add missing objects and modules to docs

pymc-devs · Feb 4, 2022 · 1005d20 · 1005d20
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diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -10,11 +10,18 @@ API Reference
    api/distributions
    api/gp
    api/model
-   api/ode
    api/samplers
+   api/vi
    api/smc
-   api/step_methods
-   api/inference
+   api/backends
+   api/data
+   api/bart
+   api/ode
+   api/tuning
+   api/math
+   api/aesaraf
+   api/shape_utils
+   api/misc
 
 --------------
 API extensions

diff --git a/docs/source/api/aesaraf.rst b/docs/source/api/aesaraf.rst
@@ -0,0 +1,25 @@
+Aesara utils
+************
+
+.. currentmodule:: pymc
+
+.. autosummary::
+   :toctree: generated/
+
+   gradient
+   hessian
+   hessian_diag
+   inputvars
+   cont_inputs
+   floatX
+   intX
+   smartfloatX
+   jacobian
+   CallableTensor
+   join_nonshared_inputs
+   make_shared_replacements
+   generator
+   set_at_rng
+   at_rng
+   take_along_axis
+   pandas_to_array
diff --git a/docs/source/api/backends.rst b/docs/source/api/backends.rst
@@ -0,0 +1,23 @@
+Storage backends
+****************
+
+.. currentmodule:: pymc
+
+.. autosummary::
+   :toctree: generated/
+
+   to_inference_data
+   predictions_to_inference_data
+
+Internal structures
+-------------------
+
+.. automodule:: pymc.backends
+
+.. autosummary::
+   :toctree: generated/
+
+   NDArray
+   point_list_to_multitrace
+   base.BaseTrace
+   base.MultiTrace
diff --git a/docs/source/api/bart.rst b/docs/source/api/bart.rst
@@ -0,0 +1,12 @@
+Bayesian Additive Regression Trees (BART)
+*****************************************
+
+.. currentmodule:: pymc
+
+.. autosummary::
+   :toctree: generated/
+
+   BART
+   PGBART
+   bart.plot_dependence
+   bart.predict
diff --git a/docs/source/api/data.rst b/docs/source/api/data.rst
@@ -0,0 +1,15 @@
+Data
+****
+
+.. currentmodule:: pymc
+
+.. autosummary::
+   :toctree: generated/
+
+   ConstantData
+   MutableData
+   get_data
+   Data
+   GeneratorAdapter
+   Minibatch
+   align_minibatches
diff --git a/docs/source/api/inference.rst b/docs/source/api/inference.rst
diff --git a/docs/source/api/math.rst b/docs/source/api/math.rst
@@ -7,9 +7,27 @@ from aesara.tensor (see there for more details). Doing any kind of math with PyM
 variables, or defining custom likelihoods or priors requires you to use these Aesara
 expressions rather than NumPy or Python code.
 
-.. currentmodule:: pymc.math
+.. currentmodule:: pymc
 
+Functions exposed in pymc namespace
+-----------------------------------
 .. autosummary::
+   :toctree: generated/
+
+   expand_packed_triangular
+   logit
+   invlogit
+   probit
+   invprobit
+   logsumexp
+
+Functions exposed in pymc.math
+------------------------------
+
+.. automodule:: pymc.math
+.. autosummary::
+   :toctree: generated/
+
    dot
    constant
    flatten
@@ -58,6 +76,3 @@ expressions rather than NumPy or Python code.
    logsumexp
    invlogit
    logit
-
-.. automodule:: pymc.math
-   :members:
diff --git a/docs/source/api/misc.rst b/docs/source/api/misc.rst
@@ -0,0 +1,19 @@
+Other utils
+***********
+
+.. currentmodule:: pymc
+
+.. autosummary::
+   :toctree: generated/
+
+   find_constrained_prior
+   DictToArrayBijection
+
+Printing
+--------
+.. autosummary::
+   :toctree: generated/
+
+   str_for_dist
+   str_for_model
+   str_for_potential_or_deterministic
diff --git a/docs/source/api/model.rst b/docs/source/api/model.rst
@@ -1,6 +1,25 @@
 Model
 -----
 
-.. currentmodule:: pymc.model
-.. automodule:: pymc.model
-   :members:
+Model creation and inspection
+-----------------------------
+
+.. currentmodule:: pymc
+.. autosummary::
+   :toctree: generated/
+
+   Model
+   model_to_graphviz
+   modelcontext
+
+Others
+------
+
+.. autosummary::
+   :toctree: generated/
+
+   Deterministic
+   Potential
+   set_data
+   Point
+   compile_fn
diff --git a/docs/source/api/ode.rst b/docs/source/api/ode.rst
@@ -2,11 +2,10 @@
 Ordinary differential equations (ODEs)
 **************************************
 
-This submodule contains tools used to perform inference on ordinary differential equations.
 
-.. currentmodule:: pymc.ode
+.. automodule:: pymc.ode
 
 .. autosummary::
+    :toctree: generated/
 
-.. automodule:: pymc.ode
-   :members: DifferentialEquation
+    DifferentialEquation
diff --git a/docs/source/api/samplers.rst b/docs/source/api/samplers.rst
@@ -1,13 +1,72 @@
-====
 Samplers
-====
+========
 
-This submodule contains functions for MCMC sampling.
+This submodule contains functions for MCMC and forward sampling.
 
 
-.. currentmodule:: pymc.sampling
+.. currentmodule:: pymc
 
 .. autosummary::
+   :toctree: generated/
 
-.. automodule:: pymc.sampling
-   :members:
+   sample
+   sample_prior_predictive
+   sample_posterior_predictive
+   sample_posterior_predictive_w
+   iter_sample
+   init_nuts
+   draw
+
+Step methods
+************
+
+.. currentmodule:: pymc
+
+HMC family
+----------
+
+.. autosummary::
+   :toctree: generated/
+
+   NUTS
+   HamiltonianMC
+
+Metropolis family
+-----------------
+
+.. autosummary::
+    :toctree: generated/
+
+    BinaryGibbsMetropolis
+    BinaryMetropolis
+    CategoricalGibbsMetropolis
+    CauchyProposal
+    DEMetropolis
+    DEMetropolisZ
+    LaplaceProposal
+    Metropolis
+    MultivariateNormalProposal
+    NormalProposal
+    PoissonProposal
+    UniformProposal
+
+MLDA family
+-----------
+
+.. autosummary::
+   :toctree: generated/
+
+   MLDA
+   DEMetropolisZMLDA
+   MetropolisMLDA
+   RecursiveDAProposal
+
+Other step methods
+------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   CompoundStep
+   EllipticalSlice
+   Slice