diff --git a/CHANGELOG.md b/CHANGELOG.md index ceb9b8e00..8eb58aef4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,9 @@ ### Maintenance and fixes * Fix bug in predictions with models using HSGP (#780) +* Fix `get_model_covariates()` utility function (#801) +* Upgrade PyMC dependency to >= 5.13 (#803) +* Use `pm.compute_deterministics()` to compute deterministics when bayeux based samplers are used (#803) ### Documentation diff --git a/bambi/__init__.py b/bambi/__init__.py index 660d6724c..fdec8ec16 100644 --- a/bambi/__init__.py +++ b/bambi/__init__.py @@ -4,7 +4,7 @@ from pymc import math -from .backend import PyMCModel +from .backend import inference_methods, PyMCModel from .config import config from .data import clear_data_home, load_data from .families import Family, Likelihood, Link @@ -25,6 +25,7 @@ "Formula", "clear_data_home", "config", + "inference_methods", "load_data", "math", ] diff --git a/bambi/backend/__init__.py b/bambi/backend/__init__.py index 6ee2a4aa3..daef1924c 100644 --- a/bambi/backend/__init__.py +++ b/bambi/backend/__init__.py @@ -1,3 +1,4 @@ from .pymc import PyMCModel +from .inference_methods import inference_methods -__all__ = ["PyMCModel"] +__all__ = ["inference_methods", "PyMCModel"] diff --git a/bambi/backend/inference_methods.py b/bambi/backend/inference_methods.py new file mode 100644 index 000000000..900d9c262 --- /dev/null +++ b/bambi/backend/inference_methods.py @@ -0,0 +1,119 @@ +import importlib +import inspect +import operator + +import pymc as pm + + +class InferenceMethods: + """Obtain a dictionary of available inference methods for Bambi + models and or the default kwargs of each inference method. + """ + + def __init__(self): + # In order to access inference methods, a bayeux model must be initialized + self.bayeux_model = bayeux_model() + self.bayeux_methods = self._get_bayeux_methods(bayeux_model()) + self.pymc_methods = self._pymc_methods() + + def _get_bayeux_methods(self, model): + # Bambi only supports bayeux MCMC methods + mcmc_methods = model.methods.get("mcmc") + return {"mcmc": mcmc_methods} + + def _pymc_methods(self): + return {"mcmc": ["mcmc"], "vi": ["vi"]} + + def _remove_parameters(self, fn_signature_dict): + # Remove 'pm.sample' parameters that are irrelevant for Bambi users + params_to_remove = [ + "progressbar", + "progressbar_theme", + "var_names", + "nuts_sampler", + "return_inferencedata", + "idata_kwargs", + "callback", + "mp_ctx", + "model", + ] + return {k: v for k, v in fn_signature_dict.items() if k not in params_to_remove} + + def get_kwargs(self, method): + """Get the default kwargs for a given inference method. + + Parameters + ---------- + method : str + The name of the inference method. + + Returns + ------- + dict + The default kwargs for the inference method. + """ + if method in self.bayeux_methods.get("mcmc"): + bx_method = operator.attrgetter(method)( + self.bayeux_model.mcmc # pylint: disable=no-member + ) + return bx_method.get_kwargs() + elif method in self.pymc_methods.get("mcmc"): + return self._remove_parameters(get_default_signature(pm.sample)) + elif method in self.pymc_methods.get("vi"): + return get_default_signature(pm.ADVI.fit) + else: + raise ValueError( + f"Inference method '{method}' not found in the list of available" + " methods. Use `bmb.inference_methods.names` to list the available methods." + ) + + @property + def names(self): + return {"pymc": self.pymc_methods, "bayeux": self.bayeux_methods} + + +def bayeux_model(): + """Dummy bayeux model for obtaining inference methods. + + A dummy model is needed because algorithms are dynamically determined at + runtime, based on the libraries that are installed. A model can give + programmatic access to the available algorithms via the `methods` attribute. + + Returns + ------- + bayeux.Model + A dummy model with a simple quadratic likelihood function. + """ + if importlib.util.find_spec("bayeux") is None: + return {"mcmc": []} + + import bayeux as bx # pylint: disable=import-outside-toplevel + + return bx.Model(lambda x: -(x**2), 0.0) + + +def get_default_signature(fn): + """Get the default parameter values of a function. + + This function inspects the signature of the provided function and returns + a dictionary containing the default values of its parameters. + + Parameters + ---------- + fn : callable + The function for which default argument values are to be retrieved. + + Returns + ------- + dict + A dictionary mapping argument names to their default values. + + """ + defaults = {} + for key, val in inspect.signature(fn).parameters.items(): + if val.default is not inspect.Signature.empty: + defaults[key] = val.default + return defaults + + +inference_methods = InferenceMethods() diff --git a/bambi/backend/pymc.py b/bambi/backend/pymc.py index 82b646ebe..75a1fe318 100644 --- a/bambi/backend/pymc.py +++ b/bambi/backend/pymc.py @@ -1,5 +1,4 @@ import functools -import importlib import logging import operator import traceback @@ -14,6 +13,7 @@ import pytensor.tensor as pt from pytensor.tensor.special import softmax +from bambi.backend.inference_methods import inference_methods from bambi.backend.links import cloglog, identity, inverse_squared, logit, probit, arctan_2 from bambi.backend.model_components import ConstantComponent, DistributionalComponent from bambi.utils import get_aliased_name @@ -47,8 +47,8 @@ def __init__(self): self.model = None self.spec = None self.components = {} - self.bayeux_methods = _get_bayeux_methods() - self.pymc_methods = {"mcmc": ["mcmc"], "vi": ["vi"]} + self.bayeux_methods = inference_methods.names["bayeux"] + self.pymc_methods = inference_methods.names["pymc"] def build(self, spec): """Compile the PyMC model from an abstract model specification. @@ -253,8 +253,13 @@ def _run_mcmc( return idata def _clean_results(self, idata, omit_offsets, include_mean, idata_from): - for group in idata.groups(): + # Before doing anything, make sure we compute deterministics. + if idata_from == "bayeux": + idata.posterior = pm.compute_deterministics( + idata.posterior, model=self.model, merge_dataset=True, progressbar=False + ) + for group in idata.groups(): getattr(idata, group).attrs["modeling_interface"] = "bambi" getattr(idata, group).attrs["modeling_interface_version"] = __version__ @@ -262,36 +267,41 @@ def _clean_results(self, idata, omit_offsets, include_mean, idata_from): offset_vars = [var for var in idata.posterior.data_vars if var.endswith("_offset")] idata.posterior = idata.posterior.drop_vars(offset_vars) - # Drop variables and dimensions associated with LKJ prior - vars_to_drop = [var for var in idata.posterior.data_vars if var.startswith("_LKJ")] - dims_to_drop = [dim for dim in idata.posterior.dims if dim.startswith("_LKJ")] + # NOTE: + # This has not had an effect for a while since we haven't been supporting LKJ prior lately. - idata.posterior = idata.posterior.drop_vars(vars_to_drop) - idata.posterior = idata.posterior.drop_dims(dims_to_drop) + # Drop variables and dimensions associated with LKJ prior + # vars_to_drop = [var for var in idata.posterior.data_vars if var.startswith("_LKJ")] + # dims_to_drop = [dim for dim in idata.posterior.dims if dim.startswith("_LKJ")] + # idata.posterior = idata.posterior.drop_vars(vars_to_drop) + # idata.posterior = idata.posterior.drop_dims(dims_to_drop) dims_original = list(self.model.coords) # Identify bayeux idata and rename dims and coordinates to match PyMC model if idata_from == "bayeux": - pymc_model_dims = [dim for dim in dims_original if "_obs" not in dim] - bayeux_dims = [ - dim for dim in idata.posterior.dims if not dim.startswith(("chain", "draw")) - ] - cleaned_dims = dict(zip(bayeux_dims, pymc_model_dims)) + cleaned_dims = { + f"{dim}_0": dim + for dim in dims_original + if not dim.endswith("_obs") and f"{dim}_0" in idata.posterior.dims + } idata = idata.rename(cleaned_dims) - # Discard dims that are in the model but unused in the posterior + # Don't select dims that are in the model but unused in the posterior dims_original = [dim for dim in dims_original if dim in idata.posterior.dims] # This does not add any new coordinate, it just changes the order so the ones # ending in "__factor_dim" are placed after the others. - dims_group = [c for c in dims_original if c.endswith("__factor_dim")] + dims_group = [dim for dim in dims_original if dim.endswith("__factor_dim")] # Keep the original order in dims_original dims_original_set = set(dims_original) - set(dims_group) - dims_original = [c for c in dims_original if c in dims_original_set] + dims_original = [dim for dim in dims_original if dim in dims_original_set] dims_new = ["chain", "draw"] + dims_original + dims_group - idata.posterior = idata.posterior.transpose(*dims_new) + + # Drop unused dimensions before transposing + dims_to_drop = [dim for dim in idata.posterior.dims if dim not in dims_new] + idata.posterior = idata.posterior.drop_dims(dims_to_drop).transpose(*dims_new) # Compute the actual intercept in all distributional components that have an intercept for pymc_component in self.distributional_components.values(): @@ -338,8 +348,7 @@ def _run_laplace(self, draws, omit_offsets, include_mean): Mainly for pedagogical use, provides reasonable results for approximately Gaussian posteriors. The approximation can be very poor for some models - like hierarchical ones. Use ``mcmc``, ``vi``, or JAX based MCMC methods - for better approximations. + like hierarchical ones. Use MCMC or VI methods for better approximations. Parameters ---------- @@ -388,10 +397,6 @@ def constant_components(self): def distributional_components(self): return {k: v for k, v in self.components.items() if isinstance(v, DistributionalComponent)} - @property - def inference_methods(self): - return {"pymc": self.pymc_methods, "bayeux": self.bayeux_methods} - def _posterior_samples_to_idata(samples, model): """Create InferenceData from samples. @@ -431,22 +436,3 @@ def _posterior_samples_to_idata(samples, model): idata = pm.to_inference_data(pm.backends.base.MultiTrace([strace]), model=model) return idata - - -def _get_bayeux_methods(): - """Gets a dictionary of usable bayeux methods if the bayeux package is installed - within the user's environment. - - Returns - ------- - dict - A dict where the keys are the module names and the values are the methods - available in that module. - """ - if importlib.util.find_spec("bayeux") is None: - return {"mcmc": []} - - import bayeux as bx # pylint: disable=import-outside-toplevel - - # Dummy log density to get access to all methods - return bx.Model(lambda x: -(x**2), 0.0).methods diff --git a/bambi/backend/terms.py b/bambi/backend/terms.py index a33b40d64..ed2a2e02c 100644 --- a/bambi/backend/terms.py +++ b/bambi/backend/terms.py @@ -110,9 +110,13 @@ def build(self, spec): response_dims = list(spec.response_component.response_term.coords) dims = list(self.coords) + response_dims + coef = self.build_distribution(self.term.prior, label, dims=dims, **kwargs) + # Squeeze ensures we don't have a shape of (n, 1) when we mean (n, ) # This happens with categorical predictors with two levels and intercept. - coef = self.build_distribution(self.term.prior, label, dims=dims, **kwargs).squeeze() + # See https://github.com/pymc-devs/pymc/issues/7246 + if len(coef.shape.eval()) == 2 and coef.shape.eval()[-1] == 1: + coef = pt.specify_broadcastable(coef, 1).squeeze() coef = coef[self.term.group_index] return coef, predictor diff --git a/bambi/families/univariate.py b/bambi/families/univariate.py index fa45c43a2..93b91785e 100644 --- a/bambi/families/univariate.py +++ b/bambi/families/univariate.py @@ -403,7 +403,7 @@ def transform_backend_eta(eta, kwargs): def transform_backend_kwargs(kwargs): # P(Y = k) = F(threshold_k - eta) * \prod_{j=1}^{k-1}{1 - F(threshold_j - eta)} p = kwargs.pop("p") - n_columns = p.type.shape[-1] + n_columns = p.shape.eval()[-1] p = pt.concatenate( [ pt.shape_padright(p[..., 0]), diff --git a/bambi/interpret/utils.py b/bambi/interpret/utils.py index cbb7bde19..b06f97c11 100644 --- a/bambi/interpret/utils.py +++ b/bambi/interpret/utils.py @@ -258,6 +258,9 @@ def get_model_covariates(model: Model) -> np.ndarray: flatten_covariates = [item for sublist in covariates for item in sublist] + # Don't include non-covariate names (#797) + flatten_covariates = [name for name in flatten_covariates if name in model.data] + return np.unique(flatten_covariates) diff --git a/bambi/models.py b/bambi/models.py index ecb57700f..74286dbed 100644 --- a/bambi/models.py +++ b/bambi/models.py @@ -267,7 +267,7 @@ def fit( Finally, ``"laplace"``, in which case a Laplace approximation is used and is not recommended other than for pedagogical use. To get a list of JAX based inference methods, call - ``model.backend.inference_methods['bayeux']``. This will return a dictionary of the + ``bmb.inference_methods.names['bayeux']``. This will return a dictionary of the available methods such as ``blackjax_nuts``, ``numpyro_nuts``, among others. init : str Initialization method. Defaults to ``"auto"``. The available methods are: @@ -307,7 +307,7 @@ def fit( ------- An ArviZ ``InferenceData`` instance if inference_method is ``"mcmc"`` (default), "laplace", or one of the MCMC methods in - ``model.backend.inference_methods['bayeux']['mcmc]``. + ``bmb.inference_methods.names['bayeux']['mcmc]``. An ``Approximation`` object if ``"vi"``. """ method = kwargs.pop("method", None) diff --git a/docs/notebooks/alternative_samplers.ipynb b/docs/notebooks/alternative_samplers.ipynb index 24d610d96..7610df6d6 100644 --- a/docs/notebooks/alternative_samplers.ipynb +++ b/docs/notebooks/alternative_samplers.ipynb @@ -15,9 +15,17 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n" + ] + } + ], "source": [ "import arviz as az\n", "import bambi as bmb\n", @@ -62,7 +70,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -74,12 +82,12 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "We can call `model.backend.inference_methods` that returns a nested dictionary of the backends and list of inference methods." + "We can call `bmb.inference_methods.names` that returns a nested dictionary of the backends and list of inference methods." ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 27, "metadata": {}, "outputs": [ { @@ -100,47 +108,16 @@ " 'flowmc_realnvp_hmc',\n", " 'flowmc_realnvp_mala',\n", " 'numpyro_hmc',\n", - " 'numpyro_nuts'],\n", - " 'optimize': ['jaxopt_bfgs',\n", - " 'jaxopt_gradient_descent',\n", - " 'jaxopt_lbfgs',\n", - " 'jaxopt_nonlinear_cg',\n", - " 'optimistix_bfgs',\n", - " 'optimistix_chord',\n", - " 'optimistix_dogleg',\n", - " 'optimistix_gauss_newton',\n", - " 'optimistix_indirect_levenberg_marquardt',\n", - " 'optimistix_levenberg_marquardt',\n", - " 'optimistix_nelder_mead',\n", - " 'optimistix_newton',\n", - " 'optimistix_nonlinear_cg',\n", - " 'optax_adabelief',\n", - " 'optax_adafactor',\n", - " 'optax_adagrad',\n", - " 'optax_adam',\n", - " 'optax_adamw',\n", - " 'optax_adamax',\n", - " 'optax_amsgrad',\n", - " 'optax_fromage',\n", - " 'optax_lamb',\n", - " 'optax_lion',\n", - " 'optax_noisy_sgd',\n", - " 'optax_novograd',\n", - " 'optax_radam',\n", - " 'optax_rmsprop',\n", - " 'optax_sgd',\n", - " 'optax_sm3',\n", - " 'optax_yogi'],\n", - " 'vi': ['tfp_factored_surrogate_posterior']}}" + " 'numpyro_nuts']}}" ] }, - "execution_count": 4, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "methods = model.backend.inference_methods\n", + "methods = bmb.inference_methods.names\n", "methods" ] }, @@ -153,7 +130,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 28, "metadata": {}, "outputs": [ { @@ -162,7 +139,7 @@ "{'mcmc': ['mcmc'], 'vi': ['vi']}" ] }, - "execution_count": 5, + "execution_count": 28, "metadata": {}, "output_type": "execute_result" } @@ -180,36 +157,36 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['tfp_hmc',\n", - " 'tfp_nuts',\n", - " 'tfp_snaper_hmc',\n", - " 'blackjax_hmc',\n", - " 'blackjax_chees_hmc',\n", - " 'blackjax_meads_hmc',\n", - " 'blackjax_nuts',\n", - " 'blackjax_hmc_pathfinder',\n", - " 'blackjax_nuts_pathfinder',\n", - " 'flowmc_rqspline_hmc',\n", - " 'flowmc_rqspline_mala',\n", - " 'flowmc_realnvp_hmc',\n", - " 'flowmc_realnvp_mala',\n", - " 'numpyro_hmc',\n", - " 'numpyro_nuts']" + "{'mcmc': ['tfp_hmc',\n", + " 'tfp_nuts',\n", + " 'tfp_snaper_hmc',\n", + " 'blackjax_hmc',\n", + " 'blackjax_chees_hmc',\n", + " 'blackjax_meads_hmc',\n", + " 'blackjax_nuts',\n", + " 'blackjax_hmc_pathfinder',\n", + " 'blackjax_nuts_pathfinder',\n", + " 'flowmc_rqspline_hmc',\n", + " 'flowmc_rqspline_mala',\n", + " 'flowmc_realnvp_hmc',\n", + " 'flowmc_realnvp_mala',\n", + " 'numpyro_hmc',\n", + " 'numpyro_nuts']}" ] }, - "execution_count": 7, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "methods[\"bayeux\"][\"mcmc\"]" + "methods[\"bayeux\"]" ] }, { @@ -242,9 +219,46 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": {}, "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "909c6a6f539145ab8348ebdeb1d42a3b", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Output()" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
