nf-core sync silently deletes ignored files
A pull request for this has already been merged.
- #3847 by @tgelafr-pfzr — merged
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
This may not be the biggest issue, but I recently found that running nf-core sync causes ignored files to be deleted.
This is a particular nuisance as it deletes editor config files such as .vscode/.
Currently the delete is performed using a simple iteration over the files in the directory, skipping the .git folder.
It could be possible to leverage the git.Repo object to skip ignored/untracked files too.
Command used and terminal output
No response
System information
nf-core tools 2.7.2
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
The issue points to the nf-core sync deletion iteration and suggests using the git.Repo object; start by reproducing nf-core sync with an ignored .vscode/ file and inspect that deletion path. Done means ignored and untracked files are retained while intended files still sync; check the linked pull request context before starting.
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
- 25/100