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RalfGRalfG
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Merge pull request #90 from CompOmics/feature/new-api
Initial work for new 4.0 API
2 parents 0409a78 + dff9b59 commit 2b0aea9

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‎.github/workflows/publish.yml‎

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name: Publish to PyPI and GitHub release
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name: Publish
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on:
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push:
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tags:
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- 'v*'
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release:
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types: [created]
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workflow_dispatch:
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inputs:
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ref:
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description: 'Git ref (branch, tag, or SHA) to build from'
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required: true
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default: 'master' # ← was 'main'
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type: string
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# Least-privilege defaults for all jobs (override per-job if needed)
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permissions:
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contents: write # to create releases and read code
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packages: write # to push container images to ghcr.io
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id-token: write # for PyPI OIDC publish
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jobs:
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python-package:
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build-python-package:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- name: Select ref
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id: select-ref
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run: |
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if [ -n "${{ github.event.inputs.ref }}" ]; then
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echo "ref=${{ github.event.inputs.ref }}" >> $GITHUB_OUTPUT
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else
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# Fallback to the event ref (e.g. refs/tags/v1.2.3 on tag pushes)
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echo "ref=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT
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fi
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- uses: actions/checkout@v4
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with:
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# Checkout the chosen ref for manual runs; for tag-push runs this will be that tag
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ref: ${{ steps.select-ref.outputs.ref }}
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- name: Derive version
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id: version
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shell: bash
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run: |
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# If the ref looks like a release tag (v*), use it as version (strip refs/tags/ if present)
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REF="${{ steps.select-ref.outputs.ref }}"
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if [[ "$GITHUB_REF" == refs/tags/v* ]]; then
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VER="${GITHUB_REF#refs/tags/}"
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elif [[ "$REF" == refs/tags/v* ]]; then
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VER="${REF#refs/tags/}"
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elif [[ "$REF" == v* ]]; then
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VER="$REF"
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else
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# Fallback for non-tag manual runs
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VER="manual-${{ github.run_number }}"
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fi
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echo "version=$VER" >> $GITHUB_OUTPUT
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echo "Resolved version: $VER"
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build flake8
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- name: Check for syntax errors
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run: |
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flake8 ./deeplc --count --select=E9,F63,F7,F82 --show-source --statistics
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- uses: actions/checkout@v6
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- name: Build package
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run: |
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python -m build . --sdist --wheel
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- uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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- uses: astral-sh/setup-uv@v7
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with:
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enable-cache: true
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- name: Upload compiled wheels
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uses: actions/upload-artifact@v4
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with:
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name: python-wheels
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path: dist/*.whl
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- name: Build
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run: uv build --no-sources
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windows-installer:
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runs-on: windows-latest
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needs: python-package
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steps:
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- uses: actions/checkout@v4
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with:
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# Match the same ref used for building the Python package
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ref: ${{ needs.python-package.outputs.ref || github.ref }}
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# If you want to avoid recomputing the ref/version here, you can
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# alternatively repeat the "Select ref" + "Derive version" steps as above
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- uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[gui] pyinstaller
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- name: Install Inno Setup
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uses: crazy-max/ghaction-chocolatey@v3
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with:
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args: install innosetup -y --allow-unofficial --force
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- name: Run pyinstaller
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run: pyinstaller ./deeplc_pyinstaller.spec --clean --noconfirm
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- name: Test built DeepLC exe
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run: dist/deeplc/deeplc.exe --ignore-gooey --help
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- name: Derive version (Windows)
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id: version
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shell: bash
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run: |
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REF="${{ github.event.inputs.ref }}"
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if [[ "$GITHUB_REF" == refs/tags/v* ]]; then
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VER="${GITHUB_REF#refs/tags/}"
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elif [[ "$REF" == refs/tags/v* ]]; then
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VER="${REF#refs/tags/}"
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elif [[ "$REF" == v* ]]; then
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VER="$REF"
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else
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VER="manual-${{ github.run_number }}"
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fi
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echo "version=$VER" >> $GITHUB_OUTPUT
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echo "Resolved version: $VER"
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- name: Run Inno Setup
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run: ISCC.exe ./deeplc_innosetup.iss /DAppVersion=${{ steps.version.outputs.version }}
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- name: Upload installer
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uses: actions/upload-artifact@v4
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with:
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name: windows-installer
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path: dist/*.exe
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- name: Upload dists
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uses: actions/upload-artifact@v7
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with:
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name: python-package-distributions
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path: dist/
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if-no-files-found: error
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git-release:
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publish-python-package:
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needs: build-python-package
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runs-on: ubuntu-latest
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needs: [python-package, windows-installer]
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# Only create a GitHub Release when the ref is a v* tag (either push or manual)
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if: startsWith(github.ref, 'refs/tags/v') || startsWith(github.event.inputs.ref, 'v')
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steps:
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- uses: actions/checkout@v4
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- name: Resolve version/tag
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id: version
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shell: bash
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run: |
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if [[ "$GITHUB_REF" == refs/tags/v* ]]; then
