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* sci-chemistry/votca-xtp: version bumpChristoph Junghans2021-09-192-0/+52
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/votca-csg: version bumpChristoph Junghans2021-09-192-0/+89
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/gromacs: Check patchesAlexey Shvetsov2021-09-151-6/+1
| | | | | Package-Manager: Portage-3.0.23, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: version bumpAlexey Shvetsov2021-09-152-0/+363
| | | | | Package-Manager: Portage-3.0.23, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/mdtraj: Fix DISTUTILS_USE_SETUPTOOLSJakov Smolić2021-09-131-2/+1
| | | | | Closes: https://bugs.gentoo.org/809767 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* **/metadata.xml: Replace http by https in DOCTYPE elementUlrich Müller2021-09-1165-65/+65
| | | | | Bug: https://bugs.gentoo.org/552720 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-chemistry/dssp: Bump to 3.0.11Pacho Ramos2021-09-022-0/+43
| | | | | | | | | | It is the latest version that seems to work with gmx do_dssp from my tests, also the one packaged in Fedora currently Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Needs boost with zlib and bzip2 supportPacho Ramos2021-09-021-1/+1
| | | | | | Closes: https://bugs.gentoo.org/802417 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Needs boost with zlib and bzip2Pacho Ramos2021-09-021-1/+1
| | | | | Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Fix boost compat for dssp-2Pacho Ramos2021-09-022-0/+42
| | | | | | | | | dssp-2 is still needed by gromacs, try to keep it whenever possible then Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Bump to 4.0.1Pacho Ramos2021-09-022-0/+34
| | | | | | | | Closes: https://bugs.gentoo.org/679142 Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Take the packagePacho Ramos2021-09-021-4/+3
| | | | | | | I use it a lot from gromacs Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/mars: Remove last-rited packageJakov Smolić2021-08-303-52/+0
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/gromacs: Needs to be rebuilt with hwlocPacho Ramos2021-08-253-3/+3
| | | | | Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/bodr: Port to EAPI 8Jakov Smolic2021-08-141-11/+4
| | | | | | Closes: https://github.com/gentoo/gentoo/pull/21980 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/easychem: Port to EAPI 8Jakov Smolic2021-08-141-8/+12
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/mustang: Port to EAPI 8Jakov Smolic2021-08-142-10/+5
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/mopac7: Port to EAPI 8Jakov Smolic2021-08-141-7/+10
| | | | | | Closes: https://bugs.gentoo.org/454896 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/theseus: Port to EAPI 8Jakov Smolic2021-08-141-13/+15
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: workaround build failure with GCC 11Sam James2021-07-271-1/+4
| | | | | Closes: https://bugs.gentoo.org/790023 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/votca-xtp: version bumpChristoph Junghans2021-07-183-0/+53
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.2 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/votca-csg: version bumpChristoph Junghans2021-07-182-0/+89
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.2 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/vmd: PYTHON_MULTI_USEDEP -> PYTHON_USEDEPDavid Seifert2021-07-171-2/+2
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gromacs: PYTHON_MULTI_USEDEP -> PYTHON_USEDEPDavid Seifert2021-07-175-10/+10
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/chemex: PYTHON_MULTI_USEDEP -> PYTHON_USEDEPDavid Seifert2021-07-171-7/+7
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Drop oldPacho Ramos2021-07-082-72/+0
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Version bumpPacho Ramos2021-07-082-0/+72
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/tinker: add pkgconfig or pkgconfig-referenced libs depsSam James2021-06-181-4/+5
| | | | | | | | | | Add dependencies for either virtual/pkgconfig, move it into BDEPEND where applicable, or add dependencies for libraries we're trying to find with pkgconfig. Package-Manager: Portage-3.0.18-prefix, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/dssp: Depend on dev-libs/boost:=[threads(+)]David Seifert2021-06-181-2/+2
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/autodock_vina: Depend on dev-libs/boost:=[threads(+)]David Seifert2021-06-181-1/+1
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/gromacs: Fix manual useAlexey Shvetsov2021-06-185-33/+52
| | | | | | Closes: https://bugs.gentoo.org/796497 Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: drop oldAlexey Shvetsov2021-06-185-1424/+0
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Allow to download manual instead of building itAlexey Shvetsov2021-06-1710-200/+279
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Needs cuda_profiler_api.h to buildPacho Ramos2021-06-153-3/+3
| | | | | | | | | | | | | | | | | Otherwise it fails with: /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2/src/gromacs/ gpu_utils/gpu_utils.cu:50:10: fatal error: cuda_profiler_api.h: No such file or directory 50 | #include <cuda_profiler_api.h> | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. CMake Error at libgromacs_generated_gpu_utils.cu.o.Gentoo.cmake:222 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-2021.2/work/gromacs-2021.2_float/src/ gromacs/CMakeFiles/libgromacs.dir/gpu_utils/./libgromacs_generated_gpu_utils.cu.o Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-libs/cbflib & sci-chemistry/rasmol: remove last-rited packagesJoonas Niilola2021-06-067-280/+0
| | | | | | | Closes: https://bugs.gentoo.org/788508 Closes: https://bugs.gentoo.org/668568 Closes: https://bugs.gentoo.org/721998 Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-chemistry/votca-ctp: subscribe to sci-libs/gsl subslotSam James2021-06-021-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/theseus: subscribe to sci-libs/gsl subslotSam James2021-06-021-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/numbat: subscribe to sci-libs/gsl subslotSam James2021-06-021-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Fix pkgcheck errorAlexey Shvetsov2021-06-0210-10/+10
| | | | | Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Version bumpAlexey Shvetsov2021-06-022-0/+351
| | | | | Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gmxapi: Remove last-rited pkgMichał Górny2021-05-313-72/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Drop oldPacho Ramos2021-05-302-109/+0
| | | | | Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Needs glu libraryPacho Ramos2021-05-301-0/+1
| | | | | | | Closes: https://bugs.gentoo.org/792600 Thanks-to: Agostino Sarubbo Package-Manager: Portage-3.0.19, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gelemental: [QA] Disable static librariesDavid Seifert2021-05-281-3/+6
| | | | | Closes: https://bugs.gentoo.org/792603 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/pymol: apbs_tools.py is not createdPacho Ramos2021-05-201-10/+12
| | | | | | | | as apbs package was dropped from the tree Closes: https://bugs.gentoo.org/790629 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2021-05-162-0/+112
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/autodock_vina: Fix build w/ boost-1.69Andreas Sturmlechner2021-05-161-4/+3
| | | | | | Closes: https://bugs.gentoo.org/789702 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/gromacs: fix cmake_src_make -> cmake_src_compileSam James2021-05-1110-10/+10
| | | | | | cmake_src_make was removed in cmake.eclass. Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: remove ALLARCHESSam James2021-05-111-1/+0
| | | | | | | | This package compiles (a lot of) C++, hence not suitable for ALLARCHES. ALLARCHES is left for architecture-independent data files or, possibly, e.g. shell scripts, Python, etc. Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/modeller: fix function/phase declaration styleSam James2021-05-041-3/+3
| | | | | Package-Manager: Portage-3.0.18-prefix, Repoman-3.0.3 Signed-off-by: Sam James <sam@gentoo.org>