You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
 
 
 
Horea Christian ab870a494b
dev-python/keyrings_alt: treeclean
2 days ago
.github/workflows .github/workflows: only run on push/PR 5 months ago
app-arch/libdeflate app-arch/libdeflate: add version 1.11 4 months ago
app-office/visidata app-office/visidata: enable py3.10 3 months ago
app-text/noweb app-text/noweb: drop UnusedInherits 9 months ago
app-vim/vim-gromacs app-vim/vim-gromacs: remove RedundantLongDescription 2 years ago
dev-cpp dev-cpp/castxml: moved to ::gentoo 4 weeks ago
dev-java/fits dev-java/jeuclid-core: treeclean 2 months ago
dev-lang dev-lang/terra: remove broken package without consumers 8 months ago
dev-libs dev-libs/optix: moved to ::gentoo 4 weeks ago
dev-ml/lacaml dev-ml/lacaml: add missing dep 1 year ago
dev-perl dev-perl/Bio-EnsEMBL: remove fundamentally broken package 8 months ago
dev-python dev-python/keyrings_alt: treeclean 2 days ago
dev-util dev-util/Tensile: moved to ::gentoo 7 months ago
dev-vcs dev-vcs/dandi-cli: updated distfile naming 2 days ago
docs virtual/{{c,}blas,lapack{,e}}: replaced by counterparts in ::gentoo. 3 years ago
eclass eclass/numeric-int64-multibuild.eclass: fix @ECLASS variable 2 years ago
licenses licenses: drop unused licenses 8 months ago
media-gfx/brlcad media-gfx/brlcad: version bump 7.32.4, many fixes 9 months ago
media-libs media-libs/charls: new package 1 month ago
metadata layout.conf: ban EAPI 6 9 months ago
net-misc/cernbox-client net-misc/cernbox-client: add 2.10.1.7389, drop 2.9.2.6206 3 months ago
profiles sci-libs/mlpack: treeclean, more recent version in ::guru 1 month ago
sci-astronomy/libthesky sci-astronomy/libthesky: relax dependency 8 months ago
sci-biology sci-biology/bidsschematools: add 0.5.1 2 days ago
sci-chemistry */*: virtual/jpeg deprecation 5 months ago
sci-electronics/minipro sci-electronics/minipro: version bump 0.5 2 months ago
sci-libs sci-libs/itk: add AdaptiveDenoising module 2 weeks ago
sci-mathematics */*: virtual/jpeg deprecation 5 months ago
sci-misc sci-misc: elmer-fem fix rpath and make compatible with qwt-6.2 4 weeks ago
sci-physics sci-physics/rivet: ESYSROOT and bracketed vars 3 weeks ago
sci-visualization sci-visualization/fsleyes-props: enable py3.10 3 months ago
scripts Drop repoman CI in favour of pkgcheck 5 months ago
sys-cluster/modules sys-cluster/lmod: lmod is now in ::gentoo 2 years ago
x11-libs/xview-bin x11-libs/xview-bin: drop UnusedInherits 9 months ago
x11-misc/envytools x11-misc/envytools: remove duplicate inherit of git-r3 2 years ago
.gitignore profiles: remove use.local.desc permanently 5 years ago
CONTRIBUTING.md *.md: update documentation: repoman --> pkgcheck and friends 5 months ago
README.md README.md: Added link for eselect install 2 weeks ago

README.md

The Gentoo Science Project Repository

pkgcheck contributions welcome chat on libera

This is an official mirror of the Gentoo Science ebuild repository, containing numerous scientific software packages.

See Project:Science for more information on the project.

Contents

  1. Installation
  1. Usage
  2. Contributing

Installation

As per the current Portage specification, ebuild repositories (a.k.a. overlays) can be managed via file collections under /etc/portage/repos.conf/, via the new plug-in sync system.

Eselect-repository Install

The overlay can be enabled via the repository extension of the Gentoo eselect utility.

emerge --ask --noreplace --verbose eselect-repository
eselect repository enable science

Eselect-repository Uninstall

To disable and remove the overlay, run:

eselect repository disable science
eselect repository remove science

Manual Install

To enable the overlay without the need for dedicated repository software, you need to have git installed:

emerge --ask --noreplace --verbose dev-vcs/git

Then you can simply download the science repository configuration file, science.conf:

wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
	-O /etc/portage/repos.conf/science

Manual Uninstall

To disable and remove the overlay, run:

rm /etc/portage/repos.conf/science
rm /var/db/repos/science -rf

Layman Install

You can also install the overlay via the layman overlay manager.

emerge --ask --noreplace --verbose app-portage/layman
layman --add science

Layman Uninstall

To delete the overlay, run:

layman --delete science

Using Packages from ::science

To start using the overlay you now only need to get the newest files, via:

emerge --sync science

To be able to install ::science packages you need to make sure that you are accepting the ~${ARCH} keyword for your respective architecture. This may already be the case globally on your system, and you can check whether this is the case by running:

grep "~$(portageq envvar ARCH)" /etc/portage/make.conf

If the above returns empty, you will need to instruct Portage to accept ~${ARCH} packages.

This can be done for ::science specifically:

mkdir -p /etc/portage/package.accept_keywords
printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/science

If the above fails with mkdir: cannot create directory ‘/etc/portage/package.accept_keywords’: File exists this means you are using a file and not a directory, and you can instead run:

printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords

Alternatively, and only if you know what you are doing, you can accept ~${ARCH} packages globally:

printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> /etc/portage/make.conf

The downside of this approach is potentially higher instability, the advantage is that often ::science packages require ~${ARCH} packages from ::gentoo as well.

Contributing

If you fork, we will merge!
We welcome new contributors and are happy to include new packages.

Areas to contribute

Resources

For a brief introduction please see our contributing guide. Further helpful resources are:

Additionally, please make sure to add the Science Project as an additional maintainer to any new packages you submit. For an example, take a look at the metadata for the Numba package - dev-python/numba/metadata.xml

Support

You can ask for help on Libera IRC in #gentoo-science. Alternatively you can report bugs on the Gentoo Bugzilla.