Table of contents

GitHub Actions: Intro

GH100 The recommended CI for scientific Python projects is GitHub Actions (GHA), although its predecessor Azure is also in heavy usage, and other popular services (Travis, Appveyor, and Circle CI) may be found in a few packages. GHA is preferred due to the flexible, extensible design and the tight integration with the GitHub permissions model (and UI). Here is a guide in setting up a new package with GHA.

GHA is made up of workflows which consist of actions. Here are some of the workflows you will probably want in your package. These should be in a file named .github/workflows/main.yml or similar.

Your main CI workflow file should begin something like this:

name: CI

      - main


This gives the workflow a nice name GH101, and defines the conditions under which it runs. This will run on all pull requests, or pushes to main. If you use a develop branch, you probably will want to include that. You can also specify specific branches for pull requests instead of running on all PRs (will run on PRs targeting those branches only).


If you use pre-commit (and you should), and you don’t want to / can’t use yet, then this is a job that will check pre-commit for you:

  name: Lint
  runs-on: ubuntu-latest
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v5
        python-version: "3.x"
    - uses: pre-commit/action@v3.0.1

If you do use, but you need this job to run a manual check, like check-manifest, then you can keep it but just use with: extra_args: --all-files --hook-stage manual check-manifest to run just this one check. You can also use needs: lint in your other jobs to keep them from running if the lint check does not pass.

Unit tests

Implementing unit tests is also easy. Since you should be following best practices listed in the previous sections, this becomes an almost directly copy-and-paste formula, regardless of the package details. You might need to adjust the Python versions to suit your taste; you can also test on different OS’s if you’d like by adding them to the matrix and inputting them into runs-on.

  runs-on: ubuntu-latest
    fail-fast: false
        - "3.8"
        - "3.11"
        - "3.12"
  name: Check Python ${{ matrix.python-version }}
    - uses: actions/checkout@v4
        fetch-depth: 0 # Only needed if using setuptools-scm

    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
        python-version: ${{ matrix.python-version }}
        allow-prereleases: true

    - name: Install package
      run: python -m pip install -e .[test]

    - name: Test package
      run: python -m pytest

A few things to note from above:

The matrix should contain the versions you are interested in. You can also test on other OS’s if you are building any extensions or are worried about your package on macOS or Windows. Fail-fast is optional.

The formula here for installing should be identical for all users; and using PEP 517/518 builds, you are even guaranteed a consistent wheel will be produced just as if you were building a final package.


GH200 GH210 If you use non-default actions in your repository (you will see some in the following pages), then it’s a good idea to keep them up to date. GitHub provided a way to do this with dependabot. Just add the following file as .github/dependabot.yml:

version: 2
  # Maintain dependencies for GitHub Actions
  - package-ecosystem: "github-actions"
    directory: "/"
      interval: "weekly"
          - "*"

This will check to see if there are updates to the action weekly, and will make a PR if there are updates, including the changelog and commit summary in the PR. If you select a name like v1, this should only look for updates of the same form (since April 2022) - there is no need to restrict updates for “moving tag” updates anymore GH211. You can also use SHA’s and dependabot will respect that too. And groups will combine actions updates GH212, which is both cleaner and sometimes required for dependent actions, like upload-artifact/download-artifact.

You can use this for other ecosystems too, including Python.

Common needs

Single OS steps

If you need to have a step run only on a specific OS, use an if on that step with runner.os:

if: runner.os != 'Windows' # also 'macOS' and 'Linux'

Using runner.os is better than matrix.<something>. You also have an environment variable $RUNNER_OS as well. Single quotes are required here.

Changing the environment in a step

If you need to change environment variables for later steps, such combining with an if condition for only for one OS, then you add it to a special file:

- run: echo "MY_VAR=1" >> $GITHUB_ENV

Later steps will see this environment variable.

Communicating between steps

You can also directly communicate between steps, by setting id:’s. Some actions have outputs, and bash actions can manually write to output:

- id: someid
  run: echo "something=true" >> $GITHUB_OUTPUT

You can now refer to this step in a later step with ${{ steps.someid.something }}. You also can get it from another job by using ${{ needs.<jobname>.outputs.something }}. The toJson() function is useful for inputing JSON - you can even generate matrices dynamically this way!

Pretty output

You can write GitHub flavored markdown to $GITHUB_STEP_SUMMARY, and it will be shown on the summary page.

You can output annotations, as well; these show up inline on the code in the PR. This can be done by setting special double-colon outputs, like echo "::error file=app.js,line=1::Missing semicolon". See pytest-github-actions-annotate-failures for a plugin to do this with pytest.

