Cellfinder workflow CLI input argument with tests

[sfmig]

A script to simulate a typical cellfinder workflow. It builds up on previous work from PRs #15 and #20 (none of which we merged).

We wanted

• to define workflows that can fetch data from GIN and also locally - note these workflows will take the required input parameters from an input config file; and
• to allow the input config to be set to some default values, but also allow them to be customised

The current solution takes the path to a configuration json file as a command line input.

If no input json file is passed as a CLI argument, the default configuration defined at brainglobe_workflows/cellfinder/default_config.json is used. This default configuration fetches data from a GIN repo, creates a .cellfinder_workflows cache subdirectory at the location the script is launched from, and saves to it the downloaded data and the output results.

Example usage

• to pass a custom configuration, run from the cellfinder_main.py parent directory:
  python cellfinder_main.py --config path/to/input/config.json
• to use the default configuration, run:
  python cellfinder_main.py

It ended up being a larger PR than I thought, apologies! But hopefully it crystallises the structure we discussed these past few days (see #9)

[codecov]

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (8665e74) 0.00% compared to head (f16c6b9) 92.56%.
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##            main      #23       +/-   ##
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+ Coverage   0.00%   92.56%   +92.56%     
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  Files          1        2        +1     
  Lines          5      121      +116     
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+ Hits           0      112      +112     
- Misses         5        9        +4     

Files	Coverage Δ
brainglobe_workflows/__init__.py	60.00% <60.00%> (ø)
brainglobe_workflows/cellfinder/cellfinder_main.py	93.96% <93.96%> (ø)

... and 1 file with indirect coverage changes

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[alessandrofelder]

Thanks a lot @sfmig
I think the source code looks good - made some minor comments!

As discussed, we may want to refactor the tests a bit in a separate PR.