Update workflows on branch

.github/pull_request_template.md

@@ -1,6 +0,0 @@
--   [ ] Closes #xxxx (Replace xxxx with the GitHub issue number)
--   [ ] Tests added and passed if fixing a bug or adding a new feature
--   [ ] All code checks passed
--   [ ] Added type annotations to new arguments/methods/functions
--   [ ] Added an entry in the latest `docs/release_notes/index.md` file if fixing a bug or adding a new feature
--   [ ] If the changes are patches for a version, I have added the `on-merge: backport to x.x.x` label

.github/workflows/build.yml

@@ -1,30 +1,29 @@
-name: Check Build
+name: Check build
 
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   package:
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v3
-
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
-
       - name: Install build dependencies
         run: python -m pip install --upgrade pip wheel twine build
-
       - name: Build package
         run: python -m build
-
       - name: Check package
         run: twine check --strict dist/*.whl

.github/workflows/test_linux_cpu.yml → .github/workflows/test_linux.yml

@@ -1,4 +1,4 @@
-name: test-linux-cpu
+name: Test (Linux)
 
 on:
   push:
@@ -15,9 +15,6 @@ concurrency:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-
-    timeout-minutes: 30
-
     defaults:
       run:
         shell: bash -e {0} # -e to fail on error
@@ -28,13 +25,14 @@ jobs:
         os: [ubuntu-latest]
         python: ["3.9", "3.10", "3.11"]
 
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
     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
         with:
@@ -46,17 +44,19 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel
 
-      - name: Install scvi-tools test dependencies
+      - name: Install dependencies
         run: |
-          pip install ".[tests]"
+          pip install --pre ".[tests]"
 
       - name: Test
         env:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes
-
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.github/workflows/test_linux_cuda.yml

@@ -1,16 +1,26 @@
-name: test-linux-cuda
+name: Test (Linux, CUDA)
 
 on:
+  push:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
+  pull_request:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
   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: [self-hosted, Linux, X64, CUDA]
-
-    timeout-minutes: 30
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
 
     strategy:
       fail-fast: false
@@ -22,9 +32,17 @@ jobs:
       image: martinkim0/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base
       options: --user root --gpus all
 
+    environment:
+      name: approved_test
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }} CUDA
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install dependencies
         run: |
@@ -33,10 +51,12 @@ jobs:
       - name: Test
         env:
           MPLBACKEND: agg
-          PLATFORM: ubuntu
+          PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes --accelerator cuda --devices auto
-
+          coverage run -m pytest -v --color=yes --accelerator cuda --devices auto
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.github/workflows/test_linux_cpu_pre.yml → .github/workflows/test_linux_pre.yml

@@ -1,10 +1,8 @@
-name: test-linux-cpu-prerelease
+name: Test (Linux, prerelease)
 
 on:
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
-  issue_comment:
-    types: [created] # runs if issue/PR has a specific comment
   workflow_dispatch:
 
 concurrency:
@@ -14,12 +12,6 @@ concurrency:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-
-    timeout-minutes: 30
-
-    # run if scheduled or pr has the comment 'test linux cpu prelease'
-    if: github.event_name == 'schedule' || (github.event.issue.pull_request != '' && contains(github.event.comment.body, 'test linux cpu prerelease'))
-
     defaults:
       run:
         shell: bash -e {0} # -e to fail on error
@@ -30,13 +22,14 @@ jobs:
         os: [ubuntu-latest]
         python: ["3.9", "3.10", "3.11", "3.12"]
 
+    name: ${{ matrix.name }} Python ${{ matrix.python }} prereleases
+
     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
         with:
@@ -48,7 +41,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel
 
-      - name: Install scvi-tools test dependencies
+      - name: Install dependencies
         run: |
           pip install --pre ".[tests]"
 
@@ -58,7 +51,9 @@ jobs:
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes
-
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.github/workflows/test_macos_cpu.yml → .github/workflows/test_macos.yml

@@ -1,10 +1,8 @@
-name: test-macos-cpu
+name: Test (MacOS)
 
 on:
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
-  issue_comment:
-    types: [created] # runs if issue/PR has a specific comment
   workflow_dispatch:
 
 concurrency:
@@ -14,12 +12,6 @@ concurrency:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-
-    timeout-minutes: 30
-
-    # run if scheduled or pr has the comment 'test macos cpu'
-    if: github.event_name == 'schedule' || (github.event.issue.pull_request != '' && contains(github.event.comment.body, 'test macos cpu'))
-
     defaults:
       run:
         shell: bash -e {0} # -e to fail on error
@@ -30,13 +22,14 @@ jobs:
         os: [macos-latest]
         python: ["3.9", "3.10", "3.11"]
 
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
     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
         with:
@@ -48,7 +41,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel
 
-      - name: Install scvi-tools test dependencies
+      - name: Install dependencies
         run: |
           pip install ".[tests]"
 
@@ -58,7 +51,9 @@ jobs:
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes
-
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.github/workflows/test_windows_cpu.yml → .github/workflows/test_windows.yml

@@ -1,10 +1,8 @@
-name: test-windows-cpu
+name: Test (Windows)
 
 on:
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
-  issue_comment:
-    types: [created] # runs if issue/PR has a specific comment
   workflow_dispatch:
 
 concurrency:
@@ -14,12 +12,6 @@ concurrency:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
-
-    timeout-minutes: 30
-
-    # run if scheduled or pr has the comment 'test windows cpu'
-    if: github.event_name == 'schedule' || (github.event.issue.pull_request != '' && contains(github.event.comment.body, 'test windows cpu'))
-
     defaults:
       run:
         shell: bash -e {0} # -e to fail on error
@@ -30,13 +22,14 @@ jobs:
         os: [windows-latest]
         python: ["3.9", "3.10", "3.11"]
 
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
     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
         with:
@@ -48,7 +41,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel
 
-      - name: Install scvi-tools test dependencies
+      - name: Install dependencies
         run: |
           pip install ".[tests]"
 
@@ -58,7 +51,9 @@ jobs:
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes
-
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3