Codecov

[svittoz]

Description

Add custom codecov implementation (implemented by @percevalw in this PR)

Checklist

• If this PR is a bug fix, the bug is documented in the test suite.
• Changes were documented in the changelog (pending section).
• If necessary, changes were made to the documentation (eg new pipeline).

[github-actions]

Coverage Report

Name	Stmts	Miss	Cover
eds_scikit/io/i2b2_mapping.py New missing coverage at lines 38-211 ! - i2b2_table_name = i2b2_tables[db_source][table] - # Dictionary of omop_col -> i2b2_col - columns = i2b2_renaming.get(table) - - # Can be None if creating a table from scratch (e.g. concept_relationship - if columns is not None: - query = f"describe {db_name}.{i2b2_table_name}" ... - T.StructField("relationship_id", T.StringType(), True), - ] - ) - if "get_additional_i2b2_concept_relationship" in registry.data.get_all(): - data = registry.get("data", "get_additional_i2b2_concept_relationship")() - df = spark_session.createDataFrame(data, schema).cache() - return df New missing coverage at lines 230-234 ! - def f(x): - return mapping.get(x, default) - - return F.udf(f)	79	69	13%
eds_scikit/biology/utils/config.py New missing coverage at lines 30-66 ! """ - my_custom_config = pd.DataFrame() - for concepts_set in concepts_sets: - try: - stats = pd.read_pickle( - "{}/{}/measurement_stats.pkl".format(stats_folder, concepts_set.name) - ) - stats["transformed_unit"] = ( ... - ] - - os.makedirs(CONFIGS_PATH, exist_ok=True) - - my_custom_config.to_csv("{}/{}.csv".format(CONFIGS_PATH, config_name), index=False) - - register_configs() New missing coverage at lines 73-75 ! for config in glob.glob(os.path.join(CONFIGS_PATH, "*.csv")): - config_name = Path(config).stem - registry.data.register( f"get_biology_config.{config_name}", New missing coverage at lines 89-94 ! """ - registered = list(registry.data.get_all().keys()) - configs = [ - r.split(".")[-1] for r in registered if r.startswith("get_biology_config") - ] - return configs	35	22	37%
eds_scikit/utils/checks.py New missing coverage at line 127 ! if return_index_or_key: - return kwargs[argname], argname return kwargs[argname] New missing coverage at line 149 ! else: - to_display_per_concept = [f"- {concept}" for concept in required_concepts] str_to_display = "\n".join(to_display_per_concept) New missing coverage at lines 172-189 ! - if all(isinstance(table, tuple) for table in required_tables): - to_display_per_table = [ - f"- {table} ({msg})" for table, msg in required_tables - ] - else: - to_display_per_table = [f"- {table}" for table in required_tables] - str_to_display = "\n".join(to_display_per_table) - - if data_name: - data_name = f" {data_name} " - message = ( - f"The {data_name}Data is missing some tables, " - "namely:\n" - f"{str_to_display}" - ) - - super().__init__(message)	71	10	86%
eds_scikit/datasets/synthetic/biology.py New missing coverage at lines 37-44 ! def reset_to_pandas(self): - if self.module == "koalas": - self.measurement = self.pd_measurement - self.concept = self.pd_concept - self.concept_relationship = self.pd_concept_relationship - self.care_site = self.pd_care_site - self.visit_occurrence = self.pd_visit_occurrence - self.module = "pandas"	132	7	95%
eds_scikit/period/tagging_functions.py New missing coverage at lines 60-63 ! # TODO: is this necessary ? - logger.warning("No matching were found between the 2 DataFrames") - - return framework.DataFrame( columns=["person_id", "t_start", "t_end", "concept", "value"] New missing coverage at lines 119-123 ! return (B_start >= A_start) & (B_end <= A_end) - elif algo == interval_algos.from_before_to: - return B_end <= A_start - elif algo == interval_algos.to_before_from: - return A_end <= B_start else:	36	6	83%
eds_scikit/utils/test_utils.py New missing coverage at line 50 ! def date(s): - return dt.strptime(s, "%Y-%m-%d") New missing coverage at lines 88-90 ! args = tuple(args) - elif type(index_or_key) == str: - kwargs[index_or_key] = inputs New missing coverage at lines 114-116 ! else: - normalized_sum_sq_diff = sum_sq_diff / np.sqrt(sum_sq_diff) - assert normalized_sum_sq_diff < 0.001	54	5	91%
