======================= Documentation Guidline ======================= BALSAMIC uses Sphinx to build the documentation, see the official documentation of Sphinx: https://www.sphinx-doc.org/en/master/index.html Following steps explains how to build documents locally. Create a conda environment: .. code-block:: conda create -n balsamic_doc -c bioconda -c conda-forge python=3.11 pip pygraphviz wkhtmltopdf conda activate balsamic_doc Install Sphinx and extensions: .. code-block:: cd /path/to/BALSAMIC python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir . cd docs pip install -r requirements.txt -r ../requirements-dev.txt Build docs: .. code-block:: sphinx-build -T -E -b html -d _build/doctrees-readthedocs -D language=en . _build/html View docs (\ ``open`` or similar command from your OS): .. code-block:: open _build/html/index.html