Release 0.6.0

Added

• New hypyp.sync module: Modular architecture for connectivity metrics
  • Extracted 9 connectivity metrics into separate classes: PLV, CCorr, ACCorr, Coh, ImCoh, PLI, WPLI, EnvCorr, PowCorr
  • BaseMetric abstract class for uniform interface across all metrics
  • get_metric(mode, optimization) function for easy metric instantiation
  • Helper functions: multiply_conjugate, multiply_conjugate_time, multiply_product
• GPU and numba backends for all 9 sync metrics:
  • numba JIT with prange: PLV, CCorr, Coh, ImCoh, PLI, wPLI, EnvCorr, PowCorr
  • PyTorch (MPS/CUDA/CPU) via batched einsum: all 9 metrics
  • Metal compute shaders (Apple Silicon): PLI, wPLI, ACCorr
  • CUDA raw kernels via CuPy (NVIDIA GPUs): all 9 metrics
• Benchmark-driven AUTO_PRIORITY table for optimization='auto', compiled from
  Mac M4 Max (131 runs) and Narval A100 (111 runs) benchmarks
• priority parameter on get_metric() and compute_sync() for custom backend ordering
• hypyp/sync/kernels/ submodule with Metal and CUDA dispatch infrastructure
• New optional dependencies: pyobjc-framework-Metal (Apple), cupy-cuda12x (NVIDIA)
• multiply_conjugate_torch and multiply_conjugate_time_torch GPU helpers

Changed

• BREAKING: accorr metric now returns raw connectivity values with shape (n_epoch, n_freq, 2*n_ch, 2*n_ch) like all other metrics. The swapaxes and epochs_average operations are now handled by compute_sync() instead of being applied inside the metric.
• Refactored compute_sync() to use the new hypyp.sync module internally

Deprecated

• _multiply_conjugate() in analyses.py - use hypyp.sync.multiply_conjugate instead (will be removed in 1.0.0)
• _multiply_conjugate_time() in analyses.py - use hypyp.sync.multiply_conjugate_time instead (will be removed in 1.0.0)
• _multiply_product() in analyses.py - use hypyp.sync.multiply_product instead (will be removed in 1.0.0)
• _accorr_hybrid() in analyses.py - use hypyp.sync.ACCorr instead (will be removed in 1.0.0)

Release v0.5.0b18

Upgraded depencies rules and updated dependencies

Release v0.5.0b17

v0.5.0b17 - Dependency Fix

Bug Fix

Fixed a critical dependency issue where scipy 1.17.0 breaks the import chain with MNE.

Details

With the latest release of scipy (v1.17.0), the sph_harm function was removed from scipy.special. The MNE version that HyPyP depends on requires this function but does not pin the scipy version in its dependencies.

Error that was occurring:

ImportError: cannot import name 'sph_harm' from 'scipy.special'

Solution:

• Added version constraint scipy = ">=1.0.0,<1.17.0" in pyproject.toml
• Updated poetry.lock accordingly

This is a temporary fix until the upstream MNE package updates its scipy compatibility.

Credits

Thanks to @patricefortin for identifying and fixing this issue (#243)

🔗 References

• PR: #243
• Related scipy commit: scipy/scipy@39b8d4d

0.5.0b16 — Dependency updates & Add adjusted CCorr

What's Changed

• Add adjusted circular correlation (accorr) connectivity metric (Zimmermann et al., 2024, doi:10.1162/imag_a_00350)
• Update multiple security dependencies (fonttools, urllib3, pymdown-extensions, pip)

Full Changelog: v0.5.0b15...v0.5.0b16

0.5.0b15 — Dependency updates & documentation refresh

0.5.0b15 — Dependency updates & documentation refresh

Release Notes

This pre-release introduces a series of dependency updates and maintenance improvements to keep the project aligned with the latest ecosystem versions.

Changes included in 0.5.0b15:

Regenerated documentation and cleaned build workflow.

Updated project version to 0.5.0b15 (Poetry).

