Committor updates

[EnricoTrizio]

Description

Adds a few new functionalities to committor code:

• Use of separate datasets for the training (i.e., boundary and variational) via the separate_boundary_dataset key
• Function to precompute the derivatives of descriptors wrt position for faster and cheaper evaluation via the SmartDerivatives class and the descriptors_derivatives key. This required an unpdate of the requirements.txt to include torch-scatter but it's easy in pip and only affects the Python code (i.e., no need to trace it nor change anything on the PLUMED side)
• Better implementation of PairwiseDistances for selected pairs with slicing_pairs key
• Added the possibility of passing the colors kwarg to the plot_isolines_2D function rather than using a greys only for contour mode
• Moved committor tutorial to the tutorials
• Created committor example when computing descriptors using alanine
• Improved tests

Additionally it also fixes some late issues with micromamba, see #155. In detail:

• We switched from the deprectated GitHub action https://github.com/mamba-org/provision-with-micromamba to the new one https://github.com/mamba-org/setup-micromamba
• we pinned a stable version of micromamba as the new one (2.0) is still not working on Windows, this will be fixed in a following PR (see Update to latest micromamba #155 )

TODO

• New test for committor using also alanine and the preprocessing + smart derivatives

Status

• Ready to go

[codecov]

Codecov Report

Attention: Patch coverage is 96.90722% with 6 lines in your changes missing coverage. Please review.

Project coverage is 92.75%. Comparing base (69e702e) to head (65f9b6e).
Report is 33 commits behind head on main.

Additional details and impacted files