Tscode

- Solved bugfix in check_objects_compenetration.
- Updated compenetration_check warning printouts, specifying the number of compenetrations found.

- Reinstated the only_refined option at the end of optimization_refining.
- Solved bugfix in operators.

- renamed python_functions.py to numba_functions.py
- Decreased compenetration check threshold for close contacts to 0.5 A from 0.95 A. In this way, topological mistakes made by GFN-FF, that bind hydrogen atoms (d~0.89 A) will not automatically flag the structures as compenetrated, as this will most likely optimize fine when the theory level is raised to GFN2 or other.

- Changed library versions

- Changed numpy version to 1.20.3
- Added saturation check

- Various small bugfixes/graphic restyling
- Stuctures are optimized at embedder.options.theory_level before running the mtd_search> operator, and a FatalError is raised if they scramble during this process. This increases the robustness of the workflow by avoiding changes in the molecular graph if the input structure is bad.
- Added a warning printout system to the Embedder class, via logging and appending strings to the embedder.warnings list.
- Added a saturation and compenetration check for input molecules, that warns about potential bad geometries.