HNN-core - v0.4.2

0.4.2 Patch Notes

Version 0.4.2 is a patch release that fixes two important bugs: one affecting LFP and CSD output (https://github.com/jonescompneurolab/hnn-core/pull/1062) and another preventing users from upgrading to the recently released NEURON 8.2.7 (https://github.com/jonescompneurolab/hnn-core/pull/1058), which also enables use of HNN-Core with Python 3.13. This also includes other, smaller bug fixes and changes.

If you have been using HNN-Core to simulate LFP or CSD output, we strongly recommend you update to this version.

We have also recently overhauled our HNN Frontpage and our new HNN Textbook website, so check them out!

New Features

• We now provide conda packages that offer significantly easier installation of HNN-Core, including an option with all features included (including MPI!). See our Installation Guide for how to install them.

• We now support Python 3.13, in addition to previously supported Python versions.

Upcoming Deprecations

• In the next minor release (0.5.x), we will be dropping Python 3.8 support for two reasons:
  1. It has reached "end-of-life" and is no longer supported, including NOT receiving any future security upgrades (see https://devguide.python.org/versions/).
  2. NEURON 8.2.7 has dropped support for Python 3.8.

If you expect that you will still require hnn_core using Python 3.8, please reach out to us on our Github Discussions page. We will likely be able to continue supporting your use-case.

Bug Fixes

• Major bugfix: Cell positions were previously starting at origin (incorrect) instead of origin + their pos_dict locations (correct). This has been fixed. This change should not affect results from dipole or single-cell output, but will affect results from LFP or CSD output. Identified and fixed by Katharina Duecker in https://github.com/jonescompneurolab/hnn-core/pull/1062.

• hnn_core/viz.py::plot_spikes_raster() now correctly titles the plot according to if dipoles are overlaid or not, by Dylan Daniels in https://github.com/jonescompneurolab/hnn-core/pull/1074.

• Update hnn_core/mod/vecevent.mod to a newer version from NEURON's source code, enabling use of NEURON's latest version (8.2.7) and Python's latest stable version (3.13). The prior version of this file would not correctly compile on Windows using NEURON 8.2.7. By Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1058.

• Fix test breakage caused by upstream dependency change in scipy.optimize, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1076.

Development Workflow Changes

• hnn_core code now follows the default ruff code formatting style, and all new contributions are expected to follow this style as well. Fortunately, there is a single command that developers need to run which automatically format their code appropriately (make format-overwrite), see the new Quality Control section of our Contributing Guide for details.

• Updates to Linkcheck Workflow frequency so it only runs on every merge to master and on the 1st and 15th of every month, by Maira Usman in https://github.com/jonescompneurolab/hnn-core/pull/1043 (new contributor!!!).

• Concurrency in Github Actions is now utilized: if you push a new commit to your existing PR branch while prior workflows are still running, the prior workflows are canceled (https://github.com/jonescompneurolab/hnn-core/pull/1015).

• You can now build and deploy new package distributions of hnn_core directly from Github to Pypi and TestPypi by pushed any new tag that begins with v (https://github.com/jonescompneurolab/hnn-core/pull/1073 and https://github.com/jonescompneurolab/hnn-core/pull/1077). Documentation for how to make a release has not been updated yet, but will be soon.

• When a developer needs to update parameters of the "default model" used in HNN, there is now both documentation and commands to help guide them. See the new "Making changes to the default network" section of our Contributing Guide (https://github.com/jonescompneurolab/hnn-core/pull/1068).

API Changes

• hnn_core.CellResponse now requires a cell_type_names argument, whereas before the argument was optional (https://github.com/jonescompneurolab/hnn-core/pull/970).

• hnn_core/optimization/optimized_evoked.py::optimized_evoked now enforces a minimum number of iterations, twelve (12). This is a temporary, possibly permanent, fix introduced in https://github.com/jonescompneurolab/hnn-core/pull/1076.

People who contributed to this release (in alphabetical order of family name):

• Dylan Daniels
• Katharina Duecker
• Mohamed W. ElSayed
• Austin E. Soplata
• Maira Usman

Changelog

• Fix tiny typo in pip MPI install documentation, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1072. (he's also responsible for the original typo...)

• Update the Linux path of our Unix unit tests to use conda for its MPI installation, NOT system packages. This makes our unit tests consistent with our recently-changed recommended installation pathways for pip MPI on Linux. By Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1071.

• Tiny docstring update to jones_2009_model that the "model" is from the Jones 2009 paper, but the "implementation" is from Neymotin 2020. Citations for both papers are included in the docstring. By Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1056.

