Developer information

This page contains information about GEMSEO development and how to contribute to it. The source code of GEMSEO is available on gitlab, this is the place where code contributions shall be submitted. Note also that it is required to accompany any contribution with a Developer Certificate of Origin, certifying that the contribution is compatible with GEMSEO software licence.

We aim to have industrial quality standards for software, in order to:

  • have a good and running software,

  • be confident about it,

  • facilitate collaborative work with the team,

  • facilitate distribution to our partners.

To meet these goals, we use best practices described below, these practices are not optional, they are fully part of the development job.

Quick start

First time setup:

  • Clone the repository:

git clone
  • Install the Requirements.

  • From the root of the git clone, run the tests for Python 3.9 and create a development environment under .tox/py39:

tox -e py39 --develop
  • Run the checks:

tox -e check


We use tox for handling the environments related to the development, be it for coding, testing, documenting, checking … This tool offers a simplified and high level interface to many ingredients used in development, while providing reproducible and isolated outcomes that are as much independent as possible of the platform and environment from which it is used.

All the settings of tox are defined in the file tox.ini. It contains the descriptions of the environments:

  • version of Python to use,

  • packages to install,

  • environment variables to set or pass from the current environment,

  • commands to execute.

All the directories created by tox are stored under .tox next to tox.ini. In particular, .tox contains the environments in directories named after the environments.


Make sure Python 3 is installed, preferably 3.9.

Install pipx first:

python -m pip install --user pipx
python -m pipx ensurepath

You may need to log out and back in for the system path update to be taken into account.

Then install tox and pre-commit:

pipx install tox
pipx install pre-commit

Finally, make sure that graphviz is installed (for rendering graphs).

How to use tox

The environments created by tox and their usage are described in the different sections below. In this section we give the common command line usages and tips.

Create and execute the environment named env and run its commands with:

tox -e env

The first invocation of this command line may take some time to proceed, further invocations will be faster because tox shall not create a new environment from scratch unless, for instance, some of the dependencies have been modified.

You may run (sequentially) more than one environment with:

tox -e env,env2,env3

Recreate an existing environment with:

tox -e env -r

This may be necessary if an environment is broken or if tox cannot figure out that a dependency has been updated (for instance with dependencies defined by a git branch).

Activate the tox environment named env with:

  • On Linux and MacOS:

source .tox/env/bin/activate
  • On Windows:


Activating environments may be useful for instance to investigate a particular issue that happens in a specific environment and not others. You may modify an activated environment just like any other environment, in case of trouble just recreate it. Be aware that the environment variables defined in tox.ini will not be set with a manually activated environment.

Show available environments with:

tox -a

Use a double -- to pass options to an underlying command, for example:

tox -e env -- ARG1 --opt1

Not all the environments allow this feature, see the specific topics below for more information.


Coding environment

Create a development environment:

tox -e py39 --develop

This will create an environment based on Python 3.9 with GEMSEO installed in editable mode, With an editable installation, GEMSEO appears installed in the development environment created by tox, but yet is still editable in the source tree.


You do not need to activate this environment for coding into GEMSEO.

Coding Style

We use the pep8 convention. The checking and formatting of the source code is done with ruff. A git commit shall have no checkers violations.

All these tools are used:

  • either automatically by the git hooks when creating a commit,

  • or manually by running tox -e check.

Coding guidelines

String formatting

Do not format strings with + or with the old printf-style formatting: format strings with format() (documentation).


Loggers shall be defined at module level and named after the module with:

LOGGER = logging.getLogger(__name__)

This means that logger names track the package/module hierarchy, and it’s intuitively obvious where events are logged just from the logger name.

Error messages

Error messages will be read by humans: they shall be explicit and valid sentences.


Use StrEnum from the strenum package for creating collections of constants that are compatible with strings. This allows to easily work with non-Python API like REST.



