✨ make file path relative w.r.t. to report_manager.py

- currently the section_dir is set with the knowleadge of the
  streamlit report structure
- Allows to execute report from everywhere on that operating system
- folder with streamlit report cannot be copied though.

Author: enryH

src/vuegen/streamlit_reportview.py

@@ -666,10 +666,17 @@ 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:
@@ -708,11 +715,14 @@ def _generate_plot_content(self, plot) -> List[str]:
                         )
                     )
                 else:
-                    fpath = get_relative_file_path(html_plot_file).as_posix()
+                    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()
                             """
                         )
@@ -779,10 +789,13 @@ 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"""
             )
 
@@ -873,11 +886,14 @@ 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,
                                         )
@@ -886,18 +902,27 @@ 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.
@@ -991,11 +1016,15 @@ 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()
                         """
                     )
@@ -1061,13 +1090,16 @@ 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()
+                    """
                     )
                 )
 
@@ -1385,7 +1417,11 @@ 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:

tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Dataframes/All_Formats.py

@@ -1,8 +1,10 @@
+from pathlib import Path
 from st_aggrid import AgGrid, GridOptionsBuilder
 from vuegen import table_utils
 import pandas as pd
 import streamlit as st
 df_index = 1
+section_dir = Path(__file__).resolve().parent.parent
 
 
 st.markdown(
@@ -20,7 +22,8 @@
     ),
     unsafe_allow_html=True)
 
-df = pd.read_csv('docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv')
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv').resolve().as_posix()
+df = pd.read_csv(file_path)
 
 
 # Displays a DataFrame using AgGrid with configurable options.
@@ -59,12 +62,14 @@
     unsafe_allow_html=True)
 
 selected_sheet = 0
-sheet_names = table_utils.get_sheet_names("docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls")
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls').resolve().as_posix()
+sheet_names = table_utils.get_sheet_names(file_path)
 selected_sheet = st.selectbox("Select a sheet to display",
                               options=sheet_names,
                 )
 
-df = pd.read_excel('docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls', sheet_name=selected_sheet)
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls').resolve()
+df = pd.read_excel(file_path, sheet_name=selected_sheet)
 
 
 # Displays a DataFrame using AgGrid with configurable options.
@@ -102,7 +107,8 @@
     ),
     unsafe_allow_html=True)
 
-df = pd.read_table('docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt')
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt').resolve().as_posix()
+df = pd.read_table(file_path)
 
 
 # Displays a DataFrame using AgGrid with configurable options.
@@ -140,7 +146,8 @@
     ),
     unsafe_allow_html=True)
 
-df = pd.read_parquet('docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet')
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet').resolve().as_posix()
+df = pd.read_parquet(file_path)
 
 
 # Displays a DataFrame using AgGrid with configurable options.
@@ -179,7 +186,8 @@
     unsafe_allow_html=True)
 
 selected_sheet = 0
-df = pd.read_excel('docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/5_example_xlsx.xlsx', sheet_name=selected_sheet)
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/5_example_xlsx.xlsx').resolve()
+df = pd.read_excel(file_path, sheet_name=selected_sheet)
 
 
 # Displays a DataFrame using AgGrid with configurable options.

tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Html/All_Html.py

@@ -1,6 +1,10 @@
+from pathlib import Path
+
 import requests
 import streamlit as st
 
+section_dir = Path(__file__).resolve().parent.parent
+
 
 st.markdown(
     (
@@ -17,8 +21,8 @@
     ),
     unsafe_allow_html=True)
 
-
-with open('docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html', 'r', encoding='utf-8') as f:
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html').resolve().as_posix()
+with open(file_path, 'r', encoding='utf-8') as f:
     html_content = f.read()
 
 st.components.v1.html(html_content, height=600, scrolling=True)
@@ -32,7 +36,8 @@
     unsafe_allow_html=True)
 
 
-with open('docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html', 'r') as html_file:
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html').resolve().as_posix()
+with open(file_path, 'r') as html_file:
     html_content = html_file.read()
 
 
@@ -58,8 +63,8 @@
     ),
     unsafe_allow_html=True)
 
-
-with open('docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html', 'r', encoding='utf-8') as f:
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html').resolve().as_posix()
+with open(file_path, 'r', encoding='utf-8') as f:
     html_content = f.read()
 
 st.components.v1.html(html_content, height=600, scrolling=True)

tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Markdown/All_Markdown.py

@@ -1,5 +1,7 @@
+from pathlib import Path
 import requests
 import streamlit as st
+section_dir = Path(__file__).resolve().parent.parent
 
 
 st.markdown(
@@ -18,7 +20,8 @@
     unsafe_allow_html=True)
 
 
-with open('docs/example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md', 'r') as markdown_file:
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md').resolve().as_posix()
+with open(file_path, 'r') as markdown_file:
     markdown_content = markdown_file.read()
 
 st.markdown(markdown_content, unsafe_allow_html=True)

tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Interactive_Networks.py

@@ -1,5 +1,7 @@
+from pathlib import Path
 import requests
 import streamlit as st
+section_dir = Path(__file__).resolve().parent.parent
 
 
 st.markdown(
@@ -26,7 +28,8 @@
     unsafe_allow_html=True)
 
 
-with open('tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/static/Man_Example.html', 'r') as html_file:
+file_path = (section_dir / '../static/Man_Example.html').resolve().as_posix()
+with open(file_path, 'r') as html_file:
     html_content = html_file.read()
 
 
@@ -53,7 +56,8 @@
     unsafe_allow_html=True)
 
 
-with open('docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md', 'r') as markdown_file:
+file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md').resolve().as_posix()
+with open(file_path, 'r') as markdown_file:
     markdown_content = markdown_file.read()
 
 st.markdown(markdown_content, unsafe_allow_html=True)

tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Static_Networks.py

@@ -1,4 +1,6 @@
+from pathlib import Path
 import streamlit as st
+section_dir = Path(__file__).resolve().parent.parent
 
 
 st.markdown(
@@ -16,8 +18,8 @@
     ),
     unsafe_allow_html=True)
 
-
-st.image('docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png',  caption='', use_column_width=True)
+plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png').resolve().as_posix()
+st.image(plot_file_path, caption='', use_column_width=True)
 
 footer = '''
 <style type="text/css">