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Refactoring trait pipeline (2/2) #48

Merged
merged 42 commits into from
Aug 2, 2023
Merged

Refactoring trait pipeline (2/2) #48

merged 42 commits into from
Aug 2, 2023

Commits on Jul 25, 2023

  1. Map convex hull traits

    @eberrigan
    eberrigan committed Jul 25, 2023
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  2. Change primary to lateral when monocots is True

    @eberrigan
    eberrigan committed Jul 25, 2023
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  3. Get tips x and y coordinates uses network map

    @eberrigan
    eberrigan committed Jul 25, 2023
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  4. Change "stem" to "root"

    @eberrigan
    eberrigan committed Jul 25, 2023
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  5. Fix tip y map

    @eberrigan
    eberrigan committed Jul 25, 2023
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  6. Change root width back to take lateral_pts

    @eberrigan
    eberrigan committed Jul 25, 2023
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  7. Changing the order of positional arguments to match others (primary i… 

    …s first)
    @eberrigan
    eberrigan committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. Fix plotting for using sleap-io API

    @eberrigan
    eberrigan committed Jul 26, 2023
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  2. Merge branch 'elizabeth/fix_plotting' into elizabeth/pipeline_cache

    @eberrigan
    eberrigan committed Jul 26, 2023
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  3. Make positional arguments consistent

    @eberrigan
    eberrigan committed Jul 26, 2023
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  4. Refactor get_base_xs to use graph

    @eberrigan
    eberrigan committed Jul 26, 2023
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  5. Map scanline_intersection_counts and use keyword arguments

    @eberrigan
    eberrigan committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. Refactor get_base_ys, get_base_length, and base_ct_density to u… 

    …se graph and add comments. Delete duplicate `primary_depth`.
    @eberrigan
    eberrigan committed Jul 27, 2023
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  2. Clean up dependencies. Fix tip_ys.

    @eberrigan
    eberrigan committed Jul 27, 2023
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  3. Refactor get_root_lengths_max for use with graph

    @eberrigan
    eberrigan committed Jul 27, 2023
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  4. Refactor get_base_tip_dist to make base and tip pts or all points o… 

    …ptional arguments
    @eberrigan
    eberrigan committed Jul 27, 2023
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  5. Delete primary_depth

    @eberrigan
    eberrigan committed Jul 27, 2023
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  6. Delete traitsgraph

    @eberrigan
    eberrigan committed Jul 27, 2023
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  7. Delete traitsgraph dependencies

    @eberrigan
    eberrigan committed Jul 27, 2023
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  8. Refactor base-related traits to use graph optionally

    @eberrigan
    eberrigan committed Jul 27, 2023
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  9. Delete traits graph dependency

    @eberrigan
    eberrigan committed Jul 27, 2023
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  10. Use get_primary_pts from series class

    @eberrigan
    eberrigan committed Jul 27, 2023
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  11. Delete get_primary_depth tests

    @eberrigan
    eberrigan committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. Fix trait map for base traits

    @eberrigan
    eberrigan committed Jul 28, 2023
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  2. Delete test for traitsgraph.py

    @eberrigan
    eberrigan committed Jul 28, 2023
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Commits on Jul 31, 2023

  1. Standardize trait definition in trait map

    @eberrigan
    eberrigan committed Jul 31, 2023
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  2. Change "graph" to "trait"

    @eberrigan
    eberrigan committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Fix docstrings in get_bases

    @eberrigan
    eberrigan committed Aug 1, 2023
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  2. Use TraitDef class

    @eberrigan
    eberrigan committed Aug 1, 2023
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  3. Fix docstrings

    @eberrigan
    eberrigan committed Aug 1, 2023
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  4. Add argument to class TraitDef whether to include in csv or if scalar

    @eberrigan
    eberrigan committed Aug 1, 2023
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  5. Change attr to attrs

    @eberrigan
    eberrigan committed Aug 1, 2023
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  6. Add lengths.py for length-related traits.

    @eberrigan
    eberrigan committed Aug 1, 2023
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  7. Add primary_max_length_pts to trait definitions

    @eberrigan
    eberrigan committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. Add pts_all_array and convex_hull trait definitions

    @eberrigan
    eberrigan committed Aug 2, 2023
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  2. Fix docstring

    @eberrigan
    eberrigan committed Aug 2, 2023
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  3. Import base-related trait to lengths.py

    @eberrigan
    eberrigan committed Aug 2, 2023
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  4. Make sure arrays of points are 2-dimensional

    @eberrigan
    eberrigan committed Aug 2, 2023
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  5. Streamline point-related functions

    @eberrigan
    eberrigan committed Aug 2, 2023
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  6. Vectorize get_node_ind

    @eberrigan
    eberrigan committed Aug 2, 2023
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  7. Add trait definitions until lateral_lengths

    @eberrigan
    eberrigan committed Aug 2, 2023
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  8. Delete unnecessary code

    @eberrigan
    eberrigan committed Aug 2, 2023
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