Dynamic build matrix in GitHub Actions

[This article was first published on cynkra, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

I wanted to try out the new fromJSON() that allows dynamic build matrices in GitHub Actions for quite some time now. Today was the day.

GitHub Actions allows automating build and deployment processes (CI/CD), tightly integrated with GitHub. A build matrix is a way to define very similar workflows that differ only by configuration parameters. Usually, a build matrix is defined directly in the .yaml files together with the workflows. This blog post shows how to define these build matrices dynamically, so that the “source of truth” for the matrix definition is outside the .yaml file.

Illustration
Photo by Markus Spiske

The configuration for a workflow is a YAML file that has a context and expression syntax with very few basic functions. Two very powerful functions are toJSON() and fromJSON():

  • toJSON() can capture pieces of the workflow configuration as JSON and pass it to your workflow code
  • fromJSON() allows injecting arbitrary configuration pieces created from JSON code

The basic setup comprises of two jobs: one that creates the workflow definition as JSON and stores it as output, and another dependent job that injects this output via fromJSON() into its matrix definition. A third job is defined for testing if outputs are passed correctly between jobs.

The original blog post contains a somewhat terse description. This blog post shows a walkthrough how I converted a static to a dynamic build matrix in the DBItest project.

Original matrix

In DBItest, we test compatibility of new or updated tests with backend packages. Each backend is run in a build matrix, which is defined as follows:

jobs:
        backend:
        strategy:
        fail-fast: false
        matrix:
        package:
        - duckdb
        - RSQLite
        - RMariaDB
        - RPostgres
        - RKazam
        

The relevant backends are defined in the Makefile, we want to get the list from there so that we can use a single source of truth.

This is a very simple build matrix, ideally suited for first experiments. The techniques shown here are applicable to build matrices of any complexity and size.

Derive and verify JSON

Our goal is to create the package: section from the above matrix in JSON format. To derive the JSON format, I use the sed stream editor, my beloved hammer that I use whenever I see a text transformation task in the shell:

echo '{ "package" : ['
        ## { "package" : [
        sed -n "/^REVDEP *:= */ { s///; p }" revdep-dev/Makefile | sed 's/ /, /g' | xargs -n 1 echo | sed -r 's/^([^,]*)(,?)$/"\1"\2/'
        ## "RMariaDB",
        ## "RSQLite",
        ## "RPostgres",
        ## "RKazam",
        ## "duckdb"
        echo "]}"
        ## ]}
        

This is not pretty, but still valid JSON when put together. We can prettify with jq ., later we will use jq -c . to condense to a single line.

(
        echo '{ "package" : ['
        sed -n "/^REVDEP *:= */ { s///; p }" revdep-dev/Makefile | sed 's/ /, /g' | xargs -n 1 echo | sed -r 's/^([^,]*)(,?)$/"\1"\2/'
        echo "]}"
        ) | jq .
        
{
        "package": [
        "RMariaDB",
        "RSQLite",
        "RPostgres",
        "RKazam",
        "duckdb"
        ]
        }
        

We verify the YAML version by piping to json2yaml which can be installed with npm install json2yaml:

---
        package:
        - "RMariaDB"
        - "RSQLite"
        - "RPostgres"
        - "RKazam"
        - "duckdb"
        

These tools are preinstalled on the workers. This avoids time-consuming installation procedures in this first job that needs to be run before the main jobs can even start.1

Define job

Once we have derived the JSON, we’re ready to define a job that creates the matrix. This must be done in the same workflow file where the matrix is defined, ideally before the main job. The job runs on ubuntu-latest, and also must clone the repository. In the bash snippet, the $matrix variable contains the JSON. It is shown and pretty-printed before it is provided as output via echo ::set-output ....

jobs:
        matrix:
        runs-on: ubuntu-latest
        outputs:
        matrix: ${{ steps.set-matrix.outputs.matrix }}
        steps:
        - uses: actions/[email protected]
        - id: set-matrix
        run: |
        matrix=$((
        echo '{ "package" : ['
        sed -n "/^REVDEP *:= */ { s///; p }" revdep-dev/Makefile | sed 's/ /, /g' | xargs -n 1 echo | sed -r 's/^([^,]*)(,?)$/"\1"\2/'
        echo " ]}"
        ) | jq -c .)
        echo $matrix
        echo $matrix | jq .
        echo "::set-output name=matrix::$matrix"
        backend:
        # Original workflow
        # ...
        

Verify output

Before plugging in the generated JSON into our build job, we add another check job to verify if the generated JSON is transported correctly across job boundaries. The needs: matrix declares that the job must wait before the first matrix job succeeds. The job’s output is queried via ${{ needs.matrix.outputs.matrix }}, the quotes ensure that bash processes this correctly. We install and use json2yaml to double-check what the YAML snippet looks like.

jobs:
        matrix:
        # job defined above
        check-matrix:
        runs-on: ubuntu-latest
        needs: matrix
        steps:
        - name: Install json2yaml
        run: |
        sudo npm install -g json2yaml
        - name: Check matrix definition
        run: |
        matrix='${{ needs.matrix.outputs.matrix }}'
        echo $matrix
        echo $matrix | jq .
        echo $matrix | json2yaml
        backend:
        # Original workflow
        # ...
        

Use output

Finally, we’re ready to use the generated JSON as a build matrix. The workflow now uses matrix: ${{fromJson(needs.matrix.outputs.matrix)}} instead of the hard-coded matrix:

jobs:
        matrix:
        # see above
        check-matrix:
        # see above
        backend:
        needs: matrix
        strategy:
        fail-fast: false
        matrix: ${{fromJson(needs.matrix.outputs.matrix)}}
        # rest unchanged
        

This gives a workflow as shown in the image below. Click on the image to view the workflow on GitHub.

GitHub Actions workflow with dependencies
Final workflow with dynamic build matrix

Next steps

For R packages, I see two use case where dynamic matrices can be useful:

  • Testing if package checks pass if one suggested package is not installed. Ideally, we remove suggested packages one by one and run in parallel.
  • Testing reverse dependencies. For some packages we may hit the limit of 256 jobs per workflow run. Allocating downstream packages to workers, minimizing the number of packages to be installed on each worker, sounds like an interesting optimization problem.

What are your use cases for dynamic build matrices? Drop us a line at [email protected]!

Caveats

Even with this simple build matrix it took more time than I would have hoped to get the bits and pieces right. Quoting is hard. Setting up the check-matrix job really saves time, I wish I had done this from the start.

Both fromJson() and fromJSON() appear to work. The internal functions from the expression syntax seem to be case-insensitive throughout.

For older versions, jq needs to be called as jq . to act as pretty-printer. For newer versions this can be omitted.

Today I also learned that workflows can be temporarily disabled. This is useful in situations where you experiment with a workflow and want to avoid running other workflows for every test.


  1. You can use any tool or ecosystem you are familiar with to come up with the JSON definition. To avoid long installation times, use a specific image for your step via uses: docker://... or implement a container action, also possible in the same repository

To leave a comment for the author, please follow the link and comment on their blog: cynkra.

R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)