[ENH] include roi based calls in CLI

[Remi-Gau]

closes #846
closes #865

• update python CLI
• update CLI help

[codecov]

Codecov Report

Merging #880 (c649993) into main (b28218a) will decrease coverage by 0.05%.
The diff coverage is 51.42%.

@@            Coverage Diff             @@
##             main     #880      +/-   ##
==========================================
- Coverage   78.71%   78.66%   -0.06%     
==========================================
  Files         238      239       +1     
  Lines        6400     6449      +49     
  Branches       37       40       +3     
==========================================
+ Hits         5038     5073      +35     
- Misses       1347     1360      +13     
- Partials       15       16       +1     

Flag	Coverage Δ
cli	38.61% <20.00%> (-1.56%)	⬇️
matlab	80.25% <93.33%> (+0.04%)	⬆️
octave	78.83% <93.33%> (?)

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Impacted Files	Coverage Δ
src/bidspm.py	30.30% <5.88%> (-2.81%)	⬇️
src/workflows/roi/bidsCreateROI.m	30.95% <87.50%> (+1.68%)	⬆️
src/cli/getOptionsFromCliArgument.m	67.21% <100.00%> (+1.69%)	⬆️
src/defaults/setDirectories.m	98.21% <100.00%> (+0.10%)	⬆️
src/parsers.py	88.23% <100.00%> (+0.73%)	⬆️
src/workflows/roi/bidsRoiBasedGLM.m	76.00% <0.00%> (-1.00%)	⬇️
src/workflows/stats/bidsResults.m	48.83% <0.00%> (-0.46%)	⬇️
src/stats/utils/fillInResultStructure.m	100.00% <0.00%> (ø)
src/defaults/checkOptions.m	96.15% <0.00%> (+0.42%)	⬆️
src/infra/getEnvInfo.m	64.86% <0.00%> (+1.35%)	⬆️
... and 4 more

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[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.96%.

Quality metrics	Before	After	Change
Complexity	4.73 ⭐	4.60 ⭐	-0.13 👍
Method Length	114.41 🙂	123.06 😞	8.65 👎
Working memory	12.33 😞	12.95 😞	0.62 👎
Quality	58.18% 🙂	57.22% 🙂	-0.96% 👎

Other metrics	Before	After	Change
Lines	668	749	81

Changed files	Quality Before	Quality After	Quality Change
src/bidspm.py	52.65% 🙂	51.92% 🙂	-0.73% 👎
src/parsers.py	76.96% ⭐	75.95% ⭐	-1.01% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
src/bidspm.py	bidspm	14 🙂	351 ⛔	29 ⛔	23.26% ⛔	Try splitting into smaller methods. Extract out complex expressions
src/bidspm.py	stats	6 ⭐	204 😞	23 ⛔	38.38% 😞	Try splitting into smaller methods. Extract out complex expressions
src/bidspm.py	preprocess	6 ⭐	185 😞	19 ⛔	42.05% 😞	Try splitting into smaller methods. Extract out complex expressions
src/bidspm.py	cli	5 ⭐	236 ⛔	13 😞	45.87% 😞	Try splitting into smaller methods. Extract out complex expressions
src/bidspm.py	create_roi	2 ⭐	142 😞	16 ⛔	52.79% 🙂	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

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• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

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