nf-core lint check that snapshots are used
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linting
modules
nf-test
- Dominant language
- Python
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Description
I think we can check for any use of md5 or contains in the assert statements and warn/fail on those. I haven't seen a reason not to use a snapshot(yet). Happy to be proven wrong, if so:
// nf-core-ignore: 186 Can't snapshot because the output is huge, etc.
{ assert process.out.npa.get(0).get(1) ==~ ".*/test.npa" },
{ assert process.out.npc.get(0).get(1) ==~ ".*/test.npc" },
{ assert path(process.out.npo.get(0).get(1)).getText().contains("# @impl: Nonpareil") },
{ assert path(process.out.npl.get(0).get(1)).md5 == "be95453a272a9f685d5695d2b391fde8" },
or something to by-pass it
Original conversation https://github.com/nf-core/modules/pull/4313/files#r1386762562
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 by locating the existing lint-check entry point for assertions and its test coverage. Add coverage for assertions using md5 or contains, including the proposed nf-core-ignore bypass, and verify that the check warns or fails as intended.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100