cdci.yml

name: CICD Python Package

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  release:
    types: [published]
  workflow_dispatch:

jobs:
  test:
    name: Unittests+streamlit
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
    steps:
      - uses: actions/checkout@v4
      - uses: psf/black@stable
        with:
          # ! for now (format output files of vuegen for streamlit)
          src: "./src"
      - uses: isort/isort-action@v1
        with:
          # ! should be removed once all imports are correctly sorted
          sort-paths: src
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip" # caching pip dependencies
          cache-dependency-path: "**/pyproject.toml"
      - name: lint package code with ruff
        run: |
          python -m pip install --upgrade pip
          pip install ruff
          ruff check src
      - name: Install dependencies for testing
        run: |
          pip install pytest
          pip install .
      - name: Run tests
        run: python -m pytest tests
      - name: Execute streamlit report
        run: |
          cd docs
          vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook
          vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml

  other-reports:
    name: Reports - ${{ matrix.os.label }}, ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12", "3.13"]
        os:
          # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/running-variations-of-jobs-in-a-workflow#example-using-a-multi-dimension-matrix
          # - runner: "macos-14"
          #   label: "macos-14-arm64"
          - runner: "ubuntu-latest"
            label: "ubuntu-latest-x64"
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip" # caching pip dependencies
          cache-dependency-path: "**/pyproject.toml"
      - name: Install dependencies
        run: |
          pip install --upgrade pip
          pip install "."
      - name: Quarto check
        run: |
          quarto check -h
          quarto check
          quarto install chromium
          quarto install tinytex --no-prompt
      - name: Execute streamlit report (to check)
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook
          # here we are testing that the generated config from the -dir call works
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml
      # repeat for easier inspection on GitHub:
      - name: quarto html report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt html
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt html
      - name: quarto pdf report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pdf -qt_checks
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pdf -qt_checks
      - name: quarto docx report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt docx
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt docx
      - name: quarto odt report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt odt
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt odt
      - name: quarto revealjs report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt revealjs
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt revealjs
      - name: quarto pptx report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pptx
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pptx
      - name: quarto jupyter report
        run: |
          cd docs
          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt jupyter
          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt jupyter
      - name: quarto html report based on predefined config file
        run: |
          cd docs
          vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/html -rt html
          # Check for changes
          if git diff ../tests/report_examples | grep .; then
            echo "Error: One or more protected files have been modified."
            exit 1
          fi
      - name: streamlit report based on predefined config file
        run: |
          cd docs
          vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg
          # Check for changes
          if git diff ../tests/report_examples | grep .; then
            echo "Error: One or more protected files have been modified."
            exit 1
          fi
      - name: check streamlit report files for chatbot API
        run: |
          vuegen -c docs/example_config_files/Chatbot_example_config.yaml -output_dir tests/report_examples/chat_bot
          if git diff tests/report_examples | grep .; then
            echo Failed for report: $format
            echo "Error: One or more protected files have been modified."
            exit 1
          fi
      - name: check for changes in report files
        run: |
          # write streamlit report to test folder 
          vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook
          # Check for changes
          if git diff tests/report_examples | grep .; then
            echo "Error: One or more protected files have been modified."
            exit 1
          fi
      - name: check for changes in quarto report files
        run: |
          # write quarto based report to test folder
          for format in html pdf docx odt revealjs pptx jupyter; do
            vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/$format  -rt $format 
            # Check for changes
            if git diff tests/report_examples | grep .; then
              echo Failed for report: $format
              echo "Error: One or more protected files have been modified."
              exit 1
            fi
          done

  publish:
    name: Publish package to PyPI
    if: startsWith(github.ref, 'refs/tags')
    permissions:
      id-token: write
    needs:
      - test
      - other-reports
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install twine and build
        run: python -m pip install --upgrade twine build
      - name: Build
        run: python -m build
      - name: Publish package distributions to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1