You can also do this by supplying matchers, which tell GitHub to look for certain patterns. Do keep in mind you can only see up to 10 matches per type per step, and a total of 50 matchers.

Common useful actions

There are a variety of useful actions. There are GitHub supplied ones:

And many other useful ones:

A couple more from Python developers; note these do not provide vX moving tags like the official actions and most other actions, but instead have release/vX branches that you can use.

There are also a few useful tools installed which can really simplify your workflow or adding custom actions. This includes system package managers (like brew, chocolaty, NuGet, Vcpkg, etc), as well as a fantastic cross platform one:

  • pipx: This is pre-installed on all runners (GitHub uses to set up other things), and is kept up to date. It enables you to use any PyPI application in a single line with pipx run <app>.

You can also run GitHub Actions locally:

  • act: Run GitHub Actions in a docker image locally.

Advanced usage

These are some things you might need.

Cancel existing runs

GH102 If you add the following, you can ensure only one run per PR/branch happens at a time, cancelling the old run when a new one starts:

  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

Anything with a matching group name will count in the same group - the ref is the “from” name for the PR. If you want, you can replace github.ref with github.event.pull_request.number || github.sha; this will still cancel on PR pushes but will build each commit on main.

Pass job

If you want support GitHub’s “merge when pass” feature, you should set up a pass job instead of listing every job you wand to require. Besides making it much easier to add and remove jobs, it also means that adding a new required job won’t make all of your past, merged PRs change from a green checkmark to an orange “pending” symbol (since there are new requirements that they didn’t pass).

As an example, if you had lint and checks jobs, use this:

  if: always()
  needs: [lint, checks]
  runs-on: ubuntu-latest
    - uses: re-actors/alls-green@release/v1
        jobs: ${{ toJSON(needs) }}

We want the job to always run, so we set if: always(). Otherwise, it might be skipped if any job it depends on is skipped, and skipped jobs count as “passing” to GitHub’s automerge (yikes!). The important part of the job is the needs: list; this tells it what is required.

We use re-actors/alls-green to evaluate whether required jobs have passed. You need to tell it what jobs are required, which you can do without repeating the needs list by taking the needs list and inputting it as json to with: jobs:.

This will also support jobs that are allowed to fail (allowed-failures:) and allowed to be skipped (allowed-skips:) too.

Just set this pass job in your required checks for your main branch. Then you’ll be able to use GitHub’s auto merge functionality.

Custom actions

You can write your own actions locally or in a shared GitHub repo in either GitHub actions syntax itself (called “composite”), JavaScript, or Docker. Combined with pipx, composite actions are very easy to write!

To create a custom action, either places it in .github/actions (Just for internal use in that repo’s workflows), or in action.yml if you want to allow others to use your repository as an action. The start of the file looks like:

name: <some name>
description: <Some description>

You can also setup inputs, which will be placed by the user in with::

    description: <Some description>
    required: true

Then you specify that the action is composite and give it the steps to run:

  using: composite

If you specify a runs: step, you have to specify shell: <something>. Otherwise, it’s basically identical to what you are used to; you can use if:, etc.

One common use case is using Python. Unless it’s the point of your action, you ideally shouldn’t change the user’s environment; suddenly changing the active Python version might come as a surprise. You can do that, though, using update-environment: false with setup-python and pipx:

- uses: actions/setup-python@v5
  id: python
    python-version: "3.11"
    update-environment: false

- name: Run some local program
  shell: bash
    pipx run --python '${{ steps.python.outputs.python-path }}' '${{
    github.action_path }}' ${{ inputs.some-input }}

You use the python-path output from setup-python to get the Python you activated. You use github.action_path to get the path to the checked-out action.

Examples of custom composite actions include:

Reusable workflows

You can also make reusable workflows. One reason to do this is it allows you to use needs or communicate values between workflows. It’s an easy way to make one workflow (which can contain multiple jobs, even a matrix) depend on another.

To use a reusable workflow, you replace the triggers with:


If you add a outputs: table to the workflow call table, you can specify outputs for other workflows to read. See other options in the docs.

Conditional workflows

Sometimes you have jobs that depend on certain files in our repository. Maybe you only want to run tests if code or tests files are changed, docs if documentation changes, etc. While GitHub does allow you to specify files in triggers, it doesn’t play well with required checks or usage across multiple workflows. Here is a way to set it up that works well with those:

Write your workflows as reusable workflows. This means they start with a trigger that allows other workflows to call them:

# reusable-tests.yml, for example

Otherwise, they look like normal workflows. Then you need another reusable workflow file to decide when to run a specific situation.

