Assorted cleanup of xfel-calibrate

Description

Now that @roscar has added some tests for the CLI, I though I'd start cleaning up the code a bit. This is a combination of various minor changes, which I'll describe inline.

How Has This Been Tested?

Run xfel-calibrate from my account on Maxwell, checked that output files, report, details from Slurm are still produced in the output folder as before.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• Refactor (refactoring code with no functionality changes)

Checklist:

• My code follows the code style of this project.

Reviewers

@roscar @ahmedk

changed the description

added 1 commit

• ba12f7b5 - No longer need to pass Slurm job ID to finalize script

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• cc8c65c7 - Use keyword argument for finalize_script

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• 1133e3b7 - Type hints say user_venv should be Path, not str

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Tests fail on CI, but pass when I run them locally...

added 2 commits

• a2403610 - Remove some unused imports
• a9345b83 - finalize script goes in run_tmp_path

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I needed to reinstall. I guess I'm used to being able to test on the local version without installing it...

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• cd20719c - Sort notebooks in test

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LGTM

And with the wonders of git worktree I didn't even need to stash stuff to review this

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• 11b41b3c - Apply suggestion to src/xfel_calibrate/finalize.py

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added 1 commit

• 09465fcb - Fix missing sys import

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enabled an automatic merge when the pipeline for 09465fcb succeeds

merged

mentioned in commit fa2d8cad

resolved all discussions