feat: first rename

example/loaders/debug_loader_function.py

@@ -9,8 +9,8 @@
 
 import pandas as pd
 
-import psycopmlutils.loaders.raw as raw_loaders
-from psycopmlutils.data_checks.raw.check_predictor_lists import check_raw_df
+import psycop_feature_generation.loaders.raw as raw_loaders
+from psycop_feature_generation.data_checks.raw.check_predictor_lists import check_raw_df
 
 
 def will_it_float(value: Any) -> bool:

example/loaders/load_coercion.py

@@ -2,7 +2,7 @@
 
 # pylint: disable=non-ascii-name
 
-import psycopmlutils.loaders.raw.load_coercion as c
+import psycop_feature_generation.loaders.raw.load_coercion as c
 
 if __name__ == "__main__":
     df = c.coercion_duration(n_rows=100)

example/loaders/load_diagnoses.py

@@ -1,7 +1,7 @@
 """Example for loading diagnoses."""
 
-import psycopmlutils.loaders.raw.load_diagnoses as d
-from psycopmlutils.data_checks.raw.check_predictor_lists import (
+import psycop_feature_generation.loaders.raw.load_diagnoses as d
+from psycop_feature_generation.data_checks.raw.check_predictor_lists import (
     check_feature_combinations_return_correct_dfs,
 )
 

example/loaders/load_medications.py

@@ -1,6 +1,6 @@
 """Example of loading medications."""
 
-import psycopmlutils.loaders.raw.load_medications as m
+import psycop_feature_generation.loaders.raw.load_medications as m
 
 if __name__ == "__main__":
     df = m.antipsychotics()

example/loaders/load_physical_visits.py

@@ -1,5 +1,5 @@
 """Example loader for physical visits."""
-import psycopmlutils.loaders.raw as r
+import psycop_feature_generation.loaders.raw as r
 
 if __name__ == "__main__":
     df = r.load_visits.physical_visits_to_psychiatry()

example/loaders/load_sql.py

@@ -1,6 +1,6 @@
 """Example of how to load IDs from sql."""
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 if __name__ == "__main__":
     VIEW = "[psycop_t2d_train]"

pyproject.toml

@@ -24,6 +24,7 @@ pre-commit = "^2.20.0"
 pytest-cov = "^3.0.0"
 flake8 = "^5.0.4"
 docformatter = "^1.5.0"
+mypy = "^0.971"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

src/application/t2d/check_feature_set_integrity.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-from psycopmlutils.data_checks.flattened.data_integrity import (
+from psycop_feature_generation.data_checks.flattened.data_integrity import (
     save_feature_set_integrity_from_dir,
 )
 

src/application/t2d/describe_features.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-from psycopmlutils.data_checks.flattened.feature_describer import (
+from psycop_feature_generation.data_checks.flattened.feature_describer import (
     save_feature_description_from_dir,
 )
 from src.application.t2d.features_blood_samples import get_lab_feature_spec

src/application/t2d/generate_features_and_write_to_disk.py

@@ -13,24 +13,24 @@
 import pandas as pd
 import psutil
 import wandb
+from psycop_feature_generation.utils import FEATURE_SETS_PATH
 from wasabi import Printer
 
-import psycopmlutils.loaders.raw  # noqa
+import psycop_feature_generation.loaders.raw  # noqa
 from application.t2d.features_blood_samples import get_lab_feature_spec
 from application.t2d.features_diagnoses import get_diagnosis_feature_spec
 from application.t2d.features_medications import get_medication_feature_spec
-from psycopmlutils.data_checks.flattened.data_integrity import (
+from psycop_feature_generation.data_checks.flattened.data_integrity import (
     save_feature_set_integrity_from_dir,
 )
-from psycopmlutils.data_checks.flattened.feature_describer import (
+from psycop_feature_generation.data_checks.flattened.feature_describer import (
     save_feature_description_from_dir,
 )
-from psycopmlutils.loaders.raw.pre_load_dfs import pre_load_unique_dfs
-from psycopmlutils.timeseriesflattener import (
+from psycop_feature_generation.loaders.raw.pre_load_dfs import pre_load_unique_dfs
+from psycop_feature_generation.timeseriesflattener import (
     FlattenedDataset,
     create_feature_combinations,
 )
-from psycopmlutils.utils import FEATURE_SETS_PATH
 
 
 def log_to_wandb(wandb_project_name, predictor_combinations, save_dir):
@@ -129,7 +129,9 @@ def split_and_save_to_disk(
     # Create splits
     for dataset_name in splits:
         if split_ids_dict is None:
-            df_split_ids = psycopmlutils.loaders.raw.load_ids(split=dataset_name)
+            df_split_ids = psycop_feature_generation.loaders.raw.load_ids(
+                split=dataset_name
+            )
         else:
             df_split_ids = split_ids_dict[dataset_name]
 

