v0.4.3

What's Changed

🐛 Bug Fixes

• Use pylapy for solving the LAP (sparse) in PointMatcher by @raphaelreme in #320
• Pass label key to overlap compute by @DragaDoncila in #325
• Fix argument to _get_mbc by @DragaDoncila in #326
• Split error annotations into basic and ctc by @DragaDoncila in #324

🧰 Maintenance

• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #318
• ci(dependabot): bump actions/cache from 4 to 5 by @dependabot[bot] in #327
• ci(dependabot): bump actions/checkout from 5 to 6 by @dependabot[bot] in #322
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #323

New Contributors

• @raphaelreme made their first contribution in #320

Full Changelog: v0.4.2...v0.4.3

What's Changed

🐛 Bug Fixes

• Use pylapy for solving the LAP (sparse) in PointMatcher by @raphaelreme in #320

🧰 Maintenance

• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #318
• ci(dependabot): bump actions/cache from 4 to 5 by @dependabot[bot] in #327
• ci(dependabot): bump actions/checkout from 5 to 6 by @dependabot[bot] in #322

Miscellaneous

• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #323
• Pass label key to overlap compute by @DragaDoncila in #325
• Fix argument to _get_mbc by @DragaDoncila in #326
• Split error annotations into basic and ctc by @DragaDoncila in #324

New Contributors

• @raphaelreme made their first contribution in #320

Full Changelog: v0.4.2...v0.4.3

v0.4.2

What's Changed

Bugfix

• Set label_key in TrackingGraph after loading geff by @msschwartz21 in #317

Full Changelog: v0.4.1...v0.4.2

v0.4.1

What's Changed

🐛 Bug Fixes

• Update to geff v1 and add type checking by @msschwartz21 in #309

🧰 Maintenance

• ci(dependabot): bump actions/checkout from 4 to 5 by @dependabot[bot] in #300
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #307
• ci(dependabot): bump actions/setup-python from 5 to 6 by @dependabot[bot] in #310

Miscellaneous

• docs: 📝 Add metrics overview table and link to in depth descriptions in overviews by @cmalinmayor in #302
• Improve error test case coverage by @msschwartz21 in #303
• feat: ✨ Complete tracks metric by @cmalinmayor in #312
• Move CellCycleAccuracy out of ctc submodule into stand alone submodule by @msschwartz21 in #305
• Add tracking graph method for clearing annotations on the graph by @msschwartz21 in #306
• Expose relax skips as an option in run_metrics by @msschwartz21 in #314
• Use Flag.value for storing flags on graph by @msschwartz21 in #315

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

🐛 Bug Fixes

• Show track errors in autodocs by fixing public/private by @msschwartz21 in #256
• Ensure point loader always returns positive integer IDs by @DragaDoncila in #283
• Refactor ctc loader to use uint ids by @msschwartz21 in #281

Miscellaneous

• Load csv into TrackingGraph by @msschwartz21 in #244
• Pin click dependency to avoid docs build failure by @DragaDoncila in #248
• Allow positions stored as lists in a single attribute by @cmalinmayor in #237
• Document branching correctness = division F1 score by @msschwartz21 in #246
• Remove graph copying in division metrics with frame buffer by @DragaDoncila in #245
• Remove get subgraph by @cmalinmayor in #252
• Move TrackGraph node attr validation into a separate function with flag by @msschwartz21 in #255
• Update links throughout repo to point to new litt org by @msschwartz21 in #258
• Address impact of sparse annotations on metrics by @msschwartz21 in #257
• Add function to expand skip edges by @DragaDoncila in #249
• Incorporate skip edge errors into basic metrics by @msschwartz21 in #264
• Add a larger test case with multiple tracks and frames by @cmalinmayor in #268
• Update some docstrings by @cmalinmayor in #267
• Add TF measure to track_overlap by @DragaDoncila in #259
• Implement cell cycle accuracy metric by @msschwartz21 in #247
• Allow skip edges in divisions by @msschwartz21 in #253
• Documentation updates by @msschwartz21 in #265
• Update test cases to remove string ids by @msschwartz21 in #282
• Improving matching performance by @JoOkuma in #276
• Track overlap tests docs by @cmalinmayor in #285
• Implement a loader for geff data by @msschwartz21 in #288
• adding CHOTA metric by @JoOkuma in #274
• Remove some ctc functions from public export by @DragaDoncila in #292
• Allow skip edge relaxation in track overlap metrics by @DragaDoncila in #289
• Implement a geff exporter for annotated graphs and traccuracy results by @msschwartz21 in #290
• Raise error if only one graph has error annotations by @DragaDoncila in #294
• Check that node ids are positive integers by @msschwartz21 in #293
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #298
• Add tests and docs for TF measure by @DragaDoncila in #297

New Contributors

• @JoOkuma made their first contribution in #276

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

✨ Features

• Add LNK metric by @DragaDoncila in #205
• Point matcher by @cmalinmayor in #209
• Implement a point to segmentation matcher by @msschwartz21 in #234

🚀 Performance

• Improve runtime of TrackOverlap metrics by @DragaDoncila in #218

🐛 Bug Fixes

• CTC loader checks dimensionality of data to set TrackingGraph loc keys by @msschwartz21 in #236

