@@ -769,11 +763,9 @@ def _show_dataframe(
dataframe_content = []
if is_report_static:
# Generate path for the DataFrame image
- df_image = os.path.join(
- static_dir, f"{dataframe.title.replace(' ', '_')}.png"
- )
+ df_image = Path(static_dir) / f"{dataframe.title.replace(' ', '_')}.png"
dataframe_content.append(
- f"df.dfi.export('{os.path.abspath(df_image)}', max_rows=10, max_cols=5)\n```\n"
+ f"df.dfi.export('{Path(df_image).resolve()}', max_rows=10, max_cols=5)\n```\n"
)
# Use helper method to add centered image content
dataframe_content.append(self._generate_image_content(df_image))
diff --git a/src/vuegen/report.py b/src/vuegen/report.py
index 8564a1d..be2315d 100644
--- a/src/vuegen/report.py
+++ b/src/vuegen/report.py
@@ -382,7 +382,7 @@ def create_and_save_pyvis_network(self, G: nx.Graph, output_file: str) -> Networ
net.show_buttons(filter_=["physics"])
# Save the network as an HTML file
- net.save_graph(output_file)
+ net.save_graph(str(output_file))
self.logger.info(f"PyVis network created and saved as: {output_file}.")
return net
diff --git a/src/vuegen/streamlit_reportview.py b/src/vuegen/streamlit_reportview.py
index 85d9a62..1a9bb76 100644
--- a/src/vuegen/streamlit_reportview.py
+++ b/src/vuegen/streamlit_reportview.py
@@ -1,5 +1,6 @@
import os
import subprocess
+from pathlib import Path
from typing import List
import pandas as pd
@@ -14,8 +15,8 @@ class StreamlitReportView(r.WebAppReportView):
"""
BASE_DIR = "streamlit_report"
- SECTIONS_DIR = os.path.join(BASE_DIR, "sections")
- STATIC_FILES_DIR = os.path.join(BASE_DIR, "static")
+ SECTIONS_DIR = Path(BASE_DIR) / "sections"
+ STATIC_FILES_DIR = Path(BASE_DIR) / "static"
REPORT_MANAG_SCRIPT = "report_manager.py"
def __init__(
@@ -93,7 +94,7 @@ def generate_report(
# Create a folder for each section
subsection_page_vars = []
section_name_var = section.title.replace(" ", "_")
- section_dir_path = os.path.join(output_dir, section_name_var)
+ section_dir_path = Path(output_dir) / section_name_var
if create_folder(section_dir_path):
self.report.logger.debug(
@@ -106,9 +107,9 @@ def generate_report(
for subsection in section.subsections:
subsection_name_var = subsection.title.replace(" ", "_")
- subsection_file_path = os.path.join(
- section_name_var, subsection_name_var + ".py"
- )
+ subsection_file_path = (
+ Path(section_name_var) / f"{subsection_name_var}.py"
+ ).as_posix() # Make sure it's Posix Paths
# Create a Page object for each subsection and add it to the home page content
report_manag_content.append(
@@ -128,9 +129,7 @@ def generate_report(
)
# Write the navigation and general content to a Python file
- with open(
- os.path.join(output_dir, self.REPORT_MANAG_SCRIPT), "w"
- ) as nav_manager:
+ with open(Path(output_dir) / self.REPORT_MANAG_SCRIPT, "w") as nav_manager:
nav_manager.write("\n".join(report_manag_content))
self.report.logger.info(
f"Created app navigation script: {self.REPORT_MANAG_SCRIPT}"
@@ -162,7 +161,7 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
[
"streamlit",
"run",
- os.path.join(output_dir, self.REPORT_MANAG_SCRIPT),
+ Path(output_dir) / self.REPORT_MANAG_SCRIPT,
],
check=True,
)
@@ -180,12 +179,12 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
f"To run the Streamlit app, use the following command:"
)
self.report.logger.info(
- f"streamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}"
+ f"streamlit run {Path(output_dir) / self.REPORT_MANAG_SCRIPT}"
)
msg = (
f"\nAll the scripts to build the Streamlit app are available at: {output_dir}\n\n"
f"To run the Streamlit app, use the following command:\n\n"
- f"\tstreamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}"
+ f"\tstreamlit run {Path(output_dir) / self.REPORT_MANAG_SCRIPT}"
)
print(msg)
@@ -242,7 +241,7 @@ def _generate_home_section(
try:
# Create folder for the home page
- home_dir_path = os.path.join(output_dir, "Home")
+ home_dir_path = Path(output_dir) / "Home"
if create_folder(home_dir_path):
self.report.logger.debug(f"Created home directory: {home_dir_path}")
else:
@@ -267,14 +266,14 @@ def _generate_home_section(
home_content.append("st.markdown(footer, unsafe_allow_html=True)\n")
# Write the home page content to a Python file
- home_page_path = os.path.join(home_dir_path, "Homepage.py")
+ home_page_path = Path(home_dir_path) / "Homepage.py"
with open(home_page_path, "w") as home_page:
home_page.write("\n".join(home_content))
self.report.logger.info(f"Home page content written to '{home_page_path}'.")
