Function to add tracklets id to graph #9

JoOkuma · 2025-05-27T18:56:47Z

There is a bug in the subgraph and node mapping that needs to be fixed.

codecov-commenter · 2025-05-27T19:09:23Z

Codecov Report

Attention: Patch coverage is 60.27397% with 29 lines in your changes missing coverage. Please review.

Project coverage is 90.93%. Comparing base (f624781) to head (fde7e45).

Files with missing lines	Patch %	Lines
src/tracksdata/graph/_rustworkx_graph.py	40.00%	11 Missing and 4 partials ⚠️
src/tracksdata/functional/_napari.py	0.00%	14 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #9      +/-   ##
==========================================
- Coverage   94.35%   90.93%   -3.43%     
==========================================
  Files          22       24       +2     
  Lines         638      706      +68     
  Branches      106      118      +12     
==========================================
+ Hits          602      642      +40     
- Misses         21       46      +25     
- Partials       15       18       +3

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github-actions · 2025-06-03T03:29:29Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     540±3ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000     5.41±0s   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   57.7±0.07s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points          158±0.3ns

github-actions · 2025-06-03T04:30:07Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     549±2ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000    5.51±0.02s 
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   58.9±0.01s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points          159±0.7ns

github-actions · 2025-06-03T17:00:22Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     530±6ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000    5.26±0.01s 
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   56.0±0.02s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points            154±2ns

github-actions · 2025-06-03T17:57:18Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     481±6ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000     4.75±0s   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   50.7±0.05s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points            149±2ns

github-actions · 2025-06-03T18:05:43Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     476±1ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000    4.78±0.01s 
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   51.0±0.03s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points          157±0.3ns

github-actions · 2025-06-03T20:18:55Z

Benchmark Results

· Discovering benchmarks
· Running 2 total benchmarks (1 commits * 1 environments * 2 benchmarks)
[ 0.00%] ·· Benchmarking existing-py_home_runner_work_tracksdata_tracksdata_.venv_bin_python3
[25.00%] ··· Running (graph_backends.GraphBackendSuite.time_simple_workflow--).
[50.00%] ··· Running (graph_backends.RustWorkXGraphBackend.time_points--).
[75.00%] ··· ...kends.GraphBackendSuite.time_simple_workflow                 ok
[75.00%] ··· ========================================================= ========= ============
                                      backend                           n_nodes              
             --------------------------------------------------------- --------- ------------
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend     1000     484±3ms   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    10000     4.79±0s   
              tracksdata.graph._rustworkx_graph.RustWorkXGraphBackend    100000   51.1±0.04s 
             ========================================================= ========= ============

[100.00%] ··· ...h_backends.RustWorkXGraphBackend.time_points          145±0.4ns

JoOkuma added 6 commits May 27, 2025 11:19

WIP getting code from ultrack

3cb82e5

fixed tests and implementation

d9ee2f7

renaming file

3a0e89b

adding missing file

1871d98

Merge branch 'jookuma/line-length' into jookuma/graph-track-id

f683b56

Merge branch 'main' into jookuma/graph-track-id

59c7fff

JoOkuma added 2 commits June 2, 2025 10:47

Merge branch 'main' into jookuma/graph-track-id

1e0d88f

adding subgraph from edge filter

8508b80

refactoring distance edges and other tests

36b7e84

Merge branch 'main' into jookuma/graph-track-id

0eda653

working version of track ids

94883e6

JoOkuma added 2 commits June 3, 2025 10:58

fixing subgraph mapping

b1a5b13

adding regression test

9177f04

WIP napari compatible format

fde7e45

JoOkuma mentioned this pull request Jun 5, 2025

Improving slicing abstraction with GraphView #16

Merged

JoOkuma closed this pull request by merging all changes into main in f0b16b8 Jun 5, 2025

JoOkuma deleted the jookuma/graph-track-id branch June 5, 2025 23:33

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Function to add tracklets id to graph #9

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JoOkuma commented May 27, 2025 •

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JoOkuma commented May 27, 2025 •

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