whitews/FlowKit: 0.8.0

New features: Support for Python 3.9 FlowKit version now available via top-level attribute __version__ GatingStrategy: optimized processing order of gates to avoid re-processing optional caching of pre-processed events to speed up processing of gates Matrix class now has an inverse method WSPBiexTransform now has an inverse method Significant speed increase for parsing FlowJo 10 WSP files with lots of bi-ex transforms Sample method plot_contour now has optional fill argument to created filled contours Sample now re-applies a transform when Sample is given a new compensation Analyzing samples in a Session using multiprocessing will now try to dynamically allocate CPUs based on available memory to avoid out of memory errors Removed features: Anomalous event detection removed from FlowKit, now lives in separate FlowQC project API changes: gates module: All gate types now take a pandas DataFrame as input (possible to use gates independently now) Sample class: subsample argument added back to Sample constructor (better to have subsample ready for plot methods) Sample plot methods (except histogram and plot channel) now default to subsample=True The various methods for getting NumPy arrays of events are now encapsulated into the single get_events methods that takes a source argument (consistent w/ other Sample methods) Method get_channel_data renamed to get_channel_events Added option to cache original events, they are no longer stored by default (saves memory) Attribute anomalous_indices renamed to flagged_indices, and now set by user for any purpose using set_flagged_events method Attribute channels changed from a dictionary to a more readable pandas DataFrame New plotting method plot_channel for plotting channel data with "events" as x-axis (similar to plotting vs Time) GatingStrategy class: gate_path is now always a tuple (not a list) Uses of gate_id replaced with gate_name: a gate ID is a tuple of (gate_name, gate_path) Method get_gate_indices renamed to get_gate_membership (since it returns a boolean array) Session class: Plotting methods no longer analyze samples, analyze_samples method must be called prior Method get_gate_indices renamed to get_gate_membership (since it returns a boolean array) Dimension class Attribute label renamed to id Method get_gate now returns the containing QuadrantGate when a Quadrant ID is given Function calculate_extent removed from public API (was never intended for external use) Bug fixes: Improved support for Windows multiprocessing now working fixed issue where parent gate results were not being properly retrieved, causing lots of re-processing fixed memory leak in points_in_polygon C extension (used for processing PolygonGate instances) fixed issue in C extension code that would sometimes cause mis-allocation of NumPy array sizes Documentation: New & comprehensive tutorial notebook series for new FlowKit users New notebook demonstrating how to create a custom Sample gate in a Session More docstrings for classes and methods Dependencies: FlowIO requirement updated to 0.9.12 (significantly faster reading of FCS files) FlowUtils requirement updated to 0.9.5 new requirement networkx >= 2.3 new requirement psutil ~= 5.8.