Select: support user-provided calibration results

[dilpath]

Currently, the design is that:

• a user can provide previously-calibrated models as user_calibrated_models
• the design of PEtab Select was changed to accommodate this. A model selection iteration now involves two stages: "calibration" and "post-calibration". pyPESTO will not see the user-provided calibration results until the "post-calibration" stage of each iteration.
• PEtab Select will put these models into the candidate space, instead of the uncalibrated versions
• pyPESTO still needs to skip these models

The purpose is that the path through model space is still reproducible, because models are not skipped.
TODO: fully handle this in PEtab Select, so pyPESTO never sees already-calibrated models, except when it asks PEtab Select for the final results.

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 91.66667% with 2 lines in your changes missing coverage. Please review.

Project coverage is 82.71%. Comparing base (d5eedc2) to head (0fdfae0).

Files with missing lines	Patch %	Lines
pypesto/select/method.py	86.66%	2 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1338      +/-   ##
===========================================
- Coverage    82.77%   82.71%   -0.06%     
===========================================
  Files          163      163              
  Lines        13907    13910       +3     
===========================================
- Hits         11511    11506       -5     
- Misses        2396     2404       +8     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[PaulJonasJost]

LGTM 👍🏼 Is the functionality provided in petab select already?

[Doresic]

Nice feature, thanks!

[dilpath]

Now handled on the PEtab Select side