Merge branch 'main' into docs_update

Author: sayalaruano

.github/workflows/cdci.yml

@@ -27,9 +27,13 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: "pip" # caching pip dependencies
           cache-dependency-path: "**/pyproject.toml"
-      - name: Install dependencies
+      - name: lint package code with ruff 
         run: |
           python -m pip install --upgrade pip
+          pip install ruff
+          ruff check src
+      - name: Install dependencies for testing
+        run: |
           pip install pytest
           pip install -e .
       - name: Run tests

gui/app.py

@@ -110,7 +110,13 @@
 
 
 def create_run_vuegen(
-    is_dir, config_path, report_type, run_streamlit, output_dir_entry, python_dir_entry
+    is_dir,
+    config_path,
+    report_type,
+    run_streamlit,
+    output_dir_entry,
+    python_dir_entry,
+    max_depth: int,
 ):
     def inner():
         kwargs = {}
@@ -125,6 +131,8 @@ def inner():
         print(f"{run_streamlit.get() = }")
         kwargs["streamlit_autorun"] = run_streamlit.get()
         kwargs["output_dir"] = output_dir_entry.get()
+        if max_depth.get():
+            kwargs["max_depth"] = int(max_depth.get())
         print("kwargs:")
         pprint(kwargs)
 
@@ -146,6 +154,16 @@ def inner():
                 messagebox.showwarning(
                     "warning", "Running locally. Ignoring set Python Path"
                 )
+        if kwargs["max_depth"] < 2:
+            messagebox.showwarning(
+                "warning", "Maximum depth must be at least 2. Setting to 2."
+            )
+            kwargs["max_depth"] = 2
+        elif kwargs["max_depth"] > 9:
+            messagebox.showwarning(
+                "warning", "Maximum depth must be at most 9. Setting to 9."
+            )
+            kwargs["max_depth"] = 9
         try:
             os.chdir(kwargs["output_dir"])  # Change the working directory
             # Define logger suffix based on report type and name
@@ -316,6 +334,40 @@ def select_directory():
 # output directory selection
 ctk_label_outdir = customtkinter.CTkLabel(app, text="Select output directory:")
 ctk_label_outdir.grid(row=row_count, column=0, columnspan=1, padx=10, pady=5)
+CTK_ENTRY_MAX_DEPTH_DEFAULT = 2
+# Maximum Depth input
+ctk_label_max_depth = customtkinter.CTkLabel(
+    app,
+    text=f"Maximum Depth: (default {CTK_ENTRY_MAX_DEPTH_DEFAULT})",
+)
+ctk_label_max_depth.grid(
+    row=row_count, column=1, columnspan=1, padx=10, pady=5, sticky="e"
+)
+
+
+max_depth = tk.IntVar(value=CTK_ENTRY_MAX_DEPTH_DEFAULT)
+
+
+def slider_event(value):
+    max_depth.set(value)
+    ctk_label_max_depth.configure(text=f"Maximum Depth: {int(value)}")
+
+
+ctk_entry_max_depth = customtkinter.CTkSlider(
+    app,
+    from_=2,
+    to=9,
+    variable=max_depth,
+    width=150,
+    command=slider_event,
+    number_of_steps=7,
+)
+ctk_entry_max_depth.set(
+    CTK_ENTRY_MAX_DEPTH_DEFAULT
+)  # Set the initial value of the slider
+ctk_entry_max_depth.grid(
+    row=row_count, column=2, columnspan=1, padx=10, pady=5, sticky="w"
+)
 row_count += 1
 ##########################################################################################
 output_dir_entry = tk.StringVar(value=str(output_dir))
@@ -380,6 +432,7 @@ def select_directory():
     run_streamlit=run_streamlit,
     output_dir_entry=output_dir_entry,
     python_dir_entry=python_dir_entry,
+    max_depth=max_depth,
 )
 run_button = customtkinter.CTkButton(
     app,

src/vuegen/__main__.py

@@ -14,9 +14,6 @@ def main():
     config_path = args.config
     dir_path = args.directory
     report_type = args.report_type
-    output_dir = args.output_directory
-    streamlit_autorun = args.streamlit_autorun
-    quarto_cheks = args.quarto_checks
 
     # Determine the report name for logger suffix
     if config_path:
@@ -47,9 +44,10 @@ def main():
         logger=logger,
         config_path=config_path,
         dir_path=dir_path,
-        output_dir=output_dir,
-        streamlit_autorun=streamlit_autorun,
-        quarto_checks=quarto_cheks,
+        output_dir=args.output_directory,
+        streamlit_autorun=args.streamlit_autorun,
+        quarto_checks=args.quarto_checks,
+        max_depth=args.max_depth,
     )
 
     # Print completion message

src/vuegen/config_manager.py

@@ -13,18 +13,23 @@ class ConfigManager:
     Class for handling metadata of reports from YAML config file and creating report objects.
     """
 
-    def __init__(self, logger: Optional[logging.Logger] = None):
+    def __init__(self, logger: Optional[logging.Logger] = None, max_depth: int = 2):
         """
         Initializes the ConfigManager with a logger.
 
