feat: properly configure logging in cli (#447)

Largely a copy/paste of work done in metakb. Small QOL increase for
running data updates.

src/therapy/cli.py

@@ -16,6 +16,7 @@
     DatabaseWriteError,
     create_db,
 )
+from therapy.log import configure_logs
 from therapy.schemas import SourceName
 
 _logger = logging.getLogger(__name__)
@@ -32,6 +33,7 @@ def check_db(db_url: str, verbose: bool = False) -> None:
     :param db_url: URL to normalizer database
     :param verbose: if true, print result to console
     """  # noqa: D301
+    configure_logs()
     db = create_db(db_url, False)
     if not db.check_schema_initialized():
         if verbose:
@@ -237,6 +239,7 @@ def update_normalizer_db(
     :param update_merged: if true, update normalized records
     :param use_existing: if True, use most recent local data instead of fetching latest version
     """  # noqa: D301
+    configure_logs()
     db = create_db(db_url, aws_instance)
 
     if update_all:

src/therapy/log.py

@@ -0,0 +1,36 @@
+"""Provide functions and utilities related to application logging."""
+
+import logging
+
+
+def _quiet_upstream_libs() -> None:
+    """Turn off debug logging for chatty upstream library loggers."""
+    for lib in (
+        "boto3",
+        "botocore",
+        "urllib3",
+    ):
+        logging.getLogger(lib).setLevel(logging.INFO)
+
+
+def configure_logs(
+    log_file: str | None = None,
+    log_level: int = logging.DEBUG,
+    quiet_upstream: bool = True,
+) -> None:
+    """Configure logging.
+
+    :param log_filename: location to put log file at
+    :param log_level: global log level to set
+    :param quiet_upstream: if True, turn off debug logging for a selection of libraries
+    """
+    if log_file is None:
+        log_file = "therapy.log"
+    if quiet_upstream:
+        _quiet_upstream_libs()
+    logging.basicConfig(
+        filename=log_file,
+        format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s",
+    )
+    logger = logging.getLogger(__package__)
+    logger.setLevel(log_level)