Version updates

All notable changes to NRV are summed up in this file.

[1.3.0] - 2025-08-21

Added

  • Added a first version of the nrv.eit sub-package: to allow simulation of electrical impedance tomography of peripheral nerve activity

  • Added Fixing Tutorial 6 — Play with EIT using NRV.

  • Added first version of EIT users’ guide

  • Version of deprecation of tests added as comment

Fixed

  • Import problem solved (fciotti suggestion), by adding nrv.nmod.utils in setup file

  • Adding static doc to the git repository in docs/_nrv (to speed up compilation and avoid time out error from readthedoc). Think to regenerate locally for future updates.

[1.2.2] - 2025-07-09

Added

  • Added utils.geom-subpackage to gather geometry related functions and classes.

  • Added elliptic and polygonal geometry for fascicles.

  • Added nmod.utils-subpackage to gather population creation and placement methods and classes.

  • Added axon_population-class to handle creation of population and interface with fascicle.

  • Added angle untis: rad (default) and degree

  • Added file: backend._extlib_interface to gather interfacing function with external libraries

  • Added MshCreator.add_from_cshape to generate cylinder with custom base.

  • Fascicle are now added from their full geometry instead of only their diameter and center

  • New method used to generated example and tutorial docs using sphinxs_gallery.

  • New directory for NRV/examples and NRV/tutorials.

  • New dependency: shapely.

Fixed

  • Impose deepcopy in load_any to prevent issue when loading multiple times a same dict.

  • Prevent to use more processes than axon number in fascicle.simulate.

  • Various Bug with tests

Removed

  • Removed fascicle.save_fascicle_configuration and fascicle.load_fascicle_configuration Deprecated since fascicle.save and fascicle.load arrived.

Depreciated

  • arguments Fascicle_D, y_c and z_c from FEM_stimulation.reshape_fascicle, now geometry is used instead

  • Attributes fascicle.A, fascicle.y_grav_center and fascicle.z_grav_center, now fascicle.geom.area, fascicle.y and fascicle.z

  • tests 513 to 517: axon pop related test are now with geometry tests between 350 and 400.

[1.2.1] - 2025-06-06

Added

  • Added backend._NRV_Mproc to handle parallel processing in NRV.

  • Added Github Action Build and Push Docker Image on Release to automatically push docker image to Docker Hub on release.

  • Example o06.

  • Added Command “-f” in NRV_test to find specific tests

Fixed

  • Cleaned doc Makefile

  • Fixing Tutorial 5.

  • Cleaning and refreshing of the docs

Removed

  • Remove backend.Mcore_handler.

  • Remove nrv2calm.

[1.2.0] - 2025-05-30

Added

  • improved eval in _FEMResults for serialized calls (added state variables).

  • spec_loader.py mostly for typing.

  • progress bars are now handled with rich.progress.

  • Added automatic translation of Tutorials to the docs in docs/tutorials.

  • automated parallel processing using multiprocessing. All parallelization are handled as a blind process for the end-user, this change has been performed with taking care for the most on backward compatibility. Documentation has been changed in consequence.

Fixed

  • axon.__init__’s kwargs: all parameters can now be set at the instantiation of the axon.

  • Fixed search_threshold_dispatcher for use in notebooks.

  • Remove deprecated function in tutorials and examples.

Removed

  • myelinated_results.find_central_node_index-method replaced by axon_results.find_central_index with, for myelinated_results, the argument node to obtain former results.

  • MCore and explicit use of mpi4py are removed, as parallel processing is handled by Python standard API.

[1.1.2] - 2024-09-12

Added

  • ui, a subpackage for user interface to separate from utils which are ment to stay internal.

  • Help restructuration to have an API description more user-friendly.

  • nrv.CONFIG as a singleton object gathering configuration related data, parameters and methods.

Fixed

  • small fix in filter_freq to avoid filtering artefact.

Removed

  • methods such as load_any_axon, load_any_electrode… (load_any_ + something) are deprecated, though not removed for backward compatibility. Please only use load_any function.

