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