Merge branch 'main' into test_all_os

Author: enryH

.github/workflows/cdci.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: CICD Python Package
 
 on:
   push:
@@ -7,6 +7,7 @@ on:
     branches: [main]
   release:
     types: [published]
+  workflow_dispatch:
 
 jobs:
   test:
@@ -20,17 +21,25 @@ jobs:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
         with:
-          jupyter: true
+          # ! 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: Install dependencies
+      - 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 -e .
       - name: Run tests
@@ -64,6 +73,7 @@ jobs:
         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
@@ -101,6 +111,44 @@ jobs:
           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: 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
@@ -128,6 +176,11 @@ jobs:
   build-executable:
     name: Build-exe-${{ 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
@@ -157,7 +210,7 @@ jobs:
       - 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
+          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 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/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.'

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Test documentation building, and publish report to GitHub Pages
+name: Docs and Report Examples
 
 on:
   push:
@@ -7,10 +7,10 @@ on:
     branches: [main]
   release:
     types: [published]
-    
+
 jobs:
   test:
-    name: Test
+    name: Test docs and report examples
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -21,24 +21,24 @@ 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: |
           python -m pip install --upgrade pip
-          pip install -e .[docs]
+          pip install .[docs]
       - name: Build references
         run: |
-            cd docs
-            sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
+          cd docs
+          sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
       - name: Build documentation
         run: |
-            cd docs
-            sphinx-build -n --keep-going -b html ./ ./_build/
+          cd docs
+          sphinx-build -n --keep-going -b html ./ ./_build/
       # --- HTML example deployment ---
       - name: Rename entry point of report to index.html
         run: |
-            mv docs/quarto_report/quarto_report.html docs/quarto_report/index.html
+          mv docs/quarto_report/quarto_report.html docs/quarto_report/index.html
       - name: Publish HTML report to GitHub Pages (gh-pages branch)
         # Only publish a new static report upon a new release -> can be changed.
         if: startsWith(github.ref, 'refs/tags')
@@ -53,13 +53,13 @@ jobs:
       #     path: docs/_build/
 
       # --- Streamlit example deployment ---
-      - name: Fix Absolute Paths in Streamlit Scripts
-        run: |
-          find docs/streamlit_report/sections -type f -name "*.py" -exec sed -i 's|/home/runner/work/vuegen/vuegen/docs/||g' {} +
+      #- name: Fix Absolute Paths in Streamlit Scripts
+      #  run: |
+      #    find docs/streamlit_report/sections -type f -name "*.py" -exec sed -i 's|/home/runner/work/vuegen/vuegen/docs/||g' {} +
       - name: Publish Streamlit report to streamlit-example branch
         if: startsWith(github.ref, 'refs/tags')
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: docs/
-          publish_branch: streamlit-report-example
+          publish_branch: streamlit-report-example

.gitignore

@@ -117,6 +117,7 @@ cython_debug/
 logs/
 vuegen/logs/
 streamlit_report/
+!tests/report_examples
 quarto_report/
 output_docker/
 
@@ -128,6 +129,5 @@ docs/images/UML_diagrams/
 docs/images/Graphical_abstract/
 docs/images/Nfcore_module_figure
 docs/presentations/
-docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/
-docs/vuegen_case_study_earth_microbiome_test.ipynb
-test.py
+basic_example_vuegen_demo_notebook_config.yaml
+earth_microbiome_vuegen_demo_notebook_config.yaml

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+  "editor.rulers": [88, 100, 120]
+}

CONTRIBUTING.md

@@ -27,16 +27,17 @@ you to share any suggestions or observations you have about this project.
 
 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.
+### 1. Reporting Issues or Suggesting Improvements
 
-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.
+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.
 
-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.
+### 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.