# Add the home page to the report manager content
report_manag_content.append(
- f"homepage = st.Page('Home/Homepage.py', title='Homepage')"
+ f"homepage = st.Page('Home/Homepage.py', title='Homepage')" # ! here Posix Path is hardcoded
)
report_manag_content.append(f"sections_pages['Home'] = [homepage]\n")
self.report.logger.info("Home page added to the report manager content.")
@@ -308,10 +307,10 @@ def _generate_sections(self, output_dir: str) -> None:
)
try:
# Create subsection file
- subsection_file_path = os.path.join(
- output_dir,
- section_name_var,
- subsection.title.replace(" ", "_") + ".py",
+ subsection_file_path = (
+ Path(output_dir)
+ / section_name_var
+ / f"{subsection.title.replace(' ', '_')}.py"
)
# Generate content and imports for the subsection
@@ -460,8 +459,8 @@ def _generate_plot_content(
networkx_graph, html_plot_file = networkx_graph
else:
# Otherwise, create and save a new pyvis network from the netowrkx graph
- html_plot_file = os.path.join(
- static_dir, f"{plot.title.replace(' ', '_')}.html"
+ html_plot_file = (
+ Path(static_dir) / f"{plot.title.replace(' ', '_')}.html"
)
pyvis_graph = plot.create_and_save_pyvis_network(
networkx_graph, html_plot_file
@@ -531,7 +530,7 @@ def _generate_plot_code(self, plot) -> str:
plot_json = json.loads(response.text)\n"""
else: # If it's a local file
plot_code = f"""
-with open('{os.path.join(plot.file_path)}', 'r') as plot_file:
+with open('{Path(plot.file_path)}', 'r') as plot_file:
plot_json = json.load(plot_file)\n"""
# Add specific code for each visualization tool
@@ -584,7 +583,7 @@ def _generate_dataframe_content(self, dataframe) -> List[str]:
try:
# Check if the file extension matches any DataFrameFormat value
- file_extension = os.path.splitext(dataframe.file_path)[1].lower()
+ file_extension = Path(dataframe.file_path).suffix.lower()
if not any(
file_extension == fmt.value_with_dot for fmt in r.DataFrameFormat
):
@@ -674,7 +673,7 @@ def _generate_markdown_content(self, markdown) -> List[str]:
else: # If it's a local file
markdown_content.append(
f"""
-with open('{os.path.join("..", markdown.file_path)}', 'r') as markdown_file:
+with open('{Path("..") / markdown.file_path}', 'r') as markdown_file:
markdown_content = markdown_file.read()\n"""
)
# Code to display md content
@@ -734,7 +733,7 @@ def _generate_html_content(self, html) -> List[str]:
# If it's a local file
html_content.append(
f"""
-with open('{os.path.join("..", html.file_path)}', 'r', encoding='utf-8') as html_file:
+with open('{Path("..") / html.file_path}', 'r', encoding='utf-8') as html_file:
html_content = html_file.read()\n"""
)
diff --git a/src/vuegen/utils.py b/src/vuegen/utils.py
index e407d34..41fa4e7 100644
--- a/src/vuegen/utils.py
+++ b/src/vuegen/utils.py
@@ -24,27 +24,20 @@
## CHECKS
-def check_path(filepath: str) -> bool:
+def check_path(filepath: Path) -> bool:
"""
Checks if the given file or folder path exists.
Parameters
---------
- filepath : str
+ filepath : Path
The file or folder path to check.
Returns
-------
bool
True if the path exists, False otherwise.
-
- Raises
- ------
- AssertionError
- If the filepath is not a valid string.
"""
- # Assert that the filepath is a string
- assert isinstance(filepath, str), f"Filepath must be a string: {filepath}"
# Check if the path exists
return os.path.exists(os.path.abspath(filepath))
@@ -87,13 +80,13 @@ def assert_enum_value(
)
-def is_url(filepath: str) -> bool:
+def is_url(filepath: Path) -> bool:
"""
Check if the provided path is a valid URL.
Parameters
----------
- filepath : str
+ filepath : Path
The filepath to check.
Returns
@@ -102,17 +95,9 @@ def is_url(filepath: str) -> bool:
True if the input path is a valid URL, meaning it contains both a scheme
(e.g., http, https, ftp) and a network location (e.g., example.com).
Returns False if either the scheme or the network location is missing or invalid.
-
- Raises
- ------
- AssertionError
- If the filepath is not a valid string.
"""
- # Assert that the filepath is a string
- assert isinstance(filepath, str), f"Filepath must be a string: {filepath}"
-
# Parse the url and return validation
- parsed_url = urlparse(filepath)
+ parsed_url = urlparse(str(filepath))
return bool(parsed_url.scheme and parsed_url.netloc)
@@ -749,22 +734,20 @@ def print_completion_message(report_type: str):
Prints a formatted completion message after report generation.
"""
border = "ā" * 65 # Creates a separator line
- print(f"\n{border}\nš Pipeline Execution Complete! š\n")
-
if report_type == "streamlit":
print(
"""š Streamlit Report Generated!
