Refactor CI to use micromamba instead of docker containers.

.github/workflows/test.yaml

@@ -0,0 +1,83 @@
+name: Test
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+
+  push:
+    branches:
+      - "trunk"
+      - "trunk-major"
+
+  workflow_dispatch:
+
+  schedule:
+  - cron:  '0 18 * * 1'
+
+jobs:
+  execute_notebooks:
+    name: Execute notebooks
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: hoomd
+        ref: trunk-minor
+        repository: glotzerlab/hoomd-blue
+        submodules: true
+
+    - name: Create Python Environment
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: test
+        environment-file: hoomd/.github/workflows/environments/py312-conda-lock.yml
+        micromamba-root-path: ${{ github.workspace }}/micromamba
+
+    - name: Configure conda environment variables
+      run: |
+        echo "PYTHONPATH=$GITHUB_WORKSPACE/hoomd/build" >> $GITHUB_ENV
+        echo "CONDA_PREFIX=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
+        echo "CMAKE_PREFIX_PATH=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
+        echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH
+  
+    - name: Configure
+      run: >-
+        cmake -B hoomd/build -S hoomd
+        -DCMAKE_BUILD_TYPE=Release
+        -DENABLE_GPU=off
+        -DENABLE_MPI=off
+        -DENABLE_TBB=off
+        -DBUILD_TESTING=off
+        -DENABLE_LLVM=off
+    - name: Compile
+      run: ninja -j $(($(getconf _NPROCESSORS_ONLN) + 2))
+      working-directory: hoomd/build
+    - name: Display hoomd version
+      run: python3 -c "import hoomd; print(hoomd.version.version, hoomd.version.git_sha1)"
+
+    - name: Checkout notebooks
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: notebooks
+    - name: List notebooks
+      run: ls **/*.ipynb
+      working-directory: notebooks
+    - name: Execute notebooks
+      run: 'for i in */; do echo "Running notebooks in: $i" && jupyter nbconvert --execute --inplace $i/*.ipynb || exit 1; done'
+      working-directory: notebooks
+
+    # This check is very basic, but we don't want to use `python -W error` as it will also catch any
+    # warnings generated inside nbconvert and its dependencies.
+    - name: Check for warnings
+      run: |
+        has_warnings=0
+        for file in **/*.ipynb
+        do
+          grep Warning $file && echo "::error file=${file}::Has deprecation warnings" && has_warnings=1
+        done
+        exit ${has_warnings}
+      working-directory: notebooks