topostats.entry_point#

Entry point for all TopoStats programs.

Parses command-line arguments and passes input on to the relevant functions / modules.

Attributes#

Functions#

write_config_with_comments(→ None)

Write a sample configuration with in-line comments.

run_toposum(→ None)

Run Plotting.

run_topostats(→ None)

Find and process all files.

create_parser(→ argparse.ArgumentParser)

Create a parser for reading options.

entry_point(→ None)

Entry point for all TopoStats programs.

create_legacy_run_topostats_parser(...)

Create a parser reading options for the 'run_topostats' processing entry point.

create_legacy_toposum_parser(→ argparse.ArgumentParser)

Create a parser reading options for the legacy 'toposum' summarize entry point.

legacy_run_topostats_entry_point(→ None)

Legacy entry point for the run_topostats processing function.

legacy_toposum_entry_point(→ None)

Legacy entry point for the toposum summarizing function.

Module Contents#

topostats.entry_point.__version__#
topostats.entry_point.write_config_with_comments(args=None) None[source]#

Write a sample configuration with in-line comments.

This function is not designed to be used interactively but can be, just call it without any arguments and it will write a configuration to ‘./config.yaml’.

Parameters:

args (Namespace) – A Namespace object parsed from argparse with values for ‘filename’.

topostats.entry_point.run_toposum(args=None) None[source]#

Run Plotting.

Parameters:

args (None) – Arguments to pass and update configuration.

topostats.entry_point.run_topostats(args: None = None) None[source]#

Find and process all files.

Parameters:

args (None) – Arguments.

topostats.entry_point.create_parser() argparse.ArgumentParser[source]#

Create a parser for reading options.

Creates a parser, with multiple sub-parsers for reading options to run ‘topostats’.

Returns:

Argument parser.

Return type:

arg.ArgumentParser

topostats.entry_point.entry_point(manually_provided_args=None, testing=False) None[source]#

Entry point for all TopoStats programs.

Main entry point for running ‘topostats’ which allows the different processing steps (‘process’, ‘filter’, ‘create_config’ etc.) to be run.

Parameters:
  • manually_provided_args (None) – Manually provided arguments.

  • testing (bool) – Whether testing is being carried out.

Returns:

Does not return anything.

Return type:

None

topostats.entry_point.create_legacy_run_topostats_parser() argparse.ArgumentParser[source]#

Create a parser reading options for the ‘run_topostats’ processing entry point.

Returns:

Arguments to be passed to ‘run_topostats’.

Return type:

arg.ArgumentParser

topostats.entry_point.create_legacy_toposum_parser() argparse.ArgumentParser[source]#

Create a parser reading options for the legacy ‘toposum’ summarize entry point.

Returns:

Arguments to be passed to ‘toposum’.

Return type:

arg.ArgumentParser

topostats.entry_point.legacy_run_topostats_entry_point(args=None, testing=False) None[source]#

Legacy entry point for the run_topostats processing function.

Parameters:
  • args (None) – Arguments.

  • testing (bool) – Whether functions is being tested.

Returns:

Does not return anything.

Return type:

None

topostats.entry_point.legacy_toposum_entry_point(args=None, testing=False) None[source]#

Legacy entry point for the toposum summarizing function.

Parameters:
  • args (None) – Arguments.

  • testing (bool) – Whether functions is being tested.

Returns:

Does not return anything.

Return type:

None