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* dev-python/astropy-healpix: remove unneeded dependencyAndrew Ammerlaan2022-01-161-2/+1
| | | | | | | this is based on the cxx healpix but does not require it Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask opennlp-maxent for removalAndrew Ammerlaan2022-01-161-0/+1
| | | | | | depends on dev-java/trove which is being removed from ::gentoo Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/llvmlite: bump version to 0.38.0YiyangWu2022-01-162-0/+61
| | | | | | | | | The llvm max slot is 11. >11 will cause compilation error Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Yiyang Wu <xgreenlandforwyy@gmail.com> Closes: https://github.com/gentoo/sci/pull/1136 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/cadquery-ocp: gles2 flag dropped from vtkAndrew Ammerlaan2022-01-161-1/+1
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fsl: drop oldAndrew Ammerlaan2022-01-153-371/+0
| | | | | | Closes: https://github.com/gentoo/sci/issues/974 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-visualization/surf-ice: drop unavailable flagAndrew Ammerlaan2022-01-151-2/+2
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/ngs: properly use the java eclassAndrew Ammerlaan2022-01-151-3/+3
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fastqc: drop useless blank lineAndrew Ammerlaan2022-01-151-1/+0
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/salmon: drop unavailable flagAndrew Ammerlaan2022-01-151-2/+2
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/pbcopper: drop unavailable flagAndrew Ammerlaan2022-01-151-2/+2
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/pbbam: drop unavailable flagAndrew Ammerlaan2022-01-151-2/+2
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-cpp/blitz: drop unavailable flagAndrew Ammerlaan2022-01-151-2/+2
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.use.mask: mask R and go flags on mlpackAndrew Ammerlaan2022-01-151-0/+6
| | | | | | | Closes: https://github.com/gentoo/sci/issues/1084 Closes: https://github.com/gentoo/sci/issues/1085 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-libs/mlpack: fix pytest-runner errorAndrew Ammerlaan2022-01-151-4/+10
| | | | | | Closes: https://github.com/gentoo/sci/issues/1086 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-mathematics/freefem++: drop conflicting flag mpiAndrew Ammerlaan2022-01-152-4/+4
| | | | | | | | conflicts with cxx Closes: https://github.com/gentoo/sci/issues/1126 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/minimap2: version bump 2.24, add python flagAndrew Ammerlaan2022-01-153-58/+64
| | | | | | Closes: https://github.com/gentoo/sci/issues/1125 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask jigsaw for removalAndrew Ammerlaan2022-01-151-0/+5
| | | | | | Closes: https://github.com/gentoo/sci/issues/1071 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/ngs: add missing dep on java compilerAndrew Ammerlaan2022-01-151-0/+1
| | | | | | Closes: https://github.com/gentoo/sci/issues/1134 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fastqc: version bump to 0.11.9Andrew Ammerlaan2022-01-155-109/+42
| | | | | | | add desktop shortcuts and stuff Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/pybedtools: bump to version 0.8.2Andrew Ammerlaan2022-01-152-23/+14
| | | | | | Closes: https://github.com/gentoo/sci/issues/983 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* profiles/updates: fix pkg moveAndrew Ammerlaan2022-01-151-1/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* profiles/updates: move sra_sdk to sra-toolsAndrew Ammerlaan2022-01-157-254/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/sra-tools: rename from sra_sdk, add version 2,11,3Andrew Ammerlaan2022-01-156-0/+226
| | | | | | Closes: https://github.com/gentoo/sci/issues/982 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/ncbi-vdb: add new dep of sra-toolsAndrew Ammerlaan2022-01-153-0/+58
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/ngs: add new dep of sra-toolsAndrew Ammerlaan2022-01-153-0/+55
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/fsl: add version 6.0.5Andrew Ammerlaan2022-01-142-0/+221
| | | | | | | No keywords, compile fails, need patches Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/fslpy: add version 3.8.1Andrew Ammerlaan2022-01-142-0/+40
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/trimesh: add version 3.9.42Andrew Ammerlaan2022-01-142-0/+66
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* Fixed thrust include path for rocm platformAntonin Riha2022-01-141-0/+1
| | | | | | Signed-off-by: Antonín Říha <riha.antonin@outlook.com> Closes: https://github.com/gentoo/sci/pull/1133 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/spm: cleanup oldAndrew Ammerlaan2022-01-143-76/+0
| | | | | | Closes: https://github.com/gentoo/sci/issues/896 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask quorum for removalAndrew Ammerlaan2022-01-141-0/+7
| | | | | | Closes: https://github.com/gentoo/sci/issues/833 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/jellyfish: fix configure phase, add missing depsAndrew Ammerlaan2022-01-141-8/+4
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask terra for removalAndrew Ammerlaan2022-01-131-0/+5
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask htsjdk for removalAndrew Ammerlaan2022-01-131-0/+4
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.use.mask: drop obsolete use maskAndrew Ammerlaan2022-01-131-5/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* layout.conf: ban EAPI 6Andrew Ammerlaan2022-01-131-2/+1
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* package.mask: mask jhdf5 for removalAndrew Ammerlaan2022-01-131-0/+2
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/pytorch-lightning: add new packageAndrew Ammerlaan2022-01-133-0/+45
| | | | | | Closes: https://github.com/gentoo/sci/issues/954 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* virtual/scalapack: cleanupAndrew Ammerlaan2022-01-132-24/+0
| | | | | | obsolete Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-libs/protobuf: cleanup old versionsAndrew Ammerlaan2022-01-1311-619/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-tcltk/togl: cleanup oldAndrew Ammerlaan2022-01-134-93/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-python/pybind11-stubgen: add version 0.10.4Andrew Ammerlaan2022-01-132-0/+20
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-mathematics/netgen: cleanup oldAndrew Ammerlaan2022-01-1311-1206/+0
| | | | | | | | | Closes: https://bugs.gentoo.org/670050 Closes: https://bugs.gentoo.org/502962 Bug: https://bugs.gentoo.org/688120 Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --force Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-mathematics/netgen: add version 6.2.2105Andrew Ammerlaan2022-01-134-1/+139
| | | | | | | | | | Bug: https://github.com/NGSolve/netgen/issues/72 Bug: https://github.com/NGSolve/netgen/issues/77 Closes: https://bugs.gentoo.org/155424 Closes: https://bugs.gentoo.org/756214 Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --force Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-astronomy/erfa: move new versions to ::gentooAndrew Ammerlaan2022-01-134-83/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* dev-libs/cudnn: move new versions to ::gentooAndrew Ammerlaan2022-01-133-43/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/abyss: move the new versions to ::gentooAndrew Ammerlaan2022-01-137-217/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* app-arch/libdeflate: version bump to 1.9Aisha Tammy2022-01-122-0/+29
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
* dev-libs/boost: remove duplicateAndrew Ammerlaan2022-01-1218-1001/+0
| | | | Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-libs/pytorch: cleanup oldAndrew Ammerlaan2022-01-125-957/+0
| | | | | | | | | | | | we finally have a working version of this again Closes: https://github.com/gentoo/sci/issues/1075 Closes: https://github.com/gentoo/sci/issues/1073 Closes: https://github.com/gentoo/sci/issues/1070 Closes: https://github.com/gentoo/sci/issues/953 Closes: https://bugs.gentoo.org/789807 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>