Merge branch 'main' into optim-prior

Author: AlexAndorra

.github/workflows/pytest.yml

@@ -46,7 +46,6 @@ jobs:
             --ignore=pymc/tests/test_dist_math.py
             --ignore=pymc/tests/test_minibatches.py
             --ignore=pymc/tests/test_pickling.py
-            --ignore=pymc/tests/test_plots.py
             --ignore=pymc/tests/test_updates.py
             --ignore=pymc/tests/test_gp.py
             --ignore=pymc/tests/test_model.py
@@ -68,7 +67,6 @@ jobs:
             pymc/tests/test_dist_math.py
             pymc/tests/test_minibatches.py
             pymc/tests/test_pickling.py
-            pymc/tests/test_plots.py
             pymc/tests/test_updates.py
             pymc/tests/test_transforms.py
 

.gitignore

@@ -18,6 +18,7 @@ tags
 # Sphinx
 _build
 docs/jupyter_execute
+docs/**/generated/*
 
 # Merge tool
 *.orig

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs/logos|pymc/tests/data)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -19,7 +19,7 @@ repos:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.29.1
+  rev: v2.31.0
   hooks:
     - id: pyupgrade
       args: [--py37-plus]

CONTRIBUTING.md

@@ -146,9 +146,9 @@ docker exec -it pymc jupyter notebook list
 ## Style guide
 
 We have configured a pre-commit hook that checks for `black`-compliant code style.
-We encourage you to configure the pre-commit hook as described in the [PyMC Python Code Style Wiki Page](https://github.com/pymc-devs/pymc/wiki/Python-Code-Style), because it will automatically enforce the code style on your commits.
+We encourage you to configure the pre-commit hook as described in the [PyMC Python Code Style Wiki Page](https://docs.pymc.io/en/latest/contributing/python_style.html), because it will automatically enforce the code style on your commits.
 
-Similarly, consult the [PyMC's Jupyter Notebook Style](https://github.com/pymc-devs/pymc/wiki/PyMC-Jupyter-Notebook-Style-Guide) guides for notebooks.
+Similarly, consult the [PyMC's Jupyter Notebook Style](https://docs.pymc.io/en/latest/contributing/jupyter_style.html) guides for notebooks.
 
 For documentation strings, we *prefer* [numpy style](https://numpydoc.readthedocs.io/en/latest/format.html) to comply with the style that predominates in our upstream dependencies.
 

docs/source/Makefile renamed to Makefile

@@ -5,7 +5,8 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
-BUILDDIR      = _build
+SOURCEDIR     = docs/source
+BUILDDIR      = docs/_build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -51,9 +52,11 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf $(SOURCEDIR)/api/**/generated
+	rm -rf docs/jupyter_execute
 
 html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) $(SOURCEDIR) $(BUILDDIR) -b html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

docs/source/404.md

@@ -28,17 +28,4 @@ do so we have moved some files around and we have
 modified the base url in order to support multi version docs
 (you'll see the version switcher at the bottom right of the page).
 
-::::{grid} 3
-:::{grid-item}
-:::
-:::{grid-item}
-```{button-link} https://docs.pymc.io/en/stable/
-:color: primary
-:expand:
-
-Back to stable version documentation
-```
-:::
-:::{grid-item}
-:::
-::::
+Back to {{ '[documentation homepage](https://docs.pymc.io/en/{}/)'.format(version_slug) }}

docs/source/api.rst

@@ -15,11 +15,34 @@ API Reference
    api/smc
    api/step_methods
    api/inference
-   api/plots
 
-Indices and tables
-===================
+--------------
+API extensions
+--------------
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+Plots, stats and diagnostics
+----------------------------
+Plots, stats and diagnostics are delegated to the
+:doc:`ArviZ <arviz:index>`.
+library, a general purpose library for
+"exploratory analysis of Bayesian models".
+
+* Functions from the `arviz.plots` module are available through ``pymc.<function>`` or ``pymc.plots.<function>``,
+but for their API documentation please refer to the :ref:`ArviZ documentation <arviz:plot_api>`.
+
+* Functions from the `arviz.stats` module are available through ``pymc.<function>`` or ``pymc.stats.<function>``,
+but for their API documentation please refer to the :ref:`ArviZ documentation <arviz:stats_api>`.
+
+ArviZ is a dependency of PyMC and so, in addition to the locations described above,
+importing ArviZ and using ``arviz.<function>`` will also work without any extra installation.
+
+Generalized Linear Models (GLMs)
+--------------------------------
+
+Generalized Linear Models are delegated to the
+`Bambi <https://bambinos.github.io/bambi>`_.
+library, a high-level Bayesian model-building
+interface built on top of PyMC.
+
+Bambi is not a dependency of PyMC and should be installed in addition to PyMC
+to use it to generate PyMC models via formula syntax.

docs/source/api/distributions/continuous.rst

@@ -2,8 +2,9 @@
 Continuous
 **********
 
-.. currentmodule:: pymc.distributions.continuous
+.. currentmodule:: pymc
 .. autosummary::
+   :toctree: generated/
 
    Uniform
    Flat
@@ -38,6 +39,3 @@ Continuous
    Moyal
    AsymmetricLaplace
    PolyaGamma
-
-.. automodule:: pymc.distributions.continuous
-   :members:

docs/source/api/distributions/discrete.rst

@@ -2,8 +2,9 @@
 Discrete
 ********
 
-.. currentmodule:: pymc.distributions.discrete
+.. currentmodule:: pymc
 .. autosummary::
+   :toctree: generated
 
    Binomial
    BetaBinomial
@@ -21,6 +22,3 @@ Discrete
    Categorical
    OrderedLogistic
    OrderedProbit
-
-.. automodule:: pymc.distributions.discrete
-   :members:

docs/source/api/distributions/mixture.rst

@@ -2,11 +2,10 @@
 Mixture
 *******
 
-.. currentmodule:: pymc.distributions.mixture
+.. currentmodule:: pymc
 .. autosummary::
+   :toctree: generated
+
    Mixture
    NormalMixture
    MixtureSameFamily
-
-.. automodule:: pymc.distributions.mixture
-   :members: