Os standalone installers (with a GUI)

.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
@@ -110,7 +112,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-  
+
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
@@ -120,3 +122,58 @@ 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 Executable to a GitHub Release
+        if: startsWith(github.ref, 'refs/tags')
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TAG_NAME=${GITHUB_REF#refs/tags/}
+          cp 
+          gh release upload "$TAG_NAME" gui/dist/vuegen_gui.*#vuegen_gui_${{ matrix.os.label }}
+        # https://cli.github.com/manual/gh_release_upload
+        # either .app or .exe depending on the OS

README.md

@@ -38,7 +38,7 @@ Also, the class diagram for the project is presented below to illustrate the arc
 
 An extended version of the class diagram with attributes and methods is available [here][vuegen-class-diag-att].
 
-The VueGen documentation is available at [vuegen.readthedocs.io][vuegen-docs], where you can find detailed information of the package’s classes and functions, installation and execution instructions, and case studies to demonstrate its functionality. 
+The VueGen documentation is available at [vuegen.readthedocs.io][vuegen-docs], where you can find detailed information of the package’s classes and functions, installation and execution instructions, and case studies to demonstrate its functionality.
 
 ## Installation
 ### Pip
@@ -120,6 +120,26 @@ docker run --rm \
   quay.io/dtu_biosustain_dsp/vuegen:docker --directory /home/appuser/Earth_microbiome_vuegen_demo_notebook --report_type streamlit
 ```
 
+## GUI
+
+We have a simple GUI for VueGen that can be run locally or through a standalone executable.
+
+```bash
+cd gui
+python app.py
+```
+
+The bundle GUI with the VueGen package is available under the releases. You will need to
+unzip the file and run `vuegen_gui` in the unpacked main folder. Most dependencies are included into
+the bundle under `_internals` using PyInstaller.
+
+Streamlit works out of the box as a purely Python based package. For `html` creation you will have to
+have a global Python installation with the `jupyter` package installed. `quarto` needs to start
+a kernel for execution. This is also true if you install `quarto` globally on your machine.
+
+More information can be found in the 
+[GUI README](https://github.com/Multiomics-Analytics-Group/vuegen/blob/os_installers/gui/README.md).
+
 ## Case studies
 VueGen’s functionality is demonstrated through two case studies:
 

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

@@ -1,29 +1,32 @@
 <!-- <div align="center">
   <img width="300px" src="images/vuegen_logo.svg">
 </div> -->
-![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg)
------------------
+
+![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png)
+
 <p align="center">
    VueGen is a Python library that automates the creation of scientific reports.
 </p>
 
-| Information | Links |
-| :--- | :--- |
-| **Package** |[ ![PyPI Latest Release](https://img.shields.io/pypi/v/vuegen.svg)](https://pypi.org/project/vuegen/) [![Supported versions](https://img.shields.io/pypi/pyversions/vuegen.svg)](https://pypi.org/project/vuegen/)|
-| **Documentation** | [![Docs](https://readthedocs.org/projects/vuegen/badge/?style=flat)](https://vuegen.readthedocs.io/)|
-| **Build** | [![CI](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml/badge.svg)](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml) [![Docs](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml/badge.svg)](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml)|
-| **Examples** | [![HTML5](https://img.shields.io/badge/html5-%23E34F26.svg?style=for-the-badge&logo=html5&logoColor=white)](https://multiomics-analytics-group.github.io/vuegen/) [![Streamlit](https://img.shields.io/badge/Streamlit-%23FE4B4B.svg?style=for-the-badge&logo=streamlit&logoColor=white)](https://multiomics-analytics-group.github.io/vuegen/)|
-| **Discuss on GitHub** | [![GitHub issues](https://img.shields.io/github/issues/Multiomics-Analytics-Group/vuegen)](https://github.com/Multiomics-Analytics-Group/vuegen/issues) [![GitHub pull requests](https://img.shields.io/github/issues-pr/Multiomics-Analytics-Group/vuegen)](https://github.com/Multiomics-Analytics-Group/vuegen/pulls) |
+| Information           | Links                                                                                                                                                                           |
+| :-------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **Package**           | [PyPI Latest Release](https://pypi.org/project/vuegen/) [Supported versions](https://pypi.org/project/vuegen/)                                                                  |
+| **Documentation**     | [Docs](https://vuegen.readthedocs.io/)                                                                                                                                          |
+| **Build**             | [CI](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml) - [Docs](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml) |
+| **Examples**          | [HTML5](https://multiomics-analytics-group.github.io/vuegen/) - [Streamlit](https://multiomics-analytics-group.github.io/vuegen/)                                               |
+| **Discuss on GitHub** | [GitHub issues](https://github.com/Multiomics-Analytics-Group/vuegen/issues) - [GitHub pull requests](https://github.com/Multiomics-Analytics-Group/vuegen/pulls)               |
 
 ## Table of contents:
+
 - [About the project](#about-the-project)
 - [Installation](#installation)
 - [Execution](#execution)
 - [Acknowledgements](#acknowledgements)
 - [Contact](#contact)
 
 ## About the project
-VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input. 
+
+VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input.
 
 The configuration file specifies the structure of the report, including sections, subsections, and various components such as plots, dataframes, markdown, html, and API calls. Reports can be generated in various formats, including documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), notebooks (Jupyter) or [Streamlit](streamlit) web applications.
 
@@ -34,6 +37,7 @@ An overview of the VueGen workflow is shown in the figure below:
   <img width="650px" src="images/vuegen_graph_abstract.png" alt="VueGen overview"/>
 </figure>
 </p> -->
+
 ![VueGen Abstract](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png)
 
 Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes:
@@ -57,7 +61,7 @@ pip install vuegen
 You can also install the package for development from this repository by running the following command:
 
