AllenInstitute / AllenInstitute/bmtk
Don't delete all contents of output_dir...
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 335
- Forks
- 102
- Avg merge
- 1d 5h
- Merged PRs (30d)
- 6
Description
Currently BMTK will delete all files & subfolders in the output_dir as specified of a Sonata file:
"output":{
"output_dir": "$OUTPUT_DIR",
...
}
including presumably the user's home directory if they specify that...
https://github.com/AllenInstitute/bmtk/blob/develop/bmtk/simulator/core/io_tools.py#L73
It would be better to only delete the files BMTK expects to generate (as is suggested by the spec: "An optional attribute named "overwrite_output_dir" provides a hint to simulators to let them know if already existing output files must be overwritten."), or better still warn the user that that dir contains files BMTK didn't create.
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
Read bmtk/simulator/core/io_tools.py around line 73 and inspect how the Sonata output_dir and overwrite_output_dir settings are handled. Define the expected output files and ensure existing unrelated files are not deleted, or that the user is warned when the directory contains files BMTK did not create.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100