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* 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>
* sci-chemistry/votca: x86 stable wrt bug #846386Agostino Sarubbo2022-06-131-1/+1
| | | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-chemistry/votca: amd64 stable wrt bug #846386Agostino Sarubbo2022-06-121-1/+1
| | | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-chemistry/openbabel: fix build with GCC 12Sam James2022-06-122-0/+36
| | | | | Closes: https://bugs.gentoo.org/851510 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/molsketch: drop 0.4.1-r1Pacho Ramos2022-06-093-72/+0
| | | | | Closes: https://bugs.gentoo.org/830529 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molsketch: Needs to be rebuilt with openbabel subslot changesPacho Ramos2022-06-091-1/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: Keyword 2022.1 arm, #834865Sam James2022-06-021-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/dssp: Keyword 3.0.11 arm, #834865Sam James2022-06-021-2/+2
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/pymol: Fix desktop file, LICENSE and restrict valuesPacho Ramos2022-05-221-0/+98
| | | | | | | | Also port to eapi8 Thanks-to: Ulrich Müller Closes: https://bugs.gentoo.org/844991 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/vmd: drop 1.9.4_alpha51Pacho Ramos2022-05-202-271/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/vmd: add 1.9.4_alpha57Pacho Ramos2022-05-202-0/+271
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: [QA] use tc-check-openmp correctlyDavid Seifert2022-05-162-2/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/tinker: [QA] tc-has-openmp → tc-check-openmpDavid Seifert2022-05-141-2/+7
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gromacs: [QA] tc-has-openmp → tc-check-openmpDavid Seifert2022-05-1412-36/+33
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gromacs: dropped unused eclassAlexey Shvetsov2022-04-282-2/+2
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: add 2022.1Alexey Shvetsov2022-04-282-0/+339
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gelemental: add 2.0.1Matthias Maier2022-04-243-0/+67
| | | | Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-chemistry/openbabel: Resurect opebabel[python]Alexey Shvetsov2022-04-151-0/+104
| | | | | | | | | File ${FILESDIR}/openbabel-python.cmake was accidently removed by astrum in 3b032e0f3d0d837c2faf2051da6257844e7ced55 Closes: https://bugs.gentoo.org/837254 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/modeller: enable py3.10Alexey Shvetsov2022-04-081-3/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: enable py3.10Alexey Shvetsov2022-04-081-17/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/openbabel-perl: Remove last-rited packageAndreas Sturmlechner2022-04-054-102/+0
| | | | | Closes: https://bugs.gentoo.org/834261 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/votca-ctp: Remove last-rited packageAndreas Sturmlechner2022-03-303-87/+0
| | | | | Closes: https://bugs.gentoo.org/773175 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/mm-align: treecleanJakov Smolić2022-03-284-55/+0
| | | | | | Closes: https://bugs.gentoo.org/834301 Closes: https://bugs.gentoo.org/723194 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/procheck: [QA] fix tc-get* quotingSam James2022-03-201-3/+3
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/mustang: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/mopac7: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/moldy: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gperiodic: [QA] fix tc-get* quotingSam James2022-03-201-2/+2
| | | | | | This can cause build problems for e.g. 32-bit (gcc -m32 ...) Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/dssp: Keyword 4.0.4 x86, #834864Jakov Smolić2022-03-171-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/dssp: Bump to 4.0.4Pacho Ramos2022-03-132-0/+32
| | | | | | Closes: https://bugs.gentoo.org/834882 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: fix WhitespaceFoundSam James2022-03-102-3/+3
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/openbabel: Drop 2.4.1-r2Andreas Sturmlechner2022-03-074-268/+0
| | | | | | Bug: https://bugs.gentoo.org/834115 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/openbabel: Stabilize 3.1.1_p20210225 x86, #834115Jakov Smolić2022-03-071-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/openbabel: Stabilize 3.1.1_p20210225 amd64, #834115Jakov Smolić2022-03-071-2/+2
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>