From b2c32349136c7780825ff14531dc1a862be42dc2 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 19 Jun 2024 14:58:23 -0400
Subject: [PATCH] Refactor CI to use micromamba instead of docker containers.

---
 .github/workflows/test.yaml |  83 +++++++++++++++++++++++
 .github/workflows/test.yml  | 127 ------------------------------------
 2 files changed, 83 insertions(+), 127 deletions(-)
 create mode 100644 .github/workflows/test.yaml
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..8443210
--- /dev/null
+++ b/.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 -GNinja
+        -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
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index e6f1595..0000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,127 +0,0 @@
-name: Test
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-on:
-  # Trigger on pull requests.
-  pull_request:
-
-  # Trigger on pushes to the mainline branches. This prevents building commits twice when the pull
-  # request source branch is in the same repository.
-  push:
-    branches:
-      - "trunk"
-      - "trunk-major"
-
-  # Trigger on request.
-  workflow_dispatch:
-
-  # Weekly builds on the trunk branch to check that the examples continue to work with the latest
-  # development version of HOOMD.
-  schedule:
-  - cron:  '0 18 * * 1'
-
-jobs:
-  start_action_runners:
-    name: Start action runners
-    runs-on: ubuntu-latest
-    steps:
-    - name: "Use jetstream2-admin/start"
-      uses: glotzerlab/jetstream2-admin/start@v1.2.5
-      with:
-        OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
-        OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
-        number: 1
-
-  execute_notebooks:
-    name: Execute notebooks
-    runs-on: [self-hosted,jetstream2,CPU]
-    container:
-      image: glotzerlab/software:nompi
-      options: -u 0
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-
-    # build the HOOMD trunk-minor branch to test the tutorials on the latest version
-    - name: Checkout
-      uses: actions/checkout@v4.1.6
-      with:
-        path: hoomd
-        ref: trunk-major
-        repository: glotzerlab/hoomd-blue
-        submodules: true
-    - name: Make build directory
-      run: mkdir build
-      working-directory: hoomd
-    - name: Configure
-      run: >-
-        cmake
-        -DCMAKE_BUILD_TYPE=Release
-        -DENABLE_GPU=off
-        -DENABLE_MPI=off
-        -DENABLE_TBB=off
-        -DBUILD_TESTING=off
-        -DENABLE_LLVM=on
-        ../
-      working-directory: hoomd/build
-    - name: Compile
-      run: make -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)"
-      env:
-        PYTHONPATH: ${{ github.workspace }}/hoomd/build
-
-    # clone the tutorials and run them
-    - name: Checkout
-      uses: actions/checkout@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
-      env:
-        PYTHONPATH: ${{ github.workspace }}/hoomd/build
-
-    # 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
-
-    # notify developers if the scheduled check fails
-    - name: Slack notification
-      if: ${{ github.event_name == 'schedule' && (failure() || cancelled()) }}
-      uses: 8398a7/action-slack@v3.16.2
-      with:
-        status: ${{ job.status }}
-        fields: workflow,job,message,commit
-        mention: channel
-        if_mention: failure,cancelled
-        channel: '#dev-hoomd-notifications'
-        username: Github Action
-        author_name: ''
-        job_name: Execute notebooks
-      env:
-        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-
-    - name: Clean HOME
-      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
-      shell: bash