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-       ".xr-attrs dt, dd {\n",
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        "\t> sample_stats"
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-     "execution_count": 8,
+     "execution_count": 7,
      "metadata": {},
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     "Different backends have different naming conventions for the parameters specific to that MCMC method. Thus, to specify backend-specific parameters, pass your own `kwargs` to the `fit` method.\n",
     "\n",
-    "Each algorithm has a `.get_kwargs()` method that tells you how it will be called, and what functions are being called."
+    "The following can be performend to identify the kwargs specific to each method."
    ]
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   {
@@ -1542,7 +1557,7 @@
     }
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    "source": [
-    "bx.Model.from_pymc(model.backend.model).mcmc.blackjax_nuts.get_kwargs()"
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    ]
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@@ -3100,7 +3153,7 @@
        "\t> sample_stats"
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@@ -3126,9 +3179,46 @@
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+      "text/plain": [
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+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "
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+      ],
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+      "text/html": [
+       "
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+       "
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+      "text/plain": [
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@@ -3140,8 +3230,8 @@
        "              
  • created_at :
    2024-04-13T05:36:30.303342+00:00
    arviz_version :
    0.18.0
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    • \n",
        "                      \n",
        "                  \n",
        "            \n",
        "            \n",
        "            
  • \n",
-       "                  \n",
-       "                  \n",
+       "                  \n",
+       "                  \n",
        "                  
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        "                  
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        "                      
  • created_at :
    2024-04-13T05:36:30.304788+00:00
    arviz_version :
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    modeling_interface_version :
    0.13.1.dev25+g1e7f677e.d20240413

    • \n",
        "                      \n",
        "                  \n",
        "            \n",
@@ -4325,7 +4415,8 @@
        "  grid-template-columns: 125px auto;\n",
        "}\n",
        "\n",
-       ".xr-attrs dt, dd {\n",
+       ".xr-attrs dt,\n",
+       ".xr-attrs dd {\n",
        "  padding: 0;\n",
        "  margin: 0;\n",
        "  float: left;\n",
@@ -4368,7 +4459,7 @@
        "\t> sample_stats"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -4394,9 +4485,46 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "sample: 100%|██████████| 1500/1500 [00:02<00:00, 551.76it/s]\n"
+      "sample: 100%|██████████| 1500/1500 [00:02<00:00, 599.25it/s]\n"
      ]
     },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "851ea515d7c54968926f9eb0dc8b30c1",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "
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+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "
    \n",
+       "
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+      ],
+      "text/plain": [
+       "\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
     {
      "data": {
       "text/html": [
@@ -4408,8 +4536,8 @@
        "              
  • created_at :
    2024-04-13T05:36:33.599519+00:00
    arviz_version :
    0.18.0
    inference_library :
    numpyro
    inference_library_version :
    0.14.0
    modeling_interface :
    bambi
    modeling_interface_version :
    0.13.1.dev25+g1e7f677e.d20240413

    • \n",
        "                      \n",
        "                  \n",
        "            \n",
        "            \n",
        "            
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-       "                  \n",
-       "                  \n",
+       "                  \n",
+       "                  \n",
        "                  
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        "                  
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        "                      
