Add code example to Potential docstrings

.github/workflows/devcontainer-docker-image.yml

@@ -22,7 +22,7 @@ jobs:
       uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
 
     - name: Setup Docker buildx
-      uses: docker/setup-buildx-action@v2.4.0
+      uses: docker/setup-buildx-action@v2.4.1
 
     - name: Prepare metadata
       id: meta
@@ -42,7 +42,7 @@ jobs:
 
     - name: Build and push Docker image
       id: docker_build
-      uses: docker/build-push-action@e551b19e49efd4e98792db7592c17c09b89db8d8
+      uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
       with:
         context: .
         file: scripts/dev.Dockerfile

.github/workflows/docker-image.yml

@@ -34,7 +34,7 @@ jobs:
               type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and load image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
         with:
           context: .
           file: scripts/Dockerfile
@@ -46,7 +46,7 @@ jobs:
            docker run --rm ${{ env.CONTAINER_NAME }} conda run -n pymc-dev python -c 'import pymc;print(pymc.__version__)'
 
       - name: Build and push
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
         with:
           context: .
           push: true

.github/workflows/tests.yml

@@ -38,66 +38,65 @@ jobs:
         python-version: ["3.10"]
         test-subset:
           - |
-            pymc/tests/test_util.py
-            pymc/tests/distributions/test_logprob.py
-            pymc/tests/test_pytensorf.py
-            pymc/tests/test_math.py
-            pymc/tests/backends/test_base.py
-            pymc/tests/backends/test_ndarray.py
-            pymc/tests/step_methods/hmc/test_hmc.py
-            pymc/tests/test_func_utils.py
-            pymc/tests/distributions/test_shape_utils.py
-            pymc/tests/distributions/test_mixture.py
+            tests/test_util.py
+            tests/test_pytensorf.py
+            tests/test_math.py
+            tests/backends/test_base.py
+            tests/backends/test_ndarray.py
+            tests/step_methods/hmc/test_hmc.py
+            tests/test_func_utils.py
+            tests/distributions/test_shape_utils.py
+            tests/distributions/test_mixture.py
 
           - |
-            pymc/tests/distributions/test_continuous.py
-            pymc/tests/distributions/test_multivariate.py
+            tests/distributions/test_continuous.py
+            tests/distributions/test_multivariate.py
 
           - |
-            pymc/tests/distributions/test_bound.py
-            pymc/tests/distributions/test_censored.py
-            pymc/tests/distributions/test_simulator.py
-            pymc/tests/sampling/test_forward.py
-            pymc/tests/sampling/test_population.py
-            pymc/tests/stats/test_convergence.py
-            pymc/tests/stats/test_log_likelihood.py
-            pymc/tests/distributions/test_distribution.py
-            pymc/tests/distributions/test_discrete.py
+            tests/distributions/test_bound.py
+            tests/distributions/test_censored.py
+            tests/distributions/test_simulator.py
+            tests/sampling/test_forward.py
+            tests/sampling/test_population.py
+            tests/stats/test_convergence.py
+            tests/stats/test_log_likelihood.py
+            tests/distributions/test_distribution.py
+            tests/distributions/test_discrete.py
 
           - |
-            pymc/tests/tuning/test_scaling.py
-            pymc/tests/tuning/test_starting.py
-            pymc/tests/distributions/test_dist_math.py
-            pymc/tests/distributions/test_transform.py
-            pymc/tests/sampling/test_mcmc.py
-            pymc/tests/sampling/test_parallel.py
-            pymc/tests/test_printing.py
+            tests/tuning/test_scaling.py
+            tests/tuning/test_starting.py
+            tests/distributions/test_dist_math.py
+            tests/distributions/test_transform.py
+            tests/sampling/test_mcmc.py
+            tests/sampling/test_parallel.py
+            tests/test_printing.py
 
           - |
-            pymc/tests/distributions/test_timeseries.py
-            pymc/tests/gp/test_cov.py
-            pymc/tests/gp/test_gp.py
-            pymc/tests/gp/test_mean.py
-            pymc/tests/gp/test_util.py
-            pymc/tests/test_model.py
-            pymc/tests/test_model_graph.py
-            pymc/tests/ode/test_ode.py
-            pymc/tests/ode/test_utils.py
-            pymc/tests/step_methods/hmc/test_quadpotential.py
+            tests/distributions/test_timeseries.py
+            tests/gp/test_cov.py
+            tests/gp/test_gp.py
+            tests/gp/test_mean.py
+            tests/gp/test_util.py
+            tests/test_model.py
+            tests/test_model_graph.py
+            tests/ode/test_ode.py
+            tests/ode/test_utils.py
+            tests/step_methods/hmc/test_quadpotential.py
 