We use the gitflow for managing git branches. For the daily work, this basically means that evolutions of GEMSEO are done in feature branches created from the develop branch and merged back into it when finished.

Initial setup

  • Create your fork of the gemseo repository on

  • Clone your fork to your local machine:

    • git clone <url of your fork>

  • Go to the directory of your fork.

  • Add the reference upstream repository to you fork with:

    • git remote add upstream

  • Get access to the IRT CI:

    • from your account on,

    • go to Settings > CI/CD and expand the Runners section,

    • under Specific runners, copy the registration token and send it to a maintainer.

Working on a new feature
  • Update your local copy of the upstream repository:

    • git fetch upstream

  • Create a new feature branch on your local clone from the up to date upstream develop branch:

    • git checkout upstream/develop -b my_new_feature_branch

  • Add commits to your feature branch.

  • On a regular basis (ideally everyday), keep your feature branch up to date with the upstream evolution of the develop branch so to make the future merge into develop easier:

    • git fetch upstream

    • git rebase upstream/develop

  • When rebasing turns to be to cumbersome, you may use merge:

    • git rebase --abort

    • git merge upstream/develop

  • Push your current local feature branch to your fork at least once a day:

    • git push origin HEAD

  • Once pushed, the gitlab CI will run the tests on your branch, you will receive an email notification in case of failure.

Finishing a feature
  • When your feature branch is ready to be merged in the upstream develop branch, your branch shall become a merge request (MR).

  • If applicable, add a changelog fragment that will be later inserted into the changelog. To do so, create one or more files named after the issue number and kind of change (added, changed, deprecated, fixed, removed or security), for instance 123.fixed.rst, in changelog/fragments.

  • MR basic information.

  • How to create a MR.

  • Assign the MR to a maintainer (AntoineD by default) which will handle the choice of the reviewers (discussed during the scrum meeting).

  • Set the milestone.

  • Set the issue relating or closing the MR, if any.

  • If for some reasons the branch of the MR requires more work, the MR may be set to Draft.

  • If a review discussion goes beyond the scope of a branch, one or more review threads of a MR may be turned into a new issue to be resolved in a future branch.

  • If a review thread has not been resolved by a new commit to the reviewed branch and shall not be dealt with in a new issue, it shall be marked as resolved by the reviewer.

  • If changes have been pushed to the branch of a MR, the reviewers shall be notified.

  • When all the MR discussion threads are resolved:

    • The reviewers shall approve the MR,

    • The MR creator shall ask the branch to be merged.

Reviewing a MR
  • You can choose how the changes of the MR branch are displayed.

  • You may leave reviews or comments on one or more lines.

  • You may make code suggestions that could be committed as is the reviewed branch.

  • Once done, you shall submit your review.

  • You shall check that your review comments have been addressed, if so you shall mark them as resolved.

  • When all the reviews have been resolved, you shall approve the MR.

Git hooks

When a commit is being created, git will perform predefined actions:

  • remove the trailing whitespaces,

  • fix the end of files,

  • check toml, yaml and json files are well formed,

  • check that no big file is committed,

  • check bad symbolic links,

  • check or fix some of the python docstrings formatting,

  • fix the Python import order,

  • fix the Python code formatting,

  • check for Python coding issues (see Coding Style),

  • fix some of the above coding issues.

  • fix outdated Python syntax,

  • check the commit message (see Commit message),

  • check for forbidden print() usage,

  • check for misused logging formatting,

  • check for .rst files issues.

  • check or fix license headers,

  • check for docstrings formatting,

  • check for docstrings coverage,

Those actions will eventually modify the files about to be committed. In this case your commit is denied and you have to check that the modifications are OK, then add the modifications to the commit staged files before creating the commit again.

