Installing Python modules on Guix
On GNU Guix [1], software binaries are stored under /gnu/store/ which
is a read-only file system. Therefore, when installing a Python module, such as
gcvb [2], simply invoking pip install does not work as it can not
access the Python directories in /gnu/store/ for writing. In this post, I
tackle all the issues faced during the installation of the gcvb benchmarking
module but, it may help you install other Python modules as well.
Rather unknown outside of a restrained group of users, the gcvb module is not
available as a standalone package through Guix channels and can not be
installed using guix install python-gcvb. This means that, one needs to
manually write the Guix package definition for gcvb in order to be able to
install the module on Guix like in the case of any other custom package.
Defining gcvb as a Guix package
Dealing with dependencies
Before writing the definition of the gcvb module itself, I must deal with
its dependencies. gcvb requires two other Python modules to work, pyyaml and
dash-bootstrap-components. Usually, the dependency modules are listed in the
setupy.py file of the target module with the install_requires,
setup_requires, tests_require, extras_require keywords. Although, you may
discover other dependencies during the build phase of the package based on the
error messages you may get.
pyyaml
This module is directly available from the official Guix channel. As such, it can be installed it the usual way using
guix install python-pyyaml
Note that, the name of the packages corresponding to Python modules is usually preceded by python-.
dash-bootstrap-components
This module can not be directly installed using guix install. Nevertheless, it
is available through pypi.org. This makes possible to use
the guix import command to generate the corresponding Guix package
description. The -r option tells the command to do the same for all of its
dependencies as well.
guix import pypi dash-bootstrap-components -r
Eventually, I save the output of the previous command to a Scheme file, i. e.
gcvb.scm, for later use.
gcvb
At this point, I can define the gcvb package itself by adding the following
at the end of the gcvb.scm file.
(define-public gcvb (package (name "gcvb") (version "0.0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jm-cc/gcvb") (commit "a62cd85c5e631524fcade39542e992f5cec577fd"))) (sha256 (base32 "00qk7v9q9xl7qlgcgswb196fyb77n3rrg4nf9ia50ix4d0hycjzd")))) (build-system python-build-system) (propagated-inputs `(("PyYAML" ,python-pyyaml))) (native-inputs `(("python-dash-bootstrap-components" ,python-dash-bootstrap-components))) (home-page "https://github.com/jm-cc/gcvb") (synopsis "Python 3 module aiming at facilitating non-regression, validation and benchmarking of simulation codes") (description "gcvb (generate compute validate benchmark) is a Python 3 module aiming at facilitating non-regression, validation and benchmarking of simulation codes. gcvb is not a complete tool of continuous integration (CI). It is rather a component of the testing part of a CI workflow. It can compare the different metrics of your computation with references that can be a file, depends of the 'configuration' or are absolute.") (license license:x11)))
My package definition is based on the definition of the itsdangerous Python
package acquired using the guix import command as explained earlier. According
to [3], I declare the pyyaml dependency as a
propagated-input and the dash-bootstrap-components as a native-input.
Including the package to a channel
In order to make the gcvb package definition publicly available, I include it
into the guix-hpc channel.
The first step, is to clone the channel's repository:
git clone https://gitlab.inria.fr/guix-hpc/guix-hpc
Then, I put the gcvb.scm file into a directory named airbus created in the
root of the repository. For the definition file to be valid, I add the following
header to the file.
;;; This module extends GNU Guix and is licensed under the same terms, those ;;; of the GNU GPL version 3 or (at your option) any later version. ;;; ;;; Copyright © 2017, 2019, 2020 Inria (define-module (airbus gcvb) #:use-module (guix) #:use-module (guix git-download) #:use-module (guix hg-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages graph) #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-web) #:use-module (gnu packages xml) #:use-module (guix utils) #:use-module (srfi srfi-1))
Please refer to
https://gitlab.inria.fr/guix-hpc/guix-hpc/-/raw/master/airbus/gcvb.scm for
the complete gcvb.scm file.
Error 404 while building the dependencies
During the build phase of gcvb I have encountered several Not found errors.
These come from broken links to the source tarballs of the gcvb dependencies
automatically generated using guix import. My workaround is to replace all of
the broken links by copying the links to the packages from
pypi.org. Pay attention to the package versions. The
hashes must remain the same.
Errors while testing dependencies
By default, when a package is built, a series of tests is executed to check the
operation of the package. Some dependency packages of gcvb require for their
test phases to work the packages that are not build yet. Moreover, the latter
have the former as dependencies which creates unsatisfiable cyclic dependencies.
This make the tests of some of the gcvb dependencies fail. My temporary
workaround is to disable the test phase for the concerned packages (using the
(arguments '(#:tests? #f) directive) in order to be able to finish the
installation of all the dependencies.
Installation
To install the package, use
guix install gcvb -L guix-hpc/
where the -L option allows you to specify the path to a local Guix channel
repository. This is useful for testing new package definitions before actually
pushing them into the channel.
Using a manifest file
For those who do not want to work with another Guix channels, you can install gcvb from a single manifest file. Just take the gcvb.scm file and use the following command to install gcvb.
guix package -m gcvb.scm
