Unwanted side effects during update
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
The modules_json_up_to_date() function installs modules that are listed in modules.json but can not be found in the directory structure. I think running this command in the update routine for another package should be considered an unwanted side effect.
There is some inherent link between the nf-core modules update command and this function.
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 nf_core/modules/update.py at lines 44-45 and inspect how modules_json_up_to_date() is called during the update routine. Trace the relationship between the general update command and the nf-core modules update command. Done means updating another package no longer installs modules missing from the directory structure, while the modules update behavior remains linked appropriately.
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
- 35/100