Streamlit and quarto relative paths, and fix plots resizing

.github/workflows/docs.yml

@@ -53,9 +53,9 @@ jobs:
       #     path: docs/_build/
 
       # --- Streamlit example deployment ---
-      - name: Fix Absolute Paths in Streamlit Scripts
-        run: |
-          find docs/streamlit_report/sections -type f -name "*.py" -exec sed -i 's|/home/runner/work/vuegen/vuegen/docs/||g' {} +
+      #- name: Fix Absolute Paths in Streamlit Scripts
+      #  run: |
+      #    find docs/streamlit_report/sections -type f -name "*.py" -exec sed -i 's|/home/runner/work/vuegen/vuegen/docs/||g' {} +
       - name: Publish Streamlit report to streamlit-example branch
         if: startsWith(github.ref, 'refs/tags')
         uses: peaceiris/actions-gh-pages@v4

.gitignore

@@ -128,6 +128,5 @@ docs/images/UML_diagrams/
 docs/images/Graphical_abstract/
 docs/images/Nfcore_module_figure
 docs/presentations/
-docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/
-docs/vuegen_case_study_earth_microbiome_test.ipynb
-test.py
+basic_example_vuegen_demo_notebook_config.yaml
+earth_microbiome_vuegen_demo_notebook_config.yaml

