add unit tests for deterministic logic#13
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lets you run the pipeline end to end without an acquisition rig. useful for smoke testing a fresh install, working on a laptop, and CI. - realtime_decoder/synthetic.py: SyntheticDataReceiver and SyntheticClient that match the surface of TrodesDataReceiver and TrodesClient. drop in replacements. non-blocking __next__ semantics so the polling loops in encoder/decoder/ripple work unchanged. - runscript.py picks the data source via config['datasource']. defaults to 'trodes' so every existing config keeps working. - config/demo_synthetic.yml is a 5 rank demo wired to the synthetic source. - README adds a 'running without acquisition hardware' section. spikes are poisson, marks gaussian, position walks a triangle wave along a single segment. not biologically realistic, the point is to exercise the data path and message plumbing. to try it: mpiexec -np 5 python -u runscript.py config/demo_synthetic.yml
most of the per-animal yamls duplicate the same sampling rates, ripple filter, gui colors, kinematics smoothing filter, mua, etc. drift is real and 'what is the canonical value of X' is currently unanswerable. - configs can declare `_extends: defaults.yml` and only override what is actually different. nested dicts deep merge key by key, lists and scalars replace. - config/defaults.yml holds the values stable across the SC*/fred/ginny configs. - runscript routes config loading through a new config_loader module that runs a small validator on the resolved dict. catches missing rank.supervisor, unknown algorithm, missing encoder.mark_dim, decoder ranks with no assignment, encoder.mark_dim != synthetic.mark_dim, etc. errors print one readable message and exit 2 before MPI workers spawn, instead of surfacing as IndexError deep in a rank. - config/demo_synthetic.yml now uses _extends, drops about 80 lines. - loader uses stdlib pyyaml instead of oyaml since python 3.7+ dicts preserve order. one fewer dep. backward compatible. verified all 16 existing per-animal configs still load and validate unchanged. follow up not in this PR: the SC*/fred/ginny configs can each be rewritten as _extends + overrides which would shrink them by roughly half. left as a separate diff so per-config behavior changes are auditable on their own.
36 tests covering the pure-python pieces of the codebase. these run on a plain `pip install pytest` without MPI or any acquisition hardware.
coverage:
- utils: normalize_to_probability (incl. nan handling), estimate_new_stats (vs numpy), apply_no_anim_boundary (1d + 2d)
- position: PositionBinStruct edges/centers/get_bin, TrodesPositionMapper (basic + clamp-above-1 edge case), KinematicsEstimator (first-sample, unsmoothed speed, FIR smoothing)
- transitions: sungod_transition_matrix shape, row sums equal 1 or 0, gap rows/cols zeroed, no NaNs in output
- config_loader: deep_merge (nested, list-replace, scalar-overrides-dict), load_config with and without _extends, circular extends detection, validate catches missing required keys / unknown algorithm / decoder rank without assignment / mark_dim mismatch with synthetic
- synthetic: receiver rejects bad datatype, lfp/spike/position emission shapes, returns None before activate, SyntheticClient fires startup callback after delay, records would-be ECU shortcut messages
tests/conftest.py installs a minimal mpi4py stub if the real mpi4py is not importable. several modules (base, position, synthetic) import mpi4py at module top, and mpi4py needs a system MPI build to install. the stub lets the deterministic tests run anywhere; if real mpi4py is present it's used instead.
setup.py: `extras_require={'test': ['pytest']}` and exclude tests from the installed package. also added pyyaml to install_requires since the config_loader uses it.
README: short Tests section.
to run:
pip install -e .[test]
pytest -q
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stacked on top of #11 (config defaults). until that lands, the diff here also shows the synthetic source + config_loader; once #10 and #11 merge GitHub will collapse this to just `tests/`, the setup.py edits, and the README section.
36 tests covering the pure-python pieces of the codebase. these run on a plain `pip install pytest` without MPI or any acquisition hardware.
what's covered
the mpi4py stub
several modules (`base`, `position`, `synthetic`) import `mpi4py` at module top, and `mpi4py` needs a system MPI build to install. that makes `pip install pytest` not enough by itself.
`tests/conftest.py` installs a minimal mpi4py stub if the real one is not importable. if real mpi4py is present (developer machine, CI image with MPI), the stub is skipped. the stub's data-path methods raise loudly if anything accidentally tries to use them in a test, so we don't get silent no-ops.
setup.py
README
to run:
```
pip install -e .[test]
pytest -q
```
not in this PR: tests for the MPI paths themselves, the ripple envelope filter (depends on ghostipy filter design), and gui_process. natural follow ups once this lands.