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* sci-biology/proda: EAPI bumpAndrew Ammerlaan2021-01-261-6/+7
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/imagej: version bump, EAPI bump, add keywordsAndrew Ammerlaan2021-01-263-43/+20
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/lattE-macchiato: drop dead packageAisha Tammy2021-01-264-300/+0
| | | | | | superseded by latte-int available on ::sage-on-gentoo Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* media-libs/embree-bin: version bump to 3.12.2Aisha Tammy2021-01-252-0/+56
| | | | | Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sys-cluster/lmod: add long descriptionAisha Tammy2021-01-252-2/+2
| | | | | Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sci-mathematics/scilab: only add -fallow-argument-mismatch if supportedAndrew Ammerlaan2021-01-253-3/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: merge fixes in 5.5.2 ebuild to the later versionsAndrew Ammerlaan2021-01-243-33/+60
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: revert ban of --as-neededFabio Rossi2021-01-241-4/+0
| | | | | | | | | | The linker flag was banned a lot of time ago, on amd64 I don't see problems at link- or run-time, so let's try without it. In case this commit might be reverted later. Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Closes: https://github.com/gentoo/sci/pull/1042 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: fix QA issuesFabio Rossi2021-01-241-1/+6
| | | | | Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: fix dependency needed for USE=mpiFabio Rossi2021-01-241-0/+1
| | | | | Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: bump to EAPI 7Fabio Rossi2021-01-241-1/+1
| | | | | Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: remove USE=bash-completionFabio Rossi2021-01-241-2/+3
| | | | | | | | Install unconditionally bash-completion file to avoid useless rebuilds. Fix also symlinks for bashcomp aliases. Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: fix linking to deprecated lapack functionsFabio Rossi2021-01-241-1/+1
| | | | | | | | Fix lapack dependency to have support for legacy functions to avoid "undefined reference to [dz]geqpf_" linking errors Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-mathematics/scilab: re-add previous version 5.5.2Fabio Rossi2021-01-2417-0/+998
| | | | | | | | As latest version 6.1.0 requires more work (missing deps in portage), re-add the old one. Ebuild is not mergeable yet. Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* licenses: add file for scilab-5.5.2Fabio Rossi2021-01-241-0/+519
| | | | | Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sys-cluster/lmod: add long descriptionAisha Tammy2021-01-242-1/+9
| | | | | Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sys-cluster/lmod: add proper formatted manpageAisha Tammy2021-01-243-5/+391
| | | | | Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sys-cluster/lmod: drop old versionAisha Tammy2021-01-242-127/+0
| | | | Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* sci-biology/germline: version bump, EAPI bumpAndrew Ammerlaan2021-01-243-45/+7
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/flexbar: version bump, cmake-utils --> cmakeAndrew Ammerlaan2021-01-243-41/+5
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/exonerate-gff3: remove keyword from live ebuildAndrew Ammerlaan2021-01-241-1/+1
| | | | | | | oops Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/exonerate-gff3: EAPI bumpAndrew Ammerlaan2021-01-242-34/+10
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/diamond: version bump 2.0.6, cmake-utils --> cmakeAndrew Ammerlaan2021-01-242-13/+4
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/dcm2niix: version bump, cmake-utils --> cmake,Andrew Ammerlaan2021-01-242-3/+3
| | | | | | | fix optfeature Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/codonw: EAPI bumpAndrew Ammerlaan2021-01-241-7/+6
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/breakdancer: remove pack, repo archived, last update 2015, does ↵Andrew Ammerlaan2021-01-242-34/+0
| | | | | | not sync Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/bam-readcount: cmake-utils --> cmake, EAPI bumpAndrew Ammerlaan2021-01-242-14/+6
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/assembly-stats: cmake-utils --> cmake, fix installAndrew Ammerlaan2021-01-241-9/+4
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/pytorch: correct protobuf-python dependencyAndrew Ammerlaan2021-01-241-1/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/Sibelia: cmake-utils --> cmakeAndrew Ammerlaan2021-01-241-5/+4
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-biology/SnpEff: fix installAndrew Ammerlaan2021-01-241-3/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/pytorch: bump to 1.7.1.Benda Xu2021-01-249-0/+413
