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Implement a basic set of node and edge errors #204

Merged
merged 16 commits into from
Feb 14, 2025
Merged

Implement a basic set of node and edge errors #204

merged 16 commits into from
Feb 14, 2025

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msschwartz21
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@msschwartz21 msschwartz21 commented Feb 10, 2025

Closes #181 by implementing a set of node and edge errors outside of the CTC errors. Currently, these errors only support one to one matching, but they could be extended to support many-to-many in the future if desired. I updated the metrics and docs accordingly.

FYI, I'm open to a name other than BasicErrors and BasicMetrics, but couldn't come up with anything better 😅

For the documentation of the metrics, I kept it pretty minimal and assumed that people know/can google precision/recall/f1, but if you think I should elaborate more let me know.

Types of Changes

What types of changes does your code introduce? Delete those that do not apply.

  • New feature or enhancement

Which topics does your change affect? Delete those that do not apply.

  • Track Errors
  • Metrics

Checklist

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  • I have read the developer/contributing docs.
  • I have added tests that prove that my feature works in various situations or tests the bugfix (if appropriate).
  • I have checked that I maintained or improved code coverage.
  • I have checked the benchmarking action to verify that my changes did not adversely affect performance.
  • I have written docstrings and checked that they render correctly in the Read The Docs build (created after the PR is opened).
  • I have updated the general documentation including Metric descriptions and example notebooks if necessary.

@msschwartz21 msschwartz21 added documentation Improvements or additions to documentation enhancement New feature or request topic: metrics topic: errors labels Feb 10, 2025
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codecov bot commented Feb 10, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.45%. Comparing base (31be450) to head (1f8b78b).
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #204      +/-   ##
==========================================
+ Coverage   95.00%   95.45%   +0.45%     
==========================================
  Files          18       20       +2     
  Lines         921     1013      +92     
==========================================
+ Hits          875      967      +92     
  Misses         46       46              

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@msschwartz21 msschwartz21 marked this pull request as ready for review February 10, 2025 20:59
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@cmalinmayor cmalinmayor left a comment

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Generally looks great, just left a few comments on the code. The tests are so sensible and complete 😄 I love it. One potential problem is that I tried to look at the docs and it seems that the build is not working in the PR? Not sure if that is just a one-time issue or if there is something actually wrong, but if you could investigate that would also be great.

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src/traccuracy/track_errors/basic.py Show resolved Hide resolved
@msschwartz21 msschwartz21 merged commit 9743fbe into main Feb 14, 2025
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@msschwartz21 msschwartz21 deleted the new-errors branch February 14, 2025 19:05
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Implement non-CTC node and edge errors
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