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- 14 commits
- 135 files changed
- 3 contributors
Commits on Aug 26, 2024
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* bump version to 0.1.1 * version needs to be 0.1.2 to match release
Commits on Oct 29, 2024
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Handle unsupported geometry types (#91)
* add test data that breaks extract_points_from_geometry * replace images filename in slp file * update OlderMonocotPipeline notebook * return empty list if unsupported geometry type * update oldermonocot pipeline * use logging statements for convex hull calculations * modify tests for two plants * check intersection for empty list, return nans * add more test for unexpected inputs to extract_points_from_geometry * include empty MultiLineString and remove duplicate test * update OlderMonocot notebook * add stunted 10 day-old rice predictions as fixture * fix paths * organize and add needed imports * update OlderMonocot pipeline notebook * black * black * test new fixture * black * black * add more unexpected types * use logging * add test for inf values * add more tests for multilinestring * add tests for nex convex hull features using rice fixture * black
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Commits on Mar 19, 2025
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Test plant trait computation for DicotPipeline (#95)
* add dicot pipeline test data * black * black * add pytest fixture for canola traits * add traits csv for soy and add pytest fixture * delete tests/data/canola_7do/my_summarized_traits.csv * fix path name for dicot trait csvs * add tests for computing dicot traits * shorten dicot compute_plant_traits test * add range and type checks and remove test_series.py error * remove failing series.py line * delete tests/test_DicotPipeline.py * fix crown and expected labeled frame instances comparison * add comma to angle traits tuple Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * remove unused variables and add docstring --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Commits on Apr 2, 2025
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Add YoungerMonocotPipeline Tests (#102)
* add tests to YoungerMonocotPipeline and add saved traits csv * add YoungerMonocotPipeline tests * update docstrings for rice traits csv files * update rice folder path * update younger monocot notebook * update sample variables * fix minor spelling errors * add comparison to fixture and add descriptive comments * correct inputs for traits involving pts_all_array * change proximal parameter in primary_angle_distal
Commits on Apr 9, 2025
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Add Return Value to Series.plot (#105)
* add return value to series.plot * update series plot logic * update comments on Series.plot() * add test to series plot function * update commends and change which plot is closed * change variable name plt to fig
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Add OlderMonocotPipeline Tests (#103)
* update OlderMonocot notebook and add pipeline outputs as csv files * update fixture and add manual trait calulcation * remove duplicate OlderMonocotPipeline test * remove unused trait pts_all_array * add camel case test * change pts_all_array to crown_pts in older monocot * add old test referencing pipeline output * remove range type and dataframe check * remove dataframe shape check * remove old test
Commits on Apr 29, 2025
Commits on May 5, 2025
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Implement PrimaryRootPipeline (#115)
* upload first implementation of PrimaryRootPipeline in notebook * add PrimaryRootPipeline into trait_pipelines.py * add missing check to get_base_ys to match get_tip_ys * update traitdefs in trait_pipelines.py and add discontinuous root notebook * remove unused traitdef pts_list * standardize behavior of tip and base functions * remove MultipleDicotPipeline class * add test for PrimaryRootPipeline and update test in tips.py * fix style * add descriptions to traitdefs * update mermaid diagram to include PrimaryRootPipeline * rewrite PrimaryRootPipeline notebook * delete unnecessary notebooks * update pipeline test to include manual calculation * minor style fixes * update description in angle traits * add tests to bases * add tips tests * add bbox helper function and tests * add new bbox traits and update notebook
Commits on May 9, 2025
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Add lateral root only pipeline (#121)
* add lateral root pipeline * add test for lateral root pipeline * fix type * add primary root pipeline and lateral root pipeline to init * add mermaid diagrms to repo * add lateral root pipeline example notebook * update mermaid graphs
Commits on May 15, 2025
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Add MultipleDicotPipeline Tests (#104)
* update MultipleDicotPipeline notebook * fix incorrect path in notebook * add first version of updated test * add summary trait check and clean up comments * update tests without fixtures * add fixtures for batch traits * add csv fixtures * sort keys in compute_multiple_dicots_traits * remove sorting and remove unused data in multiple arabidopsis * reorganize multiple arabidopsis folder and add manual vs fixture check * remove unnecessary change to iterate over dict * remove unnecessary conversion of batch dataframe columns * add md file explaining directory structure * update tests * add associations check in manual calculation * remove unnecessary string datatype conversion in dataframe
Commits on Jun 23, 2025
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Implement MultiplePrimaryRootPipeline (#117)
* upload first implementation of PrimaryRootPipeline in notebook * add PrimaryRootPipeline into trait_pipelines.py * add missing check to get_base_ys to match get_tip_ys * update traitdefs in trait_pipelines.py and add discontinuous root notebook * remove unused traitdef pts_list * standardize behavior of tip and base functions * remove MultipleDicotPipeline class * add test for PrimaryRootPipeline and update test in tips.py * fix style * add descriptions to traitdefs * update mermaid diagram to include PrimaryRootPipeline * rewrite PrimaryRootPipeline notebook * delete unnecessary notebooks * upload first implementation of multiple primary root pipeline * add group level computation to MultiplePrimaryRootPipeline * add MultipleDicotPipeline test * add tests to filter_primary_roots_with_unexpected_ct * add pipeline specific fixtures to arabidopsis test data and add batch tests * add macos to CI matrix to see if failure is OS dependent * remove macOS from CI matrix * add manual and computed output comparison in test and reorganize arabidopsis data folder * fix minor errors and duplication * add MultipleDicotPipeline tutorial notebook * add test with empty series * add plate data as test dataset * fix variable assignment * update new fixture descriptions * update compute_multiple_primary_roots_traits with per_instance flag
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