Traccuracy

<!-- Release notes generated using configuration in .github/release.yml at v0.2.0 -->

What's Changed
✨ Features
* Metrics validate that the matcher is supported by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/170
* Update node and edge annotations to be sparse by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/192
* Add dictionary mappings to the Matched class by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/201
* Compute the matching type for each dataset and use for metric validation by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/202
* Implement a basic set of node and edge errors by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/204
* Update run metrics to return results and matched object by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/208
🚀 Performance
* Extend benchmarks by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/74
* Pre-allocate numpy array and populate during reading for ctc loader by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/199
🐛 Bug Fixes
* Fix frame buffer bug where predecessors were not checked properly by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/155
* Update example notebooks and run in CI by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/196
* Bugfix: fix testing issue with GT nodes matched to NS nodes by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/200
* Incorrect daughter in division is labeled as wrong child by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/193
* Remove unnecessary casting in get_labels_with_overlap by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/197
* Warn and return nans for metrics if there are no divisions in the gt by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/198
🧰 Maintenance
* ci(dependabot): bump codecov/codecov-action from 4 to 5 by dependabot in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/168
* Canonical unit test examples: Segmentations for matching, and matched graphs without divisions by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/171
* Test CTCMatcher using standard test cases by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/174
* Add tests cases to docs using example notebook by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/172
* Test the IOU matcher using standardized segmentation test cases by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/173
* Add standard division test cases by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/175
* Test division errors using standard test cases by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/177
* Add tests for CTC node and edge track errors by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/176
* Update the test case notebook with py:percent files by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/180
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/186
📚️ Documentation
* Expand CTC DET Measure docs by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/130
* Add written documentation for errors and metrics by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/116
* Add written documentation for the ctc error types with example graphs by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/178
* Add example graph plots for division error documentation by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/189
Miscellaneous
* Speed up IoU Matcher by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/156
* Group PRs in release notes based on labels by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/160
* Reduce number of checkboxes in issue and PR templates by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/159
* Add data download to benchmark report action by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/167
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/158


**Full Changelog**: https://github.com/Janelia-Trackathon-2023/traccuracy/compare/v0.1.1...v0.2.0

What's Changed
* Add pyarrow to pyproject by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/142
* ci(dependabot): bump actions/cache from 3 to 4 by dependabot in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/140
* Fix CTC matching for emtpy frames by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/139
* ci(dependabot): bump codecov/codecov-action from 3 to 4 by dependabot in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/143
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/144
* Speed up CTCMatcher by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/148
* Remove support for python 3.8 by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/151
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/146
* ci(dependabot): bump softprops/action-gh-release from 1 to 2 by dependabot in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/145
* Add iou matcher option to use linear assignment to get one-to-one matching by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/150
* Fix multiple IOU-related bugs by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/153
* Check empty subgraph by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/141
* ci(pre-commit.ci): autoupdate by pre-commit-ci in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/154


**Full Changelog**: https://github.com/Janelia-Trackathon-2023/traccuracy/compare/v0.1.0...v0.1.1

What's Changed
* Improve rendering of cli documentation in cli and in Read The Docs by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/29
* Add report of matcher coverage by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/34
* Use appropriate label key for `gt` and `pred` graphs in `ctc` matching by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/35
* Remove detection matrix computation by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/36
* Faster matchings/metrics by maweigert in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/37
* Create Enums for our Node and Edge Attribute strings by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/46
* Eliminate use of `TrackEvents` in in CTC error calculations by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/47
* Eliminate use of `DivisionEvents` and reorganize placement of division functions by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/48
* Remove `TrackingData` by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/50
* Graph access funcs by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/51
* README update by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/55
* Add function to extract tracklets by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/56
* Use logging API by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/58
* Add basic set of performance benchmarking tests by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/62
* Improve the benchmarking workflow to generate a commit comment on PRs by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/64
* Improve benchmark action when running on repo forks by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/65
* Annotate intertrack edges in the ctc `get_edge_errors` function by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/54
* Correct benchmarking tests assertion for wrong semantic edges by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/66
* Speed up accessing nodes/edges by attribute and node/edge attributes by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/63
* Speed up CTC edge errors by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/59
* test: enable codecov by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/69
* style: update pre-commit by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/70
* docs: fix docs build, fix all build warnings, enable strict mode by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/71
* Adding track overlap metrics from `laptrack` by yfukai in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/112
* Refactor existing `Matched` into separate `Matcher` which returns `Matched` by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/103
* Refactor `Metrics` class to pass data into compute method not constructor by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/109
* Add pull request and issue templates by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/121
* Create general pr template by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/122
* Remove Pr template headers by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/123
* Fix subclass docstrings for sphinx autoapi by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/124
* fix import loop by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/125
* Update `run_metrics` to take instantiated `Matchers` and `Metrics` as input by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/118
* style: cleanup string type annotations by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/104
* Add CTC format checks in loader by bentaculum in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/119
* Create a `Results` class for storing metric output with associated metadata by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/126
* Prune tracking graph API by cmalinmayor in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/111
* Change `frame_buffer` kwarg to `max_frame_buffer` by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/136

New Contributors
* maweigert made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/37
* cmalinmayor made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/46
* bentaculum made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/58
* dependabot made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/52
* yfukai made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/112
* pre-commit-ci made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/113

**Full Changelog**: https://github.com/Janelia-Trackathon-2023/traccuracy/compare/v0.0.2...v0.1.0

What's Changed
* Correct name in documentation files by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/16
* Add `run-metrics` function by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/17
* Fix results return and support matcher kwargs by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/20
* Fix docstring for CTC loader and add test by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/21
* Add metrics_kwargs as explicit arg and fix matcher kwargs bug by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/22
* Add an example notebook for benchmarking CTC data by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/23
* Modify .py file names to prefix private modules with _ by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/24
* Remove unused ipython extension from docs by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/27
* Add support for skipped frames at divisions by adjavon in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/25
* Add basic CLI tools by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/26


**Full Changelog**: https://github.com/Janelia-Trackathon-2023/traccuracy/compare/v0.0.1...v0.0.2

What's Changed
* use numba instead of cython by tlambert03 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/3
* Add division evaluation with temporal tolerance by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/4
* Fix missing 't' for single nodes in track graph by adjavon in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/5
* Add base classes for new api by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/6
* Add label_key to TrackingGraph by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/7
* Pull code to get overlapping labels out into its own function by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/8
* Use `sphinx-autoapi` to automate api documentation by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/9
* Implement `DivisionMetrics` and `IOUMatched` classes by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/11
* Add sample tracking solution for Fluo-N2DL-HeLa ST segmentation by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/14
* Draft of README content by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/12
* Add cell tracking challenge metrics computation by DragaDoncila in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/10
* Rename `cell-tracking-metrics` to `traccuracy` by msschwartz21 in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/15

New Contributors
* tlambert03 made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/3
* msschwartz21 made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/4
* adjavon made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/5
* DragaDoncila made their first contribution in https://github.com/Janelia-Trackathon-2023/traccuracy/pull/6

**Full Changelog**: https://github.com/Janelia-Trackathon-2023/traccuracy/commits/v0.0.1