v1.3.0: modernise for Python 3.10–3.13 and bundle an updated PyDSTool

[jarmarshall]

Summary

Brings MuMoT up to date with current Python (3.10–3.13) and the current scientific Python stack (NumPy 2, SciPy, SymPy 1.14, Matplotlib, IPython 9, Notebook 7/JupyterLab), unpins dependencies, and removes the dependency on the unmaintained PyDSTool package. Also prepares the v1.3.0 release (see Release below).

PyDSTool

• A trimmed copy of PyDSTool 0.91.0 is bundled as mumot._vendor.pydstool. The first commit (f7c8a55) adds the upstream files unmodified, so git diff f7c8a55 -- mumot/_vendor shows every change; mumot/_vendor/pydstool/README.md lists them.
• Removed: AUTO, the compiled integrators (Dopri/Radau/ADMC), the Toolbox, and all distutils use.
• Ported: NumPy 2 names, SciPy API changes, a replacement (_cst.py) for the stdlib parser module removed in Python 3.10, and Python 3.13 locals() semantics (PEP 667). The _cst.py output was checked node-for-node against the real parser module on 180,000 random expressions.
• Fixed a PyCont bug: at a branch point, which branch got followed depended on floating-point rounding. It now uses the continuation tangent and the SVD null space, so the result is deterministic.

Continuation API

• New mumot/continuation.py: a backend-independent equilibrium-continuation API (SymPy symbols in, NumPy arrays out).
• MuMoTbifurcationView uses only this API and no longer does any PyDSTool name mangling. A native continuation implementation could replace PyDSTool by implementing two methods.

Dependencies and packaging

• Packaging moved to pyproject.toml (PEP 621), requiring Python ≥ 3.10.
• Dependencies have no upper bounds, but each has a tested lower bound. The new minimum_versions_job CI job installs exactly those minimum versions and runs the unit tests.
• Fresh installs on 3.10–3.13 have no conflicts (pip check) and no dependency cycles (pipdeptree -w fail).
• The one exact pin is antlr4-python3-runtime==4.11.*, which SymPy's LaTeX parser requires. It is tracked in Remove the exact antlr4-python3-runtime==4.11.* pin #418.

Code structure

• Removed the circular import between mumot.utils and the package; previously an uninstalled checkout could not be imported.
• Symbolic derivations moved from views to a new mumot.equations module, so the internal import graph is now acyclic.

Library compatibility fixes

• SymPy changed latex() on strings, simplify() evaluating derivatives, and subs() with non-numeric values. Without these fixes the van Kampen ODEs came out wrong for multi-species models.
• Matplotlib: 3D axes, tick labels and Arrow3D updated for current APIs.
• Notebook 7 and IPython 9 removed APIs MuMoT used; interactive figures now use the ipympl backend.
• Non-finite floats in widget state replaced with finite values, as non-finite values are not valid JSON in widget messages.
• Fixed complex-valued angles for the noise ellipses.
• Fixed two latent bugs: broken chmod calls and an undefined variable in utils.

CI, docs, Binder

• CI, tox, Read the Docs (config v2), Binder files and the installation docs updated.
• nbval (≥ 0.10) runs notebook cells without input history, which broke the documented %%model + mumot.parseModel(In[n]) pattern under test only. A root conftest.py makes nbval record history as Jupyter does.
• The nbval per-cell timeout is raised from 120 s to 600 s. Coverage tracing makes the symbolic noise calculations about 4× slower; without it they are no slower than in the previous release.

Release

• Binder: the README badge and all Getting Started Binder links now point at v1.3.0.
• CHANGELOG: has a complete v1.3.0 entry.
• Read the Docs: now fetches git tags, so the docs show the release version.
• about.rst: credits the bundled PyDSTool; the broken ERC link is fixed.
• Tag: the v1.3.0 tag still needs to be created on master after this PR is merged, not before. Pushing a v* tag triggers the Test PyPI and PyPI upload in CI, and the Binder links only work once the tag exists.
• Still to do by hand: reserve the DOI for this release in ORDA, then add the citation for release 1.3.0 to docs/source/about.rst.

Behaviour changes

• showNoiseEquations() and showNoiseSolutions() now render moments as ⟨η⟩, as the code intended. SymPy 1.4 silently skipped that substitution.
• The iopub rate-limit tweak was removed because it had no effect; pass --ServerApp.iopub_msg_rate_limit when starting Jupyter instead.
• AUTO-based curve types (limit-cycle continuation) are not available from the bundled PyDSTool. MuMoT never used them.

Testing

• Reference results come from the previous release run on Python 3.8 with its original pinned dependencies (SymPy 1.4, PyDSTool 0.91.0).
• Bifurcation diagrams: all 8 cases (1D/2D, folds, pitchforks, branch switching, Greek/protected symbol names) agree with the reference. Most branches match to ~1e-9; a few are traversed in the opposite direction or run slightly further along the same analytic curve.
• Symbolic outputs: all 60 comparable model getter results match the reference mathematically. These are now a unit test (tests/test_symbolic_regression.py); it fails if SymPy's default simplify is used again.
• New unit tests for the continuation API (fold, pitchfork branch switching, protected names) and for the vendored parser shim.
• CI is green on 3.10, 3.11, 3.12 and 3.13: 63 unit tests, the 5 test notebooks and the user manual (nbval), the manual's no-outputs check, and the Sphinx docs build.
• Minimum versions: minimum_versions_job installs the lowest allowed version of every dependency (Python 3.10) and passes the unit tests. Locally, the bifurcation results also match the reference on that set.
• Binder environment: reproduced the repo2docker setup locally (Python 3.12, requirements.txt, postBuild, JupyterLab 4.6 / Notebook 7). In Chromium, integrate(), stream() and bifurcation() rendered interactive ipympl figures and widgets with no errors, and a slider change redrew the figure. The real mybinder.org image build has not been tested.

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