🚧 try to add tinytex

Author: enryH

.github/workflows/cdci.yml

@@ -150,6 +150,9 @@ jobs:
       - name: Install VueGen GUI and pyinstaller
         run: |
           python -m pip install ".[gui]" pyinstaller
+      - name: Install tinytex into local quarto installation
+        run: |
+          quarto install tinytex
       - name: Build executable
         run: |
           cd gui

README.md

@@ -36,7 +36,7 @@ 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
 Vuegen is available on [PyPI][vuegen-pypi] and can be installed using pip:
@@ -102,6 +102,23 @@ 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.
+
 ## Case studies
 VueGen’s functionality is demonstrated through two case studies:
 

gui/copy_python_executable.py

@@ -201,50 +201,6 @@ def run_report(self, output_dir: str = BASE_DIR) -> None:
                 f"Quarto is not installed. Please install Quarto to run the report: {str(e)}"
             )
             raise
-        # else:
-        #     quarto_path = Path(sys._MEIPASS) / "quarto_cli" / "bin" / "quarto"
-        # _sys_exe = sys.executable
-        # set executable to the bundled python (manually added to bundle)
-        # sys.executable = str(Path(sys._MEIPASS).parent / "python")
-        # self.report.logger.info(f"quarto_path: {self.quarto_path}")
-
-        # args = [f"{quarto_path}", "render", file_path_to_qmd]
-        # subprocess.run(
-        #     args,
-        #     check=True,
-        # )
-        # self.report.logger.info(
-        #     f"Converted '{self.report.title}' '{self.report_type}' report to Jupyter Notebook after execution"
-        # )
-        # notebook_filename = Path(file_path_to_qmd).with_suffix(".ipynb")
-        # try papermill
-        # import papermill as pm
-
-        # pm.execute_notebook(
-        #     "path/to/input.ipynb",
-        #     "path/to/output.ipynb",
-        #     parameters=dict(alpha=0.6, ratio=0.1),
-        # )
-        # quarto does not try to execute ipynb files, just render them
-        # execute manually using bundled python binary
-        # https://nbconvert.readthedocs.io/en/latest/execute_api.html
-        # import nbformat
-        # from nbconvert.preprocessors import ExecutePreprocessor
-
-        # with open(notebook_filename, encoding="utf-8") as f:
-        #     nb = nbformat.read(f, as_version=4)
-        # logging.getLogger("traitlets").setLevel(logging.INFO)
-        # ep = ExecutePreprocessor(timeout=600, kernel_name="python3")
-        # nb, _ = ep.preprocess(nb, {"metadata": {"path": "./"}})
-        # with open(notebook_filename, "w", encoding="utf-8") as f:
-        #     nbformat.write(nb, f)
-        # quarto does not try execute ipynb files per default, just render these
-        # args = [f"{quarto_path}", "render", notebook_filename]
-        # subprocess.run(
-        #     args,
-        #     check=True,
-        # )
-        # sys.executable = _sys_exe
 
     def _create_yaml_header(self) -> str:
         """