Skip to content

Enable testing against external instances#1264

Draft
bernt-matthias wants to merge 3 commits into
galaxyproject:mainfrom
bernt-matthias:env-secret-testing
Draft

Enable testing against external instances#1264
bernt-matthias wants to merge 3 commits into
galaxyproject:mainfrom
bernt-matthias:env-secret-testing

Conversation

@bernt-matthias

@bernt-matthias bernt-matthias commented Jun 26, 2026

Copy link
Copy Markdown
Contributor

Split testing job in the PR workflow into two parts:

  1. test against planemo instance in github actions (as before) OR
  2. test against external instance (using an environment secret) if there is a .wt_instance with content usegalaxy.org (currently we test only against org)

In the 2nd case the workflow (or more precisely the test job) needs approval to access the environment by a configurable set of persons.

Therefore we adapted:

  • test_workflows.yml to use a secret (optionally from an environment)
  • this should automatically be used in the scheduled CI jobs running in the separate workflow repos (each needs to setup the secret)
  • The PR CI workflow_test.yml needs an extra step to check which job to run (with / without secret).

FOR CONTRIBUTOR:

  • I have read the Adding workflows guidelines
  • License permits unrestricted use (educational + commercial)
  • Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

  • .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
  • Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
  • In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
  • In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
  • In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
  • Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
  • Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
  • Changelog contains appropriate entries
  • Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

@bernt-matthias bernt-matthias changed the title Env secret testing Enable testing against external instances Jun 27, 2026
@bernt-matthias bernt-matthias marked this pull request as draft June 27, 2026 12:10
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants