Merge branch 'main' into docs_update

Author: enryH

.github/workflows/cdci.yml

@@ -7,7 +7,7 @@ on:
     branches: [main]
   release:
     types: [published]
-    
+
 jobs:
   test:
     name: Unittests+streamlit
@@ -17,14 +17,16 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable 
+      - uses: psf/black@stable
+        with:
+          jupyter: true
       - uses: isort/isort-action@v1
       - 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'
+          cache: "pip" # caching pip dependencies
+          cache-dependency-path: "**/pyproject.toml"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -37,7 +39,7 @@ jobs:
           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: Integration tests
     runs-on: ubuntu-latest
@@ -50,8 +52,8 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip' # caching pip dependencies
-          cache-dependency-path: '**/pyproject.toml'
+          cache: "pip" # caching pip dependencies
+          cache-dependency-path: "**/pyproject.toml"
       - name: Install dependencies
         run: |
           pip install --upgrade pip
@@ -70,8 +72,8 @@ jobs:
       - name: quarto pdf report
         run: |
           cd docs
-          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pdf
-          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pdf
+          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
@@ -110,7 +112,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-  
+
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
@@ -120,3 +122,77 @@ jobs:
         run: python -m build
       - name: Publish package distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+
+  build-executable:
+    name: Build-exe-${{ matrix.os.label }}
+    runs-on: ${{ matrix.os.runner }}
+    needs:
+      - test
+      - other-reports
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+        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-13"
+            label: "macos-13-x64"
+          - runner: "macos-15"
+            label: "macos-15-arm64"
+          - runner: "windows-latest"
+            label: "windows-x64"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install VueGen GUI and pyinstaller
+        run: |
+          python -m pip install ".[gui]" pyinstaller
+      - name: Install quarto tools
+        run: |
+          quarto install chromium
+          quarto install tinytex
+      - name: Build executable
+        run: |
+          cd gui
+          pyinstaller -n vuegen_gui --onefile --windowed --collect-all pyvis --collect-all streamlit --collect-all st_aggrid --collect-all customtkinter --collect-all quarto_cli --collect-all plotly --collect-all _plotly_utils --collect-all traitlets --collect-all referencing --collect-all rpds --collect-all tenacity --collect-all pyvis --collect-all pandas --collect-all numpy --collect-all matplotlib --collect-all openpyxl --collect-all xlrd --collect-all nbformat --collect-all nbclient --collect-all altair --collect-all itables --collect-all kaleido --collect-all pyarrow --collect-all dataframe_image --collect-all narwhals --collect-all PIL --collect-all vl_convert --add-data ../docs/example_data/Basic_example_vuegen_demo_notebook:example_data/Basic_example_vuegen_demo_notebook --add-data ../docs/images/vuegen_logo.png:. app.py
+        # --windowed only for mac, see:
+        # https://pyinstaller.org/en/stable/usage.html#building-macos-app-bundles
+        # 'Under macOS, PyInstaller always builds a UNIX executable in dist.'
+        # --onefile --windowed for Windows?
+        # --collect-all yaml --collect-all strenum --collect-all jinja2 --collect-all fastjsonschema --collect-all jsonschema --collect-all jsonschema_specifications
+        # replace by spec file once done...
+      - name: Upload executable
+        uses: actions/upload-artifact@v4
+        with:
+          name: vuegen_gui_${{ 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 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

.gitignore

@@ -118,6 +118,7 @@ logs/
 vuegen/logs/
 streamlit_report/
 quarto_report/
+output_docker/
 
 # VS Code
 .DS_Store

CONTRIBUTING.md

@@ -0,0 +1,71 @@
+# Contributing to VueGen
+
+[VueGen][vuegen-repo] is an open source project, and we welcome contributions of all 
+kinds via GitHub issues and pull requests: correct or improve our [documentation][vuegen-docs], report or fix bugs, propose changes, and implement new features. Please follow 
+these guidelines to make sure that your contribution is easily integrated into the project.
+
+## 1. Contributor Agreement
+
+By contributing, you agree that we may redistribute your work under [our
+license](LICENSE). In exchange, we will address your issues and/or assess
+your change proposal as promptly as we can, and help you become a member of our
+community.
+
+## 2. What to Contribute
+
+The easiest way to get started is by reporting an issue that needs to be fixed, 
+such as a bug in the code, unclear explanations, conceptual errors, or other details. 
+You can also  contribute by proposing new features or modules, improving existing 
+functionality, or suggesting other ideas that might be useful. If you’re looking for 
+inspiration, please check the [list of open issues][issues] in this repository.
+
+Feedback from beginners is especially valuable, as experienced users may overlook how 
+challenging certain aspects of the software can be for newcomers. Therefore, we encourage 
+you to share any suggestions or observations you have about this project.
+
+## 3. How to Contribute
+
+Here are the ways you can submit your suggestions and contribute to the project:
+
+1. **Reporting Issues or Suggesting Improvements:** If you have a  [GitHub][github] account 
+   (or are willing to [open one][github-join]) but are unfamiliar with Git, you can report 
+   bugs or suggest improvements by [creating an issue][new-issue]. This GitHub feature allows 
+   for discussion threads on reported issues and proposed enhancements.
+
+2. **Submitting Changes via Pull Requests:** If you are comfortable using Git and would like to
+   add or modify a functionality, you can submit a **pull request (PR)**. Instructions on how to contribute this way are provided in the next section.
+
+3. **Providing Feedback via Email:** If you don’t have a GitHub account and are
+   unfamiliar with Git, you can send feedback via email to [[email protected]][contact]. However, using GitHub is preferred, as it allows us to respond more quickly and track discussions openly.
+
+> [!NOTE]
+> The documentation for [Git][git-docs] and [GitHub][github-docs] are easy to follow, and you can learn the basics using their official guides.
+
+## 4. Creating a Pull Request
+
+If you choose to contribute via GitHub, you may want to look at [How to Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we use [GitHub flow][github-flow] to manage changes:
+
+1. Create a new branch in your desktop copy of this repository for each significant change.
+2. Commit the change in that branch.
+3. Push that branch to your fork of this repository on GitHub.
+4. Submit a pull request from that branch to the [upstream repository][vuegen-repo].
+5. If you receive feedback, make changes on your desktop and push to your branch on GitHub: the 
+   pull request will update automatically.
+
+## 5. Credits
+
+This contribution guide was modified under the [Creative Commons Attribution 4.0 International License][ccby] from the [Software Carpentry guides][soft-cp-guides].
+
+[vuegen-repo]: https://github.com/Multiomics-Analytics-Group/vuegen
+[vuegen-docs]: https://vuegen.readthedocs.io/
+[issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues
+[new-issue]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
+[github]: https://github.com
+[github-join]: https://github.com/join
+[contact]: mailto:[email protected]
+[git-docs]: https://git-scm.com/doc
+[github-docs]: https://guides.github.com/
+[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[github-flow]: https://guides.github.com/introduction/flow/
+[soft-cp-guides]: https://software-carpentry.org/lessons/
+[ccby]: https://creativecommons.org/licenses/by/4.0/