Merge branch 'pymc-devs:main' into debug_docs_and_function_helpers

Author: itsdivya1309

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

@@ -23,10 +23,10 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
 
     - name: Setup Docker buildx
-      uses: docker/setup-buildx-action@v3.0.0
+      uses: docker/setup-buildx-action@v3.2.0
 
     - name: Prepare metadata
       id: meta
@@ -38,15 +38,15 @@ jobs:
           type=raw,value=latest
 
     - name: Log into registry ${{ env.REGISTRY }}
-      uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
+      uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20
       with:
         registry: ${{ env.REGISTRY }}
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Build and push Docker image
       id: docker_build
-      uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
       with:
         context: .
         file: scripts/dev.Dockerfile

.github/workflows/dispatched_pre-commit.yml

@@ -7,7 +7,7 @@ jobs:
   runPreCommit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
         with:
           repository: ${{github.event.client_payload.pull_request.head.repo.full_name}}
           ref: ${{github.event.client_payload.pull_request.head.ref}}

.github/workflows/docker-image.yml

@@ -13,10 +13,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
 
       - name: Login to Docker Hub
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
+        uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -34,7 +34,7 @@ jobs:
               type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and load image
-        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
+        uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
         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@0565240e2d4ab88bba5387d719585280857ece09
+        uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
         with:
           context: .
           push: true

.github/workflows/pre-commit.yml

@@ -11,7 +11,7 @@ jobs:
     env:
       SKIP: no-commit-to-branch
     steps:
-    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
     - uses: actions/setup-python@v5
       with:
         python-version: "3.9"  # Run pre-commit on oldest supported Python version
@@ -22,7 +22,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:

.github/workflows/release.yml

@@ -11,7 +11,7 @@ jobs:
     env:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PYMC }}
     steps:
-    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
     - name: Set up Python
       uses: actions/setup-python@v5
       with:

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
     outputs:
       changes: ${{ steps.changes.outputs.src }}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
         with:
           fetch-depth: 0
       - uses: dorny/paths-filter@v3
@@ -48,7 +48,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         test-subset:
           - |
             tests/test_util.py
@@ -67,7 +67,6 @@ jobs:
             tests/distributions/test_multivariate.py
 
           - |
-            tests/distributions/test_bound.py
             tests/distributions/test_censored.py
             tests/distributions/test_simulator.py
             tests/sampling/test_forward.py
@@ -130,7 +129,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -174,7 +173,7 @@ jobs:
           conda activate pymc-test
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -204,7 +203,7 @@ jobs:
       run:
         shell: cmd
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -250,7 +249,7 @@ jobs:
           conda activate pymc-test &&
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -264,7 +263,7 @@ jobs:
       matrix:
         os: [macos-latest]
         floatx: [float64]
-        python-version: ["3.10"]
+        python-version: ["3.12"]
         test-subset:
           - |
             tests/sampling/test_parallel.py
@@ -287,7 +286,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -329,7 +328,7 @@ jobs:
         run: |
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -343,7 +342,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         test-subset:
           - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
       fail-fast: false
@@ -355,7 +354,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -397,7 +396,7 @@ jobs:
         run: |
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -411,7 +410,7 @@ jobs:
       matrix:
         os: [windows-latest]
         floatx: [float32]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         test-subset:
         - tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py tests/distributions/test_transform.py
       fail-fast: false
@@ -423,7 +422,7 @@ jobs:
       run:
         shell: cmd
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -469,7 +468,7 @@ jobs:
           conda activate pymc-test &&
           python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
         - --exclude=binder/
         - --exclude=versioneer.py
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.2.1
+  rev: v0.3.4
   hooks:
     - id: ruff
       args: ["--fix", "--output-format=full"]

codecov.yml

@@ -1,5 +1,7 @@
 codecov:
   require_ci_to_pass: yes
+  notify:
+    after_n_builds: 15  # This should be updated if number of test jobs changes
 
 coverage:
   precision: 2

conda-envs/environment-dev.yml

@@ -14,7 +14,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/environment-docs.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
@@ -28,6 +28,7 @@ dependencies:
 - sphinx-copybutton
 - sphinx-design
 - sphinx-notfound-page
+- sphinx-sitemap
 - sphinx>=5
 - sphinxext-rediraffe
 - watermark

conda-envs/environment-jax.yml

@@ -13,15 +13,15 @@ dependencies:
 - h5py>=2.7
 # Jaxlib version must not be greater than jax version!
 - blackjax>=1.0.0
-- jaxlib==0.4.14
-- jax==0.4.16
+- jaxlib==0.4.23
+- jax==0.4.23
 - libblas=*=*mkl
 - mkl-service
 - numpy>=1.15.0
 - numpyro>=0.8.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/environment-test.yml

@@ -17,7 +17,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/windows-environment-dev.yml

@@ -14,7 +14,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/windows-environment-test.yml

@@ -17,7 +17,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.18.1,<2.19
+- pytensor>=2.19,<2.20
 - python-graphviz
 - networkx
 - scipy>=1.4.1

docs/source/conf.py

@@ -1,6 +1,4 @@
-""" Sphinx configuration file.
-
-"""
+"""Sphinx configuration file."""
 #!/usr/bin/env python3
 #
 # pymc documentation build configuration file, created by
@@ -46,6 +44,7 @@
     "sphinx_remove_toctrees",
     "jupyter_sphinx",
     "sphinxext.rediraffe",
+    "sphinx_sitemap",
 ]
 
 # Don't auto-generate summary for class members.
@@ -108,8 +107,8 @@
 
 version = pymc.__version__
 on_readthedocs = os.environ.get("READTHEDOCS", False)
+rtd_version = os.environ.get("READTHEDOCS_VERSION", "")
 if on_readthedocs:
-    rtd_version = os.environ.get("READTHEDOCS_VERSION", "")
     if rtd_version.lower() == "stable":
         version = pymc.__version__.split("+")[0]
     elif rtd_version.lower() == "latest":
@@ -337,6 +336,8 @@ def setup(app):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = "pymc_sphinx_theme"
+html_baseurl = "https://www.pymc.io/projects/docs/"
+sitemap_url_scheme = f"{{lang}}{rtd_version}/{{link}}"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme

docs/source/contributing/developer_guide.md

@@ -66,7 +66,7 @@ We can, of course, also work out the math by hand:
 $$
 \begin{aligned}
 pdf_{\mathcal{N}}(\mu, \sigma, x) &= \frac{1}{\sigma \sqrt{2 \pi}} \exp^{- 0.5 (\frac{x - \mu}{\sigma})^2} \\
-pdf_{\mathcal{N}}(0, 5, 0.3) &= 0.070413 \\
+pdf_{\mathcal{N}}(0, 5, 2.5) &= 0.070413 \\
 ln(0.070413) &= -2.6533
 \end{aligned}
 $$