1.8.0

.github/actions/python-uv-setup/action.yml

@@ -0,0 +1,74 @@
+name: "python-uv-setup"
+description: "Common Python + uv setup, deps install, and optional debug"
+
+inputs:
+  python-version:
+    description: "Python version"
+    required: true
+  debug:
+    description: "Enable debug output"
+    required: false
+    default: "false"
+  lockfile:
+    description: "Lockfile to use"
+    required: false
+    default: "uv.lock.cpu"
+  extras:
+    description: "Extra dependency set to install"
+    required: false
+    default: "cpu"
+  dependency-groups:
+    description: "Dependency group to install"
+    required: false
+    default: "dev"
+
+runs:
+  using: "composite"
+  steps:
+    - name: System Dependencies
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+          build-essential \
+          libcairo2-dev \
+          pkg-config \
+          python3-dev \
+          python3-openssl \
+          libopenblas-dev \
+          libssl-dev
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      shell: bash
+      run: |
+        python -m pip install --upgrade uv
+        uv --version
+
+    - name: Cache uv dependencies
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/uv
+        key: ${{ runner.os }}-py${{ inputs.python-version }}-uv-${{ hashFiles('pyproject.toml', 'uv.lock.cpu') }}
+        restore-keys: |
+          ${{ runner.os }}-py${{ inputs.python-version }}-uv-
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        set -euxo pipefail
+        cp "${{ inputs.lockfile }}" uv.lock
+        uv venv .venv
+        . .venv/bin/activate
+        uv sync --extra "${{ inputs.extras }}" --group "${{ inputs.dependency-groups }}" --locked
+
+    - name: Debug - what is installed
+      if: ${{ inputs.debug == 'true' }}
+      shell: bash
+      run: |
+        . .venv/bin/activate
+        uv pip list

.github/workflows/build.yml

@@ -1,59 +1,64 @@
+# How to run manually:
+# 1. Go to the GitHub repository.
+# 2. Click the "Actions" tab.
+# 3. Select this workflow, "docker publish".
+# 4. Click "Run workflow".
+# 5. Choose the desired inputs, then click "Run workflow".
+
 name: docker publish
 
 on:
-  release:
-    types: [published]
+  workflow_dispatch:
+    inputs:
+      env:
+        description: "Deployment environment"
+        required: true
+        default: "prod"
+        type: choice
+        options:
+          - prod
+          - staging
+      target:
+        description: "Which image(s) to build"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - gpu
+          - rocm
+          - cpu-amd64
+          - cpu-arm64
 
 jobs:
-  build-gpu-image:
+  build-and-push:
     runs-on: ubuntu-24.04
-    steps:
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Log in to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-
-      - name: Checkout code
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 1
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Uses Dockerfile.gpu
+          - name: gpu
+            platform: gpu
+            arch: ""
+          # Uses Dockerfile.rocm
+          - name: rocm
+            platform: rocm
+            arch: ""
+          # Uses Dockerfile.cpu
+          - name: cpu-amd64
+            platform: cpu
+            arch: ""
+          # Uses Dockerfile.arm
+          - name: cpu-arm64
+            platform: arm
+            arch: linux/arm64
 
-      - name: Build and push Docker image (gpu)
-        run: |
-          make push-docker
-        env:
-          ENV: prod
-          PLATFORM: gpu
-  build-cpu-linux-amd64:
-    runs-on: ubuntu-24.04
     steps:
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Log in to DockerHub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
+      - name: Set up QEMU
+        if: ${{ matrix.arch == 'linux/arm64' }}
+        uses: docker/setup-qemu-action@v3
 
-      - name: Checkout code
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 1
-
-      - name: Build and push Docker image (cpu)
-        run: |
-          make push-docker
-        env:
-          ENV: prod
-          PLATFORM: cpu
-  build-cpu-linux-arm64:
-    runs-on: ubuntu-24.04
-    steps:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
@@ -64,14 +69,14 @@ jobs:
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
-      - name: Build and push Docker image (cpu)
-        run: |
-          make push-docker
+      - name: Build and push Docker image
+        if: ${{ github.event.inputs.target == 'all' || github.event.inputs.target == matrix.name }}
+        run: make push-docker
         env:
-          ARCH: linux/arm64
-          ENV: prod
-          PLATFORM: arm
+          ENV: ${{ github.event.inputs.env }}
+          PLATFORM: ${{ matrix.platform }}
+          ARCH: ${{ matrix.arch }}

.github/workflows/lint.yml

@@ -7,9 +7,13 @@ jobs:
     runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
+      - name: Update apt cache
+        run: |
+          sudo apt-get update || sudo apt-get update --fix-missing
+
       - name: System Dependencies
         run: |
           sudo apt install -y build-essential \
@@ -18,30 +22,38 @@ jobs:
             python3-dev \
             python3-openssl
       - uses: actions/checkout@v3
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Cache Python dependencies
+      - name: Install uv
+        run: |
+          python -m pip install --upgrade uv
+          uv --version
+
+      - name: Cache uv downloads
         uses: actions/cache@v3
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
+          path: ~/.cache/uv
+          key: ${{ runner.os }}-uv-${{ hashFiles('pip/*.txt') }}
           restore-keys: |
-            ${{ runner.os }}-pip-
+            ${{ runner.os }}-uv-
 
-      - name: Install dependencies
+      - name: Create venv
         run: |
-          python3.9 -m pip install --upgrade pip
-          if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
+          uv venv .venv
 
-      - name: Install ruff
+      - name: Install dependencies
         run: |
-          python3.9 -m pip install ruff
+          . .venv/bin/activate
+          if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
+          uv pip install ruff
 
       - name: Lint with ruff
         run: |
           # Check all lint rules
-          python3.9 -m ruff check atomsci/
+          . .venv/bin/activate
+          uv run ruff check atomsci/