         Parameters
         ----------
         logger : logging.Logger, optional
             A logger instance for the class. If not provided, a default logger will be created.
+        max_depth : int, optional
+            The maximum depth of the directory structure to consider when generating the report
+            config from a directory.
+            The default is 2, which means it will include sections and subsections.
         """
         if logger is None:
             logger, _ = get_logger("report")
         self.logger = logger
+        self.max_depth = max_depth
 
     def _create_title_fromdir(self, file_dirname: str) -> str:
         """
@@ -198,7 +203,7 @@ def _read_description_file(self, folder_path: Path) -> str:
         return ""
 
     def _create_subsect_config_fromdir(
-        self, subsection_dir_path: Path
+        self, subsection_dir_path: Path, level: int = 2
     ) -> Dict[str, Union[str, List[Dict]]]:
         """
         Creates subsection config from a directory.
@@ -217,7 +222,6 @@ def _create_subsect_config_fromdir(
         sorted_files = self._sort_paths_by_numprefix(
             list(subsection_dir_path.iterdir())
         )
-
         components = []
         for file in sorted_files:
             if file.is_file():
@@ -227,9 +231,17 @@ def _create_subsect_config_fromdir(
                     continue
                 # Add component config to list
                 components.append(component_config)
-            # ! if folder go into folder and pull files out?
-            # nesting level already at point 2
-            # loop of components in a folder
+            elif file.is_dir():
+                if level >= self.max_depth:
+                    self.logger.warning(
+                        "Subsection nesting level exceeded: %s. Skipping.", file.name
+                    )
+                    continue
+                # components are added to subsection
+                # ! Alternatively, one could add (sub-)sections to the subsection
+                # ? Then one could remove differentiation between sections and subsections
+                nested_components = self._create_subsect_config_fromdir(file, level + 1)
+                components.extend(nested_components["components"])
 
         subsection_config = {
             "title": self._create_title_fromdir(subsection_dir_path.name),
@@ -316,7 +328,7 @@ def create_yamlconfig_fromdir(
         sorted_sections = self._sort_paths_by_numprefix(list(base_dir_path.iterdir()))
 
         main_section_config = {
-            "title": "",  # self._create_title_fromdir("home_components"),
+            "title": "",
             "description": "Components added to homepage.",
             "components": [],
         }

src/vuegen/quarto_reportview.py

@@ -578,7 +578,7 @@ def _generate_plot_content(self, plot) -> List[str]:
                     )
                     plot_content.append(self._generate_image_content(static_plot_path))
                 else:
-                    plot_content.append(f"""fig_plotly.show()\n```\n""")
+                    plot_content.append("""fig_plotly.show()\n```\n""")
             elif plot.plot_type == r.PlotType.ALTAIR:
                 plot_content.append(self._generate_plot_code(plot))
                 if self.is_report_static:
@@ -587,15 +587,15 @@ def _generate_plot_content(self, plot) -> List[str]:
                     )
                     plot_content.append(self._generate_image_content(static_plot_path))
                 else:
-                    plot_content.append(f"""fig_altair\n```\n""")
+                    plot_content.append("""fig_altair\n```\n""")
             elif plot.plot_type == r.PlotType.INTERACTIVE_NETWORK:
                 networkx_graph = plot.read_network()
                 if isinstance(networkx_graph, tuple):
                     # If network_data is a tuple, separate the network and html file path
                     networkx_graph, html_plot_file = networkx_graph
                 elif isinstance(networkx_graph, nx.Graph) and not self.is_report_static:
                     # Get the pyvis object and create html
-                    pyvis_graph = plot.create_and_save_pyvis_network(
+                    _ = plot.create_and_save_pyvis_network(
                         networkx_graph, html_plot_file
                     )
 
@@ -805,7 +805,7 @@ def _generate_markdown_content(self, markdown) -> List[str]:
                 )
 
