petab.petablint

Command line tool to check for correct format

Functions

main()	Run PEtab validator
parse_cli_args()	Parse command line arguments

Classes

LintFormatter([fmt, datefmt, style, ...])

Custom log formatter

class petab.petablint.LintFormatter(fmt=None, datefmt=None, style='%', validate=True, *, defaults=None)

Bases: Formatter

Custom log formatter

converter()

localtime([seconds]) -> (tm_year,tm_mon,tm_mday,tm_hour,tm_min,

tm_sec,tm_wday,tm_yday,tm_isdst)

Convert seconds since the Epoch to a time tuple expressing local time. When ‘seconds’ is not passed in, convert the current time instead.

format(record)

Format the specified record as text.

The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.

formatException(ei)

Format and return the specified exception information as a string.

This default implementation just uses traceback.print_exception()

formatStack(stack_info)

This method is provided as an extension point for specialized formatting of stack information.

The input data is a string as returned from a call to traceback.print_stack(), but with the last trailing newline removed.

The base implementation just returns the value passed in.

formatTime(record, datefmt=None)

Return the creation time of the specified LogRecord as formatted text.

This method should be called from format() by a formatter which wants to make use of a formatted time. This method can be overridden in formatters to provide for any specific requirement, but the basic behaviour is as follows: if datefmt (a string) is specified, it is used with time.strftime() to format the creation time of the record. Otherwise, an ISO8601-like (or RFC 3339-like) format is used. The resulting string is returned. This function uses a user-configurable function to convert the creation time to a tuple. By default, time.localtime() is used; to change this for a particular formatter instance, set the ‘converter’ attribute to a function with the same signature as time.localtime() or time.gmtime(). To change it for all formatters, for example if you want all logging times to be shown in GMT, set the ‘converter’ attribute in the Formatter class.

usesTime()

Check if the format uses the creation time of the record.

petab.petablint.SchemaValidationError

alias of ValidationError

petab.petablint.get_major_version(problem: str | dict | Path | Problem | Problem) → int

Get the major version number of the given problem.

petab.petablint.lint_problem(problem: Problem | str | Path) → ValidationResultList

Validate a PEtab problem.

Parameters:

problem – PEtab problem to check. Instance of Problem or path to a PEtab problem yaml file.

Returns:

A list of validation results. Empty if no issues were found.

petab.petablint.main()

Run PEtab validator

petab.petablint.parse_cli_args()

Parse command line arguments

petab.petablint.validate(yaml_config: dict | str | Path, path_prefix: None | str | Path = None)

Validate syntax and semantics of PEtab config YAML

Parameters:

• yaml_config – PEtab YAML config as filename or dict.

• path_prefix – Base location for relative paths. Defaults to location of YAML file if a filename was provided for yaml_config or the current working directory.