Autoreduce v0.9

[ayush9pandey]

This PR proposes a major refactor and feature enhancement for AutoReduce:

• A revised source code structure that creates modules called System, Reduce, SSM, Solver.
• New compatibility modes for model imports: python-control NonlinearIOSystem, pyDMD system, SBML (as before)
• New examples from different application areas. Now in refactored examples folders: biological, ecological, canonical (standard examples), and cyber-physical. Credit: Jenny Tang
• A new test suite to validate new model reduction methods against standard set of model reduction examples. Credit: Jenny Tang
• Readthedocs documentation that includes examples, description of methods, and an API reference.
• CI/CD for package version control and for pypi updates
• Linting with ruff

[ayush9pandey]

@copilot review if changes described above are correctly implemented in the branch that will be merged. Note items to fix.

[Copilot]

@copilot review if changes described above are correctly implemented in the branch that will be merged. Note items to fix.

Here is a review of each item in the PR description against the current branch:

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✅ Revised source code structure with modules System, Reduce, SSM, Solver
All four modules are present:

• System → autoreduce/system/system.py
• Reduce → autoreduce/reductions/timescale.py
• SSM → autoreduce/solvers/ssm.py
• Solver (ODE) → autoreduce/solvers/ode.py

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✅ New compatibility modes: python-control NonlinearIOSystem, pyDMD, SBML

• python-control adapter: autoreduce/system/control.py with from_nonlinear_io_system()
• pyDMD reduction: autoreduce/reductions/projection/dmd.py with fit_dmd() and fit_dmdc()
• SBML: System.generate_sbml_model() / System.write_sbml() in system.py

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⚠️ New examples from biological, ecological, canonical, and cyber-physical

• examples/biological/ — ✅ present (6 notebooks + models)
• examples/ecological/ — ✅ present (Viral spread.ipynb)
• examples/canonical/ — ✅ present (Michaelis-Menten.ipynb, Parameter sensitivity.ipynb)
• examples/cyber-physical/ — ❌ missing — PR description says a cyber-physical folder should exist but it is not in the repository.

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⚠️ pyDMD model reduction: example demonstration in examples/canonical/
The DMD module (autoreduce/reductions/projection/dmd.py) is implemented, but there is no notebook in examples/canonical/ demonstrating its use. The PR description explicitly states "Example demonstration in examples/canonical" for this feature.

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✅ New test suite
Multiple test files covering system objects, ODE solvers, time-scale separation, and optional integrations (control adapter and pyDMD). All 19 tests pass (2 skipped for missing optional deps).

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✅ Readthedocs documentation
docs/ with Sphinx config, .readthedocs.yaml, and nblink files pointing to examples. API references for systems, reductions, and solvers are in place.

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✅ CI/CD for package version control and PyPI updates
Four workflows: test.yml, build.yml, lint.yml, and pypi-deploy.yml are all configured correctly.

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Items to fix:

1. examples/cyber-physical/ folder is missing — add the cyber-physical example(s) described in the PR.
2. No DMD example notebook in examples/canonical/ — add a notebook demonstrating the pyDMD-based reduction (fit_dmd / fit_dmdc) on a standard example.

[ayush9pandey]

Merging this PR will fix #10, #11, #13, #17, #18, #20, #21, #28 (and finish v0.9 milestone: https://github.com/ctsd-lab/AutoReduce/milestone/1)

[ayush9pandey]

@copilot review

[Copilot]

@copilot review

Here is the updated review against the current branch:

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✅ Revised source code structure with modules System, Reduce, SSM, Solver
All present: autoreduce/system/system.py (System), autoreduce/reductions/core.py (Reduce), autoreduce/solvers/ssm.py (SSM), autoreduce/solvers/ode.py (ODE). Public API is cleanly exported from autoreduce/__init__.py.

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✅ New compatibility modes: python-control NonlinearIOSystem, pyDMD, SBML
All three adapters are implemented and tested.

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✅ New examples: biological, ecological, canonical, and cyber-physical
All four folders now exist:

• examples/biological/ — 5 notebooks
• examples/ecological/ — Viral spread.ipynb
• examples/canonical/ — Michaelis Menten.ipynb, Parameter sensitivity.ipynb, QSS control input.ipynb
• examples/cyber-physical/ — Motor control.ipynb

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✅ New test suite
43 tests pass, 2 skipped (for optional deps). Covers system objects, ODE solver, time-scale separation, conservation laws, converters, and optional integrations.

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✅ Readthedocs documentation
docs/ with Sphinx config, .readthedocs.yaml, and nblink files for 7 example notebooks.

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✅ CI/CD for package version control and PyPI updates
Workflows: test.yml, build.yml, lint.yml, pypi-deploy.yml all configured.

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✅ Linting with ruff
One import-sort error in tests/test_converters.py was fixed in ec3c088. ruff check autoreduce tests now passes clean.

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All checklist items in the PR description are implemented. No blocking issues found.