Commit message

We use conventional commits for writing clear and useful git commit messages. The commit message should be structured as follows:

<type>(optional scope): <description>

[optional body]

[optional footer(s)]


  • <type> defines the type of change you are committing

    • feat: A new feature

    • fix: A bug fix

    • docs: Documentation only changes

    • style: Changes that do not affect the meaning of the code

    • refactor: A code change that neither fixes a bug nor adds a feature

    • perf: A code change that improves performance

    • test: Adding missing tests or correcting existing tests

    • build: Changes that affect the build system or external dependencies

    • ci: Changes to our CI configuration files and scripts

  • (optional scope) provide additional contextual information and is contained within parentheses

  • <description> is a concise description of the changes, imperative, lower case and no final dot

  • [optional body] with the motivation for the change and contrast this with previous behavior

  • [optional footer(s)] with information about Breaking Changes and reference issues that this commit closes

You may use commitizen to easily create commits that follow conventional commits. Install it with:

pip install commitizen --user

Run it and and let it drive you through with:

cz commit

Commit message examples:

feat(study): open browser when generating XDSM
fix(scenario): xdsm put back filename arg

Commit best practices

The purpose of these best practices is to ease the code reviews, commit reverting (rollback changes) bisecting (find regressions), branch merging or rebasing.

Write atomic commits

Commits should be logical, atomic units of change that represent a specific idea as well as its tests. Do not rename and modify a file in a single commit. Do not combine cosmetic and functional changes in a single commit.

Commits history

Try to keep the commit history as linear as possible by avoiding unnecessary merge commit. When possible, prefer rebasing over merging, git can help to achieve this with:

git config pull.rebase true
git config rerere.enabled true
Rework commit history

You may reorder, split or combine the commits of a branch. Such history modifications shall be done before the branch has been pushed to the main repository.


Avoid commits that break tests, only push a branch that passes all the tests for py39 on your machine.


Testing is mandatory in any engineering activity, which is based on trial and error. All developments shall be tested:

  • this gives confidence to the code,

  • this enables code refactoring with mastered consequences: tests must pass!

Tests writing guidelines

We use pytest for writing and executing all the GEMSEO tests. Older tests were written with the unittest module from the Python standard library but newer tests shall be written with pytest.


Follow the Arrange, Act, Assert, Cleanup steps by splitting the testing code accordingly. Limit the number of assertions per test functions in a consistent manner by writing more test functions. Use the pytest fixtures or import the GEMSEO ones in a _conftest.py_ file:

from gemseo.utils.pytest_conftest import skip_under_windows

Tests shall be independent, any test function shall be executable alone.


Do no create loggers in the tests, instead let pytest manage the logging and use its builtin features. Some pytest logging settings are already defined in pyproject.toml.


The information provided to the user by the error and logging messages shall be correct. Use the caplog fixture for checking the logging messages. Use pytest.raises for checking the error messages.

Skipping under Windows

Use the pytest marker like:

def test_foo():
Validation of images

For images generated by matplotlib, use the image_comparison decorator provided by the matplotlib testing tools. See tests/post/dataset/ for an example. When image comparison fails, set the environment variable GEMSEO_KEEP_IMAGE_COMPARISONS such that the result_images directory with the comparisons is available at the root of the repository.

Validation of arrays

For NumPy arrays, use the NumPy testing tools.

Generated files

Tests that create files shall use the tmp_wd fixture such that the files are created in a temporary directory instead of polluting the root directory.

Executing tests

For Python 3.9, run the tests with:

tox -e py39

Replace py39 by py310 for testing with Python 3.10. With tox, you can pass options to pytest after --, for instance:

tox -e py39 -- --last-failed --step-wise

Run the tests for several Python versions with for instance (on Linux):

tox -e py39,py310,py311

Tests coverage

For a selected python version, get the coverage information with:

tox -e py39-coverage

See pytest-cov for more information.


The documentation of the develop branch is available online: develop documentation.

Generating the doc

The documentation is written with sphinx. On Linux, generate the documentation with:

tox -e doc

Pass options to sphinx-build after --, for instance:

tox -e doc -- -vv -j2

Writing guidelines

Documenting classes, functions, methods, attributes, modules, etc… is mandatory. End users and developers shall not have to guess the purpose of an API and how to use it.


