FIX: Initialize BIDS layout after cleaning working directory

[effigies]

I saw three options.

1. Protect the PyBIDS DB from being deleted by --clean-workdir. This complicates the cleaning code.
2. Move cleaning into config.execution.init, which seems bad as I think initialization is supposed to be okay to do multiple times. Destructive filesystem operations certainly seem bad to hide in configuration init.
3. Have a separate explicit layout initialization step that we call after cleaning the work-dir.

Went for option 3.

Fixes #2721

[mgxd]

what if we just move the clean_directory logic to run before initializing the config?

[effigies]

Because the working directory could be set by passing a config file.

[mgxd]

ah yes - in that case, you probably just need to initialize the layout after this line as well

fmriprep/fmriprep/cli/workflow.py

Line 46 in ea03d25

config.load(config_file)

[effigies]

Thanks for tracking that down.

[effigies]

Tests passing. Any objections?

[mgxd]

Not a big fan of having to call 2 initialization methods (load/initialize_layout) every time we establish the config. I think load by default should call all initialization functions -perhaps what we should be able to handle is selective initialization each config section

But if you feel strongly against, config.execution.init's docstring should be updated with this change in behavior

[effigies]

The config is kind of a house of cards... I'll see what I can do.

[pep8speaks]

Hello @effigies! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-04-08 15:03:03 UTC

[mgxd]

LGTM - thanks for addressing that 😄