Respond to robot feedback

Author: jessegrabowski

pymc_extras/inference/laplace_approx/find_map.py

@@ -28,7 +28,7 @@
 )
 
 
-def _make_inital_point(model, initvals=None, random_seed=None, jitter_rvs=None):
+def _make_initial_point(model, initvals=None, random_seed=None, jitter_rvs=None):
     jitter_rvs = [] if jitter_rvs is None else jitter_rvs
 
     ipfn = make_initial_point_fn(
@@ -201,7 +201,7 @@ def find_MAP(
     frozen_model = freeze_dims_and_data(model)
     compile_kwargs = {} if compile_kwargs is None else compile_kwargs
 
-    initial_params = _make_inital_point(frozen_model, initvals, random_seed, jitter_rvs)
+    initial_params = _make_initial_point(frozen_model, initvals, random_seed, jitter_rvs)
 
     do_basinhopping = method == "basinhopping"
     minimizer_kwargs = optimizer_kwargs.pop("minimizer_kwargs", {})

pymc_extras/inference/laplace_approx/idata.py

@@ -35,7 +35,7 @@ def make_unpacked_variable_names(name, model: pm.Model) -> list[str]:
     return [f"{name}[{','.join(map(str, label))}]" for label in labels]
 
 
-def map_results_to_inferece_data(results: dict[str, Any], model: pm.Model | None = None):
+def map_results_to_inference_data(results: dict[str, Any], model: pm.Model | None = None):
     """
     Convert a dictionary of results to an InferenceData object.
 
@@ -51,7 +51,7 @@ def map_results_to_inferece_data(results: dict[str, Any], model: pm.Model | None
     idata: az.InferenceData
         An InferenceData object containing the results.
     """
-    model = pm.modelcontext(model)
+    model = pm.modelcontext(model) if model is None else model
     coords, dims = coords_and_dims_for_inferencedata(model)
 
     idata = az.convert_to_inference_data(results, coords=coords, dims=dims)
@@ -78,7 +78,7 @@ def laplace_draws_to_inferencedata(
     idata: az.InferenceData
         An InferenceData object containing the approximated posterior samples
     """
-    model = pm.modelcontext(model)
+    model = pm.modelcontext(model) if model is None else model
     chains, draws, *_ = posterior_draws[0].shape
 
     def make_rv_coords(name):
@@ -191,7 +191,7 @@ def add_fit_to_inference_data(
     idata: az.InferenceData
         The provided InferenceData, with the mean vector and covariance matrix added to the "fit" group.
     """
-    model = pm.modelcontext(model)
+    model = pm.modelcontext(model) if model is None else model
 
     variable_names, *_ = zip(*mu.point_map_info)
 
@@ -242,7 +242,7 @@ def add_data_to_inference_data(
     idata: az.InferenceData
         The provided InferenceData, with observed and constant data added.
     """
-    model = pm.modelcontext(model)
+    model = pm.modelcontext(model) if model is None else model
 
     if model.deterministics:
         expand_dims = {}
@@ -309,6 +309,7 @@ def optimizer_result_to_dataset(
     """
     if not isinstance(result, OptimizeResult):
         raise TypeError("result must be an instance of OptimizeResult")
+
     model = pm.modelcontext(model) if model is None else model
     variable_names, *_ = zip(*mu.point_map_info)
     unpacked_variable_names = reduce(

pymc_extras/inference/laplace_approx/laplace.py

@@ -34,7 +34,7 @@
 
 from pymc_extras.inference.laplace_approx.find_map import (
     _compute_inverse_hessian,
-    _make_inital_point,
+    _make_initial_point,
     find_MAP,
 )
 from pymc_extras.inference.laplace_approx.scipy_interface import scipy_optimize_funcs_from_loss
@@ -228,7 +228,6 @@ def fit_laplace(
     use_hess: bool | None = None,
     initvals: dict | None = None,
     random_seed: int | np.random.Generator | None = None,
-    return_raw: bool = False,
     jitter_rvs: list[pt.TensorVariable] | None = None,
     progressbar: bool = True,
     include_transformed: bool = True,
@@ -268,23 +267,13 @@ def fit_laplace(
          If None, the model's default initial values are used.
     random_seed : None | int | np.random.Generator, optional
         Seed for the random number generator or a numpy Generator for reproducibility
-    return_raw: bool | False, optinal
-        Whether to also return the full output of `scipy.optimize.minimize`
     jitter_rvs : list of TensorVariables, optional
         Variables whose initial values should be jittered. If None, all variables are jittered.
     progressbar : bool, optional
         Whether to display a progress bar during optimization. Defaults to True.
-    fit_in_unconstrained_space: bool, default False
-        Whether to fit the Laplace approximation in the unconstrained parameter space. If True, samples will be drawn
-        from a mean and covariance matrix computed at a point in the **unconstrained** parameter space. Samples will
-        then be transformed back to the original parameter space. This will guarantee that the samples will respect
-        the domain of prior distributions (for exmaple, samples from a Beta distribution will be strictly between 0
-        and 1).
-
-        .. warning::
-            This argument should be considered highly experimental. It has not been verified if this method produces
-            valid draws from the posterior. **Use at your own risk**.
-
+    include_transformed: bool, default True
+        Whether to include transformed variables in the output. If True, transformed variables will be included in the
+        output InferenceData object. If False, only the original variables will be included.
     gradient_backend: str, default "pytensor"
         The backend to use for gradient computations. Must be one of "pytensor" or "jax".
     chains: int, default: 2
@@ -365,7 +354,7 @@ def fit_laplace(
         # The user didn't use `use_hess` or `use_hessp` (or an optimization method that returns an inverse Hessian), so
         # we have to go back and compute the Hessian at the MAP point now.
         frozen_model = freeze_dims_and_data(model)
-        initial_params = _make_inital_point(frozen_model, initvals, random_seed, jitter_rvs)
+        initial_params = _make_initial_point(frozen_model, initvals, random_seed, jitter_rvs)
 
         _, f_hessp = scipy_optimize_funcs_from_loss(
             loss=-frozen_model.logp(jacobian=False),
@@ -405,9 +394,9 @@ def fit_laplace(
             .rename({"temp_chain": "chain", "temp_draw": "draw"})
         )
 
-        new_posterior.update(unstack_laplace_draws(new_posterior, model)).drop_vars(
-            "laplace_approximation"
-        )
+        new_posterior.update(unstack_laplace_draws(new_posterior, model))
+        new_posterior = new_posterior.drop_vars("laplace_approximation")
+
         idata.posterior.update(new_posterior)
 
     return idata