  • created_at :
    2024-04-13T05:36:33.623197+00:00
    arviz_version :
    0.18.0
    inference_library :
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    inference_library_version :
    0.14.0
    modeling_interface :
    bambi
    modeling_interface_version :
    0.13.1.dev25+g1e7f677e.d20240413

    • \n",
        "                      \n",
        "                  \n",
        "            \n",
@@ -5603,7 +5731,8 @@
        "  grid-template-columns: 125px auto;\n",
        "}\n",
        "\n",
-       ".xr-attrs dt, dd {\n",
+       ".xr-attrs dt,\n",
+       ".xr-attrs dd {\n",
        "  padding: 0;\n",
        "  margin: 0;\n",
        "  float: left;\n",
@@ -5680,7 +5809,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Tuning global sampler: 100%|██████████| 5/5 [00:51<00:00, 10.23s/it]\n"
+      "Tuning global sampler: 100%|██████████| 5/5 [00:51<00:00, 10.37s/it]\n"
      ]
     },
     {
@@ -5694,9 +5823,53 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Production run: 100%|██████████| 5/5 [00:00<00:00,  9.38it/s]\n"
+      "Production run: 100%|██████████| 5/5 [00:00<00:00, 14.38it/s]"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "1865c421a05b46109fcf06c8b7da2cf4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n"
      ]
     },
+    {
+     "data": {
+      "text/html": [
+       "
    \n"
+      ],
+      "text/plain": []
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+     "output_type": "display_data"
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+    {
+     "data": {
+      "text/html": [
+       "
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+       "
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+      ],
+      "text/plain": [
+       "\n"
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+     "metadata": {},
+     "output_type": "display_data"
+    },
     {
      "data": {
       "text/html": [
@@ -5708,8 +5881,8 @@
        "              
  • created_at :
    2024-04-13T05:37:29.798250+00:00
    arviz_version :
    0.18.0
    modeling_interface :
    bambi
    modeling_interface_version :
    0.13.1.dev25+g1e7f677e.d20240413

    • \n",
        "                      \n",
        "                  \n",
        "            \n",
@@ -6440,7 +6613,8 @@
        "  grid-template-columns: 125px auto;\n",
        "}\n",
        "\n",
-       ".xr-attrs dt, dd {\n",
+       ".xr-attrs dt,\n",
+       ".xr-attrs dd {\n",
        "  padding: 0;\n",
        "  margin: 0;\n",
        "  float: left;\n",
@@ -6503,7 +6677,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -6540,40 +6714,40 @@
        "  \n",
        "  \n",
        "    \n",
-       "      y_sigma\n",
-       "      0.945\n",
-       "      0.070\n",
-       "      0.819\n",
-       "      1.080\n",
-       "      0.002\n",
-       "      0.002\n",
-       "      1044.0\n",
-       "      667.0\n",
-       "      1.0\n",
-       "    \n",
-       "    \n",
        "      Intercept\n",
-       "      0.018\n",
-       "      0.089\n",
-       "      -0.156\n",
-       "      0.185\n",
+       "      0.023\n",
+       "      0.097\n",
+       "      -0.141\n",
+       "      0.209\n",
+       "      0.004\n",
        "      0.003\n",
-       "      0.002\n",
-       "      844.0\n",
-       "      733.0\n",
-       "      1.0\n",
+       "      694.0\n",
+       "      508.0\n",
+       "      1.00\n",
        "    \n",
        "    \n",
        "      x\n",
-       "      0.358\n",
-       "      0.105\n",
-       "      0.163\n",
-       "      0.554\n",
+       "      0.356\n",
+       "      0.111\n",
+       "      0.162\n",
+       "      0.571\n",
        "      0.004\n",
        "      0.003\n",
-       "      829.0\n",
-       "      767.0\n",
-       "      1.0\n",
+       "      970.0\n",
+       "      675.0\n",
+       "      1.00\n",
+       "    \n",
+       "    \n",
+       "      y_sigma\n",
+       "      0.950\n",
+       "      0.069\n",
+       "      0.827\n",
+       "      1.072\n",
+       "      0.002\n",
+       "      0.001\n",
+       "      1418.0\n",
+       "      842.0\n",
+       "      1.01\n",
        "    \n",
        "  \n",
        "\n",
@@ -6581,17 +6755,17 @@
       ],
       "text/plain": [
        "            mean     sd  hdi_3%  hdi_97%  mcse_mean  mcse_sd  ess_bulk  \\\n",
-       "y_sigma    0.945  0.070   0.819    1.080      0.002    0.002    1044.0   \n",
-       "Intercept  0.018  0.089  -0.156    0.185      0.003    0.002     844.0   \n",
-       "x          0.358  0.105   0.163    0.554      0.004    0.003     829.0   \n",
+       "Intercept  0.023  0.097  -0.141    0.209      0.004    0.003     694.0   \n",
+       "x          0.356  0.111   0.162    0.571      0.004    0.003     970.0   \n",
+       "y_sigma    0.950  0.069   0.827    1.072      0.002    0.001    1418.0   \n",
        "\n",
        "           ess_tail  r_hat  \n",
-       "y_sigma       667.0    1.0  \n",
-       "Intercept     733.0    1.0  \n",
-       "x             767.0    1.0  "
+       "Intercept     508.0   1.00  \n",
+       "x             675.0   1.00  \n",
+       "y_sigma       842.0   1.01  "
       ]
      },
-     "execution_count": 16,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -6602,7 +6776,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -6639,39 +6813,39 @@
        "  \n",
        "  \n",
        "    \n",