docs/index.md

@@ -35,7 +35,7 @@ vuegen_Chatbot_configfile
 
 ```{toctree}
 :maxdepth: 2
-:caption: Modules
+:caption: API Reference
 :hidden:
 
 reference/vuegen

docs/vuegen_basic_case_study.ipynb

@@ -139,10 +139,9 @@
    "outputs": [],
    "source": [
     "# Imports\n",
-    "import os\n",
     "import yaml\n",
     "from vuegen import report_generator\n",
-    "from vuegen.utils import get_logger, load_yaml_config\n",
+    "from vuegen.utils import load_yaml_config\n",
     "\n",
     "if IN_COLAB:\n",
     "    import urllib"
@@ -444,7 +443,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "vuegen_py312",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -458,9 +457,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

src/vuegen/quarto_reportview.py

@@ -8,7 +8,7 @@
 import pandas as pd
 
 from . import report as r
-from .utils import create_folder, is_url, sort_imports
+from .utils import create_folder, get_relative_file_path, is_url, sort_imports
 
 
 class QuartoReportView(r.ReportView):
@@ -365,6 +365,7 @@ def _create_yaml_header(self) -> str:
             r.ReportType.PDF: """
   pdf:
     toc: false
+    fig-align: center
     margin:
       - bottom=40mm
     include-in-header: 
@@ -568,13 +569,13 @@ def _generate_plot_content(self, plot) -> List[str]:
         try:
             if plot.plot_type == r.PlotType.STATIC:
                 plot_content.append(
-                    self._generate_image_content(plot.file_path, width=950)
+                    self._generate_image_content(plot.file_path, width="90%")
                 )
             elif plot.plot_type == r.PlotType.PLOTLY:
                 plot_content.append(self._generate_plot_code(plot))
                 if self.is_report_static:
                     plot_content.append(
-                        f"""fig_plotly.write_image("{static_plot_path.resolve().as_posix()}")\n```\n"""
+                        f"""fig_plotly.write_image("{static_plot_path.relative_to("quarto_report").as_posix()}")\n```\n"""
                     )
                     plot_content.append(self._generate_image_content(static_plot_path))
                 else:
@@ -583,7 +584,7 @@ def _generate_plot_content(self, plot) -> List[str]:
                 plot_content.append(self._generate_plot_code(plot))
                 if self.is_report_static:
                     plot_content.append(
-                        f"""fig_altair.save("{static_plot_path.resolve().as_posix()}")\n```\n"""
+                        f"""fig_altair.save("{static_plot_path.relative_to("quarto_report").as_posix()}")\n```\n"""
                     )
                     plot_content.append(self._generate_image_content(static_plot_path))
                 else:
@@ -655,8 +656,9 @@ def _generate_plot_code(self, plot, output_file="") -> str:
 response.raise_for_status()
 plot_json = response.text\n"""
         else:  # If it's a local file
+            plot_rel_path = get_relative_file_path(plot.file_path, base_path="..")
             plot_code += f"""
-with open('{(Path("..") / plot.file_path).as_posix()}', 'r') as plot_file:
+with open('{plot_rel_path.as_posix()}', 'r') as plot_file:
     plot_json = json.load(plot_file)\n"""
         # Add specific code for each visualization tool
         if plot.plot_type == r.PlotType.PLOTLY:
@@ -669,13 +671,13 @@ def _generate_plot_code(self, plot, output_file="") -> str:
 plot_json_str = json.dumps(plot_json)\n
 # Create the plotly plot
 fig_plotly = pio.from_json(plot_json_str)
-fig_plotly.update_layout(width=950, height=500)\n"""
+fig_plotly.update_layout(autosize=False, width=950, height=400, margin=dict(b=50, t=50, l=50, r=50))\n"""
         elif plot.plot_type == r.PlotType.ALTAIR:
             plot_code += """
 # Convert JSON to string
 plot_json_str = json.dumps(plot_json)\n
 # Create the plotly plot
-fig_altair = alt.Chart.from_json(plot_json_str).properties(width=900, height=400)\n"""
+fig_altair = alt.Chart.from_json(plot_json_str).properties(width=900, height=370)\n"""
         elif plot.plot_type == r.PlotType.INTERACTIVE_NETWORK:
             # Generate the HTML embedding for interactive networks
             if is_url(plot.file_path) and plot.file_path.endswith(".html"):
@@ -734,16 +736,17 @@ def _generate_dataframe_content(self, dataframe) -> List[str]:
                 )
 
             # Build the file path (URL or local file)
-            file_path = (
-                dataframe.file_path
-                if is_url(dataframe.file_path)
-                else Path("..") / dataframe.file_path
-            )
+            if is_url(dataframe.file_path):
+                df_file_path = dataframe.file_path
+            else:
+                df_file_path = get_relative_file_path(
+                    dataframe.file_path, base_path=".."
+                )
 
             # Load the DataFrame using the correct function
             read_function = read_function_mapping[file_extension]
             dataframe_content.append(
-                f"""df = pd.{read_function.__name__}('{file_path.as_posix()}')\n"""
+                f"""df = pd.{read_function.__name__}('{df_file_path.as_posix()}')\n"""
             )
 
