Merge branch 'main' into numpydoc_exponential

Author: OriolAbril

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,6 +5,6 @@ Depending on what your PR does, here are a few things you might want to address
 + [ ] what are the (breaking) changes that this PR makes?
 + [ ] important background, or details about the implementation
 + [ ] are the changes—especially new features—covered by tests and docstrings?
-+ [ ] [linting/style checks have been run](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style)
++ [ ] [linting/style checks have been run](https://docs.pymc.io/en/latest/contributing/python_style.html)
 + [ ] [consider adding/updating relevant example notebooks](https://github.com/pymc-devs/pymc-examples)
 + [ ] right before it's ready to merge, mention the PR in the RELEASE-NOTES.md

.github/workflows/nightly.yml

@@ -0,0 +1,43 @@
+name: nightly
+
+on:
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  build-and-publish-nightly:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install build
+      - name: Build the sdist
+        run: python -m build --sdist .
+        env:
+          BUILD_PYMC_NIGHTLY: true
+      - name: Publish to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN_PYMC_NIGHTLY }}
+  test-install-job:
+    needs: build-and-publish-nightly
+    runs-on: ubuntu-latest
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Give PyPI a chance to update the index
+      run: sleep 240
+    - name: Install from PyPI
+      run: |
+        pip install pymc-nightly==$(grep 'version' pymc/__init__.py | awk '{print $3}' | tr -d '"').dev$(date +"%Y%m%d")

.github/workflows/pytest.yml

@@ -48,7 +48,6 @@ jobs:
             --ignore=pymc/tests/test_step.py
             --ignore=pymc/tests/test_tuning.py
             --ignore=pymc/tests/test_transforms.py
-            --ignore=pymc/tests/test_variational_inference.py
             --ignore=pymc/tests/test_sampling_jax.py
             --ignore=pymc/tests/test_dist_math.py
             --ignore=pymc/tests/test_minibatches.py
@@ -64,7 +63,6 @@ jobs:
             --ignore=pymc/tests/test_distributions_random.py
             --ignore=pymc/tests/test_idata_conversion.py
             --ignore=pymc/tests/test_smc.py
-            --ignore=pymc/tests/test_bart.py
             --ignore=pymc/tests/test_missing.py
 
           - |
@@ -78,7 +76,7 @@ jobs:
             pymc/tests/test_updates.py
             pymc/tests/test_transforms.py
             pymc/tests/test_smc.py
-            pymc/tests/test_bart.py
+            pymc/tests/test_mixture.py
 
           - |
             pymc/tests/test_parallel_sampling.py
@@ -169,6 +167,7 @@ jobs:
             pymc/tests/test_distributions_random.py
             pymc/tests/test_distributions_moments.py
             pymc/tests/test_distributions_timeseries.py
+            pymc/tests/test_variational_inference.py
           - |
             pymc/tests/test_parallel_sampling.py
             pymc/tests/test_sampling.py

.pre-commit-config.yaml

@@ -60,3 +60,35 @@ repos:
       entry: from \.[\.\w]* import
       types: [python]
       language: pygrep
+    - id: no-internal-links
+      name: Check no internal links are in the docs
+      description: >-
+        'A quick check for the links in the intersphinx '
+        'mapping inside `docs/source/`'
+        'See docs/source/conf.py for more information.'
+      files: ^docs/source/
+      # Files that should be ignored:
+      # - index.md
+      # - 404.md
+      # - contributing/release_checklist.md
+      # The other files are under development and should be
+      # removed from the list once they are revised.
+      exclude: >
+          (?x)(index.md|
+               404.md|
+               contributing/release_checklist.md|
+               contributing/developer_guide.rst|
+               learn/examples.md)
+      entry: >
+          (?x)(arviz-devs.github.io|
+               aesara.readthedocs.io|
+               aeppl.readthedocs.io|
+               docs.pymc.io|
+               numpy.org/doc|
+               pymc-examples.readthedocs.io|
+               myst-parser.readthedocs.io|
+               myst-nb.readthedocs.io|
+               docs.python.org|
+               xarray.pydata.org)
+      language: pygrep
+      types_or: [markdown, rst, jupyter]

