Add general parameters to haddock3-cfg client

[joaomcteixeira]

You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and you comply with the following criteria:

• You have stick to Python. Talk with us before adding other programming languages to HADDOCK3
• Your PR is about CNS
• Your code is well documented: proper docstrings and explanatory comments for those tricky parts
• You structured the code into small functions as much as possible. You can use classes if there's a (state) purpose
• code follows our coding style
• You wrote tests for the new code
• tox tests pass. Run tox command inside the repository folder
• -test.cfg examples execute without errors. Inside examples/ run python run_tests.py -b
• PR does not add any install dependencies unless permission granted by the HADDOCK team
• PR does not break licensing
• Your PR is about writing documentation for already existing code 🔥
• Your PR is about writing tests for already existing code

---

Now, haddock3-cfg can also output the general parameters for modules combined with those of the requested module.

[codecov-commenter]

Codecov Report

Merging #476 (ea827a9) into main (5abbdf3) will increase coverage by 0.10%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #476      +/-   ##
==========================================
+ Coverage   72.22%   72.32%   +0.10%     
==========================================
  Files          95       95              
  Lines        6080     6103      +23     
==========================================
+ Hits         4391     4414      +23     
  Misses       1689     1689              

Impacted Files	Coverage Δ
src/haddock/clis/cli_cfg.py	83.78% <100.00%> (+4.47%)	⬆️
src/haddock/gear/yaml2cfg.py	94.82% <100.00%> (+0.28%)	⬆️
tests/__init__.py	100.00% <100.00%> (ø)
tests/test_cli_cfg.py	100.00% <100.00%> (ø)
tests/test_gear_yaml2cfg.py	100.00% <100.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5abbdf3...ea827a9. Read the comment docs.

[amjjbonvin]

Do the global parameter vary per module? If not why not have a separate listing for those instead of adding the -g option to all modules?

[joaomcteixeira]

Global parameters do not vary per module. We can have a separate listing, but it should be in the same command line. For example:

haddock-cfg -m topoaa -g -> outputs also the general parameters
haddock-cfg -G -> outputs only the general parameters

I think these options should be kept in the same command-line because in this way there's a single place to read the docs. What do you think? I can make it in this same PR.

[amjjbonvin]

Sounds like a good idea!

[joaomcteixeira]

Add what we discussed @amjjbonvin . But Instead of haddock-cfg -G we can use:

haddock-cfg -g
haddock-cfg -m MODULE
haddock-cfg -m MODULE -g