• Added support for "regeneration" of both required hierarchical JSON network files alongside documentation, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1068.

• Enable automated package release building and deployment via Github Actions to Pypi and TestPypi, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1073 and hotfix in https://github.com/jonescompneurolab/hnn-core/pull/1077.

• Version downgraded from 0.5.0dev0 to 0.4.2.devX in preparation for this release (no PR).

• Fix test breakage caused by upstream dependency change in scipy.optimize, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1076.

• hnn_core/viz.py::plot_spikes_raster() now correctly titles the plot according to if dipoles are overlaid or not, by Dylan Daniels in https://github.com/jonescompneurolab/hnn-core/pull/1074.

• Update hnn_core/mod/vecevent.mod to a newer version from NEURON's source code, enabling use of NEURON's latest version (8.2.7) and Python's latest stable version (3.13), by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1058.

• Introduce concurrency controls to Github Actions, by Maira Usman in https://github.com/jonescompneurolab/hnn-core/pull/1015.

• Major bugfix: Cell positions were previously starting at origin (incorrect) instead of origin + their pos_dict locations (correct). This has been fixed. This change should not affect results from dipole or single-cell output, but will affect results from LFP or CSD output. Identified and fixed by Katharina Duecker in https://github.com/jonescompneurolab/hnn-core/pull/1062.

• Updates to Linkcheck Workflow frequency so it only runs on every merge to master and on the 1st and 15th of every month, by Maira Usman in https://github.com/jonescompneurolab/hnn-core/pull/1043 (new contributor!!!).

• Miscellaneous link updates/fixes needed due to our overhaul of our HNN Frontpage and our new HNN Textbook website, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1055, https://github.com/jonescompneurolab/hnn-core/pull/1059, https://github.com/jonescompneurolab/hnn-core/pull/1063, and https://github.com/jonescompneurolab/hnn-core/pull/1067.

• Add support for ruff format, merge changes taken from running it, and require its use for new code contributions, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/934.

• Add conda package installation instructions, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1051.

• Add and update "Cloud" usage instructions on install page to redirect to our new Textbook website, by Austin E. Soplata in https://github.com/jonescompneurolab/hnn-core/pull/1046 and https://github.com/jonescompneurolab/hnn-core/pull/1048.

• Remove hardcoding of celltypes in hnn_core.CellResponse and add {func}~hnn_core.Network.rename_cell, by Mohamed W. ElSayed in https://github.com/jonescompneurolab/hnn-core/pull/702 and https://github.com/jonescompneurolab/hnn-core/pull/970.

Scientific Software - Peer-reviewed - Python
Published by asoplata 10 months ago

HNN-core - v0.4.1

v0.4.1

Version 0.4.1 is a bug-fixing patch release for version 0.4. This includes changes to importing of BatchSimulate due to previously-undetected install/import issues (#1034), configuration of packaging metadata format (same PR), and elimination of a discrepancy in our method of cleaning local compiled files that led to architecture-specific files being included in the Pypi 0.4 release, which caused simulations on some platforms to fail (#1035 ). The public Pypi version has already been updated to 0.4.1.

For release notes about what is new for this version and 0.4, see https://github.com/jonescompneurolab/hnn-core/releases/tag/v0.4 .

Scientific Software - Peer-reviewed - Python
Published by asoplata about 1 year ago

HNN-core - v0.4

v0.4

v0.4 represents a major milestone in development of hnn_core and the HNN ecosystem as a whole. v0.4 includes over two years of active development work by many people (>800 commits!), and brings with it many new and exciting features, including significant improvements to robustness, testing, and bug-fixing.

New Features

• hnn_core now includes a fully-tested and robust GUI of its own. The hnn_core GUI was present as a prototype in v0.3, but it is now ready for production. New features and visual improvements will still be coming to it in the future, such as the ability to use optimization. See our new Install page for ways to install it, and we have already begun incorporating it into a new, fresh series of tutorials for our upcoming revamp of the HNN website. If you have installed it, you can start the GUI using hnn-gui in your terminal/command prompt window.

• The BatchSimulate class: Thanks to Abdul Samad Siddiqui and Google Summer of Code 2024, there is now the capability to run "batches" of simulations across multiple parameter sets, enabling easy analysis and simulation of behavior across parameter sweeps. See our example for more details. Note that currently, only its loky backend is supported, and the "hnn-core[parallel]" dependencies must be installed for it to be used.

• Significant improvements to the API, documentation, and pedagogical examples especially for Optimization, among others.