           - |
-            pymc/tests/distributions/test_truncated.py
-            pymc/tests/logprob/test_abstract.py
-            pymc/tests/logprob/test_censoring.py
-            pymc/tests/logprob/test_composite_logprob.py
-            pymc/tests/logprob/test_cumsum.py
-            pymc/tests/logprob/test_joint_logprob.py
-            pymc/tests/logprob/test_mixture.py
-            pymc/tests/logprob/test_rewriting.py
-            pymc/tests/logprob/test_scan.py
-            pymc/tests/logprob/test_tensor.py
-            pymc/tests/logprob/test_transforms.py
-            pymc/tests/logprob/test_utils.py
+            tests/distributions/test_truncated.py
+            tests/logprob/test_abstract.py
+            tests/logprob/test_censoring.py
+            tests/logprob/test_composite_logprob.py
+            tests/logprob/test_cumsum.py
+            tests/logprob/test_joint_logprob.py
+            tests/logprob/test_mixture.py
+            tests/logprob/test_rewriting.py
+            tests/logprob/test_scan.py
+            tests/logprob/test_tensor.py
+            tests/logprob/test_transforms.py
+            tests/logprob/test_utils.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -165,10 +164,10 @@ jobs:
         floatx: [float64]
         python-version: ["3.8"]
         test-subset:
-          - pymc/tests/variational/test_approximations.py pymc/tests/variational/test_callbacks.py pymc/tests/variational/test_inference.py pymc/tests/variational/test_opvi.py pymc/tests/test_initial_point.py
-          - pymc/tests/test_model.py pymc/tests/sampling/test_mcmc.py
-          - pymc/tests/gp/test_cov.py pymc/tests/gp/test_gp.py pymc/tests/gp/test_mean.py pymc/tests/gp/test_util.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py pymc/tests/smc/test_smc.py pymc/tests/sampling/test_parallel.py
-          - pymc/tests/step_methods/test_metropolis.py pymc/tests/step_methods/test_slicer.py pymc/tests/step_methods/hmc/test_nuts.py pymc/tests/step_methods/test_compound.py pymc/tests/step_methods/hmc/test_hmc.py
+          - tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
+          - tests/test_model.py tests/sampling/test_mcmc.py
+          - tests/gp/test_cov.py tests/gp/test_gp.py tests/gp/test_mean.py tests/gp/test_util.py tests/ode/test_ode.py tests/ode/test_utils.py tests/smc/test_smc.py tests/sampling/test_parallel.py
+          - tests/step_methods/test_metropolis.py tests/step_methods/test_slicer.py tests/step_methods/hmc/test_nuts.py tests/step_methods/test_compound.py tests/step_methods/hmc/test_hmc.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -239,16 +238,16 @@ jobs:
         python-version: ["3.9"]
         test-subset:
           - |
-            pymc/tests/sampling/test_parallel.py
-            pymc/tests/test_data.py
-            pymc/tests/test_model.py
+            tests/sampling/test_parallel.py
+            tests/test_data.py
+            tests/test_model.py
 
           - |
-            pymc/tests/sampling/test_mcmc.py
+            tests/sampling/test_mcmc.py
 
           - |
-            pymc/tests/backends/test_arviz.py
-            pymc/tests/variational/test_updates.py
+            tests/backends/test_arviz.py
+            tests/variational/test_updates.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -306,14 +305,14 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
-  jax:
+  external_samplers:
     strategy:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
         python-version: ["3.9"]
         test-subset:
-          - pymc/tests/sampling/test_jax.py
+          - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -361,9 +360,10 @@ jobs:
           conda activate pymc-test
           pip install -e .
           python --version
-      - name: Install jax specific dependencies
+      - name: Install external samplers
         run: |
           conda activate pymc-test
+          conda install -c conda-forge nutpie
           pip install "numpyro>=0.8.0"
           pip install git+https://github.com/blackjax-devs/blackjax.git@0.7.0
       - name: Run tests
@@ -383,7 +383,7 @@ jobs:
         floatx: [float32]
         python-version: ["3.10"]
         test-subset:
-        - pymc/tests/sampling/test_mcmc.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py
+        - tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:

.pre-commit-config.yaml

@@ -34,12 +34,12 @@ repos:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
     - id: black
     - id: black-jupyter
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.16.0b1
+  rev: v2.16.2
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]

.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"

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include pymc/tests/data *
+recursive-include tests/data *
 recursive-include source *
 # because of an upload-size limit by PyPI, we're temporarily removing docs from the tarball:
 recursive-exclude docs *

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:

codecov.yml

@@ -20,7 +20,7 @@ coverage:
         base: auto
 
 ignore:
-  - "pymc/tests/*"
+  - "tests/*"
   - "pymc/_version.py"
 
 comment:

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

docs/source/api/backends.rst

@@ -18,6 +18,5 @@ Internal structures
    :toctree: generated/
 
    NDArray
-   point_list_to_multitrace
    base.BaseTrace
    base.MultiTrace

docs/source/api/data.rst

@@ -12,4 +12,3 @@ Data
    Data
    GeneratorAdapter
    Minibatch
-   align_minibatches

docs/source/api/distributions/simulator.rst

@@ -6,6 +6,4 @@ Simulator
 .. autosummary::
    :toctree: generated
 
-   SimulatorRV
    Simulator
-   KullbackLiebler

docs/source/api/distributions/timeseries.rst

@@ -6,7 +6,6 @@ Timeseries
 .. autosummary::
    :toctree: generated
 
-    AR1
     AR
     GaussianRandomWalk
     GARCH11

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

docs/source/api/math.rst

@@ -48,7 +48,7 @@ Functions exposed in pymc.math
    where
    and_
    or_
-   abs_
+   abs
    exp
    log
    cos

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

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
 

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

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/"