  build-executable:
    name: Build-binary-${{ matrix.os.label }}
    runs-on: ${{ matrix.os.runner }}
    if: |
      (github.event_name == 'push' && github.ref == 'refs/heads/main') ||
      github.event_name == 'release' ||
      startsWith(github.ref, 'refs/tags') ||
      github.event_name == 'workflow_dispatch'
    needs:
      - test
      - other-reports
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.13"]
        os:
          # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/running-variations-of-jobs-in-a-workflow#example-using-a-multi-dimension-matrix
          - runner: "macos-14"
            label: "macos-14-arm64"
          - runner: "macos-latest"
            label: "macos-15-arm64"
          - runner: "windows-latest"
            label: "windows-x64"
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: "pip" # caching pip dependencies
          cache-dependency-path: "**/pyproject.toml"
      - name: Install VueGen GUI dependencies
        run: |
          pip install --upgrade pip
          pip install ".[gui]"
      - name: Install quarto tools
        run: |
          quarto install chromium
          quarto install tinytex --no-prompt
      - name: Quarto check
        run: |
          quarto check -h
          quarto check
      # installing with vuegen lead to a subtle bug installing tinytex through quarto
      - name: Install pyinstaller
        run: pip install pyinstaller
      - name: Build executable
        run: |
          cd gui
          pyinstaller -n vuegen_gui --onefile --windowed --collect-all pyvis --collect-all streamlit --collect-all st_aggrid --collect-all customtkinter --collect-all quarto_cli --collect-all plotly --collect-all _plotly_utils --collect-all traitlets --collect-all referencing --collect-all rpds --collect-all tenacity --collect-all pandas --collect-all numpy --collect-all matplotlib --collect-all openpyxl --collect-all xlrd --collect-all nbformat --collect-all nbclient --collect-all altair --collect-all rfc3987_syntax --collect-all itables --collect-all kaleido --collect-all pyarrow --collect-all dataframe_image --collect-all narwhals --collect-all PIL --collect-all vl_convert --collect-all typing-extensions --add-data ../docs/example_data/Basic_example_vuegen_demo_notebook:example_data/Basic_example_vuegen_demo_notebook --add-data ../docs/images/logo/vuegen_logo.png:. app.py
        # --windowed only for mac, see:
        # https://pyinstaller.org/en/stable/usage.html#building-macos-app-bundles
        # 'Under macOS, PyInstaller always builds a UNIX executable in dist.'
        # --onefile --windowed for Windows?
        # --collect-all yaml --collect-all strenum --collect-all jinja2 --collect-all fastjsonschema --collect-all jsonschema --collect-all jsonschema_specifications
        # replace by spec file once done...
      - name: Upload executable
        uses: actions/upload-artifact@v4
        with:
          name: vuegen_gui_${{ matrix.os.label }}
          path: gui/dist/
      - name: Upload MacOS Executable to a GitHub Release)
        if: startsWith(matrix.os.runner, 'macos') && startsWith(github.ref, 'refs/tags')
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          echo GITHUB_REF_NAME $GITHUB_REF_NAME
          echo "Uploading vuegen_gui_${{ matrix.os.label }} to release $GITHUB_REF_NAME"
          echo "Available files in build folder: gui/dist/"
          cd gui/dist/
          ls -lh
          echo "Zip .app folder"
          zip -r vuegen_gui_${{ matrix.os.label }}.zip vuegen_gui.app
          echo "Uploading..."
          gh release upload $GITHUB_REF_NAME vuegen_gui_${{ matrix.os.label }}.zip
        # .app is folder that needs to be zipped
      - name: Upload MacOS terminal application to a GitHub Release)
        if: startsWith(matrix.os.runner, 'macos') && startsWith(github.ref, 'refs/tags')
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          echo GITHUB_REF_NAME $GITHUB_REF_NAME
          echo "Uploading vuegen_gui_${{ matrix.os.label }} to release $GITHUB_REF_NAME"
          echo "Available files in build folder: gui/dist/"
          cd gui/dist/
          ls -lh
          echo "Zip single file"
          zip -r vuegen_gui_${{ matrix.os.label }}.zip vuegen_gui
          echo "Uploading..."
          gh release upload $GITHUB_REF_NAME vuegen_gui_${{ matrix.os.label }}_terminal.zip
        # .app is folder that needs to be zipped
      - name: Upload Windows Executable to a GitHub Release
        if: startsWith(matrix.os.runner, 'windows') && startsWith(github.ref, 'refs/tags')
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          echo "GITHUB_REF_NAME in env $env:GITHUB_REF_NAME"
          $GITHUB_REF_NAME = $env:GITHUB_REF_NAME
          echo "Uploading vuegen_gui_${{ matrix.os.label }} to release $GITHUB_REF_NAME"
          echo "Available files in build folder: gui/dist/"
          ls gui/dist/
          echo "Uploading..."
          gh release upload $GITHUB_REF_NAME gui/dist/vuegen_gui.exe#vuegen_gui_${{ matrix.os.label }}.exe
        # https://cli.github.com/manual/gh_release_upload
        # .exe is a single file already