 ```bash
-pip install -e path/to/vuegen # specify location 
+pip install -e path/to/vuegen # specify location
 pip install -e . # in case your pwd is in the vuegen directory
 ```
 
@@ -91,24 +95,26 @@ vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbi
 ```
 
 The current report types supported by VueGen are:
-* Streamlit
-* HTML
-* PDF
-* DOCX
-* ODT
-* Reveal.js
-* PPTX
-* Jupyter
+
+- Streamlit
+- HTML
+- PDF
+- DOCX
+- ODT
+- Reveal.js
+- PPTX
+- Jupyter
 
 ## Acknowledgements
 
 - Vuegen was developed by the [Multiomics Network Analytics Group (MoNA)][Mona] at the [Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)][Biosustain].
 - The vuegen logo was designed based on an image created by [Scriberia][scriberia] for The [Turing Way Community][turingway], which is shared under a CC-BY licence. The original image can be found at [Zenodo][zenodo-turingway].
 
 ## Contact
+
 If you have comments or suggestions about this project, you can [open an issue][issues] in this repository.
 
-[streamlit]: https://streamlit.io/ 
+[streamlit]: https://streamlit.io/
 [vuegen-pypi]: https://pypi.org/project/vuegen/
 [quarto]: https://quarto.org/
 [quarto-cli-pypi]: https://pypi.org/project/quarto-cli/
@@ -119,5 +125,3 @@ If you have comments or suggestions about this project, you can [open an issue][
 [turingway]: https://github.com/the-turing-way/the-turing-way
 [zenodo-turingway]: https://zenodo.org/records/3695300
 [issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
-
-

docs/example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml

@@ -0,0 +1,140 @@
+report:
+  title: Earth Microbiome Vuegen Demo Notebook
+  description: "The Earth Microbiome Project (EMP) is a systematic attempt to characterize\
+    \ global microbial taxonomic and functional diversity for the benefit of the planet\
+    \ and humankind. \n  It aimed to sample the Earth\u2019s microbial communities\
+    \ at an unprecedented scale in order to advance our understanding of the organizing\
+    \ biogeographic principles that govern microbial community structure. \n  The\
+    \ EMP dataset is generated from samples that individual researchers have compiled\
+    \ and contributed to the EMP. \n  The result is both a reference database giving\
+    \ global context to DNA sequence data and a framework for incorporating data from\
+    \ future studies, fostering increasingly complete characterization of Earth\u2019\
+    s microbial diversity.\n  \n  You can find more information about the Earth Microbiome\
+    \ Project at https://earthmicrobiome.org/ and in the [original article](https://www.nature.com/articles/nature24621).\n"
+  graphical_abstract: ''
+  logo: ''
+sections:
+- title: Exploratory Data Analysis
+  description: ''
+  subsections:
+  - title: Sample Exploration
+    description: ''
+    components:
+    - title: Metadata Random Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.csv
+      description: ''
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: Animal Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_samples_map.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Plant Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Saline Samples Map
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: ALTAIR
+- title: Metagenomics
+  description: ''
+  subsections:
+  - title: Alpha Diversity
+    description: ''
+    components:
+    - title: Alpha Diversity Host Associated Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_alpha_diversity_host_associated_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Alpha Diversity Free Living Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+  - title: Average Copy Number
+    description: ''
+    components:
+    - title: Average Copy Number Emp Ontology Level2
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Average Copy Number Emp Ontology Level3
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+  - title: Nestedness
+    description: ''
+    components:
+    - title: Nestedness Random Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.csv
+      description: ''
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: All Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Plant Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.json
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: PLOTLY
+    - title: Animal Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+    - title: Non Saline Samples
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_samples.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC
+- title: Network Analysis
+  description: ''
+  subsections:
+  - title: Phyla Association Networks
+    description: ''
+    components:
+    - title: Phyla Counts Subset
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.csv
+      description: ''
+      caption: ''
+      component_type: DATAFRAME
+      file_format: CSV
+      delimiter: ','
+    - title: Phyla Correlation Network With 0.5 Threshold Edgelist
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: INTERACTIVE_NETWORK
+      csv_network_format: EDGELIST
+    - title: Phyla Correlation Network With 0.5 Threshold
+      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.png
+      description: ''
+      caption: ''
+      component_type: PLOT
+      plot_type: STATIC