Tackle Typing and Linting Errors #379
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Changes: - Replace `jnp.ones` input with `jr.normal`. - Reduce size of hidden state to 3. - Remove unused `datetime` import and commented lines. Fundamentally the problem is that the solve step can be unstable. This does not resolve that but instead chooses a set up which is less vulnerable to the instability.
- Rename to PRNGKeyT to differentiate from `jax.random` function - Change type to Array - see https://jax.readthedocs.io/en/latest/jep/9263-typed-keys.html#type-annotations-for-prng-keys
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This stops type-checkers worrying about escape-sequences.
Attributes of `HHMParameterSet` and `HMMPropertySet` are changed to read-only. This change means that instances of `NamedTuple` will implement these protocols.
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- Add annotations to the *GaussianHMMEmssions classes - Apply some small formatting changes to reduce line length in places
- Add annotations to the *GaussianMixtureHMMEmssions classes
Major changes:
- Fix an error in `_compute_all_transition_probs` which caused the
return array to be too short.
- The `filtered_probs` were being truncated twice instead of once.
- Replace `jaxtyping.Int` with `dynamax.typing.IntScalar` or `int`
- this reflects when integer scalar arrays are accepted
- `jaxtyping.[Dtype]` cannot be used directly for type checking
instead they must be used as part of an array.
- Fix the shape of `transition_matrix`:
- if transition_matrix has a leading timestep axis it should be of
length T-1 not of length T.
- Add annotation indicating that `transition_matrix` is an optional argument
- Raise ValueError when neither `transition_matrix` or `transition_fn`
provided.
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Summary
This PR is a Work In Progress.
Fix the current errors with type hints and some common linting errors.
Details
Commits
A brief categorisation of the commits:
Address review comment "Incorrect typing"
Linting Errors:
Fix Type Errors:
jr.PRNGKeywhich, as a function, isn't suitable for type hinting here.jaxtyping.Arrayas per suggestion heredynamax.typesmodule that defines a type for a key - I update this definition as per suggestion linked above.dynamax.types.PRNGKeyT(which is an alias forjaxtyping.Array) and sometimes directly asjaxtyping.Array.Enable runtime type checking:
Unrelated Changes: