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| * | ||
| !/\.nvmrc | ||
| !/\.out/ | ||
| !/dev/docker/files/ | ||
| !/rust-toolchain.toml |
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| Original file line number | Diff line number | Diff line change |
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| name: pypangraph | ||
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| on: | ||
| push: | ||
| branches: [ 'master', 'release-pypangraph' ] | ||
| paths: | ||
| - packages/pypangraph/** | ||
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| pull_request: | ||
| paths: | ||
| - packages/pypangraph/** | ||
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| repository_dispatch: | ||
| types: build | ||
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| workflow_dispatch: | ||
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| workflow_call: | ||
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| concurrency: | ||
| group: pypangraph-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number || github.ref || github.run_id }} | ||
| cancel-in-progress: true | ||
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| defaults: | ||
| run: | ||
| shell: bash -euo pipefail {0} | ||
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| env: | ||
| GITHUB_REPOSITORY_URL: ${{ github.server_url }}/${{ github.repository }} | ||
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| jobs: | ||
| build: | ||
| name: "Build PyPangraph (${{ matrix.python-version }})" | ||
| runs-on: ubuntu-24.04 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: [ "3.9", "3.10", "3.11", "3.12" ] | ||
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| steps: | ||
| - name: "Checkout code" | ||
| - uses: actions/checkout@v4 | ||
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| - name: "Set up Python ${{ matrix.python-version }}" | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: "Install dependencies" | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| python -m pip install flake8 pytest | ||
| python -m pip install . | ||
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | ||
| - name: "Lint" | ||
| run: | | ||
| # stop the build if there are Python syntax errors or undefined names | ||
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
| - name: "Test" | ||
| run: | | ||
| pytest | ||
| publish-to-pypi: | ||
| name: "Publish to PyPI" | ||
| needs: [ build ] | ||
| if: endsWith(github.ref, '/release-pypangraph') | ||
| runs-on: ubuntu-24.04 | ||
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| steps: | ||
| - name: "Checkout code" | ||
| - uses: actions/checkout@v4 | ||
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| - name: "Setup Python" | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: '3.x' | ||
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| - name: "Install dependencies" | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install build | ||
| - name: "Build package" | ||
| run: python -m build | ||
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| - name: "Publish package" | ||
| uses: pypa/gh-action-pypi-publish@release/v1 | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.NEHERLAB_BOT_PYPI_TOKEN }} | ||
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| - name: "Create git tag" | ||
| run: | | ||
| git config --global user.name "${{ secrets.NEHERLAB_BOT_GITHUB_NAME }}" | ||
| git config --global user.email "${{ secrets.NEHERLAB_BOT_GITHUB_EMAIL }}" | ||
| version=$(dasel select -r toml -w - -s ".package.version" -f "packages/pypangraph/pyproject.toml") | ||
| git tag "pypangraph-${version}" | ||
| git push origin "pypangraph-${version}" |
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|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| #!/usr/bin/env bash | ||
| set -euxo pipefail | ||
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| curl -fsSL "https://github.com/TomWright/dasel/releases/download/v1.22.1/dasel_linux_amd64" -o "/usr/bin/dasel" | ||
| curl -fsSL "https://github.com/TomWright/dasel/releases/download/v2.8.1/dasel_linux_amd64" -o "/usr/bin/dasel" | ||
| chmod +x "/usr/bin/dasel" | ||
| which dasel | ||
| dasel --version |
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| #!/usr/bin/env bash | ||
| set -euxo pipefail | ||
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| curl -fsSL -o "/usr/bin/jq" "https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64" | ||
| curl -fsSL -o "/usr/bin/jq" "https://github.com/stedolan/jq/releases/download/jq-1.7.1/jq-linux64" | ||
| chmod +x "/usr/bin/jq" | ||
| which jq | ||
| jq --version |
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| # syntax=docker/dockerfile:1 | ||
| # check=experimental=all | ||
| FROM debian:12 | ||
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| SHELL ["bash", "-euxo", "pipefail", "-c"] | ||
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| RUN set -euxo pipefail \ | ||
| && ln -s /usr/bin/pangraph /pangraph \ | ||
| && export DEBIAN_FRONTEND=noninteractive \ | ||
| && apt-get update -qq --yes \ | ||
| && apt-get install -qq --no-install-recommends --yes \ | ||
| bash \ | ||
| ca-certificates \ | ||
| curl \ | ||
| tar \ | ||
| >/dev/null \ | ||
| && apt-get autoremove --yes >/dev/null \ | ||
| && apt-get clean autoclean >/dev/null \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| RUN set -euxo pipefail \ | ||
| && export MMSEQS_VERSION="17-b804f" \ | ||
| && curl -fsSL "https://github.com/soedinglab/MMseqs2/releases/download/${MMSEQS_VERSION}/mmseqs-linux-sse41.tar.gz" \ | ||
| | tar --strip-components=2 -C "/usr/bin" -xz "mmseqs/bin/mmseqs" \ | ||
| && ls "/usr/bin/mmseqs" \ | ||
| && /usr/bin/mmseqs --help \ | ||
| && mmseqs --help | ||
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| COPY .out/pangraph-x86_64-unknown-linux-gnu /usr/bin/pangraph | ||
| RUN set -euxo pipefail \ | ||
| && ls "/usr/bin/pangraph" \ | ||
| && /usr/bin/pangraph --help \ | ||
| && pangraph --help \ |
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| #!/usr/bin/env python3 | ||
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| import argparse | ||
| import sys | ||
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| def find_release_notes(input_changelog_md: str): | ||
| release_notes = "" | ||
| found_release_notes_block = False | ||
| with open(input_changelog_md) as f: | ||
| for line in f: | ||
| if not found_release_notes_block and line.startswith("## "): | ||
| found_release_notes_block = True | ||
| release_notes += line | ||
| elif found_release_notes_block: | ||
| if line.startswith("## "): | ||
| return release_notes | ||
| else: | ||
| release_notes += line | ||
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| if __name__ == '__main__': | ||
| parser = argparse.ArgumentParser(description='Extracts last release notes section from a changelog markdown file') | ||
| parser.add_argument('input_changelog_md', type=str, help='Input changelog file in markdown format') | ||
| args = parser.parse_args() | ||
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| release_notes = find_release_notes(args.input_changelog_md) | ||
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| sys.stdout.write(release_notes) |
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