petab.core

PEtab core functions (or functions that don’t fit anywhere else)

Functions

concat_tables(tables[, file_parser])	Concatenate DataFrames provided as DataFrames or filenames, and a parser
create_combine_archive(yaml_file, filename)	Create COMBINE archive (https://co.mbine.org/documents/archive) based on PEtab YAML file.
flatten_timepoint_specific_output_overrides(...)	Flatten timepoint-specific output parameter overrides.
get_flattened_id_mappings(petab_problem)	Get mapping from unflattened to flattened observable IDs.
get_hyperparameter_replacement_id(...)	Get the full ID for a replaced hyperparameter.
get_notnull_columns(df, candidates)	Return list of df-columns in candidates which are not all null/nan.
get_observable_replacement_id(groupvars, ...)	Get the replacement ID for an observable.
get_simulation_df(simulation_file)	Read PEtab simulation table
get_visualization_df(visualization_file)	Read PEtab visualization table
is_empty(val)	Check if the value val, e.g. a table entry, is empty.
to_float_if_float(x)	Return input as float if possible, otherwise return as is
unflatten_simulation_df(simulation_df, ...)	Unflatten simulations from a flattened PEtab problem.
unique_preserve_order(seq)	Return a list of unique elements in Sequence, keeping only the first occurrence of each element
write_simulation_df(df, filename)	Write PEtab simulation table
write_visualization_df(df, filename)	Write PEtab visualization table

petab.core.concat_tables(tables: str | Path | DataFrame | Iterable[DataFrame | str | Path], file_parser: Callable | None = None) → DataFrame

Concatenate DataFrames provided as DataFrames or filenames, and a parser

Parameters:

• tables – Iterable of tables to join, as DataFrame or filename.

• file_parser – Function used to read the table in case filenames are provided, accepting a filename as only argument.

Returns:

The concatenated DataFrames

petab.core.create_combine_archive(yaml_file: str | Path, filename: str | Path, family_name: str | None = None, given_name: str | None = None, email: str | None = None, organization: str | None = None) → None

Create COMBINE archive (https://co.mbine.org/documents/archive) based on PEtab YAML file.

Parameters:

• yaml_file – Path to PEtab YAML file

• filename – Destination file name

• family_name – Family name of archive creator

• given_name – Given name of archive creator

• email – E-mail address of archive creator

• organization – Organization of archive creator

petab.core.flatten_timepoint_specific_output_overrides(petab_problem: petab.problem.Problem) → None

Flatten timepoint-specific output parameter overrides.

If the PEtab problem definition has timepoint-specific observableParameters or noiseParameters for the same observable, replace those by replicating the respective observable.

This is a helper function for some tools which may not support such timepoint-specific mappings. The observable table and measurement table are modified in place.

Parameters:

petab_problem – PEtab problem to work on. Modified in place.

petab.core.get_notnull_columns(df: DataFrame, candidates: Iterable)

Return list of df-columns in candidates which are not all null/nan.

The output can e.g. be used as input for pandas.DataFrame.groupby.

Parameters:

• df – Dataframe

• candidates – Columns of df to consider

petab.core.get_simulation_df(simulation_file: str | Path) → DataFrame

Read PEtab simulation table

Parameters:

simulation_file – URL or filename of PEtab simulation table

Returns:

Simulation DataFrame

petab.core.get_visualization_df(visualization_file: str | Path | DataFrame | None) → DataFrame | None

Read PEtab visualization table

Parameters:

visualization_file – URL or filename of PEtab visualization table to read from, or a DataFrame or None that will be returned as is.

Returns:

Visualization DataFrame

petab.core.is_empty(val) → bool

Check if the value val, e.g. a table entry, is empty.

Parameters:

val – The value to check.

Returns:

Whether the field is to be considered empty.

petab.core.to_float_if_float(x: Any) → Any

Return input as float if possible, otherwise return as is

Parameters:

x – Anything

Returns:

x as float if possible, otherwise x

petab.core.unflatten_simulation_df(simulation_df: DataFrame, petab_problem: petab.problem.Problem) → DataFrame

Unflatten simulations from a flattened PEtab problem.

A flattened PEtab problem is the output of applying flatten_timepoint_specific_output_overrides() to a PEtab problem.

Parameters:

• simulation_df – The simulation dataframe. A dataframe in the same format as a PEtab measurements table, but with the measurement column switched with a simulation column.

• petab_problem – The unflattened PEtab problem.

Returns:

The simulation dataframe for the unflattened PEtab problem.

petab.core.unique_preserve_order(seq: Sequence) → List

Return a list of unique elements in Sequence, keeping only the first occurrence of each element

Parameters:

seq – Sequence to prune

Returns:

List of unique elements in seq

petab.core.write_simulation_df(df: DataFrame, filename: str | Path) → None

Write PEtab simulation table

Parameters:

• df – PEtab simulation table

• filename – Destination file name

petab.core.write_visualization_df(df: DataFrame, filename: str | Path) → None

Write PEtab visualization table

Parameters:

• df – PEtab visualization table

• filename – Destination file name