Support and Development

Getting help and reporting issues

To get help using the signac-flow package, either send an email to or join the signac gitter chatroom.

The signac-flow package is hosted on GitHub and licensed under the open-source BSD 3-Clause license. Please use the repository’s issue tracker to report bugs or request new features.

Code contributions

This project is open-source. Users are highly encouraged to contribute directly by implementing new features and fixing issues. Development for packages as part of the signac framework should follow the general development guidelines outlined here.

A brief summary of contributing guidelines are outlined in the file as part of the repository. All contributors must agree to the Contributor Agreement before their pull request can be merged.

Set up a development environment

Start by forking the project.

We highly recommend to setup a dedicated development environment, for example with venv:

~ $ python -m venv ~/envs/signac-flow-dev
~ $ source ~/envs/signac-flow-dev/bin/activate
(signac-flow-dev) ~ $ pip install -r requirements-dev.txt -r requirements-precommit.txt

or alternatively with conda:

~ $ conda create -n signac-flow-dev python --file requirements-dev.txt --file requirements-precommit.txt
~ $ conda activate signac-flow-dev

Then clone your fork and install the package from source with:

(signac-flow-dev) ~ $ cd path/to/my/fork/of/signac-flow
(signac-flow-dev) signac-flow $ pip install -e .

The -e option stands for editable, which means that the package is directly loaded from the source code repository. That means any changes made to the source code are immediately reflected upon reloading the Python interpreter.

The pre-commit tool is used to enforce code style guidelines. To install the tool and configure pre-commit hooks, execute:

(signac-flow-dev) signac $ pip install pre-commit
(signac-flow-dev) signac $ pre-commit install

With the pre-commit hook, your code will be checked for syntax and style before you make a commit. The continuous integration pipeline for the package will perform these checks as well, so running these tests before committing / pushing will prevent the pipeline from failing due to style-related issues.

The development workflow

Prior to working on a patch, it is advisable to create an issue that describes the problem or proposed feature. This means that the code maintainers and other users get a chance to provide some input on the scope and possible limitations of the proposed changes, as well as advise on the actual implementation.

All code changes should be developed within a dedicated git branch and must all be related to each other. Unrelated changes, such as minor fixes to unrelated bugs encountered during implementation, spelling errors, and similar typographical mistakes must be developed within a separate branch.

Branches should be named after the following pattern: <prefix>/issue-<#>-optional-short-description. Choose from one of the following prefixes depending on the type of change:

  • fix/: Any changes that fix the code and documentation.
  • feature/: Any changes that introduce a new feature.
  • release/: Reserved for release branches.

If your change does not seem to fall into any of the above mentioned categories, use misc/.

Once you are content with your changes, push the new branch to your forked repository and create a pull request into the main repository. Feel free to push a branch before completion to get input from the maintainers and other users, but make sure to add a comment that clarifies that the branch is not ready for merge yet.


Prior to fixing an issue, implement unit tests that fail for the described problem. New features must be tested with unit and integration tests. To run tests, execute:

(signac-flow-dev) signac-flow $ python -m pytest tests/

Building documentation

Building documentation requires the sphinx package which you will need to install into your development environment.

(signac-flow-dev) signac-flow $ pip install Sphinx sphinx_rtd_theme

Then you can build the documentation from within the doc/ directory as part of the source code repository:

(signac-flow-dev) signac-flow $ cd doc/
(signac-flow-dev) doc $ make html


Documentation as part of the package should be largely limited to the API. More elaborate documentation on how to integrate signac-flow into a computational workflow should be documented as part of the framework documentation, which is maintained here.

Updating the changelog

To update the changelog, add a one-line description to the changelog.txt file within the next section. For example:


- Fix issue with launching rockets to the moon.

[0.6.3] -- 2018-08-22

- Fix issue related to dynamic data spaces, ...

Just add the next section in case it doesn’t exist yet.

Contributing Environments to the Package

Users are also highly encouraged to contribute environment profiles that they developed for their local environments. While there are a few steps, they are almost all entirely automated, with the exception of actually reviewing the scripts your environment generates.

Before you begin the process, make sure you have the following packages installed (in addition to signac-flow):

Once you’ve written the environment class and the template as described above, contributing the environments to the package involves the following:

  1. Create a new branch of signac-flow based on the master branch.
  2. Add your environment class to the flow/environments/ directory, and add the corresponding template to the flow/templates/ directory.
  3. Run the tests/ test script. It should fail on your environment, indicating that no reference scripts exist yet.
  4. Update the environments dictionary in the init function of tests/ The dictionary indicates the submission argument combinations that need to be tested for your environment.
  5. Run the tests/ script, which will create the appropriate reference data in the tests/template_reference_data.tar.gz tarball based on your modifications. The script should now succeed.
  6. Run the tests/ script, which will extract the tarball into a signac project folder.
  7. Run the tests/ script, which will generate docx files in the tests/compiled_scripts/ directory, one for each environment.
  8. You should see one named after your new environment class. Review the generated scripts thoroughly. This step is critical, as it ensures that the environment is correctly generating scripts for various types of submission.
  9. Once you’ve fixed any issues with your environment and template, push your changes and create a pull request. You’re done!

Deprecation Policy

While the signac-flow API is not considered stable yet (a 1.0 release has not been made), we apply the following deprecation policy:

Some features may be deprecated in future releases in which case the deprecation is announced as part of the documentation, the change log, and their use will trigger warnings. A deprecated feature is removed in the next minor version, unless it is considered part of the core API in which case a reasonable attempt at maintaining backwards compatibility is made in the next minor version, but is then completely removed in any following minor or major release.

A feature is considered to be part of the core API if it is likely to be used by the majority of existing projects.

A feature which is deprecated in version 0.x, will trigger warnings for all releases with release number 0.x.*, and will be removed in version 0.y.0. A feature, which is deprecated in version 0.x and which is considered core API will trigger warnings for versions 0.x.* and 0.y.*, limited backwards compatibility will be maintained throughout versions 0.y.*, and the feature will be removed in version 0.z.0.

For example: A feature deprecated in version 0.6, will be removed in version 0.7, unless it is considered core API, in which case, some backwards compatibility is maintained in version 0.7, and it is removed in version 0.8.