RELEASE-NOTES.md

@@ -7,15 +7,13 @@ Instead update the vNext section until 4.0.0 is out.
 ⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠⚠
 -->
 
-## PyMC vNext (4.0.0b1 → 4.0.0b2 → 4.0.0b3 → 4.0.0)
+## PyMC vNext (4.0.0b1 → 4.0.0b2 → 4.0.0b3 → 4.0.0b4 → 4.0.0)
 ⚠ The changes below are the delta between the upcoming releases `v3.11.5` →...→ `v4.0.0`.
 
-### No-yet working features
+### Not-yet working features
 We plan to get these working again, but at this point their inner workings have not been refactored.
 - Timeseries distributions (see [#4642](https://github.com/pymc-devs/pymc/issues/4642))
-- Mixture distributions (see [#4781](https://github.com/pymc-devs/pymc/issues/4781))
-- Cholesky distributions (see WIP PR [#4784](https://github.com/pymc-devs/pymc/pull/4784))
-- Variational inference submodule (see WIP PR [#4582](https://github.com/pymc-devs/pymc/pull/4582))
+- Nested Mixture distributions (see [#5533](https://github.com/pymc-devs/pymc/issues/5533))
 - Elliptical slice sampling (see [#5137](https://github.com/pymc-devs/pymc/issues/5137))
 - `BaseStochasticGradient` (see [#5138](https://github.com/pymc-devs/pymc/issues/5138))
 - `pm.sample_posterior_predictive_w` (see [#4807](https://github.com/pymc-devs/pymc/issues/4807))
@@ -74,6 +72,7 @@ All of the above apply to:
   - In the gp.utils file, the `kmeans_inducing_points` function now passes through `kmeans_kwargs` to scipy's k-means function.
   - The function `replace_with_values` function has been added to `gp.utils`.
   - `MarginalSparse` has been renamed `MarginalApprox`.
+  - Removed `MixtureSameFamily`. `Mixture` is now capable of handling batched multivariate components (see [#5438](https://github.com/pymc-devs/pymc/pull/5438)).
 - ...
 
 ### Expected breaks
@@ -129,6 +128,7 @@ This includes API changes we did not warn about since at least `3.11.0` (2021-01
 - `softmax` and `log_softmax` functions added to `math` module (see [#5279](https://github.com/pymc-devs/pymc/pull/5279)).
 - ...
 
+
 ## Documentation
 - Switched to the [pydata-sphinx-theme](https://pydata-sphinx-theme.readthedocs.io/en/latest/)
 - Updated our documentation tooling to use [MyST](https://myst-parser.readthedocs.io/en/latest/), [MyST-NB](https://myst-nb.readthedocs.io/en/latest/), sphinx-design, notfound.extension,

conda-envs/environment-dev-py37.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -24,7 +24,7 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.7
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5

conda-envs/environment-dev-py38.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -24,7 +24,7 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.8
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5

conda-envs/environment-dev-py39.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -24,7 +24,7 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.9
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5

conda-envs/environment-test-py37.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -22,5 +22,5 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.7
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - typing-extensions>=3.7.4

conda-envs/environment-test-py38.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -22,5 +22,5 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.8
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - typing-extensions>=3.7.4

conda-envs/environment-test-py39.yml

@@ -5,7 +5,7 @@ channels:
 - defaults
 dependencies:
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -22,5 +22,5 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.9
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - typing-extensions>=3.7.4

conda-envs/windows-environment-dev-py38.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
  # base dependencies (see install guide for Windows)
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -17,7 +17,7 @@ dependencies:
 - pip
 - python=3.8
 - python-graphviz
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - typing-extensions>=3.7.4
 # Extra stuff for dev, testing and docs build
 - ipython>=7.16

