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README_development.md

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Developer hints

Generate documentation with Sphinx

It is recommended to set up a separate Python virtual environment for the Sphinx run as it has additional dependencies beyond what's required by DomId (see docs/requirements.txt).

You should be able to generate documentation for DomID by running the following:

sh sh_gen_doc.sh

Sphinx will regenerate the documentation in html format, and you can find the output in the 'build' directory.

Alternative approaches

  • Alternatively, to rebuild the documentation, run the following command from the root of the repository:
sphinx-build -b html docs/ docs/build
  • There is also Makefile in the project, the shortcut command to build the documentation is to run make html from the root of the repository (which is used by sh_gen_doc.sh above).

Automated (unit) tests

For automated testing of this python package we use the pytest framework. Tests are found in the domid/tests/ directory. Tests can be executed locally with:

poetry run pytest domid

Code style and formatting

This project uses Black for code formatting, with settings as specified in the pyproject.toml file. To run automated code formatting, from the base directory of the project execute:

bash sh_format_code.sh

Using DomId with a development version of DomainLab

By default the official DomainLab release from PyPI will be used. However, you can choose to use a more recent development versions of DomainLab from the Github repository. First, you will need to edit the pyproject.toml file accordingly, for example, along the lines of:

domainlab = {git = "https://github.com/marrlab/DomainLab.git", rev = "master"}

or

domainlab = { path = "./DomainLab", develop = true}

Additional hints:

  • To use the latest version of DomainLab, it may help to run git submodule update --remote.
  • If desired, you can set DomId to use another branch of DomainLab (replace <branch_name> with the name of the branch you want to use):
git config -f .gitmodules submodule.DomainLab.branch <branch_name>
git submodule update --remote