1.2.0

Changelog

May 27 2025 Update actions ubuntu image and drop python 3.6 support #156
Mar 08 2025 Update filter defaults #153
Feb 12 2025 Debug marker style error #151 
Feb 12 2025 Add tests for Python 3.13 #150
Feb 12 2025 Dataframe memory fix #149
Feb 12 2024 Github actions #147
Dec 13 2023 Marker definition for newer matplotlib #144
Dec 12 2023 Workflow tests to support Python 3.12 #143
Jul 05 2023 Mmakefile options for distributions #138
Jun 12 2023 Clean up tutorial code in ByGroup tutorial #137
Jun 11 2023 Optimize check_min_burst_cycles #136

1.1.0

1.1.0

Improvements

• Added classes (Bycycle and Bycycle)
• Optimized runtime
• Optional edge burst detection
• Support for Python 3.9, 3.10, 3.11
• Consistency tests

Bugs

• Dataframe limiting
• Plot highlighting
• Glossary typos

1.0.0

1.0.0

Warning: 1.0.0 is a breaking release from the beta 0.X.X series.

As compared to the prior series (0.X.X), some names and module organizations have changed. This
means existing code that uses Bycycle may no longer work as currently written with the new version,
and may need updating. You should update to the new version when you are ready to update your code
to reflect the new changes.

Note that the main changes are in code organization, some names, and the addition of many new
features. The algorithm itself has not changed, and results from the new version should be roughly
equivalent to those with older versions, with a few minor exceptions.

Code Oraganization

• Increased modularity.

  • burst: burst.amp, burst.cycle, burst.dualthresh, burst.utils
  • cyclepoints: cyclepoints.extrema, cyclepoints.zerox, cyclepoints.phase
  • features: features.features, features.burst, features.shape, features.cyclepoints

• Neurodsp dependency.

  • filt.py and sim.py have been replaced with equivalent neurodsp functions.

Naming Updates

• x -> sig
• N_cycles_min -> min_n_cycles
• Fs -> fs
• Ps -> ps
• Ts -> ts
• zeroriseN -> rise_xs
• zerofallN -> decay_xs
• amplitude_fraction_threshold -> amp_fraction_threshold
• amplitude_consistency_threshold -> amp_consistency_threshold

Code Updates

The 1.X.X series adds a large number of code updates & additions, including:

• Parallel processing for 2D and 3D numpy arrays (bycycle.group):

  • compute_features_2d
  • compute_features_3d

• New plottings functions (bycycle.plts):

  • burst: plot_burst_detect_summary, plot_burst_detect_param
  • cyclepoints: plot_cyclepoints_df, plot_cyclepoints_array
  • features: plot_feature_hist, plot_feature_categorical

• Bug fixes:

  • Missing cyclepoints at the beginning/end of a signal.
  • Monotonicity computation didn't include all points in a cycle.
  • Zero-crossing off-by-one error when a signal crossed at exactly zero.

Documentation

The 1.X.X series comes with an updated documentation site.

As well as updating the tutorials, API list, and other existing documentation, there are
also (upcoming) new materials.

1.0.0rc2

1.0.0rc2

Warning: the 1.0.0 is a breaking release from the beta 0.X.X series.

As compared to the prior series (0.X.X), some names and module organizations have changed. This
means existing code that uses Bycycle may no longer work as currently written with the new version,
and may need updating. You should update to the new version when you are ready to update your code
to reflect the new changes.

Note that the main changes are in code organization, some names, and the addition of many new
features. The algorithm itself has not changed, and results from the new version should be roughly
equivalent to those with older versions, with a few minor exceptions.

Code Oraganization

• Increased modularity.

  • burst: burst.amp, burst.cycle, burst.dualthresh, burst.utils
  • cyclepoints: cyclepoints.extrema, cyclepoints.zerox, cyclepoints.phase
  • features: features.features, features.burst, features.shape, features.cyclepoints

• Neurodsp dependency.