src/psycop_feature_generation/data_checks/flattened/data_integrity.py

@@ -24,7 +24,10 @@
 )
 from wasabi import Printer
 
-from psycopmlutils.loaders.flattened import load_split_outcomes, load_split_predictors
+from psycop_feature_generation.loaders.flattened import (
+    load_split_outcomes,
+    load_split_predictors,
+)
 
 
 def pruned_data_integrity_checks(**kwargs) -> Suite:

src/psycop_feature_generation/data_checks/flattened/feature_describer.py

@@ -6,11 +6,13 @@
 
 import numpy as np
 import pandas as pd
+from psycop_feature_generation.utils import generate_feature_colname
 from wasabi import Printer
 
-from psycopmlutils.data_checks.utils import save_df_to_pretty_html_table
-from psycopmlutils.loaders.flattened.local_feature_loaders import load_split_predictors
-from psycopmlutils.utils import generate_feature_colname
+from psycop_feature_generation.data_checks.utils import save_df_to_pretty_html_table
+from psycop_feature_generation.loaders.flattened.local_feature_loaders import (
+    load_split_predictors,
+)
 
 UNICODE_HIST = {
     0: " ",

src/psycop_feature_generation/data_checks/raw/check_predictor_lists.py

@@ -5,10 +5,10 @@
 from typing import Optional, Union
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 from wasabi import Printer
 
-from psycopmlutils.data_checks.raw.check_raw_df import check_raw_df
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.data_checks.raw.check_raw_df import check_raw_df
 
 
 def check_df_conforms_to_arg_dict(

src/psycop_feature_generation/data_checks/raw/validate_raw_data.py

@@ -7,12 +7,16 @@
 import pandas as pd
 from deepchecks.tabular import Dataset
 from deepchecks.tabular.suites import data_integrity
+from psycop_feature_generation.utils import RAW_DATA_VALIDATION_PATH
 from wasabi import Printer
 
-from psycopmlutils.data_checks.flattened.data_integrity import get_name_of_failed_checks
-from psycopmlutils.data_checks.flattened.feature_describer import create_unicode_hist
-from psycopmlutils.data_checks.utils import save_df_to_pretty_html_table
-from psycopmlutils.utils import RAW_DATA_VALIDATION_PATH
+from psycop_feature_generation.data_checks.flattened.data_integrity import (
+    get_name_of_failed_checks,
+)
+from psycop_feature_generation.data_checks.flattened.feature_describer import (
+    create_unicode_hist,
+)
+from psycop_feature_generation.data_checks.utils import save_df_to_pretty_html_table
 
 
 def median_absolute_deviation(series: pd.Series) -> np.array:

src/psycop_feature_generation/featurizers/tfidf.py

@@ -3,12 +3,12 @@
 
 import dill as pkl
 import pandas as pd
+from psycop_feature_generation.utils import FEATURIZERS_PATH
 from sklearn.feature_extraction.text import TfidfVectorizer
 from wasabi import Printer
 
-from psycopmlutils.loaders.raw.load_ids import load_ids
-from psycopmlutils.loaders.raw.load_text import load_all_notes
-from psycopmlutils.utils import FEATURIZERS_PATH
+from psycop_feature_generation.loaders.raw.load_ids import load_ids
+from psycop_feature_generation.loaders.raw.load_text import load_all_notes
 
 
 def create_tfidf_vectorizer(

src/psycop_feature_generation/loaders/raw/load_coercion.py

@@ -5,9 +5,9 @@
 from typing import Optional
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 @data_loaders.register("coercion_duration")

src/psycop_feature_generation/loaders/raw/load_demographic.py

@@ -3,9 +3,9 @@
 from typing import Optional
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 # pylint: disable=missing-function-docstring
 

src/psycop_feature_generation/loaders/raw/load_diagnoses.py

@@ -9,9 +9,9 @@
 from typing import Optional, Union
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 def _load(

src/psycop_feature_generation/loaders/raw/load_ids.py

@@ -4,7 +4,7 @@
 
 import pandas as pd
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 def load_ids(split: str, n_rows: Optional[int] = None) -> pd.DataFrame:

src/psycop_feature_generation/loaders/raw/load_lab_results.py

@@ -3,10 +3,12 @@
 from typing import Optional, Union
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 
-from psycopmlutils.loaders.non_numerical_coercer import multiply_inequalities_in_df
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.non_numerical_coercer import (
+    multiply_inequalities_in_df,
+)
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 # pylint: disable=missing-function-docstring
 

