Introduce petab.v1 package

[dweindl]

As discussed in #271, we need to accommodate the changes related to the upcoming PEtab v2. The goal is to move PEtab 1.0 functionality to a petab.v1 subpackage and PEtab 2.0 functionality to a petab.v2 subpackage.

This PR moves (almost) all code from the petab package to a petab.v1 sub-package. Keeps all non-private objects importable from their previous location, but issues DeprecationWarnings.

From the next release on, all consumers should change all from petab[.$x] import $y to from petab.v1[.$x] import $y.

Fixes a couple of sphinx-issues that occurred on the way. Some obscure sphinx-failures remain, but they aren't critical.

Also adds some missing __all__s.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 79.17143% with 729 lines in your changes missing coverage. Please review.

Project coverage is 75.32%. Comparing base (e8fdf3a) to head (58d0755).
Report is 91 commits behind head on develop.

Files with missing lines	Patch %	Lines
petab/v1/math/_generated/PetabMathExprParser.py	73.02%	140 Missing and 34 partials ⚠️
petab/v1/lint.py	72.19%	67 Missing and 32 partials ⚠️
petab/v1/parameter_mapping.py	66.66%	54 Missing and 11 partials ⚠️
petab/v1/models/pysb_model.py	61.41%	44 Missing and 5 partials ⚠️
petab/v1/visualize/plotter.py	83.76%	27 Missing and 17 partials ⚠️
petab/v1/visualize/plotting.py	86.91%	21 Missing and 18 partials ⚠️
petab/v1/visualize/lint.py	56.79%	25 Missing and 10 partials ⚠️
petab/v1/parameters.py	85.63%	12 Missing and 15 partials ⚠️
petab/v1/models/model.py	69.84%	18 Missing and 1 partial ⚠️
petab/v1/core.py	89.24%	10 Missing and 7 partials ⚠️
... and 27 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #282      +/-   ##
===========================================
- Coverage    75.65%   75.32%   -0.33%     
===========================================
  Files           40       69      +29     
  Lines         4141     4256     +115     
  Branches       893      898       +5     
===========================================
+ Hits          3133     3206      +73     
- Misses         745      787      +42     
  Partials       263      263              

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[dilpath]

Nice!

I looked at most files and didn't see any issues 👍 I looked at petab/v1 less since I guess it's mostly copied.

Is it possible to include this in CI by running the tests with both like so?

import petab as petabv0
import petab.v1

petab = petabv0
# run tests
petab = petab.v1

Should the tests also be split into tests/v1 and tests/v2?

[dweindl]

I looked at petab/v1 less since I guess it's mostly copied.

Yes.

Is it possible to include this in CI by running the tests with both like so?

import petab as petabv0
import petab.v1

petab = petabv0
# run tests
petab = petab.v1

For now, I would keep running tests through the deprecated functions. If they pass there, I don't have much doubt that they will work through petab.v1, as effectively everything was moved there. Once we remove the old modules, I would switch the tests.

Should the tests also be split into tests/v1 and tests/v2?

Yes, I think that makes sense. Will do that separately, though.