| | | | | | | | | | | | | | | | | | | Add ROCm support for AMD GPUs. Remove fine-grained BLAS flags, use a general USE=blas and rely on eselect-ldso for runtime switch of blas libraries. merge USE=numpy into USE=python. Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Bug: https://bugs.gentoo.org/650804 Bug: https://github.com/gentoo/gentoo/pull/10724 Closes: https://github.com/justxi/rocm/issues/133 Closes: https://github.com/gentoo/sci/issues/1039 Closes: https://github.com/gentoo/sci/issues/1011 Package-Manager: Portage-3.0.12, Repoman-3.0.1 RepoMan-Options: --force Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* media-gfx/brlcad: add missing slashAndrew Ammerlaan2021-01-242-2/+2
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* media-libs/yocto-gl: version bump 3.3.0Andrew Ammerlaan2021-01-244-54/+40
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* media-libs/implicitmesher: update snapshotAndrew Ammerlaan2021-01-243-25/+32
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* media-gfx/brlcad: version bump 7.32.0Andrew Ammerlaan2021-01-248-351/+62
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* media-libs/imgui: version bump 1.80Andrew Ammerlaan2021-01-242-8/+10
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* media-libs/DualContouringSample: cmake-utils --> cmakeAndrew Ammerlaan2021-01-241-3/+3
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* sci-libs/miopen: quote variableAndrew Ammerlaan2021-01-241-1/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* dev-libs/half: fix headerAndrew Ammerlaan2021-01-241-1/+1
| | | | | Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
* package.use.mask: mask sci-libs/pytorch[mkl].Benda Xu2021-01-241-0/+5
| | | | | Bug: https://github.com/gentoo/sci/issues/1011 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-python/protobuf-python: add back 3.11.* for PyTorch.Benda Xu2021-01-213-0/+69
| | | | | | | | PyTorch depends on protobuf-3.11.* which is removed from ::gentoo. Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-libs/protobuf: add back 3.11.* for PyTorch.Benda Xu2021-01-216-0/+528
| | | | | | | PyTorch depends on protobuf-3.11.* which is removed from ::gentoo. Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-libs/miopen: unconditional use HIP.Benda Xu2021-01-211-1/+1
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-libs/miopen: high performance machine learning primitives.Benda Xu2021-01-213-0/+72
| | | | | | | | | Bug: https://bugs.gentoo.org/650804 Bug: https://github.com/gentoo/gentoo/pull/10724 Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Suggested-by: Wilfried Holzke <gentoo@holzke.net> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-util/rocm-clang-ocl: Clang OpenCL compilation wrapper.Benda Xu2021-01-213-0/+43
| | | | | | | | | | | | This is but a shell script wrapper. To be merged with dev-libs/rocm-opencl-runtime::gentoo. Bug: https://bugs.gentoo.org/650804 Bug: https://github.com/gentoo/gentoo/pull/10724 Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Suggested-by: Wilfried Holzke <gentoo@holzke.net> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-libs/half: half precision library.Benda Xu2021-01-213-0/+36
| | | | | | | | | | | This is a dependency of MIOpen. Bug: https://github.com/gentoo/gentoo/pull/10724 Bug: https://bugs.gentoo.org/650804 Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Suggested-by: Wilfried Holzke <gentoo@holzke.net> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-libs/rocBLAS: AMD library for BLAS on the ROCm platform.Benda Xu2021-01-214-0/+130
| | | | | | | | | | | | | To be considered landing on ::gentoo when dev-util/Tensile is available. Bug: https://bugs.gentoo.org/650804 Bug: https://github.com/gentoo/gentoo/pull/10724 Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Suggested-by: Wilfried Holzke <gentoo@holzke.net> Bug: https://github.com/justxi/rocm/issues/133 Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-util/Tensile: creating benchmark-driven backend library for GEMMsBenda Xu2021-01-213-0/+43
| | | | | | | | | | | | This ebuild is a working-in-progress that works, but having QA issues, such as installing a lot of data into python site directories. Bug: https://github.com/gentoo/gentoo/pull/10724 Bug: https://bugs.gentoo.org/650804 Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Suggested-by: Wilfried Holzke <gentoo@holzke.net> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* dev-libs/boost: add back 1.72.* for MIOpen.Benda Xu2021-01-216-0/+508
| | | | | | | | AMD MIOpen depends on boost 1.72.* which has been remove from ::gentoo. Suggested-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Package-Manager: Portage-3.0.12, Repoman-3.0.1 Signed-off-by: Benda Xu <heroxbd@gentoo.org>