Minor maintenance and sync with PyPI packaging.

No API changes are expected in this release.

0.5.0b10b13

What’s Changed
• Support for Python 3.13.
• Fixed a bug in wavelet coherence when two signals in a pair were not perfectly aligned by @patricefortin in #232
• Bumped starlette from 0.47.1 to 0.47.2 by @dependabot[bot] in #233

Security
• Removed unused future dependency (CVE-2025-50817, High severity).
• Verified and updated critical dependencies:
• urllib3 >= 2.5.0 (fixes CVE related to redirect control)
• requests >= 2.32.4 (fixes .netrc credentials leak)
• pillow >= 11.3.0 (fixes buffer overflow vulnerability)

v0.5.0b10: Feature fNIRS hyperscanning (#226)

What's Changed

Fixed

• Fixed Poetry configuration for proper package inclusion
• Resolved missing fnirs, shiny, wavelet, and xdf modules in PyPI package
• Updated pyproject.toml to PEP 621 format

Technical Changes

• Fixed packages configuration in pyproject.toml
• Ensured all sub-modules are properly included in the build

Full Changelog: v0.5.0b5...v0.5.0b9

0.5.0b5

What's Changed

• Infant data visualisation by @mg-m in #207
• Edit comments by @Ramdam17 in #209
• Bump jinja2 from 3.1.3 to 3.1.6 in /docs by @dependabot in #210
• Bump certifi from 2024.2.2 to 2024.7.4 in /docs by @dependabot in #211
• Bump tornado from 6.4 to 6.4.2 in /docs by @dependabot in #212
• Bump scikit-learn from 1.4.0 to 1.5.1 in /docs by @dependabot in #213
• Bump zipp from 3.17.0 to 3.19.1 in /docs by @dependabot in #214
• Bump jupyterlab from 3.6.7 to 3.6.8 in /docs by @dependabot in #215
• Infant visualisation translation update by @mg-m in #208
• Bump requests from 2.31.0 to 2.32.2 in /docs by @dependabot in #216
• Bump tqdm from 4.66.1 to 4.66.3 in /docs by @dependabot in #217
• Bump idna from 3.6 to 3.7 in /docs by @dependabot in #218
• Bump black from 19.10b0 to 24.3.0 in /docs by @dependabot in #219
• Bump pillow from 10.2.0 to 10.3.0 in /docs by @dependabot in #220
• Fix deprecated matplotlib.cm.get_cmap() calls for compatibility with … by @Ramdam17 in #221
• Bump tornado from 6.4.2 to 6.5.1 by @dependabot in #224
• Bump setuptools from 77.0.1 to 78.1.1 by @dependabot in #223
• Bump h11 from 0.14.0 to 0.16.0 by @dependabot in #222
• Feature XDF Import by @patricefortin in #225
• continuous wavelet transform and wavelet transform coherence implementation by @patricefortin in #229

New Contributors

• @mg-m made their first contribution in #207

Full Changelog: 0.5.0b4...0.5.0b5

0.5.0b4

What's Changed

• Add github workflow trigger on pull request by @patricefortin in #198
• Add type hinting to function signatures by @patricefortin in #196
• Variables renaming for consistency in prep.py + tests by @patricefortin in #197
• Fix flaky test and add random seed to have deterministic tests by @patricefortin in #199
• Fix numpy major version in dependencies, to avoid upgrading to 2.x.x by @patricefortin in #200
• Poetry update by @Ramdam17 in #205

New Contributors

• @patricefortin made their first contribution in #198
• @Ramdam17 made their first contribution in #205

Full Changelog: 0.5.0b2...0.5.0b4

0.5.0b2

What's Changed

• fix for various deprecation warnings
• update all dependencies for security
• adapt to the new MNE syntax for spectrum functions
• fix functions for generating synthetic data
• fix usage of alpha parameter for stats thresholding by @obergmartin in #178

Full Changelog: 0.5.0b...0.5.0b2