             # Code to display md content
-            markdown_content.append(f"""display.Markdown(markdown_content)\n```\n""")
+            markdown_content.append("""display.Markdown(markdown_content)\n```\n""")
 
         except Exception as e:
             self.report.logger.error(
@@ -926,7 +926,7 @@ def _show_dataframe(self, dataframe) -> List[str]:
         else:
             # Append code to display the DataFrame interactively
             dataframe_content.append(
-                f"""show(df, classes="display nowrap compact", lengthMenu=[3, 5, 10])\n```\n"""
+                """show(df, classes="display nowrap compact", lengthMenu=[3, 5, 10])\n```\n"""
             )
 
         return dataframe_content

src/vuegen/report.py

@@ -1,4 +1,3 @@
-import json
 import logging
 import os
 from abc import ABC, abstractmethod

src/vuegen/report_generator.py

@@ -18,6 +18,7 @@ def get_report(
     streamlit_autorun: bool = False,
     quarto_checks: bool = False,
     output_dir: Path = None,
+    max_depth: int = 2,  # section and subsection folders
 ) -> tuple[str, str]:
     """
     Generate and run a report based on the specified engine.
@@ -34,6 +35,16 @@ def get_report(
         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
+        (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.
 
     Raises
     ------
@@ -57,7 +68,7 @@ def get_report(
         logger, _ = get_logger("report", folder=_folder)
 
     # Create the config manager object
-    config_manager = ConfigManager(logger)
+    config_manager = ConfigManager(logger, max_depth=max_depth)
 
     if dir_path:
         # Generate configuration from the provided directory

src/vuegen/streamlit_reportview.py

@@ -296,7 +296,7 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
                 f"All the scripts to build the Streamlit app are available at {output_dir}"
             )
             self.report.logger.info(
-                f"To run the Streamlit app, use the following command:"
+                "To run the Streamlit app, use the following command:"
             )
             self.report.logger.info(
                 f"streamlit run {Path(output_dir) / self.REPORT_MANAG_SCRIPT}"
@@ -381,7 +381,7 @@ def _generate_home_section(
 
             # Create the home page content
             home_content = []
-            home_content.append(f"import streamlit as st")
+            home_content.append("import streamlit as st")
             if subsection_imports:
                 home_content.extend(subsection_imports)
             if self.report.description:
@@ -409,9 +409,9 @@ def _generate_home_section(
 
             # Add the home page to the report manager content
             report_manag_content.append(
-                f"homepage = st.Page('Home/Homepage.py', title='Homepage')"  # ! here Posix Path is hardcoded
+                "homepage = st.Page('Home/Homepage.py', title='Homepage')"  # ! here Posix Path is hardcoded
             )
-            report_manag_content.append(f"sections_pages['Home'] = [homepage]\n")
+            report_manag_content.append("sections_pages['Home'] = [homepage]\n")
             self.report.logger.info("Home page added to the report manager content.")
         except Exception as e:
             self.report.logger.error(f"Error generating the home section: {str(e)}")
@@ -430,7 +430,6 @@ def _generate_sections(self, output_dir: str) -> None:
 
         try:
             for section in self.report.sections[1:]:
-                section_name_var = section.title.replace(" ", "_")
                 self.report.logger.debug(
                     f"Processing section '{section.id}': '{section.title}' - {len(section.subsections)} subsection(s)"
                 )
@@ -465,7 +464,6 @@ def _generate_sections(self, output_dir: str) -> None:
                     )
                     try:
                         # Create subsection file
-                        _subsection_name = make_valid_identifier(subsection.title)
                         assert (
                             subsection.file_path is not None
                         ), "Missing relative file path to subsection"
@@ -604,11 +602,11 @@ def _generate_plot_content(self, plot) -> List[str]:
                     html_plot_file = (
                         Path(self.static_dir) / f"{plot.title.replace(' ', '_')}.html"
                     )
-                    pyvis_graph = plot.create_and_save_pyvis_network(
+                    _ = plot.create_and_save_pyvis_network(
                         networkx_graph, html_plot_file
                     )
 
-                # Add number of nodes and edges to the plor conetnt
+                # Add number of nodes and edges to the plot content
                 num_nodes = networkx_graph.number_of_nodes()
                 num_edges = networkx_graph.number_of_edges()
 

src/vuegen/utils/__init__.py

@@ -246,6 +246,16 @@ def get_parser(prog_name: str, others: dict = {}) -> argparse.Namespace:
         default=False,
         help="Check if Quarto is installed and available for report generation.",
     )
+    parser.add_argument(
+        "-mdep",
+        "--max_depth",
+        type=int,
+        default=2,
+        help=(
+            "Maximum depth for the recursive search of files in the input directory. "
+            "Ignored if a config file is provided."
+        ),
+    )
     # Parse arguments
     return parser