Merge branch 'main' into discrete-distributions-type-hints

Author: fonnesbeck

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

@@ -23,10 +23,10 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
 
     - name: Setup Docker buildx
-      uses: docker/setup-buildx-action@v3.0.0
+      uses: docker/setup-buildx-action@v3.4.0
 
     - 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@9780b0c442fbb1117ed29e0efdff1e18412f7567
       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@32945a339266b759abcbdc89316275140b0fc960
       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@d632683dd7b4114ad314bca15554477dd762a938
         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@d632683dd7b4114ad314bca15554477dd762a938
 
       - name: Login to Docker Hub
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
+        uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
         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@32945a339266b759abcbdc89316275140b0fc960
         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@32945a339266b759abcbdc89316275140b0fc960
         with:
           context: .
           push: true

.github/workflows/pre-commit.yml .github/workflows/mypy.yml.github/workflows/pre-commit.yml renamed to .github/workflows/mypy.yml

@@ -1,28 +1,18 @@
-name: pre-commit
+name: mypy
 
 on:
   pull_request:
   push:
     branches: [main]
 
 jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    env:
-      SKIP: no-commit-to-branch
-    steps:
-    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.9"  # Run pre-commit on oldest supported Python version
-    - uses: pre-commit/[email protected]
   mypy:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -52,7 +42,7 @@ jobs:
           activate-environment: pymc-test
           channel-priority: strict
           environment-file: conda-envs/environment-test.yml
-          python-version: "3.9"  # Run pre-commit on oldest supported Python version
+          python-version: "3.10"  # Run pre-commit on oldest supported Python version
           use-mamba: true
           use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
       - name: Install-pymc and mypy dependencies

.github/workflows/release.yml

@@ -11,7 +11,7 @@ jobs:
     env:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PYMC }}
     steps:
-    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+    - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -26,10 +26,10 @@ jobs:
     #    pytest --cov=./pymc --cov-report term-missing pymc/
     - name: Install release tooling
       run: |
-        pip install twine wheel
+        pip install build twine
     - name: Build package
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
     - name: Check version number match
       run: |
         echo "GITHUB_REF: ${GITHUB_REF}"

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
     outputs:
       changes: ${{ steps.changes.outputs.src }}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
         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
@@ -65,10 +65,13 @@ jobs:
           - |
             tests/distributions/test_continuous.py
             tests/distributions/test_multivariate.py
+            tests/distributions/moments/test_means.py
 
           - |
             tests/distributions/test_censored.py
+            tests/distributions/test_custom.py
             tests/distributions/test_simulator.py
+            tests/sampling/test_deterministic.py
             tests/sampling/test_forward.py
             tests/sampling/test_population.py
             tests/stats/test_convergence.py
@@ -96,10 +99,12 @@ jobs:
             tests/model/test_fgraph.py
             tests/model/transform/test_basic.py
             tests/model/transform/test_conditioning.py
+            tests/model/transform/test_optimization.py
             tests/test_model_graph.py
             tests/ode/test_ode.py
             tests/ode/test_utils.py
             tests/step_methods/hmc/test_quadpotential.py
+            tests/step_methods/test_state.py
 
           - |
             tests/backends/test_mcbackend.py
@@ -111,6 +116,7 @@ jobs:
             tests/logprob/test_censoring.py
             tests/logprob/test_composite_logprob.py
             tests/logprob/test_cumsum.py
+            tests/logprob/test_linalg.py
             tests/logprob/test_mixture.py
             tests/logprob/test_order.py
             tests/logprob/test_rewriting.py
@@ -129,7 +135,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -166,14 +172,16 @@ jobs:
         run: |
           conda activate pymc-test
           pip install -e .
-          pip install --pre -U polyagamma
+          # TODO: https://github.com/pymc-devs/pymc/issues/7417
+          pip install --pre -U 'polyagamma<1.3.7'
           python --version
+          conda list
       - name: Run tests
         run: |
           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
@@ -187,12 +195,12 @@ jobs:
       matrix:
         os: [windows-latest]
         floatx: [float64]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         test-subset:
           - 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/model/test_core.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
+          - 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 tests/step_methods/test_state.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -203,7 +211,7 @@ jobs:
       run:
         shell: cmd
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -240,16 +248,17 @@ jobs:
         run: |
           conda activate pymc-test
           pip install -e .
-          pip install --pre -U polyagamma
+          pip install --pre -U 'polyagamma<1.3.7'
           python --version
+          conda list
       - name: Run tests
         # This job uses a cmd shell, therefore the environment variable syntax is different!
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
           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
@@ -263,7 +272,7 @@ jobs:
       matrix:
         os: [macos-latest]
         floatx: [float64]
-        python-version: ["3.10"]
+        python-version: ["3.12"]
         test-subset:
           - |
             tests/sampling/test_parallel.py
@@ -286,7 +295,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -324,11 +333,12 @@ jobs:
           conda activate pymc-test
           pip install -e .
           python --version
+          conda 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@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -342,7 +352,7 @@ 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
@@ -354,7 +364,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -392,11 +402,12 @@ jobs:
           conda activate pymc-test
           pip install -e .
           python --version
+          conda 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@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
           env_vars: TEST_SUBSET
@@ -410,7 +421,7 @@ 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
@@ -422,7 +433,7 @@ jobs:
       run:
         shell: cmd
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
       - name: Cache conda
         uses: actions/cache@v4
         env:
@@ -459,16 +470,17 @@ jobs:
         run: |
           conda activate pymc-test
           pip install -e .
-          pip install --pre -U polyagamma
+          pip install --pre -U 'polyagamma<1.3.7'
           python --version
+          conda list
       - name: Run tests
         # This job uses a cmd shell, therefore the environment variable syntax is different!
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
           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

.gitignore

@@ -49,3 +49,6 @@ pythonenv*
 env/
 venv/
 .venv/
+pixi.toml
+pixi.lock
+.pixi/