• Calcium concentration can now be recorded: recorded calcium concentration from either the soma, or all sections, are enabled by setting record_ca to soma or all in hnn_core.simulate_dipole. Recordings are accessed through hnn_core.CellResponse.ca.

• There is now a new class hnn_core.viz.NetworkPlotter which can be used to visualize an entire network in 3D, including firing animations; see our example of how to use it here.

• There is now a new function hnn_core.viz.plot_drive_strength for illustrating the absolute or relative amount of strength that a particular drive provides to different cell types.

• A very large amount of polishing, bug fixes, general improvements, etc.

Deprecations

• The new Python 3.13 is not supported by hnn_core at this time, due to NEURON's current lack of support for it. This will change in the near future. We still support 3.8 through 3.12 (inclusively).

Upcoming Deprecations

• Both hnn_core.viz.plot_laminar_lfp and hnn_core.viz.plot_dipole will have their tmin and tmax arguments removed in the future. Please set the x-axis limits using methods called directly on the existing matplotlib objects, or using matplotlib.pyplot.xlim.
• hnn_core.Network's argument of legacy_mode for importing old param files will be removed in the future.
• hnn_core.Network.add_tonic_bias's argument of cell_type, along with setting the argument amplitude to a single float, will be removed in the future. Instead, set the amplitude argument to a dictionary as described in the docstring.
• hnn_core.simulate_dipole's argument of postproc for post-processing will be removed in the future. Instead, use explicit smoothing and scaling via hnn_core.Dipole methods.

API Changes

• New argument to hnn_core.Network initialization: you can now set mesh_shape to easily make a grid of different sizes of Networks.
• hnn_core.Cell initialization argument topology has had both its name changed to cell_tree and its data type significantly changed; see the API docs of Cell for details.
• hnn_core.jones_2009_model and other built-in Network Models including hnn_core.law_2021_model and hnn_core.calcium_model all accept the aforementioned mesh_shape argument like hnn_core.Network.
• The API for optimization has changed significantly. Instead of running the function optimize_evoked obtained using from hnn_core.optimization import optimize_evoked, you should use the new hnn_core.optimization.Optimizer class and its methods; see our example of evoked-response optimization here.
• hnn_core.viz.plot_spikes_hist now accepts more arguments, including invert_spike_types, color, and any **kwargs_hist which can be applied to matplotlib.axes.Axes.hist. See the docstring for details.
• hnn_core.viz.plot_spikes_raster now accepts many more arguments, including cell_types, colors, show_legend, marker_size, dpl, and overlay_dipoles. See the docstring for details.
• hnn_core.viz.plot_cell_morphology now accepts more arguments, including color and several arguments related to its position and viewing window, including pos, xlim, ylim, and zlim. See the docstring for details.
• hnn_core.viz.plot_laminar_csd now accepts more arguments, including vmin, vmax, sink, and interpolation. See the docstring for details.
• hnn_core.parallel_backends.MPIBackend now accepts many more arguments, including use_hwthreading_if_found, sensible_default_cores, override_hwthreading_option, and override_oversubscribe_option. See the docstring for details; the ability to customize it has been greatly increased.
• hnn_core.read_params now accepts a new argument file_contents which lets you pass in network configuration contents using a string.

People who contributed to this release (in alphabetical order of family name):

• Huzi Cheng
• Tianqi Cheng
• George Dang
• Dylan Daniels
• Camilo Diaz
• Katharina Duecker
• Yaroslav Halchenko
• Mainak Jas
• Dikshant Jha
• Stephanie R. Jones
• Shehroz Kashif
• Rajat Partani
• Carolina Fernandez Pujol
• Dan Toms
• Abdul Samad Siddiqui
• Austin E. Soplata
• Ryan Thorpe
• Nick Tolley

Scientific Software - Peer-reviewed - Python
Published by asoplata about 1 year ago

HNN-core - v0.4rc0

v0.4rc0

Scientific Software - Peer-reviewed - Python
Published by ntolley over 1 year ago

HNN-core - v0.3.1

NOTE

• This GitHub release was not mirrored by a PyPI release (GitHub-only).
• It was done to trigger a Zenodo release to be used by JOSS.

Scientific Software - Peer-reviewed - Python
Published by ntolley over 2 years ago

HNN-core - v0.3

v0.3

Scientific Software - Peer-reviewed - Python
Published by rythorpe about 3 years ago

HNN-core - v0.2

v0.2

Scientific Software - Peer-reviewed - Python
Published by ntolley over 4 years ago

HNN-core - v0.1

v0.1

Scientific Software - Peer-reviewed - Python
Published by jasmainak about 5 years ago