OpenFreeEnergy / OpenFreeEnergy/openfe
`--output-dir` is used to define the alchemical network JSON name but only claims settings the output directory
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 332
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
When calling plan-rbfe-network, --output-dir (or -o) is expected to just set the name of the directory. I would expect the AlchemicalNetwork JSON name to be something standardized (a bit like how ligand_network.graphml is standardized). However, the output-dir name is used for the network JSON name, which isn't what the help message says and also is rather confusing to users.
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 at the plan-rbfe-network CLI entry point and trace how --output-dir/-o is used when writing the AlchemicalNetwork JSON. Compare that behavior with the help text and the standardized ligand_network.graphml naming, then verify the command produces the agreed JSON filename while still placing outputs in the requested directory.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100