  • filt.py and sim.py have been replaced with equivalent neurodsp functions.

Naming Updates

• x -> sig
• N_cycles_min -> min_n_cycles
• Fs -> fs
• Ps -> ps
• Ts -> ts
• zeroriseN -> rise_xs
• zerofallN -> decay_xs
• amplitude_fraction_threshold -> amp_fraction_threshold
• amplitude_consistency_threshold -> amp_consistency_threshold

Code Updates

The 1.X.X series adds a large number of code updates & additions, including:

• Parallel processing for 2D and 3D numpy arrays (bycycle.group):

  • compute_features_2d
  • compute_features_3d

• New plottings functions (bycycle.plts):

  • burst: plot_burst_detect_summary, plot_burst_detect_param
  • cyclepoints: plot_cyclepoints_df, plot_cyclepoints_array
  • features: plot_feature_hist, plot_feature_categorical

• Bug fixes:

  • Missing cyclepoints at the beginning/end of a signal.
  • Monotonicity computation didn't include all points in a cycle.
  • Zero-crossing off-by-one error when a signal crossed at exactly zero.

Documentation

The 1.X.X series comes with an updated documentation site.

As well as updating the tutorials, API list, and other existing documentation, there are
also (upcoming) new materials.

1.0.0rc1

1.0.0rc

Warning: the 1.0.0 is a breaking release from the beta 0.X.X series.

As compared to the prior series (0.X.X), some names and module organizations have changed. This
means existing code that uses Bycycle may no longer work as currently written with the new version,
and may need updating. You should update to the new version when you are ready to update your code
to reflect the new changes.

Note that the main changes are in code organization, some names, and the addition of many new
features. The algorithm itself has not changed, and results from the new version should be roughly
equivalent to those with older versions, with a few minor exceptions.

Code Oraganization

• Increased modularity.

  • burst: burst.amp, burst.cycle, burst.dualthresh, burst.utils

  • cyclepoints: cyclepoints.extrema, cyclepoints.zerox, cyclepoints.phase

  • features: features.features, features.burst, features.shape, features.cyclepoints

  • The dataframe output returned from compute_features now returns:

    1. df_features: burst/shape cycle features.
    2. df_samples: cyclepoint locations as signal indices.

• Neurodsp dependency.

  • filt.py and sim.py have been replaced with equivalent neurodsp functions.

Naming Updates

• Consistency with neurodsp and PEP8 compliance:

  • x -> sig
  • N_cycles_min -> min_n_cycles
  • Fs -> fs

• PEP8

  • Ps -> ps
  • Ts -> ts
  • zeroriseN -> rise_xs
  • zerofallN -> decay_xs

• Consistency between burst detection kwargs and dataframe column names:

  • amplitude_fraction_threshold -> amp_fraction_threshold
  • amplitude_consistency_threshold -> amp_consistency_threshold

Code Updates

The 1.X.X series adds a large number of code updates & additions, including:

• Parallel processing for 2D and 3D numpy arrays (bycycle.group):

  • compute_features_2d
  • compute_features_3d

• New plottings functions (bycycle.plts):

  • burst: plot_burst_detect_summary, plot_burst_detect_param
  • cyclepoints: plot_cyclepoints_df, plot_cyclepoints_array
  • features: plot_feature_hist, plot_feature_categorical

• Bug fixes:

  • Missing cyclepoints at the beginning/end of a signal.
  • Monotonicity computation didn't include all points in a cycle.
  • Zero-crossing off-by-one error when a signal crossed at exactly zero.

Documentation

The 1.X.X series comes with an updated documentation site.

As well as updating the tutorials, API list, and other existing documentation, there are
also (upcoming) new materials.

0.1.3

This release includes bug fixes, documentation improvements, and increased testing coverage.

bug fixes

major bug fix

Remove simulation code

Merge pull request #17 from voytekresearch/rmv_sim

remove simulation code that is duplicate of neurodsp

First beta version

Complete code has been added with some tests and tutorials.

Pre-alpha testing

testing