Correct crown-curve-indices definition in trait pipeline
#83
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…not assert as equal
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WalkthroughThe changes encompass the addition of a Jupyter Notebook for visualizing plant trait pipelines using Mermaid diagrams, updates to prevent division by zero in mathematical functions, enhancements to documentation for clarity, and modifications to trait definitions in a trait pipeline. Furthermore, new tests have been introduced for serialization functionality, and existing tests have been refined for more precise validation. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Notebook
participant Mermaid
participant Pipeline
User->>Notebook: Open and interact
Notebook->>Pipeline: Generate trait data
Pipeline->>Mermaid: Create diagram
Mermaid-->>Notebook: Return diagram
Notebook-->>User: Display Mermaid diagram
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #83 +/- ##
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+ Coverage 75.80% 76.16% +0.35%
==========================================
Files 13 13
Lines 1397 1397
==========================================
+ Hits 1059 1064 +5
+ Misses 338 333 -5 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (2)
notebooks/Pipeline_mermaid_diagrams.ipynb (2)
25-29: Fix typo in docstring.There is a minor typo in the
mm_inkfunction's docstring. Replace "URL that will generate the image" with "URL that will display the image".Apply this diff to fix the typo:
def mm_ink(graphbytes): """Given a bytes object holding a Mermaid-format graph, return a URL that will generate the image.""" base64_bytes = base64.b64encode(graphbytes) base64_string = base64_bytes.decode("ascii") return "https://mermaid.ink/img/" + base64_string
64-93: Fix typo in docstring.There is a minor typo in the
generate_mermaid_graph_and_write_to_filefunction's docstring. Replace "display it" with "display it.".Apply this diff to fix the typo:
def generate_mermaid_graph_and_write_to_file(pipeline, name): """Save the Mermaid graph image to a file.""" graphbytes = graph.encode("ascii") url = mm_ink(graphbytes) response = requests.get(url) if response.status_code == 200: image_file = f"{name}_Mermaid_Graph.png" with open(image_file, 'wb') as file: file.write(response.content) print(f"{name} Mermaid graph image saved to {image_file}") else: print("Failed to fetch the Mermaid graph image.")
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (7)
- notebooks/Pipeline_mermaid_diagrams.ipynb (1 hunks)
- sleap_roots/lengths.py (1 hunks)
- sleap_roots/series.py (2 hunks)
- sleap_roots/trait_pipelines.py (2 hunks)
- tests/test_lengths.py (1 hunks)
- tests/test_series.py (2 hunks)
- tests/test_trait_pipelines.py (2 hunks)
Files skipped from review due to trivial changes (2)
- sleap_roots/series.py
- tests/test_lengths.py
Additional comments not posted (19)
sleap_roots/lengths.py (4)
Line range hint
6-32: LGTM!The function is correctly implemented and handles edge cases well.
The code changes are approved.
Line range hint
35-52: LGTM!The function is correctly implemented and handles edge cases well.
The code changes are approved.
128-129: LGTM!The function is correctly implemented and the changes enhance the robustness of the function by preventing potential runtime errors.
The code changes are approved.
Line range hint
132-151: LGTM!The function is correctly implemented and handles edge cases well.
The code changes are approved.
tests/test_trait_pipelines.py (4)
22-26: LGTM!The test function is correctly implemented and covers the necessary test cases.
The code changes are approved.
29-33: LGTM!The test function is correctly implemented and covers the necessary test cases.
The code changes are approved.
36-41: LGTM!The test function is correctly implemented and covers the necessary test cases.
The code changes are approved.
44-60: LGTM!The test function is correctly implemented and covers the necessary test cases.
The code changes are approved.
tests/test_series.py (2)
283-288: LGTM!The test function is correctly implemented and the changes improve the granularity of the tests.
The code changes are approved.
310-315: LGTM!The test function is correctly implemented and the changes improve the granularity of the tests.
The code changes are approved.
notebooks/Pipeline_mermaid_diagrams.ipynb (7)
1-13: LGTM!The import statements are correctly importing necessary modules and libraries.
The code changes are approved.
15-23: LGTM!The additional import statements are correctly importing necessary modules and libraries.
The code changes are approved.
51-63: LGTM!The
save_mermaid_graph_imagefunction is correctly implemented for saving Mermaid graph images.The code changes are approved.
