Merge branch 'main' into test_all_os

Author: enryH

README.md

@@ -34,6 +34,8 @@ Also, the class diagram for the project is presented below to illustrate the arc
 
 ![VueGen Class Diagram](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_classdiagram_noattmeth.png)
 
+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. 
 
 ## Installation
@@ -68,7 +70,7 @@ If you prefer not to install VueGen on your system, a pre-configured Docker cont
 Run VueGen using a directory with the following command:
 
 ```bash
-vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook --report_type streamlit
+vuegen --directory docs/example_data/Earth_microbiome_vuegen_demo_notebook --report_type streamlit
 ```
 
 > [!NOTE]
@@ -77,7 +79,7 @@ vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook --report_t
 It's also possible to provide a configuration file instead of a directory:
 
 ```bash
-vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml --report_type streamlit
+vuegen --config docs/example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml --report_type streamlit
 ```
 
 The current report types supported by VueGen are:
@@ -95,7 +97,7 @@ Instead of installing VueGen locally, you can run it directly from a Docker cont
 
 ```bash
 docker run --rm \
-  -v "$(pwd)/Earth_microbiome_vuegen_demo_notebook:/home/appuser/Earth_microbiome_vuegen_demo_notebook" \
+  -v "$(pwd)docs/example_data/Earth_microbiome_vuegen_demo_notebook:/home/appuser/Earth_microbiome_vuegen_demo_notebook" \
   -v "$(pwd)/output_docker:/home/appuser/quarto_report" \
   quay.io/dtu_biosustain_dsp/vuegen:docker --directory /home/appuser/Earth_microbiome_vuegen_demo_notebook --report_type streamlit
 ```
@@ -138,6 +140,7 @@ We appreciate your feedback! If you have any comments, suggestions, or run into
 [streamlit]: https://streamlit.io/ 
 [vuegen-pypi]: https://pypi.org/project/vuegen/
 [vuegen-docker-quay]: https://quay.io/repository/dtu_biosustain_dsp/vuegen
+[vuegen-class-diag-att]: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_classdiagram_withattmeth.pdf
 [vuegen-docs]: https://vuegen.readthedocs.io/
 [ci-gh-action]: https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml
 [ci-docs]: https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml

docs/images/vuegen_classdiagram_noattmeth.png

@@ -3,7 +3,7 @@ name = "vuegen"
 dynamic = ["version"]
 
 [tool.poetry]
-description = "Module to generate automatic web interface reports with visualizations"
+description = "VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications. Users simply provide a directory with output files and VueGen compiles them into a structured report."
 authors = ["MoNA group"]
 license = "MIT"
 readme = "README.md"

docs/images/vuegen_classdiagram_withattmeth.pdf

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from vuegen import report_generator
-from vuegen.utils import get_logger, get_parser
+from vuegen.utils import get_logger, get_parser, print_completion_message
 
 
 def main():
@@ -47,6 +47,9 @@ def main():
         streamlit_autorun=streamlit_autorun,
     )
 
+    # Print completion message
+    print_completion_message(report_type)
+
 
 if __name__ == "__main__":
     main()

pyproject.toml

@@ -10,7 +10,7 @@
 
 def get_report(
     report_type: str,
-    logger: logging.Logger = get_logger("report"),
+    logger: logging.Logger = None,
     config_path: str = None,
     dir_path: str = None,
     streamlit_autorun: bool = False,
@@ -36,7 +36,11 @@ def get_report(
     ValueError
         If neither 'config_path' nor 'directory' is provided.
     """
-    # Initialize the config manager object
+    # Initialize logger only if it's not provided
+    if logger is None:
+        logger = get_logger("report")
+
+    # Create the config manager object
     config_manager = ConfigManager(logger)
 
     if dir_path:

src/vuegen/__main__.py

@@ -744,6 +744,46 @@ def get_logger(log_suffix):
     return logger
 
 
+def print_completion_message(report_type: str):
+    """
+    Prints a formatted completion message after report generation.
+    """
+    border = "─" * 65  # Creates a separator line
+    print(f"\n{border}\n🎉 Pipeline Execution Complete! 🎉\n")
+
+    if report_type == "streamlit":
+        print(
+            """🚀 Streamlit Report Generated!
+
+📂 All scripts to build the Streamlit app are available at:
+    nf_container_results/streamlit_report/sections
+
+▶️ To run the Streamlit app, use the following command:
+    streamlit run nf_container_results/streamlit_report/sections/report_manager.py
+
+✨ You can extend the report by adding new files to the input directory or updating the config file.
+
+🛠️ Advanced users can modify the Python scripts directly in:
+    nf_container_results/streamlit_report/sections
+"""
+        )
+    else:
+        print(
+            f"""🚀 {report_type.capitalize()} Report Generated!
+
+📂 Your {report_type} report is available at:
+    nf_container_results/quarto_report
+
+✨ You can extend the report by adding new files to the input directory or updating the config file.
+
+🛠️ Advanced users can modify the report template directly in:
+    nf_container_results/quarto_report/quarto_report.qmd
+"""
+        )
+
+    print(border)
+
+
 ## REPORT FORMATTING
 def generate_footer() -> str:
     """