Trackpy

trackpy v0.6.2 includes bug fixes, and compatibility fixes with newer dependency versions.

A special thanks to everyone who reported the issues fixed in this release!

Bug fixes
- Fixed an issue with feature-finding in 4D image sequences (VeraMTitze, 739)
- Fixed a rare issue in which subtract_drift() with multiple particles
resulted in a Pandas indexing error. (kevin-duclos, 735)

Dependencies
- Adds official support for Python 3.12. (caspervdw, 747)
- Adds support for latest Pandas, NumPy, and SciPy (marcocaggioni, 740; nkeim, 743, vivarose and rodrigo-j-goncalves, 742; caspervdw, 747)
- Drops official support for Python 3.7 and earlier, NumPy 1.17 and earlier, Pandas 0.x, and SciPy 1.3 and earlier.

See http://soft-matter.github.io/trackpy/dev/whatsnew.html for release notes.

trackpy v0.6.1 is functionally equivalent to v0.6.0. It is being released to fix an issue with Zenodo, so that this trackpy release has a citable DOI.

See the [release notes for v0.6.0](http://soft-matter.github.io/trackpy/v0.6.0/whatsnew.html) for more information.

trackpy v0.6.1 is functionally equivalent to v0.6.0. It is being released to fix an issue with Zenodo, so that this trackpy release has a citable DOI.

See the [release notes for v0.6.0](http://soft-matter.github.io/trackpy/v0.6.0/whatsnew.html) for more information.

This release focuses on fixing bugs and some inconsistencies in the prediction
capabilities. Some existing code that used prediction may now fail to run until
a (minor) update is made.

This release includes contributions by magnunor, freemansw1, crisp-snakey,
rbnvrw, caspervdw, tacaswell, and nkeim.

Enhancements

- Linking can now use any ``DistanceMetric`` class from sklearn to compute
distances (692 by freemansw1)
- Several documentation fixes by magnunor and nkeim

API Changes

- When supplying an initial velocity guess to NearestVelocityPredict or
DriftPredict, you must also supply the pos_columns argument to identify
the names of the columns in your array. (For example,
"pos_columns = ['y', 'x']".) Otherwise, creating the predictor will
raise an exception that explains this change. If you provide pos_columns
when creating the predictor, you do not have to supply it when subsequently
using the link_df() or link_df_iter() methods to link your features.
(nkeim, 710)
- ``reconnect_traj_patch()`` is now available as ``trackpy.reconnect_traj_patch``
and is described in the API documentation. (nkeim, 648)

Bug Fixes

- When linking with prediction, the predictor now correctly uses the same
position columns as the linker, and correctly handles the pos_columns
argument if specified. (nkeim, 710)
- The link_df() method of predictor objects now works correctly. (nkeim, 710)

Dependencies

- trackpy is now being tested in conda environments with Python 3.10.
- trackpy is no longer tested with Python 3.6.
- trackpy now requires the ``looseversion`` package to work with newer scipy
(crisp-snakey, 706)
- Much work on testing and packaging infrastructure by tacaswell and caspervdw

**Note:** This release is tagged `v0.6.0.1` on GitHub to address an issue with Zenodo DOI generation. There are no other differences between the GitHub version and the `v0.6.0` packages.

This is a major release focused on enhancements. Most notably, parallel processing is now turned on by default for “trackpy.batch” and “trackpy.locate_brightfield_ring”, resulting in a large performance increase for many users. Another minor speedup changes the way in which particle numbers are generated, which may cause issues with reproducibility in some existing workflows (see “API Changes” below).

Note that Python 2 reached end-of-life in 2020, and it is no longer officially supported by trackpy. Also, trackpy dropped support for older NumPy, Scipy and Pandas. The current minimum requirements are: `python>=3.6 numpy>=1.14 scipy>=1.1 pandas>=0.22`.

See the "What's new in the package" page in the [documentation](http://soft-matter.github.io/trackpy/v0.5.0/whatsnew.html) for a full list of changes.