Changelog¶

Version 0.13.2 - March 31, 2026¶

New Features¶

biopsykit.io: Added a new fibion importer with FibionDataset support for loading Fibion recordings from EDF, CSV, or complete recording folders, including metadata-aware CSV parsing.
biopsykit.signals.ecg: Added new tpcp-based heart-rate processing helpers, including normalization, aggregation, and resampling utilities.
biopsykit.protocols.cft: Added CftFeatureExtraction to compute Cold Face Test features from heartbeat-level ECG-derived heart-rate data.

Bugfixes¶

biopsykit.io: Fixed time log import handling.
biopsykit.utils.array_handling: Fixed handling of empty masked slices.
Improved compatibility with newer pandas versions by removing inplace column replacement patterns and updating DataFrame indexing code that triggered FutureWarnings.
biopsykit.io.fibion: Corrected FibionDataset attribute annotations so dataset state is stored as instance data rather than class variables.

Improvements¶

biopsykit.protocols.plotting: Extended protocol plotting support for the new CFT feature extraction workflow.
biopsykit.signals.icg.event_extraction: Improved parameter documentation across B-point and C-point extraction algorithms.

Version 0.13.1 - June 12, 2025¶

Bugfixes¶

fix IPython import paths in biopsykit.stats

Version 0.13.0 - April 16, 2025¶

Improvements¶

biopsykit.io.biomarker: Made importing biomarker data from the laboratory (“plate-format”) more flexible and error-safe.

Internal Changes¶

Updated code to fix deprecation and future warnings in pandas and numpy.

Version 0.12.3 - March 15, 2025¶

Internal Changes¶

Migrated from poetry to uv as the main build tool. This change is due to the fact that uv is more flexible and allows for more customization. The pyproject.toml file was updated accordingly.

Version 0.12.2 - January 14, 2025¶

Bugfix¶

small bugfixes in PEP Algorithms and Biopac importer (improved error handling)

Version 0.12.1 - January 03, 2025¶

Bugfix¶

Updated pandas version constraint from “^1” to “^2” and updated all code and test cases to be compatible with newer pandas versions.

Version 0.12.0 - January 03, 2025¶

New Features¶

Added new algorithms for pre-ejection period (PEP) computation in biopsykit.signals, including algorithms for ECG Q-peak extraction (biopsykit.signals.ecg) and ICG B-point extraction (biopsykit.signals.icg). Added further utility functions (e.g., for heartbeat segmentation) and to compute the PEP using a combination of ECG and ICG data (biopsykit.signals.pep).

Version 0.11.0 - January 03, 2025¶

Changes¶

Made biopsykit compatible with matplotlib >= 3.9.

Version 0.10.2 - March 06, 2024¶

Changes¶

BaseProtocol.add_salvia_data now also accepts absolute saliva sample times as argument by setting sample_times_absolute=True.
bp.protocols.plotting.saliva_plot: removed hardcoded number of plotting colors (2) when plotting data with multiple conditions (> 2)

Version 0.10.1 - Dec 01, 2023¶

Bugfixes¶

biopsykit.classification.model_selection.SklearnPipelinePermuter: fixed bug that lead to the incorrect flattening of numpy arrays not due to a newer numpy version

Version 0.10.0 - Nov 28, 2023¶

Changes¶

biopsykit.classification.model_selection.SklearnPipelinePermuter:
- renamed method best_pipeline to best_hyperparameter_pipeline. WARNING: This is a breaking change!
- added new method to fit classification pipelines and save intermediate results to disk (fit_and_save_intermediate).
- all arguments passed to fit and fit_and_save_intermediate (except for X and y) are from now on keyword-only arguments to avoid confusion. WARNING: This is a breaking change!
- merge_permuter_instances is now a class method that accepts a list of SklearnPipelinePermuter instances or a list of file paths as argument instead of a method that merges one SklearnPipelinePermuter instance with the current instance. WARNING: This is a breaking change!
- added new method update_permuter to update an SklearnPipelinePermuter instance with new model and parameter dictionaries that can then be used to fit new pipeline permutations.

