Merge branch 'main' into test_all_os

Author: enryH

.github/workflows/cdci.yml

@@ -120,6 +120,15 @@ jobs:
             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
@@ -210,7 +219,7 @@ 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 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
+          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/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.'

bin/README.md

@@ -0,0 +1,13 @@
+# Scripts
+
+Run from project root.
+
+## Update the example reports files
+
+```bash
+bash bin/update_test_reports.sh
+```
+
+- make sure these run
+- evaluate if changes are intended and potentially commit report file changes
+  along with the corresponding code changes

bin/update_test_reports.sh

@@ -0,0 +1,21 @@
+set -e
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook
+
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/html -rt html
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/pdf -rt pdf
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/docx -rt docx
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/odt -rt odt
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/revealjs -rt revealjs
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/pptx -rt pptx
+vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/jupyter -rt jupyter
+
+# all of the above quarto based reports, can be opened from the command line with:
+# open tests/report_examples/Basic_example_vuegen_demo_notebook/pdf/quarto_report/quarto_report.pdf
+
+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
+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
+vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/pdf -rt pdf
+
+# update bot example
+vuegen -c example_config_files/Chatbot_example_config.yaml -output_dir ../tests/report_examples/chat_bot

docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml

@@ -1,8 +1,8 @@
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.

docs/example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md

@@ -1,8 +1,8 @@
 <!-- <div align="center">
-  <img width="300px" src="images/vuegen_logo.svg">
+  <img width="300px" src="images/logo/vuegen_logo.svg">
 </div> -->
 
-![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png)
+![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png)
 
 <p align="center">
    VueGen is a Python library that automates the creation of scientific reports.

docs/example_data/Basic_example_vuegen_demo_notebook/description.md

@@ -1 +1,6 @@
-A general description of the report.
+A general description of the report.
+
+It should test all major components which are available
+to be integrated into VueGen.
+
+Check our tests folder for examples of report files used to generate actual reports.

docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png

@@ -3,7 +3,7 @@
 
 # Mapping section titles to their corresponding filenames
 SECTION_MAPPING = {
-    "![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg)": "home_page.md",
+    "![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/HEAD/docs/images/logo/vuegen_logo.svg)": "home_page.md",
     "About the project": "about.md",
     "Installation": "installation.md",
     "Execution": "execution.md",
@@ -84,7 +84,7 @@ def clean_trailing_links(content):
 
 
 def process_readme(readme_path, output_dir):
-    readme = Path(readme_path).read_text()
+    readme = Path(readme_path).read_text(encoding="utf-8")
 
     # Extract links from README
     links = extract_links_from_readme(readme)
@@ -104,11 +104,11 @@ def process_readme(readme_path, output_dir):
             (output_dir / filename).write_text(myst_content)
             print(f"Generated {filename}")
         else:
-            print(f"Warning: Section '{section_title}' not found in README")
+            raise ValueError(f"Section '{section_title}' not found in README")
 
     # Include CONTRIBUTING.md with its own link references
     contrib_path = readme_path.parent / "CONTRIBUTING.md"
-    if contrib_path.exists():
+    try:
         raw_contrib = contrib_path.read_text()
         contrib_links = extract_links_from_readme(raw_contrib)
 
@@ -121,8 +121,8 @@ def process_readme(readme_path, output_dir):
         # Write output
         (output_dir / "contributing.md").write_text(contrib_converted)
         print("Generated contributing.md")
-    else:
-        print("Warning: CONTRIBUTING.md not found")
+    except FileNotFoundError as e:
+        raise FileNotFoundError(f"CONTRIBUTING.md not found at {contrib_path}") from e
 
 
 if __name__ == "__main__":

docs/split_readme.py

@@ -273,7 +273,7 @@
    },
    "outputs": [],
    "source": [
-    "vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg\"\n",
+    "vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png\"\n",
     "\n",
     "# Load the YAML file\n",
     "print(\n",
@@ -457,7 +457,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

docs/vuegen_basic_case_study.ipynb

@@ -6,8 +6,8 @@ The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/bl
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.