vuegen package

VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications. Users simply provide a directory with output files and VueGen compiles them into a structured report.

Subpackages

• vuegen.utils package
  • assert_enum_value()
  • check_path()
  • create_folder()
  • cyjs_to_networkx()
  • fetch_file_stream()
  • generate_footer()
  • generate_log_filename()
  • get_basename()
  • get_completion_message()
  • get_logger()
  • get_parser()
  • get_relative_file_path()
  • get_time()
  • init_log()
  • is_pyvis_html()
  • is_url()
  • load_yaml_config()
  • pyvishtml_to_networkx()
  • sort_imports()
  • write_yaml_config()
  • Submodules
    • vuegen.utils.variables module
      • make_valid_identifier()

Submodules

• vuegen.config_manager module
  • ConfigManager
    • ConfigManager.create_yamlconfig_fromdir()
    • ConfigManager.initialize_report()
• vuegen.constants module
• vuegen.quarto_reportview module
  • QuartoReportView
    • QuartoReportView.BASE_DIR
    • QuartoReportView.STATIC_FILES_DIR
    • QuartoReportView.generate_report()
    • QuartoReportView.run_report()
• vuegen.report module
  • APICall
    • APICall.api_url
    • APICall.method
    • APICall.headers
    • APICall.params
    • APICall.request_body
    • APICall.make_api_request()
  • CSVNetworkFormat
    • CSVNetworkFormat.ADJLIST
    • CSVNetworkFormat.EDGELIST
  • ChatBot
    • ChatBot.api_call
    • ChatBot.model
    • ChatBot.headers
    • ChatBot.params
  • Component
    • Component._id_counter
    • Component.id
    • Component.title
    • Component.component_type
    • Component.logger
    • Component.file_path
    • Component.caption
    • Component.caption
    • Component.component_type
    • Component.file_path
    • Component.id
    • Component.logger
    • Component.title
  • ComponentType
    • ComponentType.APICALL
    • ComponentType.CHATBOT
    • ComponentType.DATAFRAME
    • ComponentType.HTML
    • ComponentType.MARKDOWN
    • ComponentType.PLOT
  • DataFrame
    • DataFrame.file_format
    • DataFrame.delimiter
  • DataFrameFormat
    • DataFrameFormat.CSV
    • DataFrameFormat.PARQUET
    • DataFrameFormat.TXT
    • DataFrameFormat.XLS
    • DataFrameFormat.XLSX
    • DataFrameFormat.value_with_dot
  • Html
  • ImageFormat
    • ImageFormat.GIF
    • ImageFormat.JPEG
    • ImageFormat.JPG
    • ImageFormat.PNG
    • ImageFormat.SVG
    • ImageFormat.WEBP
    • ImageFormat.value_with_dot
  • Markdown
  • NetworkFormat
    • NetworkFormat.CSV
    • NetworkFormat.CYJS
    • NetworkFormat.GEXF
    • NetworkFormat.GML
    • NetworkFormat.GRAPHML
    • NetworkFormat.HTML
    • NetworkFormat.JPEG
    • NetworkFormat.JPG
    • NetworkFormat.PNG
    • NetworkFormat.SVG
    • NetworkFormat.TXT
    • NetworkFormat.value_with_dot
  • Plot
    • Plot.plot_type
    • Plot.csv_network_format
    • Plot.create_and_save_pyvis_network()
    • Plot.read_network()
    • Plot.save_network_image()
  • PlotType
    • PlotType.ALTAIR
    • PlotType.INTERACTIVE_NETWORK
    • PlotType.PLOTLY
    • PlotType.STATIC
  • Report
    • Report.title
    • Report.logger
    • Report.sections
    • Report.description
    • Report.graphical_abstract
    • Report.logo
    • Report.description
    • Report.graphical_abstract
    • Report.logger
    • Report.logo
    • Report.sections
    • Report.title
  • ReportType
    • ReportType.DOCX
    • ReportType.HTML
    • ReportType.JUPYTER
    • ReportType.ODT
    • ReportType.PDF
    • ReportType.PPTX
    • ReportType.REVEALJS
    • ReportType.STREAMLIT
  • ReportView
    • ReportView.id
    • ReportView.name
    • ReportView.report
    • ReportView.report_type
    • ReportView.generate_report()
    • ReportView.run_report()
  • Section
    • Section._id_counter
    • Section.id
    • Section.title
    • Section.subsections
    • Section.components
    • Section.description
    • Section.file_path
    • Section.components
    • Section.description
    • Section.file_path
    • Section.id
    • Section.subsections
    • Section.title
  • Subsection
    • Subsection._id_counter
    • Subsection.id
    • Subsection.title
    • Subsection.components
    • Subsection.description
    • Subsection.file_path
    • Subsection.components
    • Subsection.description
    • Subsection.file_path
    • Subsection.id
    • Subsection.title
  • WebAppReportView
• vuegen.report_generator module
  • get_report()
• vuegen.streamlit_reportview module
  • StreamlitReportView
    • StreamlitReportView.BASE_DIR
    • StreamlitReportView.REPORT_MANAG_SCRIPT
    • StreamlitReportView.SECTIONS_DIR
    • StreamlitReportView.STATIC_FILES_DIR
    • StreamlitReportView.generate_report()
    • StreamlitReportView.run_report()
  • write_python_file()
• vuegen.table_utils module
  • get_sheet_names()