Version 0.9.0 - Apr 25, 2023¶

Changes¶

removed biopsykit.carwatch_logs module for processing CARWatch log data (moved to own carwatch package)

Bugfixes¶

biopsykit.classification.model_selection.SklearnPipelinePermuter: some bugfixes and improvements when computing additional classification metrics
additional bugfixes in other functions

Misc¶

code changes after switching to ruff as new linter

Version 0.8.1 - Apr 04, 2023¶

Added¶

biopsykit.classification.analysis: Added functions to analyze classification results
biopsykit.classification.model_selection.SklearnPipelinePermuter: Added methods to export classification metrics as latex tables, to merge to different SklearnPipelinePermuter instances, and to compute additional classification metrics.
various new util functions

Bugfixes and Improvements¶

biopsykit.classification.model_selection.SklearnPipelinePermuter: fixing random state now works as intended and produces reproducible results for real!
biopsykit.stats.StatsPipeline: Improved behavior
biopsykit.plotting: Improved layout
minor bugfixes

Version 0.7.1 - November 30, 2022¶

Bugfixes¶

bp.io.biopac:wrong index name for dataframe export when setting parameter "index = None"

Version 0.7.0 - November 22, 2022¶

Added¶

biopsykit.io:
- Added functions to directly load aTimeLogger files (biopsykit.io.load_atimelogger_file) and to convert time log files into a dictionary with start/end times (biopsykit.io.convert_time_log_dict)
- Added support for loading data acquired from the Biopac system (biopsykit.io.biopac)
biopsykit.plotting: Added function to conveniently plot feature pairs (biopsykit.plotting.feature_pairplot), which is a wrapper function for seaborn.pairplot

Improvements¶

Adapted code to don’t show pandas future warnings anymore
biopsykit.plotting.hr_ensemble_plot: Added “is_relative” argument to style y-axis accordingly
biopsykit.stats.StatsPipeline: Improved latex export for different effect sizes
biopsykit.io.nilspod: Improved handling of loading NilsPods files
biopsykit.utils.data_processing: Added support for data dicts with tuples instead of strings as keys

Bugfixes¶

some small bugfixes

Version 0.6.1 - August 19, 2022¶

Improvements¶

biopsykit.signals.ecg.EcgProcessor: improved handling of errors occurring during ECG processing
biopsykit.plotting: Improved boxplot behavior due to the use of the new light palettes of fau-colors. See the StatsPipeline & Plotting Example for further information.

Bugfixes:¶

biopsykit.signals.imu.ActivityCounts: added timezone support (PR 31)
biopsykit.signals.imu.RestPeriods: fixed bug in computing resting periods (old implementation could lead to classifying a long period of activity as the main rest period.) (PR 32)
biopsykit.signals.imu.ActivityCounts: fixed bug(s) in computing activity counts (PR 33)
biopsykit.stats.StatsPipeline: fixed bugs in LaTeX export of result tables

Version 0.5.1 - May 24, 2022¶

New Features¶

biopsykit.classification: SklearnPipelinePermuter now supports regression

Bugfixes¶

further small bugfixes

Version 0.5.0 - April 21, 2022¶

New Features¶

biopsykit.stats: Added new statistic features:
- biopsykit.stats.multicoll: Functions to handle multicollinearity in data
- biopsykit.stats.regression: Functions for performing more “complex” regression analysis (currently: stepwise backward multiple linear regression)
biopsykit.classification: SklearnPipelinePermuter instances can now be saved as pickle files and imported again

Bugfixes¶

_ biopsykit.utils.time: Renamed time_to_datetime to time_to_timedelta (wrong function name)

Version 0.4.2 - March 18, 2022¶

Bugfixes¶

biopsykit.stats.StatsPipeline: Fixed bug of failing to generate significance brackets from within-subjects stats data
biopsykit.protocols.plotting.saliva_plot: Fixed wrong plot styling

New Features¶

biopsykit.plotting.feature_boxplot: Added legend_title parameter
biopsykit.classification.model_selection.nested_cv: Train and test indices are now saved for each fold of the nested cv
biopsykit.classification.model_selection.SklearnPipelinePermuter:
- Updated “scoring” and “refit” behavior
- Added confusion matrix, true labels, predicted labels, train and test indices per fold and flattened