95-97: LGTM!The example usage is correctly demonstrating how to use the
generate_mermaid_graph_and_write_to_filefunction.The code changes are approved.
101-110: LGTM!The example usage is correctly demonstrating how to use the
generate_mermaid_graph_and_write_to_filefunction for different pipelines.The code changes are approved.
113-375: LGTM!The output is correctly demonstrating the results of the
generate_mermaid_graph_and_write_to_filefunction for different pipelines.The code changes are approved.
413-427: LGTM!The pipeline processing and graph generation are correctly implemented.
The code changes are approved.
sleap_roots/trait_pipelines.py (2)
1977-1978: Update function reference and input traits forcrown_curve_indices.The function reference for
crown_curve_indiceshas been updated fromget_base_tip_disttoget_curve_index, and the input traits have been changed fromcrown_base_ptsandcrown_tip_ptstocrown_lengthsandcrown_base_tip_dists. This change reflects a shift in how the trait is computed, likely enhancing the underlying logic or data being processed.Ensure that the new function
get_curve_indexand the input traitscrown_lengthsandcrown_base_tip_distsare correctly defined and used elsewhere in the codebase.Run the following script to verify the function usage and input traits:
Verification successful
Verified: Function and input traits are correctly defined and used.
The function
get_curve_indexand the input traitscrown_lengthsandcrown_base_tip_distsare correctly defined and utilized in the codebase. The updates in theOlderMonocotPipelineclass reflect these changes appropriately.
get_curve_indexis defined insleap_roots/lengths.py.crown_lengthsandcrown_base_tip_distsare used insleap_roots/trait_pipelines.py.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the function `get_curve_index` and input traits `crown_lengths` and `crown_base_tip_dists`. # Test: Search for the function definition and input traits. Expect: Correct definitions and usage. rg --type python -A 5 $'def get_curve_index' rg --type python -A 5 $'crown_lengths' rg --type python -A 5 $'crown_base_tip_dists'Length of output: 221
Script:
#!/bin/bash # Description: Verify the function `get_curve_index` and input traits `crown_lengths` and `crown_base_tip_dists`. # Test: Search for the function definition and input traits. Expect: Correct definitions and usage. rg --type py -A 5 $'def get_curve_index' rg --type py -A 5 $'crown_lengths' rg --type py -A 5 $'crown_base_tip_dists'Length of output: 6545
1600-1601: Update function reference and input traits forcrown_curve_indices.The function reference for
crown_curve_indiceshas been updated fromget_base_tip_disttoget_curve_index, and the input traits have been changed fromcrown_base_ptsandcrown_tip_ptstocrown_lengthsandcrown_base_tip_dists. This change reflects a shift in how the trait is computed, likely enhancing the underlying logic or data being processed.Ensure that the new function
get_curve_indexand the input traitscrown_lengthsandcrown_base_tip_distsare correctly defined and used elsewhere in the codebase.Run the following script to verify the function usage and input traits:
Verification successful
Verification Successful: Function and Input Traits Defined Correctly
The function
get_curve_indexand the input traitscrown_lengthsandcrown_base_tip_distsare correctly defined and used in the codebase. The changes in thetrait_pipelines.pyfile align with the intended logic for computing thecrown_curve_indices. No issues were found with these updates.
get_curve_indexis defined insleap_roots/lengths.py.crown_lengthsandcrown_base_tip_distsare used insleap_roots/trait_pipelines.py.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the function `get_curve_index` and input traits `crown_lengths` and `crown_base_tip_dists`. # Test: Search for the function definition and input traits. Expect: Correct definitions and usage. rg --type python -A 5 $'def get_curve_index' rg --type python -A 5 $'crown_lengths' rg --type python -A 5 $'crown_base_tip_dists'Length of output: 221
Script:
#!/bin/bash # Description: Verify the function `get_curve_index` and input traits `crown_lengths` and `crown_base_tip_dists`. # Test: Search for the function definition and input traits. Expect: Correct definitions and usage. rg 'def get_curve_index' --glob '*.py' -A 5 rg 'crown_lengths' --glob '*.py' -A 5 rg 'crown_base_tip_dists' --glob '*.py' -A 5Length of output: 6557
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- tests/test_trait_pipelines.py (4 hunks)
Files skipped from review as they are similar to previous changes (1)
- tests/test_trait_pipelines.py
OlderMonotoPipelineandYoungerMonocotPipelineand add tests.Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Tests