1.2.0

[whitews]

FlowKit 1.2.0 is out! Major updates include support for Boolean gates in FlowJo workspaces, renaming Sample channels and making the API more user-friendly. Thanks to everyone who contributed to this release, keep the bug reports and suggestions coming!

New features:

• Workspace class now supports Boolean gates when parsing a FlowJo workspace (see Workspace not loading Boolean gates #179).
• Added get_keywords method to Workspace for getting sample keywords stored in a FlowJo workspace (see Load custom keywords from FlowJo .wsp file  #210).
• Workspace method get_gate_events now supports source kwarg to control pre-processing of returned events (see Add source kwarg to Workspace.get_gate_events #196).
• Session & GatingStrategy classes now support renaming gates via the rename_gate method (see @219).
• Session & GatingStrategy classes now support removing custom sample gates via the sample_id kwarg in the remove_gate method (see Remove a Custom Gate from GatingStrategy #221).
• Sample class now supports renaming channels via a new rename_channel method (see Support renaming a channel in Sample class #198).
• Sample class methods get_events, get_channel_events and as_dataframe support event_mask kwarg for filtering events using a Boolean array (see Add event_mask to Sample.get_events #218).
• Sample class method as_dataframe supports new col_multi_index option to control column index type.
• Matrix class now supports comparison operator for determining if 2 Matrix instances are the same (see Allow equality comparison for Matrix instances #200).
• New utils module function generate_transforms to generate a set of transforms for a Sample (see Add utility function to generate a set of transforms for a sample #162).

API changes:

• Transform class: removed id attribute. This allows more convenient use of independently using transforms outside of a GatingStrategy (see Remove id attribute from Transform classes #191).
• GatingStrategy class: added transform_id arg to add_transform method.
• Session class: added transform_id arg to add_transform method.
• Workspace class: get_transforms now returns a dictionary LUT of transform IDs and transform instances.
• Matrix class: removed id attribute. This allows more convenient use of independently using matrices outside of a GatingStrategy (see Remove id attribute from Matrix class #199).
• Session class: get_comp_matrices now returns a dictionary LUT of matrix IDs and Matrix instances.
• GatingResults class: the 'level' column of the report is now indexed at 0 (for root level).

Bug fixes:

• Ensure exporting of QuadrantGate raises NotImplementedError (see How to plot QuadrantGates? #209).
• Fixed plot_scatter error with 0 or 1 points (and 2 points with extent) (see Scatter plots error with few points #197).
• Better error for invalid gate names '.' & '..' (see GateTreeError when loading a FlowJo workspace with "." gate name #220).

Documentation:

• Added more informative docstrings for transforms
• Testing code reorganized to factor constants to new test config file (Thanks @ksebby for PR Small test refactor #213).

Dependencies:

• Drops Python 3.8 support (EOL as of Oct 2024).
• Updated dependency versions for compatibility w/ Python 3.9 - 3.12 (see requirements.txt for details).

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This discussion was created from the release 1.2.0.