š All scripts to build the Streamlit app are available at:
- nf_container_results/streamlit_report/sections
+ streamlit_report/sections
ā¶ļø To run the Streamlit app, use the following command:
- streamlit run nf_container_results/streamlit_report/sections/report_manager.py
+ streamlit run streamlit_report/sections/report_manager.py
āØ You can extend the report by adding new files to the input directory or updating the config file.
š ļø Advanced users can modify the Python scripts directly in:
- nf_container_results/streamlit_report/sections
+ streamlit_report/sections
"""
)
else:
@@ -772,12 +755,12 @@ def print_completion_message(report_type: str):
f"""š {report_type.capitalize()} Report Generated!
š Your {report_type} report is available at:
- nf_container_results/quarto_report
+ quarto_report
āØ You can extend the report by adding new files to the input directory or updating the config file.
š ļø Advanced users can modify the report template directly in:
- nf_container_results/quarto_report/quarto_report.qmd
+ quarto_report/quarto_report.qmd
"""
)
@@ -810,7 +793,7 @@ def generate_footer() -> str:
- | Ā© 2025
+ | Copyright 2025
Multiomics Network Analytics Group (MoNA)
"""
- | Ā© 2025 Multiomics Network Analytics Group (MoNA)
+ | Copyright 2025 Multiomics Network Analytics Group (MoNA)
""",
}
# Create a key based on the report type and format
@@ -413,13 +411,9 @@ def _generate_plot_content(
# Define plot path
if is_report_static:
- static_plot_path = os.path.join(
- static_dir, f"{plot.title.replace(' ', '_')}.png"
- )
+ static_plot_path = Path(static_dir) / f"{plot.title.replace(' ', '_')}.png"
else:
- html_plot_file = os.path.join(
- static_dir, f"{plot.title.replace(' ', '_')}.html"
- )
+ html_plot_file = Path(static_dir) / f"{plot.title.replace(' ', '_')}.html"
# Add content for the different plot types
try:
@@ -431,7 +425,7 @@ def _generate_plot_content(
plot_content.append(self._generate_plot_code(plot))
if is_report_static:
plot_content.append(
- f"""fig_plotly.write_image("{os.path.abspath(static_plot_path)}")\n```\n"""
+ f"""fig_plotly.write_image("{static_plot_path.resolve()}")\n```\n"""
)
plot_content.append(self._generate_image_content(static_plot_path))
else:
@@ -440,7 +434,7 @@ def _generate_plot_content(
plot_content.append(self._generate_plot_code(plot))
if is_report_static:
plot_content.append(
- f"""fig_altair.save("{os.path.abspath(static_plot_path)}")\n```\n"""
+ f"""fig_altair.save("{static_plot_path.resolve()}")\n```\n"""
)
plot_content.append(self._generate_image_content(static_plot_path))
else:
@@ -513,7 +507,7 @@ def _generate_plot_code(self, plot, output_file="") -> str:
plot_json = response.text\n"""
else: # If it's a local file
plot_code += f"""
-with open('{os.path.join("..", plot.file_path)}', 'r') as plot_file:
+with open('{Path("..") / plot.file_path}', 'r') as plot_file:
plot_json = plot_file.read()\n"""
# Add specific code for each visualization tool
if plot.plot_type == r.PlotType.PLOTLY:
@@ -527,7 +521,7 @@ def _generate_plot_code(self, plot, output_file="") -> str:
if is_url(plot.file_path) and plot.file_path.endswith(".html"):
iframe_src = output_file
else:
- iframe_src = os.path.join("..", output_file)
+ iframe_src = Path("..") / output_file
# Embed the HTML file in an iframe
plot_code = f"""
@@ -573,7 +567,7 @@ def _generate_dataframe_content(self, dataframe, is_report_static) -> List[str]:
}
try:
# Check if the file extension matches any DataFrameFormat value
- file_extension = os.path.splitext(dataframe.file_path)[1].lower()
+ file_extension = Path(dataframe.file_path).suffix.lower()
if not any(
file_extension == fmt.value_with_dot for fmt in r.DataFrameFormat
):
@@ -585,7 +579,7 @@ def _generate_dataframe_content(self, dataframe, is_report_static) -> List[str]:
file_path = (
dataframe.file_path
if is_url(dataframe.file_path)
- else os.path.join("..", dataframe.file_path)
+ else Path("..") / dataframe.file_path
)
# Load the DataFrame using the correct function
@@ -648,7 +642,7 @@ def _generate_markdown_content(self, markdown) -> List[str]:
else: # If it's a local file
markdown_content.append(
f"""
-with open('{os.path.join("..", markdown.file_path)}', 'r') as markdown_file:
+with open('{Path("..") / markdown.file_path}', 'r') as markdown_file:
markdown_content = markdown_file.read()\n"""
)
@@ -694,7 +688,7 @@ def _generate_html_content(self, html) -> List[str]:
iframe_src = (
html.file_path
if is_url(html.file_path)
- else os.path.join("..", html.file_path)
+ else Path("..") / html.file_path
)
iframe_code = f"""