Version 0.4.1 - January 24, 2022¶

Bugfixes¶

biopsykit.signals.imu.static_moment_detection: Now returning an empty dataframe with correct column names when detecting no static moments
biopsykit.classification.model_selection.SkleanPipelinePermuter: Pipelines are now correctly sorted by their mean test scores
biopsykit.protocols.plotting.saliva_plot: Fixed bug when attempting to plot saliva data without sample times _ biopsykit.plotting.feature_boxplots: Updated plotting color configuration: If an alpha value smaller than 1.0 is passed, the saturation is by default set to 1.0 to still have a nice color shading despite the transparency
biopsykit.protocols.TSST: Changed default TSST test time from 20 to 15 min

Version 0.4.0 - January 05, 2022¶

New Features¶

biopsykit.stats.StatsPipeline:
- added new functions StatsPipeline.results_to_latex_table and StatsPipeline.stats_to_latex to convert statistical analysis results to LaTeX tables and to inline LaTeX code, respectively.
- changed argument stats_type to stats_effect_type.
  WARNING: This is a breaking change! The use of stats_type is deprecated and will be removed in 0.5.0!
biopsykit.colors: Removed biopsykit.colors module and replaced it with colors from the new fau_colors package.
WARNING: This is a breaking change!

Bugfixes¶

biopsykit.signals.imu.static_moment_detection: end indices of static moments are inclusive instead of exclusive

Misc¶

biopsykit.utils.array_handling: if overlap_percent > 1 it is converted to a fraction [0.0, 1.0]

Version 0.3.7 - December 03, 2021¶

Misc¶

Updated dependencies: now using scikit-learn >=1.0

Version 0.3.6 - December 01, 2021¶

New Features¶

biopsykit.io.ecg: Added functions to write a dictionary of dataframes to a series of csv files (and vice versa).
biopsykit.classification.model_selection: Model selection now also supports to perform randomized-search instead of grid-search for hyperparameter optimization of machine learning pipelines

Bugfixes¶

biopsykit.questionnaires.psqi: Fixed bug in computing Pittsburgh Sleep Quality Index (PSQI)

Version 0.3.5 – November 05, 2021¶

Bugfixes¶

further bugfixes (incorrect handling of duplicate index values) for Sleep Analyzer import data using biopsykit.io.sleep_analyzer.load_withings_sleep_analyzer_raw_file()

Version 0.3.4 – November 04, 2021¶

New Features¶

added function biopsykit.utils.time.extract_time_from_filename() that can parse time information from a filename
added function biopsykit.metadata.gender_counts()

Bugfixes¶

fixed bug when importing Sleep Analyzer data using biopsykit.io.sleep_analyzer.load_withings_sleep_analyzer_raw_file()
biopsykit.io.load_time_log(): time log dataframes imported using this function will now have “phase” as column name

Misc¶

updated the minimum version of the pingouin dependency to 0.5.0 because it’s strongly recommended from the authors of pingouin (https://pingouin-stats.org/changelog.html#v0-5-0-october-2021)
switched from doit to poethepoet as task runner.

Version 0.3.2 – October 12, 2021¶

final version of BioPsyKit for submission to the Journal of Open Source Software.
improved documentation (e.g., included Example Gallery)

Version 0.3.1 – October 5, 2021¶

biopsykit.utils.file_handling.get_subject_dirs(): replaced glob-style matching of regex strings by re-style matching. This allows more flexibility when filtering for directories that match a specific pattern.
biopsykit.questionnaires:
- fixed wrong implementation of ASQ (biopsykit.questionnaires.asq)
- added modified version of the ASQ (ASQ_MOD, biopsykit.questionnaires.asq_mod) according to (Kramer et al., 2019)
implemented changes as result of JOSS submission, including:
- improved handling of example data
- improved interface for multi-test comparison in StatsPipeline
- improved colormap handling
- new function to load dataframes in long-format (biopsykit.io.load_long_format_csv)

Version 0.3.0 – September 1, 2021¶

initial commit

Contributing to BioPsyKit biopsykit