             # Display the dataframe
@@ -798,9 +801,10 @@ def _generate_markdown_content(self, markdown) -> List[str]:
 markdown_content = response.text\n"""
                 )
             else:  # If it's a local file
+                md_rel_path = get_relative_file_path(markdown.file_path, base_path="..")
                 markdown_content.append(
                     f"""
-with open('{(Path("..") / markdown.file_path).as_posix()}', 'r') as markdown_file:
+with open('{md_rel_path.as_posix()}', 'r') as markdown_file:
     markdown_content = markdown_file.read()\n"""
                 )
 
@@ -822,6 +826,39 @@ def _generate_markdown_content(self, markdown) -> List[str]:
         )
         return markdown_content
 
+    def _show_dataframe(self, dataframe) -> List[str]:
+        """
+        Appends either a static image or an interactive representation of a DataFrame to the content list.
+
+        Parameters
+        ----------
+        dataframe : DataFrame
+            The DataFrame object containing the data to display.
+
+        Returns
+        -------
+        list : List[str]
+            The list of content lines for the DataFrame.
+        """
+        dataframe_content = []
+        if self.is_report_static:
+            # Generate path for the DataFrame image
+            df_image = (
+                Path(self.static_dir) / f"{dataframe.title.replace(' ', '_')}.png"
+            )
+            dataframe_content.append(
+                f"df.dfi.export('{Path(df_image).relative_to('quarto_report').as_posix()}', max_rows=10, max_cols=5, table_conversion='matplotlib')\n```\n"
+            )
+            # Use helper method to add centered image content
+            dataframe_content.append(self._generate_image_content(df_image))
+        else:
+            # Append code to display the DataFrame interactively
+            dataframe_content.append(
+                """show(df, classes="display nowrap compact", lengthMenu=[3, 5, 10])\n```\n"""
+            )
+
+        return dataframe_content
+
     def _generate_html_content(self, html) -> List[str]:
         """
         Adds an HTML component to the report.
@@ -843,14 +880,13 @@ def _generate_html_content(self, html) -> List[str]:
 
         try:
             # Embed the HTML in an iframe
-            iframe_src = (
-                html.file_path
-                if is_url(html.file_path)
-                else Path("..") / html.file_path
-            )
+            if is_url(html.file_path):
+                html_file_path = html.file_path
+            else:
+                html_file_path = get_relative_file_path(html.file_path, base_path="..")
             iframe_code = f"""
 <div style="text-align: center;">
-<iframe src="{iframe_src}" alt="{html.title}" width="800px" height="630px"></iframe>
+<iframe src="{html_file_path.as_posix()}" alt="{html.title}" width="950px" height="530px"></iframe>
 </div>\n"""
             html_content.append(iframe_code)
 
@@ -866,7 +902,7 @@ def _generate_html_content(self, html) -> List[str]:
         return html_content
 
     def _generate_image_content(
-        self, image_path: str, alt_text: str = "", width: int = 650, height: int = 400
+        self, image_path: str, alt_text: str = "", width: str = "90%"
     ) -> str:
         """
         Adds an image to the content list in an HTML format with a specified width and height.
@@ -889,47 +925,10 @@ def _generate_image_content(
         """
         if is_url(image_path):
             src = image_path
-            return (
-                f"""![]({src}){{fig-alt={alt_text} width={width} height={height}}}\n"""
-            )
         else:
-            src = Path(image_path).resolve()
-            return (
-                f"""![](/{src}){{fig-alt={alt_text} width={width} height={height}}}\n"""
-            )
-
-    def _show_dataframe(self, dataframe) -> List[str]:
-        """
-        Appends either a static image or an interactive representation of a DataFrame to the content list.
-
-        Parameters
-        ----------
-        dataframe : DataFrame
-            The DataFrame object containing the data to display.
+            src = get_relative_file_path(image_path, base_path="..").as_posix()
 
-        Returns
-        -------
-        list : List[str]
-            The list of content lines for the DataFrame.
-        """
-        dataframe_content = []
-        if self.is_report_static:
-            # Generate path for the DataFrame image
-            df_image = (
-                Path(self.static_dir) / f"{dataframe.title.replace(' ', '_')}.png"
-            )
-            dataframe_content.append(
-                f"df.dfi.export('{Path(df_image).resolve().as_posix()}', max_rows=10, max_cols=5, table_conversion='matplotlib')\n```\n"
-            )
-            # Use helper method to add centered image content
-            dataframe_content.append(self._generate_image_content(df_image))
-        else:
-            # Append code to display the DataFrame interactively
-            dataframe_content.append(
-                """show(df, classes="display nowrap compact", lengthMenu=[3, 5, 10])\n```\n"""
-            )
-
