🎨 module string, line length, unused arguments,

Author: enryH

src/vuegen/__init__.py

@@ -1 +1,6 @@
+"""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."""
+
 __version__ = "1.0.0"

src/vuegen/__main__.py

@@ -1,3 +1,5 @@
+"""Command-line interface for VueGen report generation."""
+
 import sys
 from pathlib import Path
 

src/vuegen/report_generator.py

@@ -1,3 +1,5 @@
+"""Main API entry point for generating reports using VueGen."""
+
 import logging
 import shutil
 import sys
@@ -28,23 +30,25 @@ def get_report(
     report_type : str
         The report type. It should be one of the values of the ReportType Enum.
     logger : logging.Logger, optional
-        A logger object to track warnings, errors, and info messages. If not provided, a default logger will be created.
+        A logger object to track warnings, errors, and info messages. If not provided,
+        a default logger will be created.
     config_path : str, optional
         Path to the YAML configuration file.
     dir_path : str, optional
         Path to the directory from which to generate the configuration file.
     streamlit_autorun : bool, optional
-        Whether to automatically run the Streamlit report after generation (default is False).
-    quarto_checks : bool, optional
-        Whether to perform checks for Quarto report generation for TeX and Chromium installation
+        Whether to automatically run the Streamlit report after generation
         (default is False).
+    quarto_checks : bool, optional
+        Whether to perform checks for Quarto report generation for TeX and Chromium
+        installation (default is False).
     output_dir : Path, optional
         The directory where the report folder will be generated.
         If not provided, the current directory will be used.
     max_depth : int, optional
-        The maximum depth of the directory structure to consider when generating the report.
-        The default is 2, which means it will include sections and subsections. The parater
-        is only used when 'dir_path' is used.
+        The maximum depth of the directory structure to consider when generating the
+        report. The default is 2, which means it will include sections and subsections.
+        The parater is only used when 'dir_path' is used.
 
     Raises
     ------
@@ -80,7 +84,7 @@ def get_report(
 
     if dir_path:
         # Generate configuration from the provided directory
-        yaml_data, base_folder_path = config_manager.create_yamlconfig_fromdir(dir_path)
+        yaml_data, _ = config_manager.create_yamlconfig_fromdir(dir_path)
         # yaml_data has under report a title created based on the directory name
         config_path = write_yaml_config(yaml_data, output_dir)
         logger.info("Configuration file generated at %s", config_path)
@@ -89,7 +93,7 @@ def get_report(
     report_config = load_yaml_config(config_path)
 
     # Load report object and metadata
-    report, report_metadata = config_manager.initialize_report(report_config)
+    report, _ = config_manager.initialize_report(report_config)
 
     # Validate and convert the report type to its enum value
     report_type = assert_enum_value(ReportType, report_type, logger)
@@ -112,12 +116,12 @@ def get_report(
         if shutil.which("quarto") is None and not hasattr(
             sys, "_MEIPASS"
         ):  # ? and not getattr(sys, "frozen", False)
-            logger.error(
-                "Quarto is not installed. Please install Quarto before generating this report type."
-            )
-            raise RuntimeError(
-                "Quarto is not installed. Please install Quarto before generating this report type."
+            msg = (
+                "Quarto is not installed. Please install Quarto before generating this "
+                "report type."
             )
+            logger.error(msg)
+            raise RuntimeError(msg)
         report_dir = output_dir / "quarto_report"
         static_files_dir = report_dir / "static"
         quarto_report = QuartoReportView(

src/vuegen/table_utils.py

@@ -1,3 +1,5 @@
+"""Reading tabular data using pandas."""
+
 import pandas as pd
 
 from . import report as r

src/vuegen/utils/variables.py

@@ -1,3 +1,5 @@
+"""Create valid variable names for Python identifiers."""
+
 import re