Add prerelease, cuda, macos, windows test workflows (#134)

- Adds CUDA, macOS, and Windows test workflows that run on schedule,
manually, or by adding appropriate labels to a PR
- Separates prerelease tests into its own workflow that runs on schedule

.github/workflows/build.yaml

@@ -1,4 +1,4 @@
-name: Check Build
+name: Build
 
 on:
   push:
@@ -14,11 +14,11 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies

.github/workflows/test.yaml → .github/workflows/test_linux.yaml

@@ -1,12 +1,10 @@
-name: Test
+name: Test (Linux)
 
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
-  schedule:
-    - cron: "0 5 1,15 * *"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -22,26 +20,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - os: ubuntu-latest
-            python: "3.9"
-          - os: ubuntu-latest
-            python: "3.11"
-          - os: ubuntu-latest
-            python: "3.11"
-            pip-flags: "--pre"
-            name: PRE-RELEASE DEPENDENCIES
+        os: [ubuntu-latest]
+        python: ["3.9", "3.10", "3.11"]
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }}
+    name: Integration
 
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"
@@ -50,9 +41,11 @@ jobs:
       - name: Install test dependencies
         run: |
           python -m pip install --upgrade pip wheel
+
       - name: Install dependencies
         run: |
-          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+          pip install --pre ".[dev,test]"
+
       - name: Test
         env:
           MPLBACKEND: agg
@@ -64,4 +57,6 @@ jobs:
         run: |
           coverage report
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_linux_cuda.yaml

@@ -0,0 +1,66 @@
+name: Test (Linux, CUDA)
+
+on:
+  pull_request:
+    branches: [main]
+    types: [labeled, synchronize, opened]
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    # if PR has label "cuda tests" or "all tests" or if scheduled or manually triggered
+    if: >-
+      (
+        contains(github.event.pull_request.labels.*.name, 'cuda tests') ||
+        contains(github.event.pull_request.labels.*.name, 'all tests') ||
+        contains(github.event_name, 'schedule') ||
+        contains(github.event_name, 'workflow_dispatch')
+      )
+    runs-on: [self-hosted, Linux, X64, CUDA]
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.11"]
+        cuda: ["11"]
+
+    container:
+      image: scverse/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base
+      options: --user root --gpus all
+
+    name: Integration (CUDA)
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_linux_pre.yaml

@@ -0,0 +1,72 @@
+name: Test (Linux, prereleases)
+
+on:
+  pull_request:
+    branches: [main]
+    types: [labeled, synchronize, opened]
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    # if PR has label "cuda tests" or "all tests" or if scheduled or manually triggered
+    if: >-
+      (
+        contains(github.event.pull_request.labels.*.name, 'prerelease tests') ||
+        contains(github.event.pull_request.labels.*.name, 'all tests') ||
+        contains(github.event_name, 'schedule') ||
+        contains(github.event_name, 'workflow_dispatch')
+      )
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.9", "3.10", "3.11", "3.12"]
+
+    name: Integration (Prereleases)
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install --pre ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_macos.yaml

@@ -0,0 +1,61 @@
+name: Test (MacOS)
+
+on:
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest]
+        python: ["3.9", "3.10", "3.11"]
+
+    name: Integration
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_macos_m1.yaml

@@ -0,0 +1,61 @@
+name: Test (MacOS M1)
+
+on:
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-14]
+        python: ["3.9", "3.10", "3.11"]
+
+    name: Integration
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}