Flowkit

BUGFIX: Fixed case where some transforms fail when given a 1-D numpy array of events (issue 71)

New features:

* Experimental support for exporting FlowJo 10 workspace files (limited to single sample groups)
* Added support for FlowJo 10 biex transform
* Added inverse transform methods for most transformations
* implement `ignore_transforms` option for parsing FJ10 workspaces
* Sample.apply_transform supports customized transforms per channel via dictionary
* Create Sample instances from Pandas DataFrame w/MultiIndex columns
* Sample: store original events unprocessed

API changes:

* Sample: added attributes `scatter_indices` & `time_index`
* Sample: `apply_transform` method now has option to include scatter channels
* GatingStrategy: `get_gate_ids` now returns a list of tuples containing the gate ID & list of ancestors (gate path)
* GatingStrategy: new method `get_root_gates` for ...
* GatingStrategy: simplify GatingStrategy methods for retrieving gates,
* GatingStrategy: added new convenience method get_child_gates
* Session: new method `get_group_comp_matrices`
* Session: all method arguments referencing a sample group name are now consistent ('group_name')
* Session: new method to get all gate IDs & paths for a sample
* Session: new method `get_group_transforms` for retrieving group transformations
* Session: new method `export_wsp` for exporting a sample group's gating strategy as a FlowJo 10 workspace
* Session: new methods for retrieving Sample specific comp matrices & transforms for a group
* Session: new method for retrieving gated events for a Sample
* Compensation utility functions moved to FlowUtils
* make sample utils functions public
* expose calculate_extent function for flowkit-extras

Bug fixes:

* Clearer error message when requesting sub-sampled events from `get_channel_data` when Sample has not been sub-sampled
* Fixed issue where gain was incorrectly applied to time channel data
* Allow re-use of gates on different branches at any level
* Applying re-used gates requires the Gate instance to know the full path
* Fixed plot_scatter for cases where the event arrays are empty
* Session.get_group_samples() now only returns loaded samples

Documentation:

* Added more docstrings for Sample, Session, Transform methods
* Updated tutorial notebooks
* Added notebook for calculating mean fluorescence intensity (MFI) per channel for gated populations

Dependencies:

* Support for Python 3.8
* Removed MulticoreTSNE dependency
* Removed sklearn dependency
* Most transform implementations moved to FlowUtils

New features:

* GatingStrategy & Session classes now support re-using gate IDs in different gate hierarchy branches (i.e. having a child gate "IFNg+" under both a "CD4+" and "CD8+" gate)
* Added support for FlowJo 10 ellipsoid gates
* Plotting of gates in Session class now plots only events from the parent gate
* Added plotting of Quadrant gates
* Added bokeh hover tool to scatter plots
* Re-enabled multiprocessing by default for faster processing of gates in a Session
* Updated plot colormap for better contrast with gate boundaries

API changes:

* Major cleanup of public/private modules for cleaner API
* New Quadrant class for cleaner API when creating QuadrantGate instances
* New `wsp_transforms` module containing FlowJo specific Transform sub-classes
* GatingStrategy, Session - added `get_transform` and `get_comp_matrix` methods
* GatingStrategy, Session - added `gate_path` kwarg for ambiguous gates in `get_gate` & `get_gate_indices`
* Session: add `sample_id` option to `analyze_samples` to process a single Sample
* Session: added `ignore_missing_files` option to `import_flowjo_workspace` method for suppressing warnings about missing FCS files when importing a FlowJo WSP file
* Gate class - added `get_dimension` method
* Sample: rename Sample method to `as_dataframe` (consistent with Matrix class), & added options to re-order and rename columns in output DataFrame
* Sample: 'fcs' is no longer the default ID when adding a compensation matrix (it is reserved for the embedded comp matrix from the `spill` metadata value)
* Matrix: `fluorochromes` argument is now optional
* Matrix: new method `as_dataframe` to get comp matrix as a Pandas DataFrame
* Dimension: 'uncompensated' is now the default value when creating Dimension instances

Bug fixes:

* Properly support time channel data when `timestep` keyword is present in FCS metadata
* Fixed display of plotted ellipses (corrected angle)
* Fixed parsing of compensated dimension references in FlowJo WSP files
* Fixed import of CSV compensation files with commented header
* Fixed creation of Sample instances from Pandas DataFrame
* Fixed parsing of FlowJo gate IDs for some WSP variants

Documentation:

* Documentation now on [ReadTheDocs](https://flowkit.readthedocs.io/en/latest/)
* Many more docstrings for classes and methods
* Added contribution guidelines
* New tutorial notebook to demonstrate loading of FlowJo workspaces & programmatically replicating the gating strategy
* New example notebook showing compensation and Matrix class usage

New features:

* Plotting of gates in Session class: limited to polygon, rectangle, range, and ellipse gates.
* Session now supports importing FlowJo workspace files, though support is limited to WSP files with linear, log, logicle transforms, and only polygon & rectangle gates.
* Session class now supports multiple gating strategies via the implementation of "sample groups", similar to how FlowJo works.
* Sample class now allows retrieving events as Pandas DataFrames, with multi-index columns as the PnN and PnS labels

API changes:

* Session: add get methods for sample IDs, sample groups, and gate IDs
* More consistent handling of Matrix class as input to compensation methods
* Expose parse_gating_xml function
* Expose plot_channel function

Bug fixes:

* Handle case where a Sample has no keyword for original filename
* Fix re-subsampling after applying Sample filters
* Ensure correct fluoro order when parsing a comp matrix from a CSV file

API changes:

* New Session method for adding samples after a Session instance has been created

Bug Fixes:

* Sample export failed to create file

New features:

* Programmatically add gates, transforms, and compensation matrices to a GatingStrategy
* Export a GatingML 2.0 compliant document from a GatingStrategy

API improvements:

* Gate sub-classes no longer require a GatingStrategy in their constructor, allowing re-use of instantiated gates
* New convenience methods in the Session class for getting parent gates and creating gates, transforms, and comp matrices
* Better x & y axis labels in scatter plot (includes marker names, if available)

Bug fixes:

* Fixed bug in GatingStrategy method get_gate_by_reference where an existing QuadrantGate could not be found
* Fixed bug in parsing spillover matrix from a $SPILL keyword value of an FCS file