1.0.0

[whitews]

Version 1.0.0 is a major milestone for the FlowKit project. This release adds support for custom sample gates in FlowJo 10 workspaces. As a major release, this version has significant API changes. Please read the release notes below and review the documentation for all the API changes.

New features:

• New dedicated Workspace class for importing FlowJo 10 workspaces. This class is essentially a read-only class for easily importing & extracting gating information from .wsp files.
• Importing .wsp files now supports 'eventsInside' flag for FlowJo gates (see Account for "EventInside" parameter in flowjo gate definition #135)
• Session & GatingStrategy classes now support custom gates by specifying a sample_id when adding a gate to the gate tree.
• Session & GatingStrategy classes now support removing gates from the gate tree via a new remove_gate method. The method includes an option to retain downstream (descendant) gates.
• Sample class adds method get_index_sorted_locations for FACs Diva index sorted files (see Retrieve index sorted information from FCS files (if available) #112)
• Sample class adds id attribute, allowing identification of samples created from NumPy arrays or pandas DataFrames.
• Sample class supports sorting (samples will be sorted by id attribute)
• Sample class constructor supports new arguments for controlling behavior in cases where there is a discrepancy in the data offset location (see Offset error not detected #136)
• Sample method plot_scatter adds highlight_indices option for highlighting events using a Boolean array.
• Transform classes now support comparison for determining if 2 transforms are equivalent (i.e. have the same parameters).

Removed features:

• Removed calculate_compensation_from_beads, the function was moved to the flowkit_extras package (see Remove creating compensation from bead samples #123)
• Session class no longer imports FlowJo 10 workspaces, this functionality now lives in the dedicated Workspace class
• Session class no longer uses sample groups, simplifying the API. Sample groups were needed for FlowJo workspaces.

API changes:

• New exceptions module containing custom FlowKit exceptions and warnings. This module also imports FlowIO exceptions so users can import all of them from one source.
• Session method get_group_samples was removed. group_name option removed from all Session methods.
• Session and GatingStrategy method get_child_gates was removed. A new method get_child_gate_ids was added. Gate instances are only available via get_gate.
• Session and GatingStrategy method get_parent_gate was removed. A new method get_parent_gate_id was added. Gate instances are only available via get_gate.
• GatingStrategy now has a is_custom_gate method for determining whether a Gate ID, Sample ID combination has a custom gate or the template gate.
• Session & Sample plot_scatter methods now take an optional bin_width argument to control the smoothness of the color density
• Gate classes no longer take the parent_gate_name argument. Gate relationships are handled completely by the GatingStrategy class.
• Gate classes have a new get_dimension_ids for retrieving Dimension IDs.
• Vertex class was removed. PolygonGate vertices are now just tuples of floats.

Bug fixes:

• Fix sample export of orig data for FCS files with data type int
• Fixed case where adding gates directly under QuadrantGate was possible. Adding a child gate to a QuadrantGate directly is not allowed, they must be added a one of the Quadrant instances.
• Fix parsing of FlowJo workspaces where a sample has no gate data.
• Fixed color density in scatter plots to correct missing 1st bin & poor coloring for data sets with outliers (see plot_scatter() density coloring is distorted #139)

Documentation:

• Docstring for Sample method subsample_events corrected to reflect that the method does not return anything (see subsample_events() does not return anything #129)
• Top-level functions & exceptions were added to the documentation
• All tutorial & advanced notebooks were updated for compatibility with the new API.

Dependencies:

• FlowIO requirement updated to 1.1.1
  latest seaborn changes API, lock down version
• Removed statsmodels dependency (see Remove creating compensation from bead samples #123)
• Other dependency minimum versions updated for Python 3.7 - 3.10 support (See requirements.txt for details)

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This discussion was created from the release 1.0.0.