-       "      y_sigma\n",
-       "      0.948\n",
-       "      0.067\n",
-       "      0.824\n",
-       "      1.073\n",
+       "      Intercept\n",
+       "      0.023\n",
+       "      0.097\n",
+       "      -0.157\n",
+       "      0.205\n",
        "      0.001\n",
        "      0.001\n",
-       "      8107.0\n",
-       "      5585.0\n",
+       "      6785.0\n",
+       "      5740.0\n",
        "      1.0\n",
        "    \n",
        "    \n",
-       "      Intercept\n",
-       "      0.025\n",
-       "      0.095\n",
-       "      -0.152\n",
-       "      0.200\n",
+       "      x\n",
+       "      0.360\n",
+       "      0.105\n",
+       "      0.169\n",
+       "      0.563\n",
        "      0.001\n",
        "      0.001\n",
-       "      6772.0\n",
-       "      5624.0\n",
+       "      6988.0\n",
+       "      5116.0\n",
        "      1.0\n",
        "    \n",
        "    \n",
-       "      x\n",
-       "      0.361\n",
-       "      0.104\n",
-       "      0.157\n",
-       "      0.551\n",
+       "      y_sigma\n",
+       "      0.946\n",
+       "      0.067\n",
+       "      0.831\n",
+       "      1.081\n",
        "      0.001\n",
        "      0.001\n",
-       "      6682.0\n",
-       "      5414.0\n",
+       "      7476.0\n",
+       "      5971.0\n",
        "      1.0\n",
        "    \n",
        "  \n",
@@ -6680,17 +6854,17 @@
       ],
       "text/plain": [
        "            mean     sd  hdi_3%  hdi_97%  mcse_mean  mcse_sd  ess_bulk  \\\n",
-       "y_sigma    0.948  0.067   0.824    1.073      0.001    0.001    8107.0   \n",
-       "Intercept  0.025  0.095  -0.152    0.200      0.001    0.001    6772.0   \n",
-       "x          0.361  0.104   0.157    0.551      0.001    0.001    6682.0   \n",
+       "Intercept  0.023  0.097  -0.157    0.205      0.001    0.001    6785.0   \n",
+       "x          0.360  0.105   0.169    0.563      0.001    0.001    6988.0   \n",
+       "y_sigma    0.946  0.067   0.831    1.081      0.001    0.001    7476.0   \n",
        "\n",
        "           ess_tail  r_hat  \n",
-       "y_sigma      5585.0    1.0  \n",
-       "Intercept    5624.0    1.0  \n",
-       "x            5414.0    1.0  "
+       "Intercept    5740.0    1.0  \n",
+       "x            5116.0    1.0  \n",
+       "y_sigma      5971.0    1.0  "
       ]
      },
-     "execution_count": 6,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -6701,7 +6875,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -6739,38 +6913,38 @@
        "  \n",
        "    \n",
        "      Intercept\n",
-       "      0.022\n",
-       "      0.097\n",
-       "      -0.149\n",
-       "      0.217\n",
+       "      0.024\n",
+       "      0.095\n",
+       "      -0.162\n",
+       "      0.195\n",
        "      0.001\n",
        "      0.001\n",
-       "      7412.0\n",
-       "      5758.0\n",
+       "      6851.0\n",
+       "      5614.0\n",
        "      1.0\n",
        "    \n",
        "    \n",
        "      x\n",
-       "      0.359\n",
-       "      0.105\n",
-       "      0.159\n",
-       "      0.555\n",
+       "      0.362\n",
+       "      0.104\n",
+       "      0.176\n",
+       "      0.557\n",
        "      0.001\n",
        "      0.001\n",
-       "      7406.0\n",
-       "      5967.0\n",
+       "      9241.0\n",
+       "      6340.0\n",
        "      1.0\n",
        "    \n",
        "    \n",
        "      y_sigma\n",
-       "      0.947\n",
-       "      0.069\n",
-       "      0.822\n",
+       "      0.946\n",
+       "      0.068\n",
+       "      0.826\n",
        "      1.079\n",
        "      0.001\n",
        "      0.001\n",
-       "      7371.0\n",
-       "      5405.0\n",
+       "      7247.0\n",
+       "      5711.0\n",
        "      1.0\n",
        "    \n",
        "  \n",
@@ -6779,17 +6953,17 @@
       ],
       "text/plain": [
        "            mean     sd  hdi_3%  hdi_97%  mcse_mean  mcse_sd  ess_bulk  \\\n",
-       "Intercept  0.022  0.097  -0.149    0.217      0.001    0.001    7412.0   \n",
-       "x          0.359  0.105   0.159    0.555      0.001    0.001    7406.0   \n",
-       "y_sigma    0.947  0.069   0.822    1.079      0.001    0.001    7371.0   \n",
+       "Intercept  0.024  0.095  -0.162    0.195      0.001    0.001    6851.0   \n",
+       "x          0.362  0.104   0.176    0.557      0.001    0.001    9241.0   \n",
+       "y_sigma    0.946  0.068   0.826    1.079      0.001    0.001    7247.0   \n",
        "\n",
        "           ess_tail  r_hat  \n",
-       "Intercept    5758.0    1.0  \n",
-       "x            5967.0    1.0  \n",
-       "y_sigma      5405.0    1.0  "
+       "Intercept    5614.0    1.0  \n",
+       "x            6340.0    1.0  \n",
+       "y_sigma      5711.0    1.0  "
       ]
      },
-     "execution_count": 17,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -6800,7 +6974,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -6837,39 +7011,39 @@
        "  \n",
        "  \n",
        "    \n",
-       "      y_sigma\n",
-       "      0.946\n",
-       "      0.067\n",
-       "      0.825\n",
-       "      1.076\n",
-       "      0.001\n",
-       "      0.001\n",
-       "      6260.0\n",
-       "      5213.0\n",
-       "      1.00\n",
-       "    \n",
-       "    \n",
        "      Intercept\n",
-       "      0.013\n",
-       "      0.093\n",