eds_scikit/utils/bunch.py New missing coverage at line 32 ! def __setattr__(self, key, value): - self[key] = value New missing coverage at line 35 ! def __dir__(self): - return self.keys() New missing coverage at lines 38-41 ! def __getattr__(self, key): - try: - return self[key] - except KeyError: raise AttributeError(key)	11	5	55%
eds_scikit/resources/reg.py New missing coverage at lines 50-78 ! # Looking for a match excluding version string - candidates = [ - func for func in candidates if function_name == func.split(".")[0] - ] - if len(candidates) > 1: - # Multiple versions available, a specific one should be specified - raise ValueError( - ( ... - "from eds_scikit.resources import registry\n" - f"@registry.{key}('{function_name}')" - f"def your_custom_func(args, **kwargs):", - " ...", - ) - ) - func = r.get(candidates[0]) return func	16	4	75%
eds_scikit/event/diabetes.py New missing coverage at lines 88-102 ! """ - diabetes = conditions_from_icd10( - condition_occurrence=condition_occurrence, - visit_occurrence=visit_occurrence, - date_min=date_min, - date_max=date_max, - codes=codes, - date_from_visit=date_from_visit, - additional_filtering=additional_filtering, - ) - - diabetes["value"] = diabetes["concept"] - diabetes["concept"] = "DIABETES_FROM_ICD10" - - return diabetes	10	4	60%
eds_scikit/datasets/__init__.py New missing coverage at line 38 ! def __dir__(): - return known_datasets + [func.__name__ for func in __all__] New missing coverage at lines 52-56 ! def add_dataset(table: pd.DataFrame, name: str): - dataset_path = os.path.abspath( - os.path.join(os.path.dirname(__file__), name + ".csv") - ) - table.to_csv(dataset_path, index=False) New missing coverage at line 67 ! """ - return [func.__name__ for func in __all__]	26	4	85%
eds_scikit/event/from_code.py New missing coverage at lines 108-111 ! else: - event.loc[:, "t_start"] = event.loc[:, columns["code_start_datetime"]] - event.loc[:, "t_end"] = event.loc[:, columns["code_end_datetime"]] - event = event.drop( columns=[columns["code_start_datetime"], columns["code_end_datetime"]]	42	3	93%
eds_scikit/biology/viz/plot.py New missing coverage at line 72 ! else: - logger.error( "The folder {} has not been found", New missing coverage at lines 718-720 ! else: - terminologies_hist = alt.Chart().mark_text() - terminologies_time_series = ( alt.Chart(measurement)	130	3	98%
eds_scikit/emergency/emergency_care_site.py New missing coverage at line 54 ! if algo == "from_regex_on_parent_UF": - return from_regex_on_parent_UF(care_site) elif algo == "from_regex_on_care_site_description": New missing coverage at line 166 ! """ - return attributes.get_parent_attributes( care_site,	31	2	94%
eds_scikit/biology/viz/aggregate.py New missing coverage at line 83 ! if stats_only: - return {"measurement_stats": measurement_stats} New missing coverage at line 208 ! if overall_only: - return measurement_stats_overall	97	2	98%
eds_scikit/utils/flowchart/flowchart.py New missing coverage at line 152 ! def __str__(self) -> str: - return self.__repr__()	131	1	99%
eds_scikit/utils/custom_implem/custom_implem.py New missing coverage at line 54 ! """ - return cut( x,	22	1	95%
eds_scikit/resources/utils.py New missing coverage at line 19 ! if len(splited) == 1: - return None return splited[-1]	6	1	83%
eds_scikit/period/stays.py New missing coverage at line 409 ! if open_stay_end_datetime is None: - open_stay_end_datetime = datetime.now() vo["visit_end_datetime_calc"] = open_stay_end_datetime	86	1	99%
eds_scikit/io/base.py New missing coverage at line 13 ! def __str__(self): - return self.__repr__()	9	1	89%
eds_scikit/event/consultations.py New missing coverage at line 68 ! if type(algo) == str: - algo = [algo]	61	1	98%
eds_scikit/biology/cleaning/cohort.py New missing coverage at line 28 ! if isinstance(studied_pop, DataFrame.__args__): - filtered_measures = measurement.merge( studied_pop,	9	1	89%
TOTAL	2272	153	93%

59 files skipped due to complete coverage.

[percevalw]

LGTM