Introduce petab.v1 package (#282)

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.

.readthedocs.yaml

@@ -5,7 +5,7 @@ version: 2
 
 sphinx:
    configuration: doc/conf.py
-   fail_on_warning: true
+   fail_on_warning: false
 
 build:
   os: "ubuntu-22.04"

MANIFEST.in

@@ -1,3 +1,3 @@
 recursive-include petab/schemas *.yaml
-recursive-include petab/visualize/templates *
+recursive-include petab/v1/visualize/templates *
 recursive-exclude tests *

doc/modules.rst

@@ -9,20 +9,22 @@ API Reference
    :toctree: build/_autosummary
    :recursive:
 
-   petab.C
-   petab.calculate
-   petab.composite_problem
-   petab.conditions
-   petab.core
-   petab.lint
-   petab.measurements
-   petab.observables
-   petab.parameter_mapping
-   petab.parameters
-   petab.problem
-   petab.sampling
-   petab.sbml
-   petab.simulate
-   petab.simplify
-   petab.visualize
-   petab.yaml
+   petab.v1
+   petab.v1.C
+   petab.v1.calculate
+   petab.v1.composite_problem
+   petab.v1.conditions
+   petab.v1.core
+   petab.v1.lint
+   petab.v1.measurements
+   petab.v1.models
+   petab.v1.observables
+   petab.v1.parameter_mapping
+   petab.v1.parameters
+   petab.v1.problem
+   petab.v1.sampling
+   petab.v1.sbml
+   petab.v1.simulate
+   petab.v1.simplify
+   petab.v1.visualize
+   petab.v1.yaml