Issuefixes

[VGPReys]

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---

This PR aims at closing three issues:

• With the addition of a regular expression that checks the presence of upper case True and False in the .toml input file and lowering them on-the-fly, this closes Booleans with capitals #575
• Also by checking values types and ranges/choices, by comparing values present in the defaults.yaml and parameter = value present in the user provided .cfg file, this closes check values in cfg files against .yaml files  #487
• Finally, a bunch of copies of the workflow haddock3 input files are now written in the data directory of the run. This includes the original inputed file, the regular expression cleaned file and the enhanced full parameter file, which includes all default parameters in addition to the ones provided by the user. This closes Adding the config file to the data dir of a run #578

Accordingly, additionnal tests were added, while some other test were modified to fit the new implementation.

Finally, run_tests.py ran without errors and the comparisons by compare-runs.py returned only No errors found - OKAY!.

[codecov-commenter]

Codecov Report

Patch coverage: 64.17% and project coverage change: -0.22 ⚠️

Comparison is base (69ee732) 74.51% compared to head (934d32b) 74.29%.

❗ Current head 934d32b differs from pull request most recent head aec8259. Consider uploading reports for the commit aec8259 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #658      +/-   ##
==========================================
- Coverage   74.51%   74.29%   -0.22%     
==========================================
  Files         111      111              
  Lines        7572     7691     +119     
==========================================
+ Hits         5642     5714      +72     
- Misses       1930     1977      +47     

Impacted Files	Coverage Δ
src/haddock/gear/prepare_run.py	48.52% <45.67%> (-1.33%)	⬇️
src/haddock/gear/config.py	79.59% <62.50%> (-1.93%)	⬇️
src/haddock/gear/yaml2cfg.py	93.84% <83.33%> (-1.40%)	⬇️
tests/test_gear_config.py	100.00% <100.00%> (ø)
tests/test_gear_prepare_run.py	99.33% <100.00%> (+0.10%)	⬆️
tests/test_modules_general.py	97.27% <100.00%> (+0.12%)	⬆️

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[mgiulini]

added a few comments, I will test it asap!

[mgiulini]

I would return something here, like the paths to the saved file

[mgiulini]

is there any particular reason to have two different dict objects in output?

[VGPReys]

There is the original one cfg that only contains the ['default'] value and used in other parts of the code.
While the ycfg one contrains verything present in the default.yaml file loaded as a dict, used for the analysis of the agreement (type, range, choices, sizes) between user provided configuration and authorized one.

[rvhonorato]

Sorry I have absolutely no idea about this part of the code, will trust your judgment 🤞🏽

[mgiulini]

Runs nicely on a couple of examples, great addition @VGPReys!