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Planemo CI action

Installs planemo, discovers changed workflows and tools, and allows to lint, test or deploy them.

The reference use cases of this action are the pull request and continuous integration workflows of the intergalactic utility comission (IUC).

The action runs in one of six modes which are controled with the mode input. Possible values are:

  • setup: This is the default.
    • Optionally do a fake planemo test run to fill .cache/pip and .planemo for caching.
    • Determine the relevant commit range.
    • Determine the set of relevant repositories and tools.
    • Determine the number of chunks and the chunk list.
  • lint: Lint tools with planemo shed_lint (resp. workflows with planemo workflow_lint) and check presence of repository metadata files (.shed.yml).
  • test: Test tools or workflows with planemo test.
  • combine: Combine the outputs from individual tool tests (planemo merge_test_reports) and create html/markdown reports (planemo test_reports).
  • check: Check if any of the tool tests failed.
  • deploy: Deploy tools to a toolshed using planemo shed_update and workflows to a github namespace, resp.

If none of these modes is set then a setup mode runs.

In all modes required software will be installed automatically, i.e. planemo and jq. The version of planemo can be controlled with the input planemo-version (default "planemo", i.e. the latest version).

Assumptions

The action currently only works on github actions workflows using an Ubuntu image.

Assumptions on the repository

Two files .tt_skip and .tt_biocontainer_skip containing paths (or prefixes of paths) can be used to skip or modify the testing for tools.

Tools/workflows in a path that has a prefix in:

  • .tt_skip are ignored in all modes
  • .tt_biocontainer_skip are not tested using containers but conda is used for resolving requirements.

Tools and workflows are discovered in all directories, except for packages/ and deprecated/. These directories may be absent.

A global .lint_skip file and per repo .lint_skip files can be used to list tool/workflow linters that should be skipped.

Setup mode

This mode runs if no other mode is selected. It:

  • runs planemo test on a mock tool (if create-cache is set to true)

  • determines the relevant set of tool/workflow repositories and tools with planemo ci_find_repos and planemo ci_find_tools, respectively.

    • for push and pull_request events (using GITHUB_EVENT_NAME) tools and repositories that changed in the commit range
    • all tools and repositories otherwise

  • calulates the number of chunks to use for tool testing and the list of chunks

Optional inputs:

  • workflows: look for workflows instead of tools
  • create-cache (default false)
  • galaxy-branch (default latest Galaxy release)
  • galaxy-source (default galaxyproject)
  • max-chunks (default 20)
  • python-version (default "3.11")

Outputs:

  • commit-range: The used commit range.
  • tool-list: List of tools (empty if workflows is true).
  • repository-list List of repositories.
  • chunk-count: Number of chunks to use.
  • chunk-list: List of chunks

Lint mode

Calls planemo shed_lint for each repository and checks if each tool is in a repository (i.e. metadata like .shed.yml is present).

Required inputs:

  • repository-list
  • tool-list

Optional inputs:

  • report_level: all|warn|error (default: all)
  • fail_level: warn|error (default: error)
  • additional-planemo-options: additional options passed to planemo lint. Here this is used to overwrite the warn level of planemo lint.

Output:

  • creates a file lint_report.txt

Test mode

Runs planemo test for each tool in a chunk using ci_find_tools. Note that none of the tests will produce a non-zero exit code even if the tests fail. Success needs to be checked with the check mode after combining the outputs of the chunks.

Required inputs:

  • repository-list: List of repositories
  • workflows: test workflows
  • setup-cvmfs: setup CVMFS (only useful for testing workflows)
  • chunk: Current chunk
  • chunk-count: Maximum chunk

Optional inputs:

  • database_connection
  • galaxy-branch
  • galaxy-source
  • python-version
  • additional-planemo-options: additional options passed to planemo test, see for instance here
  • galaxy-slots: number of slots (threads) to use in Galaxy jobs (sets the GALAXY_SLOTS environment variable)
  • test_timeout: Maximum runtime of a single test in seconds, default: 86400

Output:

The test mode creates a directory upload/ containing the test results as json file.

Combine test outputs mode

Combines the test result of the chunked tests and create html or markdown reports.

Required input:

  • json files need to be placed in a directory artifacts/.

Optional inputs:

  • html-report (default: false)
  • markdown-report (default: false)

Output:

  • statistics: (text) historam of the number of tests that passed, errored, failed, skipped.

A directory upload/ containing the combined test results as json file and optionally as html/markdow files (named tool_test_output.[json|html|md]).

Test combined outputs mode

Check the combined outputs for failed test runs. If a failed test is found exit code 1 is returned.

Required input:

tool test results in upload/tool_test_output.json

Output:

statistics: Text containg the number of successful and failed tests

Deploy mode

Deploy all repositories to a toolshed.

Required inputs:

  • workflows: deploy workflows to github namespace
  • workflow-namespace
  • shed-target toolshed name (e.g. "toolshed" or "testtoolshed")
  • shed-key API key for the toolshed