Fix/thicknesses_

[AngRodrigues]

Summary of major changes:

• Thickness outputs from all thickness calculators are now merged
• LPF version pinned to 1.4
• Added folder with datasets in map2loop/_datasets/geodata_files/hamersley. The idea behind this is to have a data loading function, e.g., at the moment load_hamersley_geology() returns a gdf with the geology; structure and dtm are available, and others will be added later on. This is quite useful for tests, but should also be useful for when we implement [Feature Request] - create map2loop project from geopandas array not file paths #74. The only thing about this is the location, which implies a long import: from map2loop._datasets.geodata_files.hamersley import load_hamersley_geology. Happy to change the file location - does anyone has a suggestion?
• Minimum fault length is now a parameter of the config file, and it actually removes the faults with length under defined value.
• Removed the project.set_minimum_fault_length method to avoid users setting the parameter twice.
• added all_basal_contacts object which are abnormal+basal contacts , and basal_contacts holds only the basal. Reconstruction of sampled_basal_contacts is based on basal_contacts
• changed the thickness_calculator_alpha to be coherent with the logic of the other thickness calculators
• added tests for some of the functions in mapdata.py
• added tests for thickness_compute in project.py
• rewrote tests for all thickness calculators independently (now without having to run the project)

summary of other minor modifications:

• tmpfile is now used to create the localGdalfile
• changed to f"" strings where possible
• change from os.path.join to pathlib.Path where possible
• added geopandas to csv converter in mapdata (it was on a #TODO)
• added check and error message to make sure that all units in user_defined_stratigraphic_column are in the geology file (otherwise project creation fails; at least now user has a warning).
• renamed distance to stratigraphic_distance in basal_contacts creation
• removed set_ and get_thickness_calculator
• rectified minor typos in the thickness calculators
• added a Linalgerror catch/pass for the InterpolatedStructure

Fixes #86
Fixes #110
Fixes #111
Fixes #12

Type of change

• Bug fix (non-breaking change which fixes an issue)
• Test improvement

How Has This Been Tested?

The branch is fix/thicknesses_AR_2.

Checklist:

• This branch is up-to-date with master
• All gh-action checks are passing
• I have performed a self-review of my own code
• My code follows the style guidelines of this project
• I have commented my code, particularly in hard-to-understand areas
• I have added tests that prove my fix is effective or that my feature works
• My tests run with pytest from the map2loop folder
• New and existing tests pass locally with my changes

[lachlangrose]

I haven't reviewed or tested the code but I have made some suggestions within the code.

My main comment for this PR is that the changes to the thickness calculators have not been implemented in the modular framework of map2loop. Instead of setting the list of thickness calculators within the method calling the thickness calculators, the list of thickness calculators should be managed by the project class. The default list can be hard coded using the current three, but the user should be able to call set_thickness_calculators and provide a custom list of thickness calculators.

This would mean, if the thicknesss calculators have any parameters e.g. the threshold angle for the structure point, or the interpolator type for the interpolated structure these could be set by the user and the thickness calculator objects can be set.

[AngRodrigues]

I think the documentation doesn't need to be built for all branches. We can make it only run on master release. I am also not sure whether documentation build/deploy should just be a manually run item that is triggered on release but can also just be run manually. This could be the same issue as the package building, it really only needs to run on master not on other branches.

@lachlangrose, I agree. Added these changes to the workflow in this PR; left the sdist jobs so that the tests run on the branch.

[AngRodrigues]

Edits on 1/11/2024:

• updated methods for minimum_fault_length
• minimum fault length calculated from project's bbox, if not defined by user in the config_dictionary.
• thickness outputs can be still merged, but modularity has been added as suggested. User can set up to 5 thickness calculators (default is InterpolatedStructure).
• Methods set_thickness_calculator and get_thickness_calculator are available again, and used likeso:

from map2loop.thickness_calculator import ThicknessCalculatorAlpha, InterpolatedStructure, StructuralPoint

[..set up the project..]

project.set_thickness_calculator([StructuralPoint(), InterpolatedStructure()])
project.get_thickness_calculator()

Output:
['StructuralPoint', 'InterpolatedStructure']

• LPF stores results and name of the thickness calculator as a new field in the LPF. This works with the LPF branch here - https://github.com/Loop3D/LoopProjectFile/tree/fix_thicknesses
• Added ignore codes both for lithology and faults (works by feature name, and similar to the existing method). Added methods for set and get with _ignore_lithology_codes() and _ignore_fault_codes(). Example of working example code to achieve this can be seen in map2loop/tests/project/test_ignore_codes_setters_getters.py.
• Added and updated appropriate tests for all new added features.
• updated CI to run docs and builds workflows only on master branch.
• added small fixes for:

• Fixes add DependecyCheckerClass #143
• Fixes [Documentation] - update readme #137
• Fixes [Bug] - CI failing due to GA server time out #119

@lachlangrose @rabii-chaarani the PR is ready for re-review now.
Thank you!