imagej / imagej/pyimagej

Arguments passed to `run_plugin` replace backslash with forward slash

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Dominant language
Python
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Description

I was using `BigStitcher` from `pyimagej` on Windows and needed to pass in paths. But, `BigStitcher` would choke on the paths claiming it can't find files there.

I traced down the issue to `pyimagej` automatically replacing backslashes with a forward slash. When I removed this, BigStitcher finally worked.

https://github.com/imagej/pyimagej/blob/17fdca871234d230c8f1b2f70b950beb4a22c779/src/imagej/__init__.py#L712

Should this replacement be optional, perhaps guarded behind a switch, like `ij1_style`!? I ended up replicating the format code and passing in `args` as a string, without this replacement.

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Research direction

Read src/imagej/__init__.py around line 712 and trace how run_plugin formats its arguments. Reproduce the Windows-path case with BigStitcher, then determine how an optional replacement setting should affect the resulting arguments; done means backslash paths work without breaking the existing behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
56/100

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