-        return dataframe_content
+        return f"""![]({src}){{fig-alt={alt_text} width={width}}}\n"""
 
     def _generate_component_imports(self, component: r.Component) -> List[str]:
         """

src/vuegen/streamlit_reportview.py

@@ -9,7 +9,7 @@
 from streamlit.web import cli as stcli
 
 from . import report as r
-from .utils import create_folder, generate_footer, is_url
+from .utils import create_folder, generate_footer, get_relative_file_path, is_url
 from .utils.variables import make_valid_identifier
 
 
@@ -585,8 +585,9 @@ def _generate_plot_content(self, plot) -> List[str]:
         # Add content for the different plot types
         try:
             if plot.plot_type == r.PlotType.STATIC:
+                plot_rel_path = get_relative_file_path(plot.file_path)
                 plot_content.append(
-                    f"\nst.image('{plot.file_path}', caption='{plot.caption}', use_column_width=True)\n"
+                    f"\nst.image('{plot_rel_path.as_posix()}', caption='{plot.caption}', use_column_width=True)\n"
                 )
             elif plot.plot_type == r.PlotType.PLOTLY:
                 plot_content.append(self._generate_plot_code(plot))
@@ -601,7 +602,7 @@ def _generate_plot_content(self, plot) -> List[str]:
                     # Otherwise, create and save a new pyvis network from the netowrkx graph
                     html_plot_file = (
                         Path(self.static_dir) / f"{plot.title.replace(' ', '_')}.html"
-                    )
+                    ).resolve()
                     _ = plot.create_and_save_pyvis_network(
                         networkx_graph, html_plot_file
                     )
@@ -616,13 +617,13 @@ def _generate_plot_content(self, plot) -> List[str]:
                         f"""
 response = requests.get('{html_plot_file}')
 response.raise_for_status()
-html_data = response.text\n"""
+html_content = response.text\n"""
                     )
                 else:
                     plot_content.append(
                         f"""
-with open('{html_plot_file}', 'r') as f:
-    html_data = f.read()\n"""
+with open('{Path(html_plot_file).relative_to(Path.cwd())}', 'r') as html_file:
+    html_content = html_file.read()\n"""
                     )
 
                 # Append the code for additional information (nodes and edges count)
@@ -669,8 +670,9 @@ def _generate_plot_code(self, plot) -> str:
 response.raise_for_status()
 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_code = f"""
-with open('{Path(plot.file_path).as_posix()}', 'r') as plot_file:
+with open('{plot_rel_path.as_posix()}', 'r') as plot_file:
     plot_json = json.load(plot_file)\n"""
 
         # Add specific code for each visualization tool
@@ -693,7 +695,7 @@ def _generate_plot_code(self, plot) -> str:
 control_layout = st.checkbox('Add panel to control layout', value=True)
 net_html_height = 1200 if control_layout else 630
 # Load HTML into HTML component for display on Streamlit
-st.components.v1.html(html_data, height=net_html_height)\n"""
+st.components.v1.html(html_content, height=net_html_height)\n"""
         return plot_code
 
     def _generate_dataframe_content(self, dataframe) -> List[str]:
@@ -739,8 +741,14 @@ def _generate_dataframe_content(self, dataframe) -> List[str]:
 
             # Load the DataFrame using the correct function
             read_function = read_function_mapping[file_extension]
+
+            # Build the file path (URL or local file)
+            if is_url(dataframe.file_path):
+                df_file_path = dataframe.file_path
+            else:
+                df_file_path = get_relative_file_path(dataframe.file_path)
             dataframe_content.append(
-                f"""df = pd.{read_function.__name__}('{dataframe.file_path}')\n"""
+                f"""df = pd.{read_function.__name__}('{df_file_path.as_posix()}')\n"""
             )
 
             # Displays a DataFrame using AgGrid with configurable options.
@@ -817,9 +825,10 @@ def _generate_markdown_content(self, markdown) -> List[str]:
 markdown_content = response.text\n"""
                 )
             else:  # If it's a local file
+                md_rel_path = get_relative_file_path(markdown.file_path)
                 markdown_content.append(
                     f"""
-with open('{(Path("..") / markdown.file_path).as_posix()}', 'r') as markdown_file:
+with open('{md_rel_path.as_posix()}', 'r') as markdown_file:
     markdown_content = markdown_file.read()\n"""
                 )
             # Code to display md content
@@ -875,11 +884,11 @@ def _generate_html_content(self, html) -> List[str]:
 response.raise_for_status()
 html_content = response.text\n"""
                 )
-            else:
-                # If it's a local file
+            else:  # If it's a local file
+                html_rel_path = get_relative_file_path(html.file_path)
                 html_content.append(
                     f"""
-with open('{(Path("..") / html.file_path).as_posix()}', 'r', encoding='utf-8') as html_file:
+with open('{html_rel_path.as_posix()}', 'r', encoding='utf-8') as html_file:
     html_content = html_file.read()\n"""
                 )