Multiomics-Analytics-Group · enryH · Jul 18, 2025 · Jul 9, 2025 · Jul 9, 2025 · Jul 9, 2025
diff --git a/.github/workflows/cdci.yml b/.github/workflows/cdci.yml
@@ -118,6 +118,15 @@ jobs:
             echo "Error: One or more protected files have been modified."
             exit 1
           fi
+      - name: streamlit report based on predefined config file
+        run: |
+          cd docs
+          vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg
+          # Check for changes
+          if git diff ../tests/report_examples | grep .; then
+            echo "Error: One or more protected files have been modified."
+            exit 1
+          fi
       - name: check streamlit report files for chatbot API
         run: |
           vuegen -c docs/example_config_files/Chatbot_example_config.yaml -output_dir tests/report_examples/chat_bot
@@ -208,7 +217,7 @@ jobs:
       - 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 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 --collect-all typing-extensions --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
+          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 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 --collect-all typing-extensions --add-data ../docs/example_data/Basic_example_vuegen_demo_notebook:example_data/Basic_example_vuegen_demo_notebook --add-data ../docs/images/logo/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.'

diff --git a/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml b/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml
@@ -1,8 +1,8 @@
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.

diff --git a/...ple_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md b/...ple_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
@@ -1,8 +1,8 @@
 <!-- <div align="center">
-  <img width="300px" src="images/vuegen_logo.svg">
+  <img width="300px" src="images/logo/vuegen_logo.svg">
 </div> -->
 
-![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png)
+![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png)
 
 <p align="center">
    VueGen is a Python library that automates the creation of scientific reports.

diff --git a/docs/split_readme.py b/docs/split_readme.py
@@ -3,7 +3,7 @@
 
 # Mapping section titles to their corresponding filenames
 SECTION_MAPPING = {
-    "![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg)": "home_page.md",
+    "![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/HEAD/docs/images/logo/vuegen_logo.svg)": "home_page.md",
     "About the project": "about.md",
     "Installation": "installation.md",
     "Execution": "execution.md",

diff --git a/docs/vuegen_basic_case_study.ipynb b/docs/vuegen_basic_case_study.ipynb
@@ -273,7 +273,7 @@
    },
    "outputs": [],
    "source": [
-    "vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg\"\n",
+    "vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png\"\n",
     "\n",
     "# Load the YAML file\n",
     "print(\n",
@@ -443,7 +443,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "vuegen_py312",
    "language": "python",
    "name": "python3"
   },
@@ -457,7 +457,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/vuegen_basic_case_study_configfile.md b/docs/vuegen_basic_case_study_configfile.md
@@ -6,8 +6,8 @@ The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/bl
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.

diff --git a/gui/Makefile b/gui/Makefile
@@ -39,7 +39,7 @@ bundle:
 	--collect-all vl_convert \
 	--collect-all typing-extensions \
 	--add-data ../docs/example_data/Basic_example_vuegen_demo_notebook:example_data/Basic_example_vuegen_demo_notebook \
-	--add-data ../docs/images/vuegen_logo.png:. \
+	--add-data ../docs/images/logo/vuegen_logo.png:. \
 	app.py
 
 

diff --git a/src/vuegen/report_generator.py b/src/vuegen/report_generator.py
@@ -108,9 +108,10 @@ def get_report(
             report_type=report_type,
             streamlit_autorun=streamlit_autorun,
             static_dir=static_files_dir,
+            sections_dir=sections_dir,
         )
-        st_report.generate_report(output_dir=sections_dir)
-        st_report.run_report(output_dir=sections_dir)
+        st_report.generate_report()
+        st_report.run_report()
     else:
         # Check if Quarto is installed
         if shutil.which("quarto") is None and not hasattr(

diff --git a/src/vuegen/streamlit_reportview.py b/src/vuegen/streamlit_reportview.py
@@ -50,6 +50,7 @@ def __init__(
         report_type: r.ReportType,
         streamlit_autorun: bool = False,
         static_dir: str = STATIC_FILES_DIR,
+        sections_dir: str = SECTIONS_DIR,
     ):
         """Initialize ReportView with the report and report type.
 
