modules test on a private modules server requires --git-remote
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- Python
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Description
Description of the bug
I have setup a private version of the modules repository, with the files in the same sort of structure.
When trying to develop on a clone of that repo, I find that nf-core modules create modulename works fine, but nf-core modules test modulename gives an error:
Cannot find directory 'modules/nf-core/modulename'. Should be TOOL/SUBTOOL or TOOL
Adding --git-remote to point at the URL for the repo that I have currently checked out, does indeed work.
I also had issues with nf-core modules lint modulename initially without adding the --git-remote option, but it is currently working for me without adding the --git-remote.
@awgymer on slack said:
Ok it’s this line. Rather than use the org_path it’s choosing to use the self.modules_repo.repo_path value which, I am pretty sure, is just the org_path but for the remote. And since you haven’t explicitly set the remote is defaulted to nf-core.
Command used and terminal output
nf-core modules test modulename
`Cannot find directory 'modules/nf-core/modulename'. Should be TOOL/SUBTOOL or TOOL `
System information
nf-core 2.14.2.dev0
nextflow 24.04.2.5914
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 with the modules test handling in nf_core/components/components_test.py at lines 126-127, then reproduce nf-core modules test modulename against a private modules repository without --git-remote. Compare the repository path used by modules create and modules lint; done means testing the checked-out private repository works without explicitly passing its remote, with regression coverage for that command.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100