🧰 Maintenance

• Add workflow for generating a test case coverage report by @msschwartz21 in #217
• Configure pixi for traccuracy by @msschwartz21 in #220
• Drop python 39 by @cmalinmayor in #227
• Add tests for correct usage of gap-closing or frame-skip edges by @DragaDoncila in #127
• Add python 312 and 313 by @cmalinmayor in #230
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #238

📚️ Documentation

• Update docs to use exclusively Myst Md by @msschwartz21 in #222
• Update dev docs with instructions to use pixi for building docs by @msschwartz21 in #232

Miscellaneous

• Replace black with ruff-format in precommit by @msschwartz21 in #221
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #203
• Remove pixi lock file and add to gitignore by @cmalinmayor in #229
• Fully type traccuracy by @msschwartz21 in #231
• Sort nodes to ensure point matcher is deterministic by @cmalinmayor in #243
• Limit CLI to CTC only by @msschwartz21 in #242

Full Changelog: v0.2.0...v0.3.0

v0.2.0

What's Changed

✨ Features

• Metrics validate that the matcher is supported by @msschwartz21 in #170
• Update node and edge annotations to be sparse by @msschwartz21 in #192
• Add dictionary mappings to the Matched class by @msschwartz21 in #201
• Compute the matching type for each dataset and use for metric validation by @msschwartz21 in #202
• Implement a basic set of node and edge errors by @msschwartz21 in #204
• Update run metrics to return results and matched object by @msschwartz21 in #208

🚀 Performance

• Extend benchmarks by @bentaculum in #74
• Pre-allocate numpy array and populate during reading for ctc loader by @cmalinmayor in #199

🐛 Bug Fixes

• Fix frame buffer bug where predecessors were not checked properly by @cmalinmayor in #155
• Update example notebooks and run in CI by @msschwartz21 in #196
• Bugfix: fix testing issue with GT nodes matched to NS nodes by @msschwartz21 in #200
• Incorrect daughter in division is labeled as wrong child by @msschwartz21 in #193
• Remove unnecessary casting in get_labels_with_overlap by @cmalinmayor in #197
• Warn and return nans for metrics if there are no divisions in the gt by @msschwartz21 in #198

🧰 Maintenance

• ci(dependabot): bump codecov/codecov-action from 4 to 5 by @dependabot in #168
• Canonical unit test examples: Segmentations for matching, and matched graphs without divisions by @cmalinmayor in #171
• Test CTCMatcher using standard test cases by @msschwartz21 in #174
• Add tests cases to docs using example notebook by @msschwartz21 in #172
• Test the IOU matcher using standardized segmentation test cases by @msschwartz21 in #173
• Add standard division test cases by @msschwartz21 in #175
• Test division errors using standard test cases by @msschwartz21 in #177
• Add tests for CTC node and edge track errors by @msschwartz21 in #176
• Update the test case notebook with py:percent files by @msschwartz21 in #180
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #186

📚️ Documentation

• Expand CTC DET Measure docs by @DragaDoncila in #130
• Add written documentation for errors and metrics by @msschwartz21 in #116
• Add written documentation for the ctc error types with example graphs by @msschwartz21 in #178
• Add example graph plots for division error documentation by @msschwartz21 in #189

Miscellaneous

• Speed up IoU Matcher by @bentaculum in #156
• Group PRs in release notes based on labels by @msschwartz21 in #160
• Reduce number of checkboxes in issue and PR templates by @msschwartz21 in #159
• Add data download to benchmark report action by @bentaculum in #167
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #158

Full Changelog: v0.1.1...v0.2.0

v0.1.1

What's Changed

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

Full Changelog: v0.1.0...v0.1.1

v0.1.0

What's Changed

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

New Contributors

• @maweigert made their first contribution in #37
• @cmalinmayor made their first contribution in #46
• @bentaculum made their first contribution in #58
• @dependabot made their first contribution in #52
• @yfukai made their first contribution in #112
• @pre-commit-ci made their first contribution in #113

Full Changelog: v0.0.2...v0.1.0

v0.0.2

What's Changed

• Correct name in documentation files by @msschwartz21 in #16
• Add run-metrics function by @DragaDoncila in #17
• Fix results return and support matcher kwargs by @msschwartz21 in #20
• Fix docstring for CTC loader and add test by @DragaDoncila in #21
• Add metrics_kwargs as explicit arg and fix matcher kwargs bug by @msschwartz21 in #22
• Add an example notebook for benchmarking CTC data by @msschwartz21 in #23
• Modify .py file names to prefix private modules with _ by @msschwartz21 in #24
• Remove unused ipython extension from docs by @msschwartz21 in #27
• Add support for skipped frames at divisions by @adjavon in #25
• Add basic CLI tools by @DragaDoncila in #26

Full Changelog: v0.0.1...v0.0.2

v0.0.1

What's Changed

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

New Contributors

• @tlambert03 made their first contribution in #3
• @msschwartz21 made their first contribution in #4
• @adjavon made their first contribution in #5
• @DragaDoncila made their first contribution in #6

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