Added some example notebooks

[along4]

This pull request involves several updates to the pleiades project, focusing on enhancing the Isotope and IsotopeParameters classes, updating the SAMMY parameter file handling, and adding logging capabilities. The most important changes include adding logging, updating the IsotopeParameters class, and modifying the SAMMY parameter file handling.

Logging Enhancements:

• src/pleiades/sammy/parameters/isotope.py: Added logging initialization with file logging and replaced ValueError raises with _log_and_raise_error to log errors before raising exceptions. [1] [2] [3] [4]

Class and Method Updates:

• src/pleiades/core/models.py: Modified the Isotope class to remove the upper limit constraint on the abundance field.
• src/pleiades/sammy/parameters/isotope.py: Updated the IsotopeParameters class to include detailed comments and added a new where_am_i variable for better logging context. [1] [2] [3]

SAMMY Parameter File Handling:

• src/pleiades/sammy/parameters/isotope.py: Added notes indicating that the extended format is currently not supported and updated the spin group parsing logic. [1] [2] [3] [4] [5]
• src/pleiades/sammy/notes/parfile_notes.md: Added documentation outlining the structure and usage of the parfile.py module, including imports, logger initialization, enums, classes, and methods.

Notebook Updates:

• notebook/samexm/ex012/ex012a.ipynb: Added a new Jupyter notebook based on example 12 from the SAMMY repository, including code cells for importing modules, reading SAMMY parameters, and writing them to an output file.
• notebook/samexm/ex012/ex012a.par: Updated the parameter file with new data values for SAMMY parameters.

[KedoKudo]

@along4 Thanks for fixing the issues (and apologize for not being able to review it due to other commitments) . There are still three left as reported by pre-commit:

• notebook/samexm/ex027/ex027.ipynb is empty
• src/pleiades/sammy/parameters/isotope.py:153:43: ARG003 Unused class method argument: extended
  • If it is clear that extended format will never be supported, we can safely remove it from the function signature.
  • Alternatively, a warning or "not implemented" error can be used to inform the users
• src/pleiades/sammy/parameters/radius.py:663:9: F841 Local variable where_am_i is assigned to but never used
  • it seems like a log entry for where_am_i is missing, but if this is not needed anymore, it is better to remove it.

[along4]

@KedoKudo, no worries! I had time today to work out most of the bugs before the merge.

I think I am going to work on the parameters a bit more tonight and tomorrow. I would like to get an update functionality going to merge parfiles soon.