feat: Perform all mesh-doctor checks at once

[alexbenedicto]

Closes #94

The goal of this PR is to create 2 new features called all_checks and main_checks that will be able to call every mesh-doctor feature already implemented that only performed "quality" checking of the mesh such as collocated_nodes, element_volumes.
The current list of all "checks" available is the following:
[ collocated_nodes, element_volumes, non_conformal, self_intersecting_elements, supported_elements ].

So now, using this following line:

mesh-doctor -i mesh_to_analyze.vtu all_checks

Is equivalent (currently) to performing these checks successively:

mesh-doctor -i mesh_to_analyze.vtu collocated_nodes
mesh-doctor -i mesh_to_analyze.vtu element_volumes
mesh-doctor -i mesh_to_analyze.vtu non_conformal
mesh-doctor -i mesh_to_analyze.vtu self_intersecting_elements
mesh-doctor -i mesh_to_analyze.vtu supported_elements

If you want to only perform the fastest checks, using this following line:

mesh-doctor -i mesh_to_analyze.vtu main_checks

Is equivalent (currently) to performing these checks successively:

mesh-doctor -i mesh_to_analyze.vtu collocated_nodes
mesh-doctor -i mesh_to_analyze.vtu element_volumes
mesh-doctor -i mesh_to_analyze.vtu self_intersecting_elements

The code was designed in a way to allow any new future "check" action to be easily added.

Major changes

1. While creating this PR, it felt appropriate to rename the folder "checks" by "actions" which is less ambiguous regarding the capabilities of mesh-doctor which can also perform operations on the mesh. The name "all_checks" makes now more sense.

2. Previously, most of the "check" actions did not have default parameters to use them which is now the case + every one of their argparse keyword is now unique amongst all features. You cannot encounter two times the keyword "tolerance" in the "check" actions.

3. import logging as now been replaced by the internal logging system configured in geos-utils which closes Improve mesh_doctor logging #41 .
   Add all parameters used as output in log.

4. Automatic documentation for mesh-doctor instead of hard-coded command line bash.
   Update documentation.

[paloma-martinez]

Thank you for this work, it will be very useful.

Could you separate the different checks in the log ? It is a bit crowded, the different sections would appear more clearly with just an additional line break for example

[dkachuma]

I haven't actually tried this but it looks good.

[paloma-martinez]

The log modification looks good to me.

I agree with the removal of expensive checks from default behaviour, but I find the term all_checks a bit misleading now...
I'd like to suggest adding another option that actually performs all tests and rename the one that only does the 3 main checks, so that we would have something like:

• main_checks that performs [ collocated_nodes, element_volumes, self_intersecting_elements ]
• all_checks that does [ collocated_nodes, element_volumes, non_conformal, self_intersecting_elements, supported_elements ], maybe with a warning that it may be long

[alexbenedicto]

@paloma-martinez Thank you for the feedback.
This can indeed be ambiguous and might need this new "main_checks" to be added as you suggest. It is only the code implementation that I need to think about to avoid maintaining two different mesh-doctor features "all_checks" and "main_checks" if the difference is only about what checks are called.

[dkachuma]

Looks good