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VER="${GITHUB_REF#refs/tags/}"
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elif [[ "${{ github.event.inputs.ref }}" == v* ]]; then
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VER="${{ github.event.inputs.ref }}"
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else
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echo "This job should only run for v* tags."
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exit 1
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fi
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echo "version=$VER" >> $GITHUB_OUTPUT
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echo "Resolved version: $VER"
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permissions:
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id-token: write
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- name: Download artifacts
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uses: actions/download-artifact@v4
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with:
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path: dist
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- name: Create GitHub Release
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# The docker action infers the tag from GITHUB_REF; set it explicitly for manual runs.
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uses: docker://antonyurchenko/git-release:v6
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DRAFT_RELEASE: "false"
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PRE_RELEASE: "false"
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CHANGELOG_FILE: "CHANGELOG.md"
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# Provide a synthetic tag ref for manual runs with input v*
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GITHUB_REF: refs/tags/${{ steps.version.outputs.version }}
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with:
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args: |
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dist/**/*.exe
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dist/**/*.whl
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build-streamlit-image:
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runs-on: ubuntu-latest
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needs: python-package
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steps:
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- uses: actions/checkout@v4
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- id: latest_release
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uses: pozetroninc/github-action-get-latest-release@master
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with:
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owner: compomics
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repo: DeepLC
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- name: Login to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push to ghcr.io
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uses: docker/build-push-action@v5
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with:
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context: streamlit
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push: true
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tags: |
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ghcr.io/compomics/deeplc-streamlit:${{ steps.latest_release.outputs.release }}
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ghcr.io/compomics/deeplc-streamlit:latest
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- name: Download dists
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uses: actions/download-artifact@v8
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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# windows-installer:
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# runs-on: windows-latest
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# needs: python-package
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# steps:
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# - uses: actions/checkout@v6
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# - uses: actions/setup-python@v5
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# with:
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# python-version: '3.11'
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# - name: Install dependencies
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# run: |
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# python -m pip install --upgrade pip
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# pip install .[gui] pyinstaller
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# - name: Install Inno Setup
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# uses: crazy-max/ghaction-chocolatey@v3
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# with:
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# args: install innosetup -y --allow-unofficial --force
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# - name: Run pyinstaller
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# run: pyinstaller ./deeplc_pyinstaller.spec --clean --noconfirm
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# - name: Test built DeepLC exe
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# run: dist/deeplc/deeplc.exe --ignore-gooey --help
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# - name: Run Inno Setup
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# run: ISCC.exe ./deeplc_innosetup.iss /DAppVersion=${{ github.ref_name }}
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# - name: Upload installer
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# uses: actions/upload-artifact@v4
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# with:
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# name: windows-installer
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# path: dist/*.exe
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# - name: Upload installer to release
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# uses: svenstaro/upload-release-action@v2
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# with:
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# repo_token: ${{ secrets.GITHUB_TOKEN }}
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# tag: ${{ github.ref }}
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# file_glob: true
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# file: dist/*.exe
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# build-streamlit-image:
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# runs-on: ubuntu-latest
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# needs: publish-python-package
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# steps:
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# - uses: actions/checkout@v6
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# - name: Login to GitHub Container Registry
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# uses: docker/login-action@v3
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# with:
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# registry: ghcr.io
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# username: ${{ github.repository_owner }}
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# password: ${{ secrets.GITHUB_TOKEN }}
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# - name: Build and push to ghcr.io
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# uses: docker/build-push-action@v5
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# with:
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# context: streamlit
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# push: true
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# tags: |
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# ghcr.io/compomics/deeplc-streamlit:${{ github.ref }}
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# ghcr.io/compomics/deeplc-streamlit:latest

‎.github/workflows/test.yml‎

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name: Python package test
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name: Test
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on:
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push:
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pull_request:
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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test:
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lint-python-package:
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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: Lint
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uses: astral-sh/ruff-action@v3
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with:
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src: "deeplc"
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- name: Check formatting
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uses: astral-sh/ruff-action@v3
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with:
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args: "format --check --diff deeplc"
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src: "deeplc"
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test-python-package:
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needs: lint-python-package
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
1335
matrix:
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system: [["3.11", "ubuntu-latest"], ["3.12", "ubuntu-latest"]]
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runs-on: ${{ matrix.system[1] }}
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.system[0] }}
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uses: actions/setup-python@v5
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- uses: actions/checkout@v6
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- uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.system[0] }}
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- name: Install dependencies
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run: |
24-
python -m pip install --upgrade pip
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pip install flake8 pytest
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pip install --editable .[test]
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- name: Lint with flake8
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run: |
29-
# stop the build if there are Python syntax errors or undefined names
30-
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
35-
pytest
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enable-cache: true
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- name: Install the project
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run: uv sync --all-extras --dev
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- name: Run tests
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run: uv run pytest
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- name: Prune cache
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run: uv cache prune --ci

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