-       "      -0.165\n",
+       "      0.015\n",
+       "      0.100\n",
+       "      -0.186\n",
        "      0.190\n",
+       "      0.004\n",
        "      0.003\n",
-       "      0.002\n",
-       "      924.0\n",
-       "      1302.0\n",
+       "      758.0\n",
+       "      1233.0\n",
        "      1.02\n",
        "    \n",
        "    \n",
        "      x\n",
-       "      0.359\n",
-       "      0.103\n",
-       "      0.166\n",
-       "      0.556\n",
+       "      0.361\n",
+       "      0.105\n",
+       "      0.174\n",
+       "      0.565\n",
        "      0.001\n",
        "      0.001\n",
-       "      5132.0\n",
-       "      5790.0\n",
+       "      5084.0\n",
+       "      4525.0\n",
+       "      1.00\n",
+       "    \n",
+       "    \n",
+       "      y_sigma\n",
+       "      0.951\n",
+       "      0.070\n",
+       "      0.823\n",
+       "      1.079\n",
+       "      0.001\n",
+       "      0.001\n",
+       "      5536.0\n",
+       "      5080.0\n",
        "      1.00\n",
        "    \n",
        "  \n",
@@ -6878,17 +7052,17 @@
       ],
       "text/plain": [
        "            mean     sd  hdi_3%  hdi_97%  mcse_mean  mcse_sd  ess_bulk  \\\n",
-       "y_sigma    0.946  0.067   0.825    1.076      0.001    0.001    6260.0   \n",
-       "Intercept  0.013  0.093  -0.165    0.190      0.003    0.002     924.0   \n",
-       "x          0.359  0.103   0.166    0.556      0.001    0.001    5132.0   \n",
+       "Intercept  0.015  0.100  -0.186    0.190      0.004    0.003     758.0   \n",
+       "x          0.361  0.105   0.174    0.565      0.001    0.001    5084.0   \n",
+       "y_sigma    0.951  0.070   0.823    1.079      0.001    0.001    5536.0   \n",
        "\n",
        "           ess_tail  r_hat  \n",
-       "y_sigma      5213.0   1.00  \n",
-       "Intercept    1302.0   1.02  \n",
-       "x            5790.0   1.00  "
+       "Intercept    1233.0   1.02  \n",
+       "x            4525.0   1.00  \n",
+       "y_sigma      5080.0   1.00  "
       ]
      },
-     "execution_count": 18,
+     "execution_count": 16,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -6908,25 +7082,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Last updated: Fri Mar 01 2024\n",
+      "Last updated: Sat Apr 13 2024\n",
       "\n",
       "Python implementation: CPython\n",
-      "Python version       : 3.11.7\n",
-      "IPython version      : 8.21.0\n",
+      "Python version       : 3.12.2\n",
+      "IPython version      : 8.20.0\n",
       "\n",
-      "arviz     : 0.17.0\n",
-      "bambi     : 0.13.1.dev16+g9a1387a7.d20240204\n",
-      "numpy     : 1.26.3\n",
-      "pandas    : 2.2.0\n",
-      "bayeux    : 0.1.9\n",
-      "matplotlib: 3.8.2\n",
+      "bambi : 0.13.1.dev25+g1e7f677e.d20240413\n",
+      "pandas: 2.2.1\n",
+      "numpy : 1.26.4\n",
+      "bayeux: 0.1.10\n",
+      "arviz : 0.18.0\n",
       "\n",
       "Watermark: 2.4.3\n",
       "\n"
@@ -6955,7 +7128,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,
diff --git a/pyproject.toml b/pyproject.toml
index 262482de1..f8b5ac674 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ dependencies = [
     "formulae>=0.5.3",
     "graphviz",
     "pandas>=1.0.0",
-    "pymc>=5.12.0",
+    "pymc>=5.13.0",
 ]
 
 [project.optional-dependencies]
diff --git a/tests/test_alternative_samplers.py b/tests/test_alternative_samplers.py
index 6222f3df3..be260b6bd 100644
--- a/tests/test_alternative_samplers.py
+++ b/tests/test_alternative_samplers.py
@@ -7,7 +7,9 @@
 
 
 MCMC_METHODS = [getattr(bx.mcmc, k).name for k in bx.mcmc.__all__]
-MCMC_METHODS_FILTERED = [i for i in MCMC_METHODS if not any(x in i for x in ("flowmc", "chees", "meads"))]
+MCMC_METHODS_FILTERED = [
+    i for i in MCMC_METHODS if not any(x in i for x in ("flowmc", "chees", "meads"))
+]
 
 
 @pytest.fixture(scope="module")
@@ -30,6 +32,24 @@ def data_n100():
     return data
 
 
+def test_inference_method_names_and_kwargs():
+    names = bmb.inference_methods.names
+
+    # Check PyMC inference method family
+    assert "mcmc" in names["pymc"].keys()
+    assert "vi" in names["pymc"].keys()
+
+    # Check bayeu inference method family. Currently, only MCMC methods are supported
+    assert "mcmc" in names["bayeux"].keys()
+
+    # Ensure get_kwargs method raises an error if a non-supported method name is passed
+    with pytest.raises(
+        ValueError,
+        match="Inference method 'not_a_method' not found in the list of available methods. Use `bmb.inference_methods.names` to list the available methods.",
+    ):
+        bmb.inference_methods.get_kwargs("not_a_method")
+
+
 def test_laplace():
     data = pd.DataFrame(np.repeat((0, 1), (30, 60)), columns=["w"])
     priors = {"Intercept": bmb.Prior("Uniform", lower=0, upper=1)}
@@ -56,7 +76,7 @@ def test_vi():
         (mode_n.item(), std_n.item()), (mode_a.item(), std_a.item()), decimal=2
     )
 
-# 
+
 @pytest.mark.parametrize("sampler", MCMC_METHODS_FILTERED)
 def test_logistic_regression_categoric_alternative_samplers(data_n100, sampler):
     model = bmb.Model("b1 ~ n1", data_n100, family="bernoulli")
diff --git a/tests/test_interpret.py b/tests/test_interpret.py
index f9be28957..083e001a0 100644
--- a/tests/test_interpret.py
+++ b/tests/test_interpret.py
@@ -2,12 +2,14 @@
 This module contains tests for the helper functions of the 'interpret' sub-package.
