live ebuildPacho Ramos2024-07-311-3/+3
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/votca: support py3.12Pacho Ramos2024-07-311-2/+2
| | | | | Closes: https://bugs.gentoo.org/929764 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: sync live ebuildPacho Ramos2024-07-301-4/+8
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: enable py3.12Pacho Ramos2024-07-301-1/+1
| | | | | Closes: https://bugs.gentoo.org/929759 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/propka: add 3.5.1Pacho Ramos2024-07-302-0/+29
| | | | | Closes: https://bugs.gentoo.org/929761 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/procheck: treecleanArthur Zamarin2024-07-195-182/+0
| | | | | Bug: https://bugs.gentoo.org/928067 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/aqua: treecleanArthur Zamarin2024-07-194-191/+0
| | | | | Bug: https://bugs.gentoo.org/928068 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/xyza2pipe: treecleanArthur Zamarin2024-07-194-211/+0
| | | | | Bug: https://bugs.gentoo.org/934232 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/namd: treecleanArthur Zamarin2024-07-195-271/+0
| | | | | | | | Bug: https://bugs.gentoo.org/686856 Bug: https://bugs.gentoo.org/686858 Bug: https://bugs.gentoo.org/686860 Bug: https://bugs.gentoo.org/934228 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/autodock_vina: Stabilize 1.2.5 amd64, #935909Arthur Zamarin2024-07-131-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/autodock_vina: fix build w/ boost-1.85Sam James2024-07-122-0/+22
| | | | | Closes: https://bugs.gentoo.org/932237 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/vmd: Fix compat with numpy-2 and don't mess with linkingPacho Ramos2024-07-111-0/+263
| | | | | | | | | | | Ebuild forcing linking flags break some utils, point to new location for numpy2 include files Closes: https://bugs.gentoo.org/929763 Thanks-to: he.ousia Closes: https://bugs.gentoo.org/835604 Thanks-to: Hypoon Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Stabilize 2k_p2-r9 amd64, #935856Jakov Smolić2024-07-111-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/wxmacmolplt: drop 7.5-r1Pacho Ramos2024-07-053-60/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/xds-bin: drop 20170930Arthur Zamarin2024-07-052-49/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/xds-bin: add 20240831Markus Meier2024-07-052-1/+59
| | | | | | Bug: https://bugs.gentoo.org/934365 Authored-by: Markus Meier <markus.meier74@gmail.com> Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/openbabel: drop 3.1.1_p20210225Andreas Sturmlechner2024-06-291-280/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* */*: delete some utterly bogus remote-idsEli Schwartz2024-06-281-3/+0
| | | | | | | | | | | | Added in a global rewrite that was apparently not tested as well as it ideally could have been, since it added some pretty wild changes. Non-exhaustive -- I caught these in passing and haven't really vetted the tree. Fixes: 67064ef687e8b3a61f5a4698ae1b029e2e70822c Fixes: 92715265f5e37292e57673f39c5372a268778c44 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/chemex: fix mysterious overdependency on tomliEli Schwartz2024-06-272-2/+0
| | | | | | | | | | | | | | | | | In upstream version 2024.02.09 some "refactoring" was done: https://github.com/gbouvignies/ChemEx/commit/97d6896836e4d5c23e0eff7b1dc1646e3f69ac9e It dropped support for python 3.10 and required the stdlib tomllib rather than trying tomli. And sure enough, when 2024.02.16 was added to ::gentoo, it excluded 3.10 support for this exact reason. But it didn't state why, and it didn't remove the out of date tomli dependency. Remove it now. Bug: https://bugs.gentoo.org/929756 Fixes: c5f2c621136bfc67183c410a60713763fd0f7bdf Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Add ~riscv keywordAlexey Shvetsov2024-06-234-4/+4
| | | | | | Tested on visionfive2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/threeV: EAPI 6 -> 8Arthur Zamarin2024-06-211-12/+5
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/chemex: drop 2022.3.6, 2024.02.16Pacho Ramos2024-06-163-90/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2024.05.3Pacho Ramos2024-06-162-0/+46
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/elem: unkeyword 1.0.3-r3 for sparcArthur Zamarin2024-06-131-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/elem: EAPI 6 -> 8Arthur Zamarin2024-06-131-2/+2
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>