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jbohnslavjbohnslav
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Merge pull request #174 from jbohnslav/cleanup
Modernize deepethogram: Python 3.11, uv, unified Docker, Modal GPU tests
2 parents a77c77c + b4f3511 commit 81d5415

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‎.dockerignore‎

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

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

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

‎.github/workflows/claude.yml‎

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

‎.github/workflows/gpu-tests.yml‎

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

‎.github/workflows/gpu.yml‎

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‎.github/workflows/main.yml‎

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

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