Modernize deepethogram: Python 3.11, uv, unified Docker, Modal GPU tests

.dockerignore

@@ -1,16 +1,47 @@
-**/.git
-**/.gitignore
-**/.vscode
-**/coverage
-**/.env
-**/.aws
-**/.ssh
-Dockerfile
-docker-compose.yml
-**/.DS_Store
-**/venv
-**/env
-build/*
-dist/*
-docs/*
-docker/
+**
+
+!README.md
+!MANIFEST.in
+!pyproject.toml
+!uv.lock
+!pytest.ini
+!setup_tests.py
+!deepethogram/
+!deepethogram/**
+!tests/
+!tests/**
+!docker/
+!docker/Dockerfile
+!docker/build_and_test.sh
+
+.git/
+.github/
+.gitignore
+.venv/
+venv/
+env/
+.env
+.aws/
+.ssh/
+.vscode/
+.idea/
+.kd/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.nox/
+.tox/
+__pycache__/
+*.py[cod]
+*.so
+.DS_Store
+coverage
+.coverage
+.coverage.*
+htmlcov/
+build/
+dist/
+docs/
+paper.pdf
+deepethogram.egg-info/
+tests/DATA/

.github/workflows/claude-code-review.yml

@@ -0,0 +1,44 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    if: |
+      github.event.pull_request.author_association == 'OWNER' ||
+      github.event.pull_request.author_association == 'MEMBER' ||
+      github.event.pull_request.author_association == 'COLLABORATOR'
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    permissions:
+      contents: read
+      pull-requests: write
+      issues: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
+          plugins: 'code-review@claude-code-plugins'
+          prompt: '/code-review:code-review --comment ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
+          use_sticky_comment: true
+          track_progress: true
+          claude_args: '--allowedTools "Bash(gh pr:*),Bash(gh api:*),Bash(gh diff:*)"'

.github/workflows/claude.yml

@@ -0,0 +1,66 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      github.event.sender.type == 'User' &&
+      (
+        (github.event_name == 'issue_comment' &&
+         contains(github.event.comment.body, '@claude') &&
+         (github.event.comment.author_association == 'OWNER' ||
+          github.event.comment.author_association == 'MEMBER' ||
+          github.event.comment.author_association == 'COLLABORATOR')) ||
+        (github.event_name == 'pull_request_review_comment' &&
+         contains(github.event.comment.body, '@claude') &&
+         (github.event.comment.author_association == 'OWNER' ||
+          github.event.comment.author_association == 'MEMBER' ||
+          github.event.comment.author_association == 'COLLABORATOR')) ||
+        (github.event_name == 'pull_request_review' &&
+         contains(github.event.review.body, '@claude') &&
+         (github.event.review.author_association == 'OWNER' ||
+          github.event.review.author_association == 'MEMBER' ||
+          github.event.review.author_association == 'COLLABORATOR')) ||
+        (github.event_name == 'issues' &&
+         (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')) &&
+         (github.event.issue.author_association == 'OWNER' ||
+          github.event.issue.author_association == 'MEMBER' ||
+          github.event.issue.author_association == 'COLLABORATOR'))
+      )
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    permissions:
+      contents: read
+      pull-requests: write
+      issues: write
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          claude_args: '--allowedTools "Bash(gh pr:*),Bash(gh api:*),Bash(gh diff:*)"'

.github/workflows/gpu-tests.yml

@@ -0,0 +1,86 @@
+name: GPU Tests
+
+on:
+  workflow_dispatch:
+
+jobs:
+  gpu-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.0.0
+        with:
+          enable-cache: true
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Run GPU tests on Modal
+        env:
+          # Required repository secrets:
+          #   MODAL_TOKEN_ID
+          #   MODAL_TOKEN_SECRET
+          MODAL_TOKEN_ID: ${{ secrets.MODAL_TOKEN_ID }}
+          MODAL_TOKEN_SECRET: ${{ secrets.MODAL_TOKEN_SECRET }}
+          DEG_MODAL_GPU: T4
+        run: uvx --from modal modal run modal_gpu_test.py --write-junit pytest-gpu.xml
+
+      - name: Upload pytest XML
+        if: always()
+        uses: actions/upload-artifact@v6
+        with:
+          name: pytest-gpu-xml
+          path: pytest-gpu.xml
+          if-no-files-found: ignore
+
+      - name: Summarize pytest results
+        if: always()
+        run: |
+          python - <<'PY'
+          import os
+          import xml.etree.ElementTree as ET
+          from pathlib import Path
+
+          summary_path = Path(os.environ["GITHUB_STEP_SUMMARY"])
+          xml_path = Path("pytest-gpu.xml")
+
+          if not xml_path.exists():
+              summary_path.write_text("GPU pytest report was not produced.\n")
+              raise SystemExit(0)
+
+          root = ET.parse(xml_path).getroot()
+          testsuite = root if root.tag == "testsuite" else root.find("testsuite")
+          if testsuite is None:
+              summary_path.write_text("Unable to parse GPU pytest report.\n")
+              raise SystemExit(0)
+
+          tests = int(testsuite.attrib.get("tests", 0))
+          failures = int(testsuite.attrib.get("failures", 0))
+          errors = int(testsuite.attrib.get("errors", 0))
+          skipped = int(testsuite.attrib.get("skipped", 0))
+          passed = tests - failures - errors - skipped
+
+          summary_path.write_text(
+              "\n".join(
+                  [
+                      "## GPU Pytest Results",
+                      "",
+                      "| Metric | Count |",
+                      "| --- | ---: |",
+                      f"| Passed | {passed} |",
+                      f"| Failed | {failures} |",
+                      f"| Errors | {errors} |",
+                      f"| Skipped | {skipped} |",
+                      f"| Total | {tests} |",
+                      "",
+                      "Full JUnit XML is attached as the `pytest-gpu-xml` workflow artifact.",
+                      "",
+                  ]
+              )
+          )
+          PY

.github/workflows/main.yml

@@ -13,52 +13,44 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-latest, macos-13]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
 
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v8.0.0
       with:
-        python-version: '3.7'
+        enable-cache: true
 
-    - name: Install FFMPEG (Ubuntu)
-      if: matrix.os == 'ubuntu-20.04'
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+
+    - name: Install system dependencies (Ubuntu)
+      if: matrix.os == 'ubuntu-latest'
       run: |
         sudo apt-get update
-        sudo apt-get install -y ffmpeg
+        sudo apt-get install -y ffmpeg libegl1 libopengl0 libgl1
 
     - name: Install FFMPEG (Windows)
       if: matrix.os == 'windows-latest'
       run: |
-        choco install ffmpeg
+        choco install ffmpeg -y
 
     - name: Install FFMPEG (macOS)
-      if: matrix.os == 'macos-13'
+      if: matrix.os == 'macos-latest'
       run: |
         brew install ffmpeg
 
-    - name: Install PySide2
-      run: |
-        python -m pip install --upgrade pip
-        pip install "pyside2==5.13.2"
-
-    - name: Install PyTorch CPU
-      run: |
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-
-    - name: Install package and test dependencies
-      run: |
-        python -m pip install --upgrade "pip<24.0"
-        pip install -r requirements.txt
-        pip install pytest pytest-cov
-        python setup.py develop
+    - name: Install dependencies
+      run: uv sync --locked --dev
 
     - name: Setup test data
-      run: |
-        python setup_tests.py
+      run: uv run python setup_tests.py
 
     - name: Run CPU tests
-      run: |
-        pytest -v -m "not gpu" tests/
+      env:
+        QT_QPA_PLATFORM: offscreen
+      run: uv run pytest -v -m "not gpu" tests/