pyneuroml.io module#

Methods related to IO.

File: pyneuroml/io.py

pyneuroml.io.confirm_file_exists(filename: str) → None#

Check if a file exists, exit if it does not.

Parameters:: filename (str) – the filename to check

pyneuroml.io.confirm_lems_file(filename: str) → None#

Confirm that file exists and is a LEMS file before proceeding with processing.

Parameters:: filename (list of strings) – Names of files to check

pyneuroml.io.confirm_neuroml_file(filename: str) → None#

Confirm that file exists and is a NeuroML file before proceeding with processing.

Parameters:: filename (str) – Names of files to check

pyneuroml.io.read_lems_file(lems_file_name: str, include_includes: bool = False, fail_on_missing_includes: bool = False, debug: bool = False) → Model#

Read LEMS file using PyLEMS. See WARNING below.

WARNING: this is a general function that uses PyLEMS to read any files that are valid LEMS even if they are not valid NeuroML. Therefore, this function is not aware of the standard NeuroML LEMS definitions.

To validate NeuroML LEMS files which need to be aware of the NeuroML standard LEMS definitions, please use the validate_neuroml2_lems_file function instead.

pyneuroml.io.read_neuroml2_file(nml2_file_name: str, include_includes: bool = False, verbose: bool = False, already_included: list | None = None, optimized: bool = False, check_validity_pre_include: bool = False) → NeuroMLDocument#

Read a NeuroML2 file into a nml.NeuroMLDocument

Parameters:

nml2_file_name (str) – file of NeuroML 2 file to read
include_includes (bool) – toggle whether files included in NML file should also be included/read
verbose (bool) – toggle verbosity
already_included (list) – list of files already included
optimized (bool) – toggle whether the HDF5 loader should optimise the document
check_validity_pre_include (bool) – check each file for validity before including

Returns:

nml.NeuroMLDocument object containing the read NeuroML file(s)

pyneuroml.io.write_lems_file(lems_model: Model, lems_file_name: str, validate: bool = False) → None#

Write a lems_model.Model to file using pyLEMS.

Parameters:

lems_model (lems_model.Model) – LEMS model to write to file
lems_file_name (str) – name of file to write to
validate (bool) – toggle whether written file should be validated

pyneuroml.io.write_neuroml2_file(nml2_doc: NeuroMLDocument, nml2_file_name: str, validate: bool = True, verbose_validate: bool = False, hdf5: bool = False) → bool | Tuple[bool, str] | None#

Write a NeuroMLDocument object to a file using libNeuroML.

Parameters:

nml2_doc (NeuroMLDocument) – NeuroMLDocument object to write to file
nml2_file_name (str) – name of file to write to
validate (bool) – toggle whether the written file should be validated
verbose_validate (bool) – toggle whether the validation should be verbose
hdf5 (bool) – write to HDF5 file