# reusable-change-detection.yml
        value: ${{ || false }}
      # More here if you have more situations to detect

You start by specifying outputs when running this. You’ll want one output per situation you want to detect. The value will be output from our change-detection job below, and defaults to “false” if we don’t output anything.

Now, we need our job:

    runs-on: ubuntu-latest
      run-tests: ${{ || false }}
      # more here if you have more situations to detect

      - uses: actions/checkout@v4

      - name: Changed test-related files
        if: github.event_name == 'pull_request'
        id: changed-tests-files
        uses: Ana06/get-changed-files@v2.3.0
          format: "json"
          filter: |

      - name: Set a flag for running the tests
        if: >-
          github.event_name != 'pull_request' ||
          steps.changed-tests-files.outputs.added_modified_renamed != '[]'
        id: tests-changes
        run: echo "run-tests=true" >> "${GITHUB_OUTPUT}"

      # Add 2 more steps per situation you have to detect

This has a bit of boilerplate (mostly around passing variables around), but what it’s doing is fairly simple. Instead of stepping through it, let’s look at what it’s trying to do. First, you need to find a list of all changed files in the current PR. That’s done using Ana06/get-changed-files (which does not provide a v2 or v2.2 moving tag). That list is then filtered using filter:. It is returned as json (otherwise you will not be able to support filenames with spaces in them). The return list doesn’t actually matter; in the next step, we simply check to see if it’s empty ([] in json). If we are not in a PR or if there are returned files, we set run-tests=true; otherwise, we don’t (if we are in a PR and there were no matches).

Everything else in the job is about getting the output from the step changed-tests-files to tests-changes, then from there into the reusable workflow output as run-tests.

Someone probably could write an action (maybe even an composite action using either gh or shell: python) that could directly report changes true/false instead of a file list, saving the two step process and greatly simplifying this.

If you have more situations, you just repeat these two steps with different ids and inputs.

Finally, you write the overarching CI workflow that combines the reusable workflows, something like ci.yml:

      - main

    uses: ./.github/workflows/reusable-change-detection.yml

    needs: change-detection
    if: fromJSON(
    uses: ./.github/workflows/reusable-tests.yml

  # more here if you need more

    if: always()
      - change-detection
      - tests
    runs-on: ubuntu-latest

      - name: Decide whether the needed jobs succeeded or failed
        uses: re-actors/alls-green@release/v1
          allowed-skips: >-
              && ''
              || '
          jobs: ${{ toJSON(needs) }}

If you have more situations, add another ${{ ... }} above, after the first one, and add them to the needs list. This is really just injecting “tests” only if the “tests” job is being skipped into allowed-skips.

Some examples of repos using this method are:

GitHub pages

GitHub has finished moving their pages build infrastructure to Actions, and they now provide the ability to directly push to Pages from Actions. This replaced the old workarounds of (force) pushing output to a branch or to separate repository.

Before starting, make sure in the Pages settings the source is set to “Actions”.

You’ll probably want this job to run on both your main branch, as well as workflow_dispatch, just in case you want to manually trigger a rebuild. You should set the permission so that the built-in GITHUB_TOKEN can write to pages:

  contents: read
  pages: write
  id-token: write

GH103 You probably only want one deployment at a time, so you can use:

  group: "pages"
  cancel-in-progress: true

Now you’ll want three custom actions in your steps:. First, you need to configure Pages.

- name: Setup Pages
  id: pages
  uses: actions/configure-pages@v5

Notice this action sets an id:; this will allow you to use the outputs from this action later; specifically, may want to use ${{ steps.pages.outputs.base_path }} when building (you can also get origin, base_url, or host - see the action config).

- name: Upload artifact
  uses: actions/upload-pages-artifact@v3

This actions defaults to uploading _site, but you can give any with: path: if you want, including "." which is the whole repository.

Finally, you’ll need to deploy the artifact (named github-pages) to Pages. You can make this a custom job with needs: pointing at your previous job (in this example, the previous job is called build):

    name: github-pages
    url: ${{ steps.deployment.outputs.page_url }}
  runs-on: ubuntu-latest
  needs: [build]
    - name: Deploy to GitHub Pages
      id: deployment
      uses: actions/deploy-pages@v4

The deploy-pages job gives a page_url, which is the same as base_url on the configure step, and can be set in the environment. If you want to do everything in one job, you only need one of these.

See the official starter workflows for examples. Some other examples include:

Changelog generation

Not directly part of Actions, but also in .github is .github/release.yml, which lets you [configure the changelog generation][gh-changelog] button when you make a release. The following config will remove dependabot and pre-commit-ci PRs for you:

      - dependabot
      - pre-commit-ci