diff --git a/docs/source/api/math.rst b/docs/source/api/math.rst index 26c2f66370..67b487194d 100644 --- a/docs/source/api/math.rst +++ b/docs/source/api/math.rst @@ -67,11 +67,7 @@ Functions exposed in pymc.math sgn ceil floor - det matrix_inverse - extract_diag - matrix_dot - trace sigmoid logsumexp invlogit diff --git a/docs/source/api/model/core.rst b/docs/source/api/model/core.rst index 0b46573a3f..6324ede164 100644 --- a/docs/source/api/model/core.rst +++ b/docs/source/api/model/core.rst @@ -6,8 +6,6 @@ Model creation and inspection :toctree: generated/ Model - model_to_graphviz - model_to_networkx modelcontext Others @@ -22,3 +20,14 @@ Others set_data Point compile_fn + + +Graph visualization +------------------- + +.. currentmodule:: pymc.model_graph +.. autosummary:: + :toctree: generated/ + + model_to_networkx + model_to_graphviz diff --git a/docs/source/api/pytensorf.rst b/docs/source/api/pytensorf.rst index af7b70f041..2eb12feaae 100644 --- a/docs/source/api/pytensorf.rst +++ b/docs/source/api/pytensorf.rst @@ -1,7 +1,7 @@ PyTensor utils ************** -.. currentmodule:: pymc +.. currentmodule:: pymc.pytensorf .. autosummary:: :toctree: generated/ diff --git a/docs/source/api/samplers.rst b/docs/source/api/samplers.rst index 5e53a6518a..a62ffb285e 100644 --- a/docs/source/api/samplers.rst +++ b/docs/source/api/samplers.rst @@ -4,27 +4,39 @@ Samplers This submodule contains functions for MCMC and forward sampling. -.. currentmodule:: pymc +.. currentmodule:: pymc.sampling.forward .. autosummary:: :toctree: generated/ - sample sample_prior_predictive sample_posterior_predictive - sample_posterior_predictive_w - sampling.jax.sample_blackjax_nuts - sampling.jax.sample_numpyro_nuts - init_nuts draw + +.. currentmodule:: pymc.sampling.mcmc + +.. autosummary:: + :toctree: generated/ + + sample + init_nuts + +.. currentmodule:: pymc.sampling.jax + +.. autosummary:: + :toctree: generated/ + + sample_blackjax_nuts + sample_numpyro_nuts + + Step methods ************ -.. currentmodule:: pymc - HMC family ---------- +.. currentmodule:: pymc.step_methods.hmc .. autosummary:: :toctree: generated/ @@ -34,6 +46,7 @@ HMC family Metropolis family ----------------- +.. currentmodule:: pymc.step_methods .. autosummary:: :toctree: generated/ @@ -53,6 +66,7 @@ Metropolis family Other step methods ------------------ +.. currentmodule:: pymc.step_methods .. autosummary:: :toctree: generated/ diff --git a/pymc/distributions/transforms.py b/pymc/distributions/transforms.py index fca5f6a984..bdb63285c9 100644 --- a/pymc/distributions/transforms.py +++ b/pymc/distributions/transforms.py @@ -57,7 +57,7 @@ def __getattr__(name): warnings.warn(f"{name} has been deprecated, use ordered instead.", FutureWarning) return ordered - if name in ("univariate_sum_to_1, multivariate_sum_to_1"): + if name in ("univariate_sum_to_1", "multivariate_sum_to_1"): warnings.warn(f"{name} has been deprecated, use sum_to_1 instead.", FutureWarning) return sum_to_1