Build docs in simplified environment (#6537)

michaelosthege · web-flow · commit 2978b40342e9 · 2023-02-20T08:02:24.000-08:00
* Build docs in simplified environment

* Fix docs build

* Remove private API section from docs
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ python:
      path: .
 
 conda:
-  environment: "conda-envs/environment-dev.yml"
+  environment: "conda-envs/environment-docs.yml"
 
 build:
   os: "ubuntu-20.04"
diff --git a/Makefile b/Makefile
@@ -55,9 +55,6 @@ clean:
 	rm -rf $(SOURCEDIR)/api/generated
 	rm -rf $(SOURCEDIR)/api/**/generated
 	rm -rf $(SOURCEDIR)/api/**/classmethods
-	rm -rf $(SOURCEDIR)/contributing/private_api/generated
-	rm -rf $(SOURCEDIR)/contributing/private_api/**/generated
-	rm -rf $(SOURCEDIR)/contributing/private_api/**/classmethods
 	rm -rf docs/jupyter_execute
 
 html:
diff --git a/conda-envs/environment-docs.yml b/conda-envs/environment-docs.yml
@@ -0,0 +1,35 @@
+# "dev" conda envs are to be used by devs in setting their local environments
+name: pymc-docs
+channels:
+- conda-forge
+- defaults
+dependencies:
+# Base dependencies
+- arviz>=0.13.0
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- pytensor=2.9.1
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for docs build
+- ipython>=7.16
+- jax
+- jupyter-sphinx
+- myst-nb
+- numpydoc
+- pre-commit>=2.8.0
+- sphinx-copybutton
+- sphinx-design
+- sphinx-notfound-page
+- sphinx>=1.5
+- sphinxext-rediraffe
+- watermark
+- sphinx-remove-toctrees
+- pip:
+  - git+https://github.com/pymc-devs/pymc-sphinx-theme
+  - numdifftools>=0.9.40
diff --git a/docs/source/api/backends.rst b/docs/source/api/backends.rst
@@ -18,6 +18,5 @@ Internal structures
    :toctree: generated/
 
    NDArray
-   point_list_to_multitrace
    base.BaseTrace
    base.MultiTrace
diff --git a/docs/source/api/data.rst b/docs/source/api/data.rst
@@ -12,4 +12,3 @@ Data
    Data
    GeneratorAdapter
    Minibatch
-   align_minibatches
diff --git a/docs/source/api/distributions/simulator.rst b/docs/source/api/distributions/simulator.rst
@@ -6,6 +6,4 @@ Simulator
 .. autosummary::
    :toctree: generated
 
-   SimulatorRV
    Simulator
-   KullbackLiebler
diff --git a/docs/source/api/distributions/timeseries.rst b/docs/source/api/distributions/timeseries.rst
@@ -6,7 +6,6 @@ Timeseries
 .. autosummary::
    :toctree: generated
 
-    AR1
     AR
     GaussianRandomWalk
     GARCH11
diff --git a/docs/source/api/distributions/transforms.rst b/docs/source/api/distributions/transforms.rst
@@ -16,8 +16,6 @@ Transform instances are the entities that should be used in the
     simplex
     logodds
     log_exp_m1
-    ordered_univariate
-    ordered_multivariate
     log
     sum_to_1
     circular
diff --git a/docs/source/api/math.rst b/docs/source/api/math.rst
@@ -48,7 +48,7 @@ Functions exposed in pymc.math
    where
    and_
    or_
-   abs_
+   abs
    exp
    log
    cos
diff --git a/docs/source/api/pytensorf.rst b/docs/source/api/pytensorf.rst
@@ -21,6 +21,4 @@ PyTensor utils
    join_nonshared_inputs
    make_shared_replacements
    generator
-   set_at_rng
-   at_rng
-   pandas_to_array
+   convert_observed_data
diff --git a/docs/source/api/samplers.rst b/docs/source/api/samplers.rst
@@ -15,7 +15,6 @@ This submodule contains functions for MCMC and forward sampling.
    sample_posterior_predictive_w
    sampling.jax.sample_blackjax_nuts
    sampling.jax.sample_numpyro_nuts
-   iter_sample
    init_nuts
    draw
 
diff --git a/docs/source/api/vi.rst b/docs/source/api/vi.rst
@@ -9,7 +9,6 @@ Variational Inference
 
    ADVI
    ASVGD
-   NFVI
    SVGD
    FullRankADVI
    ImplicitGradient
@@ -26,7 +25,6 @@ Approximations
    Empirical
    FullRank
    MeanField
-   NormalizingFlow
    sample_approx
 
 OPVI
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -125,7 +125,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # configure notfound extension to not add any prefix to the urls
 notfound_urls_prefix = "/projects/docs/en/latest/"
diff --git a/docs/source/contributing/index.md b/docs/source/contributing/index.md
@@ -101,7 +101,6 @@ review_pr_pymc_examples
 :maxdepth: 1
 :caption: Reference content
 
-private_api/index
 python_style
 jupyter_style
 pr_checklist
diff --git a/docs/source/contributing/private_api/index.md b/docs/source/contributing/private_api/index.md
diff --git a/docs/source/contributing/private_api/tests.rst b/docs/source/contributing/private_api/tests.rst

-Original file line number
+Diff line change
    where
    and_
    or_
 -   abs_
 +   abs
    exp
    log
    cos
Original file line number	Diff line number	Diff line change
`@@ -125,7 +125,7 @@`
`125`	`125`	`#`
`126`	`126`	`# This is also used if you do content translation via gettext catalogs.`
`127`	`127`	`# Usually you set "language" from the command line for these cases.`
`128`		`-language = None`
	`128`	`+language = "en"`
`129`	`129`
`130`	`130`	`# configure notfound extension to not add any prefix to the urls`
`131`	`131`	`notfound_urls_prefix = "/projects/docs/en/latest/"`