Add quality control property for batch processing over genotypes #76
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Actionable comments posted: 1
Actionable comments outside the diff hunks (3)
tests/test_series.py (2)
Line range hint
2-2: Remove the unused import ofnumpy.- import numpy as np
Line range hint
79-79: Rename the secondtest_series_namefunction to avoid redefinition and clarify its purpose.- def test_series_name(series_instance): + def test_series_name_from_instance(series_instance):sleap_roots/series.py (1)
Line range hint
359-359: Replace type comparison withisinstance()for better practice.- if type(data_folders) != list: + if not isinstance(data_folders, list):
sleap_roots/series.py
Outdated
| @property | ||
| def qc_fail(self) -> bool: | ||
| """Flag to indicate if the series failed QC from the CSV.""" | ||
| if not self.csv_path or not Path(self.csv_path).exists(): | ||
| print("CSV path is not set or the file does not exist.") | ||
| return np.nan | ||
| df = pd.read_csv(self.csv_path) | ||
| try: | ||
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | ||
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | ||
| except IndexError: | ||
| print(f"No QC flag found for series {self.series_name} in CSV.") | ||
| return np.nan |
There was a problem hiding this comment.
Change the return value of qc_fail to False when the CSV path is not set or the QC flag is not found, to maintain consistency with the expected boolean return type.
- return np.nan
+ return False
- return np.nan
+ return FalseCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| @property | |
| def qc_fail(self) -> bool: | |
| """Flag to indicate if the series failed QC from the CSV.""" | |
| if not self.csv_path or not Path(self.csv_path).exists(): | |
| print("CSV path is not set or the file does not exist.") | |
| return np.nan | |
| df = pd.read_csv(self.csv_path) | |
| try: | |
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | |
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | |
| except IndexError: | |
| print(f"No QC flag found for series {self.series_name} in CSV.") | |
| return np.nan | |
| @property | |
| def qc_fail(self) -> bool: | |
| """Flag to indicate if the series failed QC from the CSV.""" | |
| if not self.csv_path or not Path(self.csv_path).exists(): | |
| print("CSV path is not set or the file does not exist.") | |
| return False | |
| df = pd.read_csv(self.csv_path) | |
| try: | |
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | |
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | |
| except IndexError: | |
| print(f"No QC flag found for series {self.series_name} in CSV.") | |
| return False |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #76 +/- ##
==========================================
- Coverage 74.92% 74.58% -0.34%
==========================================
Files 13 13
Lines 1312 1326 +14
==========================================
+ Hits 983 989 +6
- Misses 329 337 +8 ☔ View full report in Codecov by Sentry. |
| if not self.csv_path or not Path(self.csv_path).exists(): | ||
| print("CSV path is not set or the file does not exist.") | ||
| return np.nan | ||
| df = pd.read_csv(self.csv_path) | ||
| try: | ||
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | ||
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | ||
| except IndexError: | ||
| print(f"No QC flag found for series {self.series_name} in CSV.") | ||
| return np.nan |
There was a problem hiding this comment.
Change the return value of qc_fail to False when the CSV path is not set or the QC flag is not found, to maintain consistency with the expected boolean return type.
- return np.nan
+ return False
- return np.nan
+ return FalseCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| if not self.csv_path or not Path(self.csv_path).exists(): | |
| print("CSV path is not set or the file does not exist.") | |
| return np.nan | |
| df = pd.read_csv(self.csv_path) | |
| try: | |
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | |
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | |
| except IndexError: | |
| print(f"No QC flag found for series {self.series_name} in CSV.") | |
| return np.nan | |
| if not self.csv_path or not Path(self.csv_path).exists(): | |
| print("CSV path is not set or the file does not exist.") | |
| return False | |
| df = pd.read_csv(self.csv_path) | |
| try: | |
| # Match the series_name (or plant_qr_code in the CSV) to fetch the QC flag | |
| return df[df["plant_qr_code"] == self.series_name]["qc_cylinder"].iloc[0] | |
| except IndexError: | |
| print(f"No QC flag found for series {self.series_name} in CSV.") | |
| return False |
eberrigan
deleted the
elizabeth/Add-quality-control--property-for-batch-processing-over-genotypes
branch
qc_failproperty toSeriesqc_failflag to remove unwanted samplesSummary by CodeRabbit
New Features
qc_failproperty in theSeriesclass to indicate quality control failures during trait computations.Bug Fixes
Tests
qc_failproperty with tests to accurately identify series failing quality control.