Update dependency flowkit to v1.2.1

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
flowkit	1.0.1 -> 1.2.1

---

Release Notes

whitews/flowkit (flowkit)

v1.2.1

Compare Source

BUGFIX: Fixes regression in loading resources, dropping pkg_resources and using importlib (thanks to @​tristan-ranff for PR #​224)

v1.2.0

Compare Source

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 #​179).
• Added get_keywords method to Workspace for getting sample keywords stored in a FlowJo workspace (see #​210).
• Workspace method get_gate_events now supports source kwarg to control pre-processing of returned events (see #​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 #​221).
• Sample class now supports renaming channels via a new rename_channel method (see #​198).
• Sample class methods get_events, get_channel_events and as_dataframe support event_mask kwarg for filtering events using a Boolean array (see #​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 #​200).
• New utils module function generate_transforms to generate a set of transforms for a Sample (see #​162).

API changes:

• Transform class: removed id attribute. This allows more convenient use of independently using transforms outside of a GatingStrategy (see #​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 #​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 #​209).
• Fixed plot_scatter error with 0 or 1 points (and 2 points with extent) (see #​197).
• Better error for invalid gate names '.' & '..' (see #​220).

Documentation:

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

v1.1.2

Compare Source

• BUGFIX: Fix typo in Matrix.fluorochromes attribute. Thanks to @​okolupaev for reporting #​206!

v1.1.1

Compare Source

• BUGFIX: Fix ModuleNotFoundError for pkg_resources package in newer Python versions. Now using importlib when available for loading non-code resources. Thanks to @​tristan-ranff for PR #​192!

v1.1.0

Compare Source

Hey FlowKit community! Lots of changes in this release, including support for Python 3.11 & 3.12. The major updates: we've moved to a src based structure using pyproject.toml and finally converted all plotting functions to Bokeh (dropping matplotlib and Seaborn as requirements). Read the notes below for all the changes.

Special thanks to @​hbhargava7 and @​laserson for their contributions to this release!

New features:

• New utility function read_multi_dataset_fcs for reading FCS files with multiple data sets (returns a list of Sample instances).
• Workspace class now has an option to load FCS files from the URI parameter embedded in the WSP file (Many thanks to @​hbhargava7 for PR #​168).
• Sample.plot_scatter_matrix now displays histograms along the diagonal (Thanks @​laserson for the suggestion in #​169).
• Exporting FlowJo 10 workspaces now supports the WSPBiexTransform.
• Sample.plot_scatter adds event_mask option to filter the plotted events.
• Sample.plot_contours & Sample.plot_channel methods now use Bokeh.
• Custom heatmap color palette was improved (it's subtle but has better visual contrast between density levels).

API changes:

• Sample.plot_histogram method adds data_min, data_max, and x_range kwargs for filtering data ranges and controlling the view range.
• Removed argument ignore_transforms in parse_wsp utility function.
• Transforms from a GatingML document are no longer imported as undocumented "GML" sub-classes, instead using the documented Transform sub-classes.
• Added kwarg gate_path to plot_scatter method in both Session & Workspace.
• sample_id argument now required for GatingStrategy.is_custom_gate method.
• Rename plot_scatter argument highlight_indices to highlight_mask (since it takes a Boolean array and not a list of indices).
• plot_scatter argument dim_ids split to x_label & y_label for specifying axis labels.
• plot_gate argument dim_ids split to x_label & y_label for specifying axis labels.

Bug fixes:

• Fixed KeyError in Workspace.summary method when a sample has no gates (see #​155).
• Fixed WSP export of "range" RectangleGate instances (see #​157).
• Fix ValueError thrown when compensating a Sample specifying null channels via null_channel_list (see #​175).
• Fix Session.plot_scatter method where mixed compensations are specified for x & y channels (rare).

Documentation:

• Switched to ReadTheDocs theme for documentation.
• Clarify docstrings for null channel usage (see Sample & Matrix constructor docs).
• All notebooks validated and updated for the new release.

Dependencies:

• Dropped support for Python 3.7, added support for Python 3.11 & 3.12.
• FlowIO updated to >=1.3.0,<1.4
• FlowUtils updated to >=1.1.0,<1.2
• Matplotlib & Seaborn removed as dependencies. All plotting now uses the Bokeh library (>=3.1).
• Pandas updated to >=2.0
• Added new dependency contourpy (the library matplotlib uses).
• Other dependency minimum versions updated for Python 3.8 - 3.12 support (See requirements.txt for details).

---

Configuration

📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

---

• If you want to rebase/retry this PR, check this box

---

This PR was generated by Mend Renovate. View the repository job log.