v0.7

trackpy v0.7 includes an enhancement/bug fix to how MSD calculations handle gaps
in trajectories. The msd() and imsd() functions now output NaN values (instead
of zeros) for portions of their output that could not be measured. The emsd()
function now properly de-weights missing data, and so its output may be
significantly different (and more accurate) when gaps are numerous and large.

Bug fixes

• MSD properly handles gaps in trajectories (@vivarose, #773)
• Fix plot_traj(colorby='frame') for intermittent particles. (@T0T0R, #777)
• Let imsd() use output of subtract_drift() (@nkeim, #785)

Enhancements

• Clarify what parameters are keyword-only in documentation of link functions
  (@anntzer, #789)

v0.7rc1

trackpy v0.7 includes an enhancement/bug fix to how MSD calculations handle gaps
in trajectories. The msd() and imsd() functions now output NaN values (instead
of zeros) for portions of their output that could not be measured. The emsd()
function now properly de-weights missing data, and so its output may be
significantly different (and more accurate) when gaps are numerous and large.

Bug fixes

• MSD properly handles gaps in trajectories (@vivarose, #773)
• Fix plot_traj(colorby='frame') for intermittent particles. (@T0T0R, #777)
• Let imsd() use output of subtract_drift() (@nkeim, #785)

Enhancements

• Clarify what parameters are keyword-only in documentation of link functions
  (@anntzer, #789)

v0.6.4

This is a maintenance release for compatibility with numpy 2.0. Note that the optional PyTables dependency is not yet compatible with numpy 2.0. For details and updates, see PyTables/PyTables#1172

v0.6.3

trackpy v0.6.3 is a minor compatibility update for newer Pandas verisons. See http://soft-matter.github.io/trackpy/dev/whatsnew.html

v0.6.3rc1

trackpy v0.6.3 is a minor compatibility update for newer Pandas verisons. See http://soft-matter.github.io/trackpy/dev/whatsnew.html

v0.6.2

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.

0.6.2rc1

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

v0.6.1

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 for more information.

v0.6.1rc1

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 for more information.

v0.6.0

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.