Guix science packages

This GNU Guix channel provides recent versions of scientific software, which cannot be included upstream.

See Specifying Additional Channels in the Guix manual for instructions how to add it to your installation or simply add the following snippet to your channels.scm:

(channel
  (name 'guix-science)
  (url "https://codeberg.org/guix-science/guix-science.git")
  (introduction
   (make-channel-introduction
    "b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"
    (openpgp-fingerprint
     "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"))))

Binary substitutes for x86_64-linux are available from https://guix.bordeaux.inria.fr, see Getting Substitutes from Other Servers in the official manual. The signing key can be imported using:

$ guix archive --authorize <<EOF
(public-key
 (ecc
  (curve Ed25519)
  (q #89FBA276A976A8DE2A69774771A92C8C879E0F24614AAAAE23119608707B3F06#)))
EOF

Licensing

Like Guix itself, Guix-Science is distributed under the terms of the GNU General Public License, version 3 or (at your option) any later version.

A copy of the license is included in the COPYING file, and each source file contains an SPDX header confirming its license.

Copyright is held by the diverse group of copyright holders for the many contributions made to Guix-Science over time.

Contributing

Contributors agree to provide their changes under the same license as the rest of Guix-Science—see licensing.

We accept software fulfilling the following criteria:

• Free and open source. Use guix-science-nonfree otherwise.
• Related to scientific research or teaching.
• Not upstreamable to Guix proper per their rules—e.g., due to excessive vendoring.

• Built entirely from source, with the following exceptions:

  1. JavaScript code is allowed to be taken as-is, including pre-built/minified JavaScript, as a pragmatic way out of the JavaScript dystopia;
  2. Packages such as build systems and compilers that have no known bootstrap path may be built starting from a binary seed (a pre-built binary of said compiler or build system).

Submissions of unfinished packaging attempts are welcome as well, as there is a good chance that others can help finish the work. Please prefix pull requests for unfinished contributions with WIP.

When obtaining a fresh checkout of this repository, run the following command:

guix git authenticate b1fe5aaff3ab48e798a4cce02f0212bc91f423dc "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"

The command authenticates your checkout and installs Git hooks such that git pull and git push automatically authenticate it from there on.

Hacking this repository

Package definitions are stored in guix-science/packages/*.scm, each .scm file being a Guile module containing several package definitions.

A new package definition can be added in the relevant module.

For example, after adding a package definition such as:

(define-public my-package-variable
  (package
    (name "my-package-name")
    ... ))

can be built using the following command:

guix build -L /path/to/guix/science/checkout my-package-name

Note that generally the same string is used for the package name and the Guile variable that points to the package object.

You can learn more about working with a channel in the Guix manual.

When submitting a new package or a modification to a package, make sure to run:

guix lint -L /path/to/your/guix/science/checkout <package-name>

This repository follows Guix's Packaging Guidelines, refer to them when contributing.

In particular, commit messages follow the GNU Coding Standards as in Guix upstream. The title format should be module_name: Add package_name. for newly added packages or module_name: package_name: Description. for package modifications. The message should list each modified file, mentioning each modified/added variable with a description of the modifications.

Please make sure that explanations about the code are included in the code as comments and not in Git log descriptions.

As a first example, this would be the commit message when adding the hello package in the utils module located at guix-science/packages/utils.scm:

utils: Add hello.

* guix-science/packages/utils.scm (hello): New variable.

This would be the commit message when updating the previously added hello package to version 1.2.3:

utils: hello: Update to 1.2.3.

* guix-science/packages/utils.scm (hello): Update to 1.2.3.

Please check this repository's commit log for further examples.

Deprecation policy

When a package is broken for more than one month, it can be deprecated and removed from the repository.

The deprecation mechanism is the following:

• Open an PR removing the deprecated package. Don't mark it as WIP: so team members are notified.
• Add a deprecation tag to the PR.
• Add a due date -- one month from the creation of the PR.
• After the due date, if the package has not been fixed, it will be effectively removed (the PR will be merged).

If you maintain another channel depending on Guix-Science, please consider joining the companion team.