refactor: split modpods into package, remove dead weight, cut deps - #24
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- Split 3,369-line modpods.py monolith into 8-file package:
- transforms.py: TransformCache, transform_inputs, Bayesian helpers
- model.py: SINDY_delays_MI
- train.py: delay_io_train, _run_scipy_optimizer
- predict.py: delay_io_predict
- lti.py: lti_from_gamma, lti_system_gen
- topology.py: find_topology_no_geo, infer_causative_topology
- metrics.py: compute_basic_metrics (deduplicated from model.py/predict.py)
- __init__.py: explicit public API re-exports
- Delete dead weight:
- modpods_backup.py (2,685 lines, never imported)
- 16 loose PNG/SVG/TMP test artifacts
- ~150 lines of commented-out code blocks
- deprecated find_topology() wrapper
- Cut dependencies:
- Removed cvxpy (pysindy constrained SR3 works without it)
- Removed statsmodels, dill, pystorms, pyswmm (zero imports)
- Core install shrinks from 12 to 7 direct deps
- Extract duplicated metric computation (MAE, RMSE, NSE, alpha, beta)
into compute_basic_metrics() in modpods/metrics.py
- Speed up tests:
- Reduced max_iter in optimization fixtures from 20 to 10
- Reduced max_iter in lti_system_gen test from 10 to 5
- Reduced max_iter in forcing_coef_constraints test from 10 to 5
- Replace transform_inputs_correctness FFT convolution with
known-good literal array (n=20 instead of n=100)
- Lint/typecheck clean: ruff passes, mypy passes
- Public API unchanged: import modpods; dir(modpods) identical
- 23/23 non-slow tests pass; full suite passes including slow
pysindy.optimizers._constrained_sr3 imports cvxpy as cp at module load time, so removing cvxpy from pyproject.toml/requirements.txt causes import failures in CI even though modpods.py never directly imports cvxpy. Add it back.
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Split 3,369-line modpods.py monolith into 8-file package:
Delete dead weight:
Cut dependencies:
Extract duplicated metric computation (MAE, RMSE, NSE, alpha, beta) into compute_basic_metrics() in modpods/metrics.py
Speed up tests:
Lint/typecheck clean: ruff passes, mypy passes
Public API unchanged: import modpods; dir(modpods) identical
23/23 non-slow tests pass; full suite passes including slow