conda-envs/windows-environment-test-py38.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
  # base dependencies (see install guide for Windows)
 - aeppl=0.0.26
-- aesara=2.3.8
+- aesara=2.4.0
 - arviz>=0.11.4
 - blas
 - cachetools>=4.2.1
@@ -21,7 +21,7 @@ dependencies:
 - pip
 - python=3.8
 - python-graphviz
-- scipy>=1.4.1,<1.8.0
+- scipy>=1.4.1
 - typing-extensions>=3.7.4
 # Extra stuff for testing
 - ipython>=7.16

docs/source/Advanced_usage_of_Aesara_in_PyMC.rst

@@ -102,7 +102,7 @@ Good reasons for defining a custom `Op` might be the following:
   and sufficiently parallelizable to make the cost worth it.
   We would definitely like to hear about any such examples.
 
-Aesara has extensive `documentation, <https://aesara.readthedocs.io/en/latest/extending/index.html>`_
+Aesara has extensive :doc:`documentation <aesara:index>`
 about how to write new Ops.
 
 

docs/source/PyMC_and_Aesara.rst

@@ -17,7 +17,7 @@ their posterior probability density up to a constant factor. We then use
 symbolic manipulations of this function to also get access to its gradient.
 
 For a thorough introduction to Aesara see the
-`aesara docs <https://aesara.readthedocs.io/en/latest/>`_,
+:doc:`aesara docs <aesara:index>`,
 but for the most part you don't need detailed knowledge about it as long
 as you are not trying to define new distributions or other extensions
 of PyMC. But let's look at a simple example to get a rough
@@ -81,7 +81,7 @@ like NumPy arrays. Most NumPy functions are available in `aesara.tensor`
 can be found in `at.nlinalg` and `at.slinalg` (the NumPy and SciPy
 operations respectively). Some support for sparse matrices is available
 in `aesara.sparse`. For a detailed overview of available operations,
-see `the aesara api docs <https://aesara.readthedocs.io/en/latest/library/tensor/index.html>`_.
+see :mod:`the aesara api docs <aesara.tensor>`.
 
 A notable exception where Aesara variables do *not* behave like
 NumPy arrays are operations involving conditional execution.

docs/source/api.rst

@@ -15,7 +15,6 @@ API Reference
    api/smc
    api/backends
    api/data
-   api/bart
    api/ode
    api/tuning
    api/math

docs/source/api/bart.rst

@@ -1,3 +1,4 @@
+.. _api_distributions:
 *************
 Distributions
 *************

docs/source/api/distributions.rst

@@ -8,4 +8,3 @@ Mixture
 
    Mixture
    NormalMixture
-   MixtureSameFamily

docs/source/api/distributions/mixture.rst

@@ -49,6 +49,7 @@
     "notfound.extension",
     "sphinx_copybutton",
     "sphinx_remove_toctrees",
+    "jupyter_sphinx",
 ]
 
 # Don't auto-generate summary for class members.
@@ -74,8 +75,10 @@
     "MultiTrace": ":class:`~pymc.backends.base.MultiTrace`",
     "BaseTrace": ":class:`~pymc.backends.base.BaseTrace`",
     "Point": ":class:`~pymc.Point`",
+    "Model": ":class:`~pymc.Model`",
     "SMC_kernel": ":ref:`SMC Kernel <smc_kernels>`",
     "Aesara_Op": ":class:`Aesara Op <aesara.graph.op.Op>`",
+    "tensor_like": ":term:`tensor_like`",
 }
 
 # Show the documentation of __init__ and the class docstring

docs/source/conf.py

@@ -6,7 +6,7 @@ To build the docs, run these commands at pymc repository root:
 $ pip install -r requirements-dev.txt  # Make sure the dev requirements are installed
 $ make clean  # clean built docs from previous runs and intermediate outputs
 $ make html   # Build docs
-$ python -m http.server --directory ../_build/  # Render docs
+$ python -m http.server --directory docs/_build/  # Render docs
 ```
 
 Check the printed url where docs are being served and open it.