ci: pre-commit hook to auto-format yaml files

.github/workflows/ci.yml

@@ -4,9 +4,9 @@ name: CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 env:
   PYTEST_ADDOPTS: "--cov=numpyro --cov-append"
@@ -17,37 +17,37 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10","3.13"]
+        python-version: ["3.9", "3.10", "3.13"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        sudo apt install -y pandoc gsfonts
-        python -m pip install --upgrade pip
-        pip install jaxlib
-        pip install jax
-        pip install '.[doc,test]'
-        pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install -r docs/requirements.txt
-        pip freeze
-    - name: Lint with mypy and ruff
-      if: matrix.python-version != '3.9'
-      run: |
-        make lint
-    - name: Build documentation
-      if: matrix.python-version != '3.9'
-      run: |
-        make docs
-    - name: Test documentation
-      if: matrix.python-version != '3.9'
-      run: |
-        make doctest
-        python -m doctest -v README.md
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo apt install -y pandoc gsfonts
+          python -m pip install --upgrade pip
+          pip install jaxlib
+          pip install jax
+          pip install '.[doc,test]'
+          pip install https://github.com/pyro-ppl/funsor/archive/master.zip
+          pip install -r docs/requirements.txt
+          pip freeze
+      - name: Lint with mypy and ruff
+        if: matrix.python-version != '3.9'
+        run: |
+          make lint
+      - name: Build documentation
+        if: matrix.python-version != '3.9'
+        run: |
+          make docs
+      - name: Test documentation
+        if: matrix.python-version != '3.9'
+        run: |
+          make doctest
+          python -m doctest -v README.md
 
 
   test-modeling:
@@ -59,46 +59,46 @@ jobs:
         python-version: ["3.9", "3.13"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        sudo apt install -y graphviz
-        python -m pip install --upgrade pip
-        # Keep track of pyro-api master branch
-        pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
-        pip install jaxlib
-        pip install jax
-        pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install -e '.[dev,test]'
-        pip freeze
-    - name: Test with pytest
-      run: |
-        CI=1 pytest -vs -k "not test_example" --durations=100 --ignore=test/infer/ --ignore=test/contrib/
-    - name: Test x64
-      run: |
-        JAX_ENABLE_X64=1 pytest -vs test/test_distributions.py -k "powerLaw or Dagum"
-    - name: Test tracer leak
-      if: matrix.python-version == '3.13'
-      env:
-        JAX_CHECK_TRACER_LEAKS: 1
-      run: |
-        pytest -vs test/infer/test_mcmc.py::test_chain_inside_jit
-        pytest -vs test/infer/test_mcmc.py::test_chain_jit_args_smoke
-        pytest -vs test/infer/test_mcmc.py::test_reuse_mcmc_run
-        pytest -vs test/infer/test_mcmc.py::test_model_with_multiple_exec_paths
-        pytest -vs test/test_distributions.py::test_mean_var -k Gompertz
-
-    - name: Coveralls
-      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
-      uses: coverallsapp/github-action@v2
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel: true
-        flag-name: test-modeling
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo apt install -y graphviz
+          python -m pip install --upgrade pip
+          # Keep track of pyro-api master branch
+          pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
+          pip install jaxlib
+          pip install jax
+          pip install https://github.com/pyro-ppl/funsor/archive/master.zip
+          pip install -e '.[dev,test]'
+          pip freeze
+      - name: Test with pytest
+        run: |
+          CI=1 pytest -vs -k "not test_example" --durations=100 --ignore=test/infer/ --ignore=test/contrib/
+      - name: Test x64
+        run: |
+          JAX_ENABLE_X64=1 pytest -vs test/test_distributions.py -k "powerLaw or Dagum"
+      - name: Test tracer leak
+        if: matrix.python-version == '3.13'
+        env:
+          JAX_CHECK_TRACER_LEAKS: 1
+        run: |
+          pytest -vs test/infer/test_mcmc.py::test_chain_inside_jit
+          pytest -vs test/infer/test_mcmc.py::test_chain_jit_args_smoke
+          pytest -vs test/infer/test_mcmc.py::test_reuse_mcmc_run
+          pytest -vs test/infer/test_mcmc.py::test_model_with_multiple_exec_paths
+          pytest -vs test/test_distributions.py::test_mean_var -k Gompertz
+
+      - name: Coveralls
+        if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          flag-name: test-modeling
 
 
   test-inference:
@@ -110,48 +110,48 @@ jobs:
         python-version: ["3.9", "3.13"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        # Keep track of pyro-api master branch
-        pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
-        pip install jaxlib
-        pip install jax
-        pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install -e '.[dev,test]'
-        pip freeze
-    - name: Test with pytest
-      run: |
-        pytest -vs --durations=20 test/infer/test_mcmc.py
-        pytest -vs --durations=20 test/infer --ignore=test/infer/test_mcmc.py --ignore=test/contrib/test_nested_sampling.py
-        pytest -vs --durations=20 test/contrib --ignore=test/contrib/stochastic_support/test_dcc.py
-    - name: Test x64
-      run: |
-        JAX_ENABLE_X64=1 pytest -vs test/infer/test_mcmc.py -k x64
-    - name: Test chains
-      run: |
-        XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/infer/test_mcmc.py -k "chain or pmap or vmap"
-        XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/contrib/test_tfp.py -k "chain"
-        XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/contrib/stochastic_support/test_dcc.py
-        XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/infer/test_hmc_gibbs.py -k "chain"
-    - name: Test custom prng
-      run: |
-        JAX_ENABLE_CUSTOM_PRNG=1 pytest -vs test/infer/test_mcmc.py
-    - name: Test nested sampling
-      run: |
-        JAX_ENABLE_X64=1 pytest -vs test/contrib/test_nested_sampling.py
-    - name: Coveralls
-      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
-      uses: coverallsapp/github-action@v2
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel: true
-        flag-name: test-inference
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Keep track of pyro-api master branch
+          pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
+          pip install jaxlib
+          pip install jax
+          pip install https://github.com/pyro-ppl/funsor/archive/master.zip
+          pip install -e '.[dev,test]'
+          pip freeze
+      - name: Test with pytest
+        run: |
+          pytest -vs --durations=20 test/infer/test_mcmc.py
+          pytest -vs --durations=20 test/infer --ignore=test/infer/test_mcmc.py --ignore=test/contrib/test_nested_sampling.py
+          pytest -vs --durations=20 test/contrib --ignore=test/contrib/stochastic_support/test_dcc.py
+      - name: Test x64
+        run: |
+          JAX_ENABLE_X64=1 pytest -vs test/infer/test_mcmc.py -k x64
+      - name: Test chains
+        run: |
+          XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/infer/test_mcmc.py -k "chain or pmap or vmap"
+          XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/contrib/test_tfp.py -k "chain"
+          XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/contrib/stochastic_support/test_dcc.py
+          XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs test/infer/test_hmc_gibbs.py -k "chain"
+      - name: Test custom prng
+        run: |
+          JAX_ENABLE_CUSTOM_PRNG=1 pytest -vs test/infer/test_mcmc.py
+      - name: Test nested sampling
+        run: |
+          JAX_ENABLE_X64=1 pytest -vs test/contrib/test_nested_sampling.py
+      - name: Coveralls
+        if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          flag-name: test-inference
 
 
   examples:
@@ -163,40 +163,40 @@ jobs:
         python-version: ["3.13"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install jaxlib
-        pip install jax
-        pip install https://github.com/pyro-ppl/funsor/archive/master.zip
-        pip install -e '.[dev,examples,test]'
-        pip freeze
-    - name: Test with pytest
-      run: |
-        CI=1 XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs -k test_example
-    - name: Coveralls
-      if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
-      uses: coverallsapp/github-action@v2
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel: true
-        flag-name: examples
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install jaxlib
+          pip install jax
+          pip install https://github.com/pyro-ppl/funsor/archive/master.zip
+          pip install -e '.[dev,examples,test]'
+          pip freeze
+      - name: Test with pytest
+        run: |
+          CI=1 XLA_FLAGS="--xla_force_host_platform_device_count=2" pytest -vs -k test_example
+      - name: Coveralls
+        if: github.repository == 'pyro-ppl/numpyro' && matrix.python-version == '3.13'
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          flag-name: examples
 
 
   finish:
 
     needs: [test-modeling, test-inference, examples]
     runs-on: ubuntu-latest
     steps:
-    - name: Coveralls finished
-      uses: coverallsapp/github-action@v2
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel-finished: true
-        carryforward: "test-modeling,test-inference,examples"
+      - name: Coveralls finished
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel-finished: true
+          carryforward: "test-modeling,test-inference,examples"
 

.github/workflows/publish.yml

@@ -11,7 +11,7 @@ name: Upload Python Package
 
 on:
   release:
-    types: [ published ]
+    types: [published]
 
 jobs:
   deploy:

.pre-commit-config.yaml

@@ -34,5 +34,11 @@ repos:
     hooks:
       - id: codespell
         stages: [pre-commit, commit-msg]
-        args:
-          [--ignore-words-list, "Teh,aas,ans,dout", --check-filenames, --skip, "*.ipynb"]
+        args: [--ignore-words-list, "Teh,aas,ans,dout", --check-filenames, --skip, "*.ipynb"]
+
+  # Format yaml files
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.20.0
+    hooks:
+      - id: yamlfmt
+        args: [-formatter, retain_line_breaks=true]

.readthedocs.yaml

@@ -6,11 +6,11 @@ build:
     python: "3.10"
 
 sphinx:
-   configuration: docs/source/conf.py
+  configuration: docs/source/conf.py
 
 formats:
-   - pdf
+  - pdf
 
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - requirements: docs/requirements.txt