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.
 
 
 
Benda Xu 7bcde49d0d
dev-python/protobuf-python: add back 3.11.* for PyTorch.
2 days ago
.github/workflows make workflows trigger daily 5 days ago
app-arch/libdeflate app-arch/libdeflate: version bump 4 months ago
app-office/visidata app-office/visidata: new package 2 weeks ago
app-text app-text/noweb: new dep 1 week ago
app-vim/vim-gromacs Second try to clean spaces in metadata.xml 3 years ago
dev-cpp dev-cpp/castxml: fix metadata 3 weeks ago
dev-java dev-java/flexdock: update homepage 3 days ago
dev-lang dev-lang/terra: remove unused test flag 4 days ago
dev-libs dev-libs/protobuf: add back 3.11.* for PyTorch. 2 days ago
dev-ml/lacaml dev-ml/lacaml: version bump, fix fetch and homepage 1 week ago
dev-perl dev-perl/BTLib: update homepage 3 days ago
dev-python dev-python/protobuf-python: add back 3.11.* for PyTorch. 2 days ago
dev-tcltk/togl dev-tcltk/togl: version bump to 2.0 3 months ago
dev-util dev-util/rocm-clang-ocl: Clang OpenCL compilation wrapper. 3 days ago
docs virtual/{{c,}blas,lapack{,e}}: replaced by counterparts in ::gentoo. 1 year ago
eclass eclass/ remove unused eclass 4 days ago
licenses license/ remove unused licenses 4 days ago
media-gfx/brlcad media-gfx/brlcad: use https homepage 1 week ago
media-libs media-libs/mmg: drop old version 1 month ago
metadata metadata/news/2020-12-20-visa-packages-removed 1 month ago
net-misc/cernbox-client net-misc/cernbox-client: Drop old version. 2 weeks ago
profiles dev-java/hdf-java: remove obsolete pack 4 days ago
sci-astronomy sci-astronomy/wcslib: landed on to ::gentoo. 2 months ago
sci-biology sci-biology/nitime: bump python compat 3 days ago
sci-chemistry sci-chemistry/gamess: update homepage 3 days ago
sci-electronics/minipro sci-electronics/tnt: drop dead package 3 months ago
sci-libs sci-libs/miopen: unconditional use HIP. 2 days ago
sci-mathematics sci-mathematics/ripser: update homepage 3 days ago
sci-misc sci-misc/foma: remove pack, duplicate of dev-libs/foma::gentoo 3 days ago
sci-physics sci-physics/fullprof-bin: use https 4 days ago
sci-visualization sci-visualization/fsleyes: fix postinst/postrm phases 3 days ago
scripts dev-lang/path64: dropped package broken for non-bootstrap install 2 weeks ago
sys-apps/ndctl sys-apps/ndctl: drop old version 1 month ago
sys-cluster sys-cluster/lmod: version bump to 8.4.20 1 week ago
sys-kernel/dkms sys-kernel/dkms: dynamic kernel module support 1 month ago
virtual/scalapack virtual/blacs: remove obsolete virtual 2 weeks ago
x11-libs x110libs/tr: remove pack, upstream has dissapeared 1 week ago
x11-misc/envytools x11-misc/envytools: add dated ebuild + EAPI 7 4 days ago
.gitignore profiles: remove use.local.desc permanently 3 years ago
.travis.yml Travis CI - add pkgcheck scan 3 months ago
CONTRIBUTING.md Fix broken Markdown headings 3 years ago
README.md readme add links to contribute 3 days ago

README.md

The Gentoo Science Project Repository

pkgcheck repoman contributions welcome chat on freenode

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

Manual Install

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

To enable the overlay without the need for additional software, you first need to have git installed:

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

Then you need to add the science repository configuration by downloading the science.conf file:

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

Manual Uninstall

To uninstall the overlay, simply 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 --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

find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done

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 Freenode IRC in #gentoo-science. Alternatively you can report bugs on the GitHub issues page.