v2: Paths as pathlib.Path & validate assignment

[dweindl]

For petab.v2 pydantic models, change path attributes to pathlib.Path, and validate assignments.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.88%. Comparing base (f9bad6a) to head (b6f7136).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #410      +/-   ##
==========================================
+ Coverage   73.86%   73.88%   +0.02%     
==========================================
  Files          62       62              
  Lines        6764     6771       +7     
  Branches     1194     1196       +2     
==========================================
+ Hits         4996     5003       +7     
  Misses       1308     1308              
  Partials      460      460              

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[dilpath]

For multiple e.g. measurement tables, are the (relative) paths stored with the table names? If so, is there a method for users to add a table via a path, to a pre-existing list of measurement tables? If not, how should multiple tables be written to disk? Manually specify each individual table filename each write?

[dweindl]

For multiple e.g. measurement tables, are the (relative) paths stored with the table names?

Not yet.

If not, how should multiple tables be written to disk? Manually specify each individual table filename each write?

To be decided.

[dweindl]

We should probably drop ProblemConfig from petab.Problem and keep only the relevant info there, and then store relative paths in the *Table objects. Anything else will be rather inconvenient. With having those filepaths in both the *Table objects and ProblemConfig things will get out of sync.

[dilpath]

Yes, moving the information to the table objects sounds nice to me 👍 Default filenames so that we can still have some kind of problem.to_files_generic would also be nice.