[1.1.1] - 2024-08-05

Added

  • Updated the way axons post-processing is handled during fascicle and nerve simulation:

    • These must now be defined as functions instead of external Python scripts.

    • For backward compatibility, some built-in postprocessing functions can be called using str (see builtin_postproc_functions).

    • The postproc_script attribute has been retained to set the postprocessing as either str or function regardless of the type.

    • The postproc function must at least take an axon_results as argument and return an axon_results, evantual key arguments can be added to the postproc_kwargs attribute.

  • Add block_summary method in axons_results which returns axon block characteristics: blocked, onset response, number of onset APs.

  • Add getAPspeed and get_avg_AP_speed methods in axons_results to measure AP propagation velocity. Should be used instead of speed (deprecated method).

  • Add is_blocked method in axons_results to detect AP propagation block. Should be used instead of block (deprecated method).

  • Add is_recruited method in axons_results to detect AP in an axon.

  • Add optional normalize bool parameter in get_recruited_axons, get_recruited_axons_greater_than, get_recruited_axons_lesser_than methods from fascicle_results.

  • Action potential (AP) analysis methods added in axons_results (split_APs, count_APs, get_start_APs, detect_AP_collisions, etc). See usage in example 18.

  • Several plot functions added in axons_results (raster_plot, colormap_plot and plot_x_t).

  • self.save_path from fascicle and nerve is passed to postprocessing_function/scripts if specified and used to save data from postprocessing_function/scripts.

  • Fascicles and Nerve return nerve_results and fascicle_results by default (self.return_parameters_only and self.save_results are false at init).

  • Updated tutorials and examples with newest features, removed use of deprecated methods/functions.

  • Add NRV_examples.py and NRV_tutorials.py to run all examples/tutorials.

  • Reorganized Example folder.

  • reworked rasterize method of the axon_result class.

  • deprecated functions of CL_postprocessing.

  • Add the axon_block_threshold function in CL_simulations to evaluate block thresholds with arbitrary stimulation settings.

  • deprecated block_threshold_point_source and block_threshold_from_axon``from ``CL_simulations as they are replaced by the more generalized version axon_block_threshold.

  • Add the axon_AP_threshold function in CL_simulations to evaluate activation thresholds with arbitrary stimulation settings (see Example 16).

  • deprecated firing_threshold_point_source and firing_threshold_from_axon``from ``CL_simulations as they are replaced by the more generalized version axon_AP_threshold.

  • Added CL simulation documentation.

  • Added the search_threshold_dispatcher function to parallelize the exploration to parameter effect on threshold + doc & example (see Example 17).

  • Doc gallery for examples. Examples have been relocated to docs/examples.

Fixed

  • issues with mcore optimization.

  • Fix duplicate node count in node_index of myelinated axons.

  • fit_to_size parameter in fill_with_population is not considered if fascicle diameter is None.

  • remove_outliers parameter in fill_with_population is not called if fascicle diameter is None.

[1.1.0] - 2024-05-27

Added

  • Significant improvement in the documentation.

  • first simulations for nerve EIT direct models -> not documented yet, technical tests pass, still under scientific tests and development.

  • classes for results and more.

  • modification of post-processing architecture.

  • progress bar for parallel computing with process specific toolbars.

  • decorator for single-core function definition.

Fixed

  • issues with type hints on documentation generation.

  • code troubles with DOLFINx v0.8.0 now resolved, versions below are not supported anymore.

  • most of the parameters of fascicles (and nerve) can now also be set at the instantiation. (see doc).

[1.0.1] - 2024-01-26

Fixed

  • issue #38:

    • Now FEMSimulation results are saved in a folder ending in .bp which can also be opened in ParaView (-5.12.0 or higher).

    • DOLFINx v0.6.0 and v0.8.0 are now supported.

[1.0.0] - 2024-01-12

[0.9.16] - 2023-12-12

Added

  • Automatic versioning for dev team.

  • this tracking file.

Fixed

  • automated releases,.

  • automatic push on pypi.