Bioconda documentation

main docs: https://bioconda.github.io

This repository stores the source code for the bioconda docs at https://bioconda.github.io.

When pull requests in this repo are merged into the main branch, the docs are built and pushed to the bioconda.github.io repo for public hosting.

Note that prior to 2023-02-28, this documentation source was in the bioconda-utils repo, but has been split out for simplicity and ease of maintenance.

Why keep this separate from the from bioconda.github.io where the built docs live? Because this source code is relatively small, but the built docs are rather large. If we worked on the source over in bioconda.github.io, even if the source lived on a different branch, every time it was cloned we would be pulling full git history (including the large built docs). This separate repo allows us to keep editing the documentation lightweight.

Notes on pull requests

• Inspect the built docs for each job. When a pull request is submitted for a branch, and on every subsequent push to the branch, the documentation will be built and uploaded as an artifact to the job. This is a file, doc.zip, that can be found on the GitHub Actions page for that job. This is a convenient way of checking formatting issues in the built documentation, without requiring a full local setup.

• By default, only 10 recipes' README.html pages will be built. This dramatically speeds up the build process (by >10x) for faster iteration times. If you need to build all recipe README.html pages for some reason, you can include the text [build all recipes] in the commit message of the commit you want to build everything for.

Building docs locally

Make an environment containing the bioconda-utils package. E.g.,

mamba create \
  env -n bioconda-docs \
  bioconda-utils \
  --channel conda-forge \
  --channel bioconda \
  --strict-channel-priority

With that environment activated (i.e., conda activate bioconda-docs), in the top level of this repo, run:

make BIOCONDA_FILTER_RECIPES=10 html SPHINXOPTS="-T -j1"

The output will be found in build/html.

Note that you can set BIOCONDA_FILTER_RECIPES to some other number; omitting it completely will build all recipes' README.html pages which can take a while.

Points of interest

• Docs are built with Sphinx
• the source/_ext directory has Sphinx extensions for building the recipe README html files (along with making backlinks for dependencies' READMEs) and for a .. details:: directive.

Update frequency

These docs are automatically built each day, after pulling the latest changes to bioconda-recipes. This means that newly-added recipes or recently-updated recipes will not show up in the package index for a day or so.