Add thickness likelihood module and refactor existing likelihood functions

[Leguark]

Add Likelihood Module with Thickness and Gravity Functions

This PR introduces a new module structure for likelihood functions in gempy_probability:

• Create dedicated likelihoods module with implementations for:

  • apparent_thickness_likelihood - Moved from model examples
  • apparent_thickness_likelihood_II - New implementation that calculates thickness based on lithology ID and distance
  • gravity_inversion_likelihood - Basic implementation for gravity inversion

• Add test for the new thickness likelihood function that demonstrates how to:

  • Set up a custom grid for a well
  • Calculate thickness using the new method
  • Visualize the results

• Update development logs to mark completed tasks and add new ones

The new structure improves code organization and provides more flexible thickness calculation options.

[Leguark]

• Add better plotting API and update gradient tests #12
• Add probabilistic modeling API with model factory and runner #11
• [ENH] Refactor gravity inversion pipeline and add flexibility #10
• Add example files for gravity and petrophysics inversion #9
• Add benchmarking tests and examples generator for performance analysis #8
• Add thickness likelihood module and refactor existing likelihood functions #7 👈 (View in Graphite)
• Add posterior analysis functionality with saving and visualization #6
• Add probabilistic model examples and tests for GemPy #5
• Reorganize gempy_probability package structure and update imports #4
• Update version to 2025.1.0 and refactor version import #3
• main

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[Leguark]

Merge activity

• Jun 12, 8:22 AM UTC: A user started a stack merge that includes this pull request via Graphite.
• Jun 12, 8:32 AM UTC: Graphite rebased this pull request as part of a merge.
• Jun 12, 8:34 AM UTC: @Leguark merged this pull request with Graphite.