 Tests here do not test any of the plotting functionality.
 """
+
 import numpy as np
 import pandas as pd
 import pytest
 
 import bambi as bmb
 from bambi.interpret.helpers import data_grid, select_draws
+from bambi.interpret.utils import get_model_covariates
 
 
 CHAINS = 4
@@ -190,3 +192,18 @@ def test_select_draws_no_effect(request, mtcars, condition):
         assert draws.shape == (CHAINS, DRAWS, 14)
     elif id == "3":
         assert draws.shape == (CHAINS, DRAWS, 2)
+
+
+# ------------------------------------------------------------------------------------------------ #
+#                                         Tests for utils                                          #
+# ------------------------------------------------------------------------------------------------ #
+
+
+def test_get_model_covariates():
+    """Tests `get_model_covariates()` does not include non-covariate names"""
+    # See issue 797
+    df = pd.DataFrame({"y": np.arange(10), "x": np.random.normal(size=10)})
+    knots = np.linspace(np.min(df["x"]), np.max(df["x"]), 4 + 2)[1:-1]
+    formula = "y ~ 1 + bs(x, degree=3, knots=knots)"
+    model = bmb.Model(formula, df)
+    assert set(get_model_covariates(model)) == {"x"}
diff --git a/tests/test_models.py b/tests/test_models.py
index 717abe7e3..3bdcf4a39 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -192,13 +192,13 @@ def test_cell_means_parameterization(self, crossed_data):
     def test_2_factors_saturated(self, crossed_data):
         model = bmb.Model("Y ~ threecats*fourcats", crossed_data)
         idata = self.fit(model)
-        assert list(idata.posterior.data_vars) == [
+        assert set(idata.posterior.data_vars) == {
             "Intercept",
             "threecats",
             "fourcats",
             "threecats:fourcats",
             "Y_sigma",
-        ]
+        }
         assert list(idata.posterior["threecats_dim"].values) == ["b", "c"]
         assert list(idata.posterior["fourcats_dim"].values) == ["b", "c", "d"]
         assert list(idata.posterior["threecats:fourcats_dim"].values) == [
@@ -214,12 +214,12 @@ def test_2_factors_saturated(self, crossed_data):
     def test_2_factors_no_intercept(self, crossed_data):
         model = bmb.Model("Y ~ 0 + threecats*fourcats", crossed_data)
         idata = self.fit(model)
-        assert list(idata.posterior.data_vars) == [
+        assert set(idata.posterior.data_vars) == {
             "threecats",
             "fourcats",
             "threecats:fourcats",
             "Y_sigma",
-        ]
+        }
         assert list(idata.posterior["threecats_dim"].values) == ["a", "b", "c"]
         assert list(idata.posterior["fourcats_dim"].values) == ["b", "c", "d"]
         assert list(idata.posterior["threecats:fourcats_dim"].values) == [
@@ -235,7 +235,7 @@ def test_2_factors_no_intercept(self, crossed_data):
     def test_2_factors_cell_means(self, crossed_data):
         model = bmb.Model("Y ~ 0 + threecats:fourcats", crossed_data)
         idata = self.fit(model)
-        assert list(idata.posterior.data_vars) == ["threecats:fourcats", "Y_sigma"]
+        assert set(idata.posterior.data_vars) == {"threecats:fourcats", "Y_sigma"}
         assert list(idata.posterior["threecats:fourcats_dim"].values) == [
             "a, a",
             "a, b",
@@ -255,7 +255,7 @@ def test_2_factors_cell_means(self, crossed_data):
     def test_cell_means_with_covariate(self, crossed_data):
         model = bmb.Model("Y ~ 0 + threecats + continuous", crossed_data)
         idata = self.fit(model)
-        assert list(idata.posterior.data_vars) == ["threecats", "continuous", "Y_sigma"]
+        assert set(idata.posterior.data_vars) == {"threecats", "continuous", "Y_sigma"}
         assert list(idata.posterior["threecats_dim"].values) == ["a", "b", "c"]
         self.predict_oos(model, idata)
 
@@ -477,7 +477,7 @@ def test_group_specific_categorical_interaction(self, crossed_data):
         idata = self.fit(model)
         self.predict_oos(model, idata)
 
-        assert list(idata.posterior.data_vars) == [
+        assert set(idata.posterior.data_vars) == {
             "Intercept",
             "continuous",
             "Y_sigma",
@@ -485,7 +485,7 @@ def test_group_specific_categorical_interaction(self, crossed_data):
             "threecats:fourcats|site_sigma",
             "1|site",
             "threecats:fourcats|site",
-        ]
+        }
         assert list(idata.posterior["threecats:fourcats|site"].coords) == [
             "chain",
             "draw",