MacOs and Windows standalone GUIs installers (#73)

First graphical user interface (GUI) for vuegen.

Code base was adjusted to improve output file location, passing of configuration paths, logging in a continiously running application and allowing Windows compatibility of used paths.

Single commits
* 🚧 start with bundleing cli tool

* ✨ with pyvis added the basic example works using the cli

* 🚧🐛 streamlit not easy to run from within vuegen script

- sys.exectuable is vuegen script, not the original Python Interpreter
 -> not easy to run `pthon -m streamlit run file.py`
- manually starting and building streamlit_run command does not connect to browser atm

* ✨ start streamlit without subprocess - runs from self-contained app

* 🐛 ensure that networking is properly enabled

- network URL assigned.
- localhost not on port 3000, but 8501 it seems

* 🎨 make Streamlit report aware of where it runs

- keep also subprocess option in code for local development

* 🐛 add st_aggrid as it is imported, not installed

import st_aggrid
but
pip install streamlit-aggrid

it is a "hidden" import as the main script is not using it (as pyvis or streamlit itself)

* 🚧 start testing of bundeling for quarto

- some form of binaries have to be passed, along addtional dependencies

* 📝 add current spec file

* ✨: First simple working example of a GUI (streamlit local)

- can start streamlit when not package as exectuable from GUI
- use grid to define layout

ToDo: Move to class-based layout

* ✨ add basic GUI command

- creates relative large executable (740 MB)

* 🎨 set default to running streamlit app directly

* 🎨 format app script further

* ⏪ undo deletion of dependencies

* ✨🎨 Try to build executable on ubuntu (+ formating)

* 🐛 cli different than on MAC, ⚡ speed up testing for now

- only run againt Python 3.11

* 🐛 install vuegen itself with gui deps

* 🎨 introduce labels for runner images

to be able to specify what is what more easily

* ✨ add other runner OS platforms with labels

* 🐛 poetry optional dependencies need to be explicit, fix name of job

- extras need to be specified as additinal dependencies
- build name of job correctly

* 🐛 colon not allowed in name...

* ⏪ undo command change

* ✨ define basic example as default, ship it with bundle

Always have something to run.

* 🎨 make process label somehow fit UI limitations

- for GitHub Actions View in the browser

* 🐛 acutally get variable value, not test instance exist

- before the existence was just tested, leading to always True (?)

* ⏪ restore main branch commands (render, not convert)

* 🚚🔥 remove cli exectuable for GUI bundle only

- 🚚 move some hints to GUI README

* 🔧 Only show streamlit for now (quarto not yet bundled)

* 🚧 add quarto execution for bundle

- execution still fails
- convert and render without execution?
- add all report types to GUI (for testing)
- do not stop app when quarto is not in PATH

* ✨ get quarto html output from bundle

- use quarto (pandoc?) to convert qmd to ipynb
- use nbconvert and a copied Python executable to execute notebook
- use quarto (pandoc?) ot convert executed ipynb to desired format

* 🐛 add bundle dependencies, RadioButton toggle

- radiobutton values are not correctly used in bundled app when built in runner
- works locally (woth local bundle, and direct execution of app)

* 🐛 fix command om cdci

* :arg: reduce console output (global logging level is DEBUG?)

* 🐛 use macos-15 explicitly

* 🎨 format and rename callback factory

* 📝 add hint to execution procedure

* 🐛 try to fix python executable path

- just copy what ever is pointing to sys.executable
- move to binaries folder

Locally this all works, but it might be that the lcoal Python exe is somehow 'valid' (signed, etc)

* 🎨 format helper script

* 🚧 move python file to main folder

* 🚧 try to use miniconda action for python exe

* 🚧 inspect conda on GitHub Actions runners

* 🚧 find the documented test environment

* 🐛 test environment not auto-activated

* 🚧 try to activate test env...

