CI Inventory

Changed on 2023-05-02: Use mergify instead of AutoMerge.yml GitHub Action

Changed on 2023-06-06: Start using build-failures workflow

Changed on 2024-03-04: Start using linux-aarch64 in bulk and recipe tests

Changed on 2024-07-05: Start using osx-arm64 in bulk and recipe tests

This page documents the various moving parts that, together, make Bioconda work. We rely on a mixture of free services to spread the workload and to maintain flexibility over the long term in case a service becomes unusable.

Note

For the platform column, we use the conda designations when conda packages are built. Otherwise we use operating system. See Understanding platform nomenclature for more info on this.

Name	Runs on	Controlled from	Trigger	Code references	Platform	Description
Recipe tests	Azure Pipelines, CircleCI	bioconda-recipes	on push	azure-pipeline.yml (linux-64, osx-64); config.yml (linux-aarch64, osx-arm64)	linux-64, osx-64, linux-aarch64, osx-arm64	These are the most-run tests: these are what run on every change on pull requests to bioconda-recipes, and they must pass before the recipe is merged into the master branch.
Comment responder	GitHub Actions	bioconda-recipes	@BiocondaBot mentions	CommentResponder.yml	Linux	Runs the bioconda-bot container (quay.io/bioconda/bot) with different image tags (merge, comment, update, repost) in response to comments. This allows fast response time (rather than, say, restoring a cache each time).
Master branch tests	Azure Pipelines, CircleCI	bioconda-recipes	push to master (bioconda-recipes)	azure-pipeline-master.yml (linux-64, osx-64); config.yml (linux-aarch64, osx-arm64)	linux-64, osx-64, linux-aarch64, osx-arm64	Runs when a PR is merged to the master branch. The already-built artifacts are retrieved from the PR and uploaded to the bioconda channel. Container(s) are uploaded to quay.io/biocontainers. If artifacts are not found, it will build the recipe(s) as a fallback.
Mergify	mergify	bioconda-recipes	Successful tests on an autobumped recipe	.mergify.yml	Linux	If a recipe was autobumped, the tests passed, and it’s been more than 3 days, then automatically merge the updated recipe.
Autobump bot	CircleCI	bioconda-utils	hourly	config.yml	Linux	Checks upstream repository for version updates, if so, creates a new bioconda-recipes recipe with the updated version and an updated hash, and opens a new pull request with various templated info and with the “autobump” label applied.
Build failures	GitHub Actions	bioconda-recipes	daily	build-failures.yaml	Linux	Runs bioconda-utils list-build-failures to generate and publish a wiki page listing prioritized failures.
Docs	GitHub Actions	bioconda-docs	daily, or on push	docs.yml	Linux	Build sphinx documentation (including updated READMEs for every recipe) and pushes the changes to [bioconda.github.io](https://github.com/bioconda/bioconda.github.io).
bioconda-utils tests	GitHub Actions	bioconda-utils	on push	GithubActionTests.yml	linux-64, osx-64	Unit tests and functional tests for bioconda-utils.
Docker image test	GitHub Actions	bioconda-utils	on push	build-image.yml, Dockerfile	Linux	Ensures that bioconda-utils can run inside a newly-built container.
Check public containers	GitHub Actions	bioconda-utils	manually	changevisibility.yml	Linux	Checks quay.io to see if any containers are mistakenly private; if so makes them public
Conventional PRs	GitHub Actions	bioconda-utils	bioconda-utils PR open/reopen/edit/sync	conventional-prs.yml	Linux	Enforces “conventional commit” tags in the title of PRs, like “docs:”, “fix:”, “ci:”, and so on in bioconda-utils. This enables better automation of releases.
Release-please	GitHub Actions	bioconda-utils	push to master on bioconda-utils	release-please.yml	Linux	Collects PRs that have been merged to master since the last release into a separate, special PR. Merging that special PR is what triggers a new release.
Nightly maintenance	Azure Pipelines	bioconda-recipes	daily	azure-pipeline-nightly.yml	Linux, macOS	Various maintenance tasks: build and upload the bioconda-repodata-patches package; try to build and upload any remaining packages (runs bioconda-utils build on all recipes)
Bulk	GitHub Actions	bioconda-recipes	push to bulk branch of bioconda-utils	Bulk.yml (linux-64, osx-64, osx-arm64); config.yml (linux-aarch64)	linux-64, osx-64, linux-aarch64, osx-arm64	If pushing to the special bulk branch, this workflow will run. It uses special bioconda-utils functionality to split the full DAG into sub-DAGs and submits them to independent parallel jobs. When recipes sucessfully build, they are immediately uploaded. Use with caution. Typically used when migrating (e.g., bioconductor updates, pinning updates)
Compile stats for plots	GitHub Actions	bioconda-stats	several times a day	packages-anaconda-org.yml	Linux	Builds a zip file containing TSVs for each package, which are inspected and compiled into json files in bioconda-plots.
Generate plots	GitHub Actions	bioconda-plots	daily	generate-plots.yml; test-plots.yml runs minor tests on the plot-generating code.	Linux	Using stats compiled in bioconda-stats, builds json files for each package that are used by plotting code on bioconda.github.io recipe pages.