Merge pull request #99 from CDCgov/rr-95-use-logging

Rr 95 use logging

Author: ryanraaschCDC

cfa/dataops/catalog.py

@@ -1,6 +1,7 @@
 """building a validated datasource namespace"""
 
 import json
+import logging
 import os
 import pkgutil
 from collections.abc import Sequence
@@ -42,6 +43,10 @@
 _config = ConfigParser()
 _config.read(os.path.join(_here, "config.ini"))
 
+logger = logging.getLogger(__name__)
+if not logger.handlers:
+    logger.addHandler(logging.NullHandler())
+
 
 def get_all_catalogs() -> list:
     """Get a list of all available dataops catalogs.
@@ -57,8 +62,10 @@ def get_all_catalogs() -> list:
         for module_finder, modname, ispkg in pkgutil.iter_modules(catalog_pkg.__path__):
             if ispkg:
                 catalogs.append((catalog_nspace, modname, module_finder.path))
-    except ModuleNotFoundError:
-        print(f"No catalogs exist in namespace {catalog_nspace}")
+    except ModuleNotFoundError as e:
+        if e.name != catalog_nspace:
+            raise
+        logger.warning("No catalogs exist in namespace %s", catalog_nspace)
 
     return catalogs
 
@@ -340,6 +347,7 @@ def _get_version_blobs(
                 raise ValueError(
                     f"Version {version} not found in available versions: {available_versions}"
                 )
+            logger.info(f"Using version: {version}")
             if print_version:
                 print(f"Using version: {version}")
             if isinstance(version, list):
@@ -424,6 +432,7 @@ def get_dataframe(
         output: Literal["pandas", "pd"] = "pandas",
         version_spec: str | None = None,
         selection: Literal["newest", "oldest"] = "newest",
+        print_version: bool = False,
     ) -> pd.DataFrame: ...
 
     @overload
@@ -432,6 +441,7 @@ def get_dataframe(
         output: Literal["polars", "pl"],
         version_spec: str | None = None,
         selection: Literal["newest", "oldest"] = "newest",
+        print_version: bool = False,
     ) -> pl.DataFrame: ...
 
     @overload
@@ -440,13 +450,15 @@ def get_dataframe(
         output: Literal["pl_lazy", "lazy"],
         version_spec: str | None = None,
         selection: Literal["newest", "oldest"] = "newest",
+        print_version: bool = False,
     ) -> pl.LazyFrame: ...
 
     def get_dataframe(
         self,
         output: Literal["pandas", "pd", "polars", "pl", "pl_lazy", "lazy"] = "pandas",
         version_spec: str | None = None,
         selection: Literal["newest", "oldest"] = "newest",
+        print_version: bool = False,
     ) -> pd.DataFrame | pl.DataFrame | pl.LazyFrame:
         """Get the data as a pandas or polars dataframe
 
@@ -456,6 +468,7 @@ def get_dataframe(
             version_spec (str, optional): the version of the data to get.
                 Defaults to "latest".
             selection (Literal["newest", "oldest", "all"], optional): whether to get the newest, oldest, or all matching versions. Defaults to "newest".
+            print_version (bool, optional): whether to log the resolved version information. Defaults to False.
 
         Raises:
             ValueError: if output is not one of
@@ -472,7 +485,7 @@ def get_dataframe(
             )
         # Fetch version blobs once and validate before deriving file extension.
         version_blobs = self._get_version_blobs(
-            version_spec=version_spec, selection=selection
+            version_spec=version_spec, selection=selection, print_version=print_version
         )
         if not version_blobs:
             raise ValueError(
@@ -627,7 +640,7 @@ def save_dataframe(
             )
         if file_format in ["json", "jsonl"] and path_after_prefix.endswith(".json"):
             path_after_prefix = path_after_prefix[:-5] + ".jsonl"
-            print("Changing file extension to .jsonl for line-delimited JSON.")
+            logger.info("Changing file extension to .jsonl for line-delimited JSON.")
         if isinstance(df, pd.DataFrame):
             if file_format == "parquet":
                 pq_bytes = df.to_parquet(index=False, compression="snappy")

changelog.md

@@ -7,6 +7,10 @@ and this project adheres to [Calendar Versioning](https://calver.org/).
 The versioning pattern is `YYYY.MM.DD.micro(a/b/{none if release})
 
 ---
+## [2026.07.20.0]
+
+- change most print statements to logging
+
 ## [2026.06.30.0]
 
 - changed SimpleNamespace to CatalogNamespace for more helpful type hints

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cfa.dataops"
-version = "2026.06.30.0"
+version = "2026.07.20.0"
 description = "Data cataloging, ETL, modeling, verification, and validation for CFA"
 authors = [
     { name = "Phil Rogers", email = "ap66@cdc.gov" },

tests/test_blob_endpoint_save_methods.py

@@ -128,25 +128,23 @@ def test_save_pandas_dataframe_json(self, mocker, blob_endpoint, sample_pandas_d
         assert isinstance(call_args[1]["file_buffer"], bytes)
 
     def test_save_pandas_dataframe_json_auto_extension_fix(
-        self, mocker, blob_endpoint, sample_pandas_df, capsys
+        self, mocker, blob_endpoint, sample_pandas_df, caplog
     ):
         """Test that .json extension is automatically changed to .jsonl"""
         mock_write = mocker.patch.object(blob_endpoint, "write_blob")
 
-        blob_endpoint.save_dataframe(
-            df=sample_pandas_df,
-            path_after_prefix="data/output.json",
-            file_format="json",
-            auto_version=False,
-        )
+        with caplog.at_level("INFO"):
+            blob_endpoint.save_dataframe(
+                df=sample_pandas_df,
+                path_after_prefix="data/output.json",
+                file_format="json",
+                auto_version=False,
+            )
 
         mock_write.assert_called_once()
         call_args = mock_write.call_args
         assert call_args[1]["path_after_prefix"] == "data/output.jsonl"
-
-        # Check that warning message was printed
-        captured = capsys.readouterr()
-        assert "Changing file extension to .jsonl" in captured.out
+        assert "Changing file extension to .jsonl" in caplog.text
 
     def test_save_polars_dataframe_parquet(
         self, mocker, blob_endpoint, sample_polars_df