src/psycop_feature_generation/loaders/raw/load_medications.py

@@ -2,10 +2,10 @@
 from typing import Optional
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 from wasabi import msg
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 # pylint: disable=missing-function-docstring
 

src/psycop_feature_generation/loaders/raw/load_t2d_outcomes.py

@@ -5,10 +5,10 @@
 from typing import Optional
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 from wasabi import msg
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 @data_loaders.register("t2d")

src/psycop_feature_generation/loaders/raw/load_text.py

@@ -10,9 +10,9 @@
 
 import dill as pkl
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 def get_all_valid_note_types() -> set[str]:

src/psycop_feature_generation/loaders/raw/load_visits.py

@@ -3,10 +3,10 @@
 from typing import Optional
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 from wasabi import msg
 
-from psycopmlutils.loaders.raw.sql_load import sql_load
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.loaders.raw.sql_load import sql_load
 
 
 @data_loaders.register("physical_visits_to_psychiatry")

src/psycop_feature_generation/loaders/raw/pre_load_dfs.py

@@ -4,10 +4,10 @@
 from typing import Any, Union
 
 import pandas as pd
+from psycop_feature_generation.utils import data_loaders
 from wasabi import Printer
 
-from psycopmlutils.data_checks.raw.check_raw_df import check_raw_df
-from psycopmlutils.utils import data_loaders
+from psycop_feature_generation.data_checks.raw.check_raw_df import check_raw_df
 
 
 def load_df(predictor_df: str, values_to_load: Union[str, None] = None) -> pd.DataFrame:

src/psycop_feature_generation/loaders/synth/raw/load_synth_data.py

@@ -3,8 +3,7 @@
 from typing import Optional
 
 import pandas as pd
-
-from psycopmlutils.utils import PROJECT_ROOT, data_loaders
+from psycop_feature_generation.utils import PROJECT_ROOT, data_loaders
 
 
 def load_raw_test_csv(filename: str, n_rows: Optional[int] = None) -> pd.DataFrame:

src/psycop_feature_generation/loaders/utils.py

@@ -1,6 +1,6 @@
 """Example of how to get tfidf vocab."""
 
-from psycopmlutils.utils import FEATURIZERS_PATH
+from psycop_feature_generation.utils import FEATURIZERS_PATH
 
 # pylint: disable=missing-function-docstring
 

tests/helpers/utils_for_testing.py

@@ -7,9 +7,10 @@
 import numpy as np
 import pandas as pd
 from pandas import DataFrame
-
-from psycopmlutils.timeseriesflattener.flattened_dataset import FlattenedDataset
-from psycopmlutils.utils import data_loaders, generate_feature_colname
+from psycop_feature_generation.timeseriesflattener.flattened_dataset import (
+    FlattenedDataset,
+)
+from psycop_feature_generation.utils import data_loaders, generate_feature_colname
 
 
 def convert_cols_with_matching_colnames_to_datetime(

tests/test_check_raw_df/test_check_raw_df.py

@@ -3,7 +3,7 @@
 import pytest
 from utils_for_testing import str_to_df  # noqa pylint: disable=import-error
 
-from psycopmlutils.data_checks.raw.check_raw_df import check_raw_df
+from psycop_feature_generation.data_checks.raw.check_raw_df import check_raw_df
 
 # pylint: disable=missing-function-docstring
 

tests/test_data/flattened/generated_with_outcome/create_synth_flattened_with_outcome.py

@@ -2,8 +2,7 @@
 from pathlib import Path
 
 import numpy as np
-
-from psycopmlutils.synth_data_generator.synth_prediction_times_generator import (
+from psycop_feature_generation.synth_data_generator.synth_prediction_times_generator import (
     generate_synth_data,
 )
 

tests/test_data/raw/create_synth_prediction_times.py

@@ -1,9 +1,9 @@
 """Generate dataframe with prediction times."""
 
-from psycopmlutils.synth_data_generator.synth_col_generators import (
+from psycop_feature_generation.synth_data_generator.synth_col_generators import (
     generate_data_columns,
 )
-from psycopmlutils.utils import PROJECT_ROOT
+from psycop_feature_generation.utils import PROJECT_ROOT
 
 if __name__ == "__main__":
     # Get project root directory

tests/test_data/raw/create_synth_raw_binary.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-from psycopmlutils.synth_data_generator.synth_col_generators import (
+from psycop_feature_generation.synth_data_generator.synth_col_generators import (
     generate_data_columns,
 )