Merge branch 'pymc-devs:main' into rename-twitter-to-x

Author: star1327p

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

@@ -28,27 +28,27 @@ jobs:
         persist-credentials: false
 
     - name: Setup Docker buildx
-      uses: docker/setup-buildx-action@v3.7.1
+      uses: docker/setup-buildx-action@v3.10.0
 
     - name: Prepare metadata
       id: meta
-      uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
+      uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
       with:
         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
         tags: |
           type=sha,enable=true,prefix=git-
           type=raw,value=latest
 
     - name: Log into registry ${{ env.REGISTRY }}
-      uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
+      uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
       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@32945a339266b759abcbdc89316275140b0fc960
+      uses: docker/build-push-action@14487ce63c7a62a4a324b0bfb37086795e31c6c1
       with:
         context: .
         file: scripts/dev.Dockerfile

.github/workflows/docker-image.yml

@@ -18,14 +18,14 @@ jobs:
           persist-credentials: false
 
       - name: Login to Docker Hub
-        uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
+        uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
         with:
           images: |
               name=pymc/pymc,enable=true
@@ -36,7 +36,7 @@ jobs:
               type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and load image
-        uses: docker/build-push-action@32945a339266b759abcbdc89316275140b0fc960
+        uses: docker/build-push-action@14487ce63c7a62a4a324b0bfb37086795e31c6c1
         with:
           context: .
           file: scripts/Dockerfile
@@ -48,7 +48,7 @@ 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@32945a339266b759abcbdc89316275140b0fc960
+        uses: docker/build-push-action@14487ce63c7a62a4a324b0bfb37086795e31c6c1
         with:
           context: .
           push: true

.github/workflows/mypy.yml

@@ -26,7 +26,6 @@ jobs:
       - name: Install-pymc and mypy dependencies
         run: |
           pip install -e .
-          pip install --pre -U polyagamma
           python --version
       - name: Run mypy
         run: |

.github/workflows/pr-auto-label.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Sync labels with closing issues
-      uses: wd60622/[email protected].3
+      uses: williambdean/[email protected].4
       with:
         exclude: "help wanted,needs info,beginner friendly"
       env:

.github/workflows/release.yml

@@ -20,7 +20,7 @@ jobs:
         with:
           fetch-depth: 0
           persist-credentials: false
-      - uses: hynek/build-and-inspect-python-package@14c7e53f5d033cfa99f7af916fa59a6f7f356394  # v2.11.0
+      - uses: hynek/build-and-inspect-python-package@b5076c307dc91924a82ad150cdd1533b444d3310  # v2.12.0
         with:
           # Prove that the packages were built in the context of this workflow.
           attest-build-provenance-github: true
@@ -38,12 +38,12 @@ jobs:
       id-token: write
     steps:
       - name: Download Distribution Artifacts
-        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16  # v4.1.8
+        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093  # v4.3.0
         with:
           # The build-and-inspect-python-package action invokes upload-artifact.
           # These are the correct arguments from that action.
           name: Packages
           path: dist
       - name: Publish Package to PyPI
-        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70  # v1.12.3
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc  # v1.12.4
         # Implicitly attests that the packages were uploaded in the context of this workflow.

.github/workflows/tests.yml

@@ -54,9 +54,9 @@ jobs:
     if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-latest]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
           - |
             tests/test_util.py
@@ -158,15 +158,13 @@ jobs:
       - name: Install-pymc
         run: |
           pip install -e .
-          # TODO: https://github.com/pymc-devs/pymc/issues/7417
-          pip install --pre -U 'polyagamma<1.3.7'
           python --version
           micromamba list
       - name: Run tests
         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@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -210,7 +208,6 @@ jobs:
       - name: Install-pymc
         run: |
           pip install -e .
-          pip install --pre -U 'polyagamma<1.3.7'
           python --version
           micromamba list
       - name: Run tests
@@ -219,7 +216,7 @@ 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@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -233,7 +230,7 @@ jobs:
       matrix:
         os: [macos-latest]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
           - |
             tests/sampling/test_parallel.py
@@ -277,23 +274,27 @@ 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@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
 
-  external_samplers:
+  alternative_backends:
     needs: changes
     if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-latest]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
-          - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
+          - |
+            tests/distributions/test_random_alternative_backends.py
+            tests/sampling/test_jax.py
+            tests/sampling/test_mcmc_external.py
+
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -308,7 +309,7 @@ jobs:
           persist-credentials: false
       - uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: conda-envs/environment-jax.yml
+          environment-file: conda-envs/environment-alternative-backends.yml
           create-args: >-
             python=${{matrix.python-version}}
           environment-name: pymc-test
@@ -323,11 +324,11 @@ 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@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
-          name: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
+          name: Alternative backend tests - ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
 
   float32:
@@ -337,7 +338,7 @@ jobs:
       matrix:
         os: [windows-latest]
         floatx: [float32]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         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
@@ -363,7 +364,6 @@ jobs:
       - name: Install-pymc
         run: |
           pip install -e .
-          pip install --pre -U 'polyagamma<1.3.7'
           python --version
           micromamba list
       - name: Run tests
@@ -372,7 +372,7 @@ 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@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -382,13 +382,13 @@ jobs:
   all_tests:
     if: ${{ always() }}
     runs-on: ubuntu-latest
-    needs: [ changes, ubuntu, windows, macos, external_samplers, float32 ]
+    needs: [ changes, ubuntu, windows, macos, alternative_backends, float32 ]
     steps:
       - name: Check build matrix status
         if: ${{ needs.changes.outputs.changes == 'true' &&
                 ( needs.ubuntu.result != 'success' ||
                   needs.windows.result != 'success' ||
                   needs.macos.result != 'success' ||
-                  needs.external_samplers.result != 'success' ||
+                  needs.alternative_backends.result != 'success' ||
                   needs.float32.result != 'success' ) }}
         run: exit 1

.gitignore

@@ -52,3 +52,6 @@ venv/
 pixi.toml
 pixi.lock
 .pixi/
+
+.jupyter/
+.claude/

.mailmap

@@ -38,7 +38,7 @@ repos:
     - id: sphinx-lint
       args: ["."]
 - repo: https://github.com/lucianopaz/head_of_apache
-  rev: "0.1.0"
+  rev: "0.1.1"
   hooks:
     - id: head_of_apache
       args:
@@ -49,7 +49,7 @@ repos:
         - --exclude=versioneer.py
         - --last-year-present
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.2
+  rev: v0.11.7
   hooks:
     - id: ruff
       args: [--fix, --show-fixes]

.pre-commit-config.yaml

@@ -296,8 +296,8 @@ Thanks to our contributors
 
 .. |Binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/pymc-devs/pymc/main?filepath=%2Fdocs%2Fsource%2Fnotebooks
-.. |Build Status| image:: https://github.com/pymc-devs/pymc/workflows/pytest/badge.svg
-   :target: https://github.com/pymc-devs/pymc/actions
+.. |Build Status| image:: https://github.com/pymc-devs/pymc/workflows/tests/badge.svg
+   :target: https://github.com/pymc-devs/pymc/actions?query=workflow%3Atests+branch%3Amain
 .. |Coverage| image:: https://codecov.io/gh/pymc-devs/pymc/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/pymc-devs/pymc
 .. |Dockerhub| image:: https://img.shields.io/docker/automated/pymc/pymc.svg