@@ -86,8 +87,9 @@ def __init__(
         }
 
         self.static_dir = static_dir
+        self.section_dir = sections_dir
 
-    def generate_report(self, output_dir: str = SECTIONS_DIR) -> None:
+    def generate_report(self, output_dir: str = None) -> None:
         """
         Generates the Streamlit report and creates Python files for each section
         and its subsections and plots.
@@ -98,6 +100,10 @@ def generate_report(self, output_dir: str = SECTIONS_DIR) -> None:
             The folder where the generated report files will be saved
             (default is SECTIONS_DIR).
         """
+        if output_dir is not None:
+            # ? does this imply changes to the static dir
+            self.section_dir = Path(output_dir).resolve()
+        output_dir = Path(self.section_dir)
         self.report.logger.debug(
             "Generating '%s' report in directory: '%s'", self.report_type, output_dir
         )
@@ -274,6 +280,27 @@ def generate_report(self, output_dir: str = SECTIONS_DIR) -> None:
 
             # Create Python files for each section and its subsections and plots
             self._generate_sections(output_dir=output_dir)
+
+            # Save README.md to the output directory
+            fpath = self.section_dir.parent / "README.md"
+            with open(fpath, "w", encoding="utf-8") as f:
+
+                f.write(
+                    textwrap.dedent(
+                        f"""\
+                    # Streamlit Report
+
+                    This report was generated using the Vuegen library.
+                    Executed from: `{Path.cwd()}`
+
+                    Written to: `{self.section_dir.resolve()}`
+
+                    Folder cannot be moved from above path, but can be executed
+                    from anywhere on the system.
+                    """
+                    )
+                )
+
         except Exception as e:
             self.report.logger.error(
                 "An error occurred while generating the report: %s",
@@ -282,7 +309,7 @@ def generate_report(self, output_dir: str = SECTIONS_DIR) -> None:
             )
             raise
 
-    def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
+    def run_report(self, output_dir: str = None) -> None:
         """
         Runs the generated Streamlit report.
 
@@ -291,6 +318,9 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
         output_dir : str, optional
             The folder where the report was generated (default is SECTIONS_DIR).
         """
+        if output_dir is not None:
+            self.report.logger.warning("The output_dir parameter is deprecated.")
+        output_dir = Path(self.section_dir)
         if self.streamlit_autorun:
             self.report.logger.info(
                 "Running '%s' %s report.", self.report.title, self.report_type
@@ -657,10 +687,17 @@ def _generate_plot_content(self, plot) -> List[str]:
                 # If the file path is a URL, keep the file path as is
                 if is_url(plot.file_path):
                     plot_file_path = plot.file_path
+                    plot_content.append(f"plot_file_path = '{plot_file_path}'")
                 else:  # If it's a local file
-                    plot_file_path = get_relative_file_path(plot.file_path).as_posix()
+                    plot_file_path = get_relative_file_path(
+                        plot.file_path, relative_to=self.section_dir
+                    ).as_posix()
+                    plot_content.append(
+                        f"plot_file_path = (section_dir / '{plot_file_path}')"
+                        ".resolve().as_posix()"
+                    )
                 plot_content.append(
-                    f"\nst.image('{plot_file_path}', "
+                    "st.image(plot_file_path,"
                     f" caption='{plot.caption}', use_column_width=True)\n"
                 )
             elif plot.plot_type == r.PlotType.PLOTLY:
@@ -699,11 +736,14 @@ def _generate_plot_content(self, plot) -> List[str]:
                         )
                     )
                 else:
-                    fpath = Path(html_plot_file).resolve().relative_to(Path.cwd())
+                    fpath = get_relative_file_path(
+                        html_plot_file, relative_to=self.section_dir
+                    ).as_posix()
                     plot_content.append(
                         textwrap.dedent(
                             f"""
-                            with open('{fpath}', 'r') as html_file:
+                            file_path = (section_dir / '{fpath}').resolve().as_posix()
+                            with open(file_path, 'r') as html_file:
                                 html_content = html_file.read()
                             """
                         )
@@ -770,10 +810,13 @@ def _generate_plot_code(self, plot) -> str:
                 plot_json = json.loads(response.text)\n"""
             )
         else:  # If it's a local file
-            plot_rel_path = get_relative_file_path(plot.file_path)
+            plot_rel_path = get_relative_file_path(
+                plot.file_path, relative_to=self.section_dir
+            ).as_posix()
             plot_code = textwrap.dedent(
                 f"""
-                with open('{plot_rel_path.as_posix()}', 'r') as plot_file:
+                file_path = (section_dir / '{plot_rel_path}').resolve().as_posix()
+                with open(file_path, 'r') as plot_file:
                     plot_json = json.load(plot_file)\n"""
             )
 
