[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.7.4'
+    rev: 'v0.9.1'
     hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
@@ -25,7 +25,7 @@ repos:
       types_or: [python, jupyter]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
     - id: mypy
       entry: python3 -m mypy --config-file pyproject.toml

cycquery/__init__.py

@@ -6,3 +6,12 @@
 from cycquery.mimiciii import MIMICIIIQuerier
 from cycquery.mimiciv import MIMICIVQuerier
 from cycquery.omop import OMOPQuerier
+
+__all__ = [
+    "DatasetQuerier",
+    "EICUQuerier",
+    "GEMINIQuerier",
+    "MIMICIIIQuerier",
+    "MIMICIVQuerier",
+    "OMOPQuerier",
+]

cycquery/base.py

@@ -17,7 +17,6 @@
 )
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)
@@ -113,6 +112,7 @@ def __init__(
         database: str = "",
         schemas: Optional[List[str]] = None,
     ) -> None:
+        """Initialize the querier."""
         config = DatasetQuerierConfig(
             database=database,
             user=user,

cycquery/eicu.py

@@ -9,7 +9,6 @@
 from cycquery.base import DatasetQuerier
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)

cycquery/gemini.py

@@ -10,7 +10,6 @@
 from cycquery.interface import QueryInterface
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)

cycquery/interface.py

@@ -13,7 +13,6 @@
 from cycquery.utils.file import save_dataframe
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)

cycquery/mimiciii.py

@@ -11,7 +11,6 @@
 from cycquery.interface import QueryInterface
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)

cycquery/mimiciv.py

@@ -14,7 +14,6 @@
 from cycquery.util import get_column
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)

cycquery/omop.py

@@ -11,7 +11,6 @@
 from cycquery.utils.common import to_list
 from cycquery.utils.log import setup_logging
 
-
 # Logging.
 LOGGER = logging.getLogger(__name__)
 setup_logging(print_level="INFO", logger=LOGGER)
@@ -66,6 +65,7 @@ def __init__(
         port: int = 5432,
         schema_name: str = "omop",
     ) -> None:
+        """Initialize OMOP querier."""
         super().__init__(
             database=database,
             user=user,