Speed up `nf-core modules` pytests
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- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
The pytests for the nf-core modules commands are very slow. I believe this partly due to that every test pulls several remote git repositories in the setUp method. Since all objects that are created by the setUp method are not used by every test, this is unnecessary. We should therefore either move the creation of install objects etc. either to the individual tests or create a test class per modules command with a simpler setUp function. Creating individual classes would also make it easier to test an individual command.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in tests/test_modules.py, especially the setUp method at lines 38–66, and inspect which created objects each modules-command test uses. Run the relevant pytest tests to establish the current runtime, then reduce unnecessary remote repository pulls by moving setup closer to the tests or separating commands into test classes. Done means the tests remain covered and run faster, with individual commands easier to test.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- testing-qa
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100