@@ -864,11 +907,14 @@ def _generate_dataframe_content(self, dataframe) -> List[str]:
                 sheet_names = table_utils.get_sheet_names(df_file_path.as_posix())
                 if len(sheet_names) > 1:
                     # If there are multiple sheets, ask the user to select one
-                    fpath = df_file_path.as_posix()
+                    fpath = get_relative_file_path(
+                        dataframe.file_path, relative_to=self.section_dir
+                    ).as_posix()
                     dataframe_content.append(
                         textwrap.dedent(
                             f"""\
-                        sheet_names = table_utils.get_sheet_names("{fpath}")
+                        file_path = (section_dir / '{fpath}').resolve().as_posix()
+                        sheet_names = table_utils.get_sheet_names(file_path)
                         selected_sheet = st.selectbox("Select a sheet to display",
                                                       options=sheet_names,
                                         )
@@ -877,18 +923,27 @@ def _generate_dataframe_content(self, dataframe) -> List[str]:
                     )
 
             # Load the DataFrame using the correct function
-            read_function = read_function_mapping[file_extension]
+            df_file_path = get_relative_file_path(
+                dataframe.file_path, relative_to=self.section_dir
+            ).as_posix()
+            read_function = read_function_mapping[file_extension].__name__
             if file_extension in [
                 r.DataFrameFormat.XLS.value_with_dot,
                 r.DataFrameFormat.XLSX.value_with_dot,
             ]:
                 dataframe_content.append(
-                    f"df = pd.{read_function.__name__}('{df_file_path.as_posix()}',"
-                    " sheet_name=selected_sheet)\n"
+                    textwrap.dedent(
+                        f"""\
+                    file_path = (section_dir / '{df_file_path}').resolve()
+                    df = pd.{read_function}(file_path, sheet_name=selected_sheet)
+                    """
+                    )
                 )
             else:
                 dataframe_content.append(
-                    f"df = pd.{read_function.__name__}('{df_file_path.as_posix()}')\n"
+                    f"file_path = (section_dir / '{df_file_path}'"
+                    ").resolve().as_posix()\n"
+                    f"df = pd.{read_function}(file_path)\n"
                 )
             # ! Alternative to select box: iterate over sheets in DataFrame
             # Displays a DataFrame using AgGrid with configurable options.
@@ -982,11 +1037,15 @@ def _generate_markdown_content(self, markdown) -> List[str]:
                     )
                 )
             else:  # If it's a local file
-                md_rel_path = get_relative_file_path(markdown.file_path)
+                md_rel_path = get_relative_file_path(
+                    markdown.file_path, relative_to=self.section_dir
+                ).as_posix()
+
                 markdown_content.append(
                     textwrap.dedent(
                         f"""
-                        with open('{md_rel_path.as_posix()}', 'r') as markdown_file:
+                        file_path = (section_dir / '{md_rel_path}').resolve().as_posix()
+                        with open(file_path, 'r') as markdown_file:
                             markdown_content = markdown_file.read()
                         """
                     )
@@ -1052,13 +1111,16 @@ def _generate_html_content(self, html) -> List[str]:
                     )
                 )
             else:  # If it's a local file
-                html_rel_path = get_relative_file_path(html.file_path).as_posix()
+                html_rel_path = get_relative_file_path(
+                    html.file_path, relative_to=self.section_dir
+                ).as_posix()
                 html_content.append(
                     textwrap.dedent(
-                        f"""
-                        with open('{html_rel_path}', 'r', encoding='utf-8') as f:
-                            html_content = f.read()
-                        """
+                        f"""\
+                    file_path = (section_dir / '{html_rel_path}').resolve().as_posix()
+                    with open(file_path, 'r', encoding='utf-8') as f:
+                        html_content = f.read()
+                    """
                     )
                 )
 
@@ -1376,7 +1438,11 @@ def _generate_component_imports(self, component: r.Component) -> List[str]:
         }
 
         component_type = component.component_type
-        component_imports = ["import streamlit as st"]
+        component_imports = [
+            "import streamlit as st",
+            "from pathlib import Path",
+            "section_dir = Path(__file__).resolve().parent.parent",
+        ]
 
         # Add relevant imports based on component type and visualization tool
         if component_type == r.ComponentType.PLOT: