From 2d7cb0b9a2c68c7fc264a33812064ba83f52be96 Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Thu, 23 Nov 2023 18:30:24 +0100 Subject: [PATCH 1/6] Remove old import from autosummary doc pages --- docs/source/api/math.rst | 4 ---- docs/source/api/model/core.rst | 1 - docs/source/api/pytensorf.rst | 1 - docs/source/api/samplers.rst | 2 -- 4 files changed, 8 deletions(-) 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..f8b5db4123 100644 --- a/docs/source/api/model/core.rst +++ b/docs/source/api/model/core.rst @@ -7,7 +7,6 @@ Model creation and inspection Model model_to_graphviz - model_to_networkx modelcontext Others diff --git a/docs/source/api/pytensorf.rst b/docs/source/api/pytensorf.rst index af7b70f041..71c2b4755c 100644 --- a/docs/source/api/pytensorf.rst +++ b/docs/source/api/pytensorf.rst @@ -16,7 +16,6 @@ PyTensor utils floatX intX smartfloatX - constant_fold CallableTensor join_nonshared_inputs make_shared_replacements diff --git a/docs/source/api/samplers.rst b/docs/source/api/samplers.rst index 5e53a6518a..2bc7614de7 100644 --- a/docs/source/api/samplers.rst +++ b/docs/source/api/samplers.rst @@ -13,8 +13,6 @@ This submodule contains functions for MCMC and forward sampling. sample_prior_predictive sample_posterior_predictive sample_posterior_predictive_w - sampling.jax.sample_blackjax_nuts - sampling.jax.sample_numpyro_nuts init_nuts draw From eaaef5461e89f59262c352ac55047df7d344e99f Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Thu, 23 Nov 2023 18:30:49 +0100 Subject: [PATCH 2/6] Fix small error --- pymc/distributions/transforms.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 726c67ea92b9a736d0f8f326903b949b9bdf1f7c Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Thu, 23 Nov 2023 18:43:52 +0100 Subject: [PATCH 3/6] Correct place for model_to_networkx & model_to_graphviz --- docs/source/api/model/core.rst | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/docs/source/api/model/core.rst b/docs/source/api/model/core.rst index f8b5db4123..16ed7902bc 100644 --- a/docs/source/api/model/core.rst +++ b/docs/source/api/model/core.rst @@ -6,7 +6,6 @@ Model creation and inspection :toctree: generated/ Model - model_to_graphviz modelcontext Others @@ -21,3 +20,14 @@ Others set_data Point compile_fn + + +Graph visualisation +------------------- + +.. currentmodule:: pymc.model_graph +.. autosummary:: + :toctree: generated/ + + model_to_networkx + model_to_graphviz From b01e778dc73c2c1170494c2099528d43373dbfd1 Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Thu, 23 Nov 2023 18:47:37 +0100 Subject: [PATCH 4/6] Correct currentmodule source for pytensorf.rst --- docs/source/api/pytensorf.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/api/pytensorf.rst b/docs/source/api/pytensorf.rst index 71c2b4755c..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/ @@ -16,6 +16,7 @@ PyTensor utils floatX intX smartfloatX + constant_fold CallableTensor join_nonshared_inputs make_shared_replacements From feb9f2ca903dca7275592e8e8ace9eab4a098b81 Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Fri, 24 Nov 2023 19:48:55 +0100 Subject: [PATCH 5/6] Update docs/source/api/model/core.rst Co-authored-by: Thomas Wiecki --- docs/source/api/model/core.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/api/model/core.rst b/docs/source/api/model/core.rst index 16ed7902bc..6324ede164 100644 --- a/docs/source/api/model/core.rst +++ b/docs/source/api/model/core.rst @@ -22,7 +22,7 @@ Others compile_fn -Graph visualisation +Graph visualization ------------------- .. currentmodule:: pymc.model_graph From 4cd807ca65341a991dccd06ea2fd46eb39dbfc3f Mon Sep 17 00:00:00 2001 From: Denis Kataev Date: Tue, 28 Nov 2023 21:18:38 +0100 Subject: [PATCH 6/6] Fix sampling & jax docs imports --- docs/source/api/samplers.rst | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/docs/source/api/samplers.rst b/docs/source/api/samplers.rst index 2bc7614de7..a62ffb285e 100644 --- a/docs/source/api/samplers.rst +++ b/docs/source/api/samplers.rst @@ -4,25 +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 - 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/ @@ -32,6 +46,7 @@ HMC family Metropolis family ----------------- +.. currentmodule:: pymc.step_methods .. autosummary:: :toctree: generated/ @@ -51,6 +66,7 @@ Metropolis family Other step methods ------------------ +.. currentmodule:: pymc.step_methods .. autosummary:: :toctree: generated/