Use the Google Style Docstrings format for documenting the code. This Example Google Style Docstrings shows how to write such docstrings.

Type hints

The type hints are used when generating the functions and methods documentation, they will also be used gradually to check and improved the code quality with the help of a type checker like mypy. See Example Google Style Docstrings for a typical example.

Functions and methods arguments shall use standard duck typing. In practice, use Iterable or Sequence etc… instead of list when appropriate, similarly for Mapping instead of dict. For *args and **kwargs arguments, use only the value types with no container.

Return types shall match exactly the type of the returned object.

Type hinting may cause circular imports, if so, use the special constant TYPE_CHECKING that’s False by default and True when type checking:

from typing import TYPE_CHECKING

    from gemseo import create_discipline

Line feeds

Use semantic line feeds by starting a new line at the end of each sentence, and splitting sentences themselves at natural breaks between clauses, a text file becomes far easier to edit and version control. You can have a look at the current page’s source for instance.


Have a look to the uncertainty module for an example of proper code documentation.

Check that the examples run correctly with:

tox -e py39 -- tests/ -m doc_examples


We use semantic versioning for defining the version numbers of GEMSEO. Given a version number MAJOR.MINOR.PATCH, we increment the:

  1. MAJOR version when we make incompatible API changes,

  2. MINOR version when we add functionality in a backwards compatible manner, and

  3. PATCH version when we make backwards compatible bug fixes.


Use pyperf to create valid benchmark, mind properly tuning the system for the benchmark (see the docs).


The Python standard library provides a profiler, mind using it with controlled system like for benchmarking. The profiling data could be analyzed with one of these tools:

Configure PyCharm

PyCharm is one of the best tools for writing Python code. We provide some configuration files to help configuring it for developing GEMSEO.

Code style

Configure PyCharm to match the code style used by GEMSEO. Download this file, open the PyCharm settings, go to Editor > Code Style > Python and select Import Scheme...:


Check and format

Some tools used by the Git hooks can be executed in order to be notified of code issues earlier and avoid having to fix files when creating a commit.

Install the Ruff plugin by opening the PyCharm settings, and searching in Plugins > Marketplace. Then, activate all the options and provide the path to the ruff executable that shall be in the following directory relative to the root of the git clone of gemseo:

  • On Linux and MacOS: .tox/check/bin/ruff.

  • On Windows: .tox\check\Scripts\ruff.exe.


For AutoPyDiscipline functions, ruff will refactor the return line in an incompatible manner. You shall append # noqa: RET504 to the return line.

Environment variables

Configure PyCharm so that the test environments do not open graphical windows during test execution:

  1. Click on Run > Edit Configurations… in the main menu.

  2. Click

    • on Edit configuration templates… on the bottom left and then on Python tests > pytest in the tree on the left to set the environment variables for all the Python test environments,

    • or on Python tests > {configuration name} to set the environment variables for a specific Python test environment.

  3. Open the section Configuration > Environment on the right.

  4. Write MPLBACKEND=AGG in the text field Environment variables (or click on the button in this field and add a new environment variable with MPLBACKEND as name and AGG as value).

Configure VSCode

vscode could serve as an alternative to PyCharm. To configure it for developing GEMSEO, we offer the base settings.json and extensions.json, which need to be placed within the local .vscode directory.

Download Configuration Files

  • settings.json: This file primarily contains Python rules for code style, formatting, debugging, testing, and indexing. You can download it here.

  • extensions.json: This file provides useful extension recommendations when browsing the Marketplace. You can download it here.


Place both downloaded files in the .vscode directory of your project.


Modify settings.json according to your preferences. You can adjust the settings either globally (User parameters) or per project (Workspace parameters).


Ensure you install all recommended extensions mentioned in extensions.json. These extensions enhance the functionality and productivity of vscode for Python development.