* 🚧 get environment to be activated

* 🚧 modify default shell params

* 🚧 use quarto native functionality

- require users to have a Python base installation with jupyter installed
  - pip install jupyter

Then quarto manages to pick up local dependencies and run the notebook (to test)

* 🚧 try to add tinytex

* 🐛 check for dependencies

* 🐛 try to add both tools on the fly (chromnium and tinyte) needed for pdfs, docx, pptx, etc

* 🐛 close parantheses (merge error)

* 🐛 make Windows Path for bundled quarto executable

- install quarto on server (as it seems to fail in conda envs which I use locally)

* 🚧 test further options

* 🎨 add file directory selection - allow to specify a directory

- added Alberto's directory selection dialog
- added the report generator functionality as suggested by Alberto
- success needs to be printed manually. quarto errors are not propagated to our app... (exist code of subprocess run)

* 🚧 test now with onefile

- importing vuegen.generate_report increased the MAC OS file size
- or it was the windowed option?

* 🚧 test also non-windowed app

* 🐛 set default static dir only on main methods, pass parameter on other hidden methods

- will allow to set static dir on app or cli

* 🐛 allow to specify log directory

* ✨ allow to set output directory, pass on to get_report

- initialize logging directory at output directory

* 🎨 separate by row, cont. increments

* 🐛 fix #89 - check if output was actually created

* 🚧 allow to set Python Path manually

- manipulate PATH and add logs

* 🐛 set generic kernel name

- otherwise it uses local defaults on device

* 🎨 fix typo in function name

* 🎨 use isostandard for log file format

- but relace colons with hypens in hour:minutes:seconds

* ✨ this let's the interpreter look for the packages in the shipped folder

- but they need to be present as full modules (which means that `.py` and not `.so` files are present?
- will be large... but that is a side note

Use Python=3.12 where pyvis examples should work in streamlit

* 🐛 only add folder as import, not the zip file

* 🐛 fix cdci

* 🚧 build for python 3.12 with jupyter installed

- conda base 3.12 with jupyter installed needed to execute
- other than that 'only' vuegen required packges

* 🚧 add makefile to document local build on mac

- Makefile also has environment packages listed which could be added (be aware to use package folder name, not PyPI name, e.g. PIL and not pillow)
- should work with local python environment with jupyter installed
- switched to windowed build

* 🐛 example data not in normal writable file path for bundled app, put config to output folder?

- could be an option (to discuss)
- config file is where output is, not where report
- could be otherwise an option to be specified

* 🐛 svg from readme cannot be rendered

* 🐛 reset logger (relevant for GUI)

- logging.basicConfig only has an effect the first time
- executed from GUI, the logs were created but empty the second time

* 💥 Write config file based on directory to output directory of report

- read-only situation of result directories: One cannot always write to directory which contains the results if -dir option is used
- ✨ Return paths for easier reporting
- adapt example notebooks accordingly

* ✨ improve folder dialog for PythonPath, set str explicitly for Windows

- On windows the Path set by the user globally are probably seen (it seems)
- check if a path is set for directory dialog, if not start at home directory

* 🎨 set default logger_id (so not all loggers are set to debug)

* 🐛 do not overwrite _PATH

- otherwise bundled quarto is set twice if python env is selected

* 🎨 add logo to app and clean-up app.py

- for debugging do not build windowed app for now

* 🎨 do not reset directories when nothing is set, adj. app size

* ✨ cache python exectutable set previously

- only require users to setup python environment once
- 📝 start describing how to use bundled app

* 🎨 format, escape pagemark

* ✨ copy example data to vuegen_gui dir in home directory, lib for png export of altair fig

- address windows pandoc issue: "pandoc: openBinaryFile: does not exist (No such file or directory)"
- add library vl-convert-python needed for altair fig exported as static png

* 🎨 remove comment and sort

* 🐛 use selected logger, not always root to reset handlers

- handlers were not reset if not root logger was used

* ✨ document and restore all actions, use windowed build

* 🐛 add 'save' tag to ensure that altair plots can be exported

* 🎨 format docs as they were adapted

- api changes needed to be reflected in docs.
- format docs
- enforce using action

* 📝 link README of GUI

* 🚧 gh release upload for adding executables to release?

* 🎨 no time zone in log file name, use onefile for windows

- time zone names on windows are too long
- onefile on Windows should lead to only one exe
- see if option leads to okay option for .app on MAC

* 🎨 remove some comments and fix docstring

---------

Co-authored-by: enryh <[email protected]>

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
@@ -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

@@ -41,7 +41,7 @@ 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
 
@@ -131,6 +131,26 @@ 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