Merge df89c5a into e07916b

src/hats/catalog/association_catalog/partition_join_info.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-import warnings
+import logging
 from pathlib import Path
 
 import numpy as np
@@ -19,6 +19,8 @@
 )
 from hats.pixel_math.healpix_pixel import HealpixPixel
 
+logger = logging.getLogger(__name__)
+
 
 class PartitionJoinInfo:
     """Association catalog metadata with which partitions matches occur in the join"""
@@ -158,7 +160,7 @@ def read_from_dir(cls, catalog_base_dir: str | Path | UPath | None = None) -> Pa
         if file_io.does_file_or_directory_exist(partition_join_info_file):
             pixel_frame = PartitionJoinInfo._read_from_csv(partition_join_info_file)
         elif file_io.does_file_or_directory_exist(metadata_file):
-            warnings.warn("Reading partitions from parquet metadata. This is typically slow.")
+            logger.info("Reading partitions from parquet metadata. This is typically slow.")
             pixel_frame = PartitionJoinInfo._read_from_metadata_file(metadata_file)
         else:
             raise FileNotFoundError(

src/hats/catalog/partition_info.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-import warnings
+import logging
 from pathlib import Path
 
 import numpy as np
@@ -19,6 +19,8 @@
 )
 from hats.pixel_math import HealpixPixel
 
+logger = logging.getLogger(__name__)
+
 
 class PartitionInfo:
     """Container class for per-partition info."""
@@ -132,7 +134,7 @@ def read_from_dir(cls, catalog_base_dir: str | Path | UPath | None) -> Partition
         if file_io.does_file_or_directory_exist(partition_info_file):
             pixel_list = PartitionInfo._read_from_csv(partition_info_file)
         elif file_io.does_file_or_directory_exist(metadata_file):
-            warnings.warn("Reading partitions from parquet metadata. This is typically slow.")
+            logger.info("Reading partitions from parquet metadata. This is typically slow.")
             pixel_list = PartitionInfo._read_from_metadata_file(metadata_file)
         else:
             raise FileNotFoundError(
@@ -240,6 +242,7 @@ def _read_from_csv(cls, partition_info_file: str | Path | UPath) -> PartitionInf
             for order, pixel in zip(
                 data_frame[cls.METADATA_ORDER_COLUMN_NAME],
                 data_frame[cls.METADATA_PIXEL_COLUMN_NAME],
+                strict=False,
             )
         ]
 

src/hats/inspection/almanac.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
+import logging
 import os
-import warnings
 
 import pandas as pd
 
@@ -37,6 +37,7 @@ def __init__(self, include_default_dir=True, dirs=None):
         self.files = {}
         self.entries = {}
         self.dir_to_catalog_name = {}
+        self.logger = logging.getLogger(__name__)
         self._init_files(include_default_dir=include_default_dir, dirs=dirs)
         self._init_catalog_objects()
         self._init_catalog_links()
@@ -102,7 +103,7 @@ def _init_catalog_objects(self):
                 else:
                     full_name = catalog_info.catalog_name
                 if full_name in self.entries:
-                    warnings.warn(f"Duplicate catalog name ({full_name}). Try using namespaces.")
+                    self.logger.warning(f"Duplicate catalog name ({full_name}). Try using namespaces.")
                 else:
                     self.entries[full_name] = catalog_info
                     self.dir_to_catalog_name[catalog_info.catalog_path] = full_name
@@ -124,7 +125,7 @@ def _init_catalog_links(self):
                 if catalog_entry.primary:
                     object_catalog = self._get_linked_catalog(catalog_entry.primary, catalog_entry.namespace)
                     if not object_catalog:
-                        warnings.warn(
+                        self.logger.warning(
                             f"source catalog {catalog_entry.catalog_name} missing "
                             f"object catalog {catalog_entry.primary}"
                         )
@@ -136,7 +137,7 @@ def _init_catalog_links(self):
                 ## Association table MUST have a primary and join catalog
                 primary_catalog = self._get_linked_catalog(catalog_entry.primary, catalog_entry.namespace)
                 if not primary_catalog:
-                    warnings.warn(
+                    self.logger.warning(
                         f"association table {catalog_entry.catalog_name} missing "
                         f"primary catalog {catalog_entry.primary}"
                     )
@@ -149,7 +150,7 @@ def _init_catalog_links(self):
                     catalog_entry.namespace,
                 )
                 if not join_catalog:
-                    warnings.warn(
+                    self.logger.warning(
                         f"association table {catalog_entry.catalog_name} missing "
                         f"join catalog {catalog_entry.join}"
                     )
@@ -160,7 +161,7 @@ def _init_catalog_links(self):
                 ## Margin catalogs MUST have a primary catalog
                 primary_catalog = self._get_linked_catalog(catalog_entry.primary, catalog_entry.namespace)
                 if not primary_catalog:
-                    warnings.warn(
+                    self.logger.warning(
                         f"margin table {catalog_entry.catalog_name} missing "
                         f"primary catalog {catalog_entry.primary}"
                     )
@@ -171,15 +172,15 @@ def _init_catalog_links(self):
                 ## Index tables MUST have a primary catalog
                 primary_catalog = self._get_linked_catalog(catalog_entry.primary, catalog_entry.namespace)
                 if not primary_catalog:
-                    warnings.warn(
+                    self.logger.warning(
                         f"index table {catalog_entry.catalog_name} missing "
                         f"primary catalog {catalog_entry.primary}"
                     )
                 else:
                     catalog_entry.primary_link = primary_catalog
                     primary_catalog.indexes.append(catalog_entry)
             else:  # pragma: no cover
-                warnings.warn(f"Unknown catalog type {catalog_entry.catalog_type}")
+                self.logger.warning(f"Unknown catalog type {catalog_entry.catalog_type}")
 
     def _get_linked_catalog(self, linked_text, namespace) -> AlmanacInfo | None:
         """Find a catalog to be used for linking catalogs within the almanac.

src/hats/inspection/visualize_catalog.py

@@ -5,7 +5,7 @@
 
 from __future__ import annotations
 
-import warnings
+import logging
 from typing import TYPE_CHECKING, Type
 
 import astropy.units as u
@@ -36,6 +36,8 @@
     from hats.catalog import Catalog
     from hats.catalog.healpix_dataset.healpix_dataset import HealpixDataset
 
+logger = logging.getLogger(__name__)
+
 
 def _read_point_map(catalog_base_dir):
     """Read the object spatial distribution information from a healpix FITS file.
@@ -235,13 +237,10 @@ def get_fov_moc_from_wcs(wcs: WCS) -> MOC | None:
     y_px = np.append(y_px, y[-1, :-1])
     y_px = np.append(y_px, y[1:, 0][::-1])
 
-    # Disable the output of warnings when encoutering NaNs.
-    warnings.filterwarnings("ignore")
     # Inverse projection from pixel coordinate space to the world coordinate space
     viewport = pixel_to_skycoord(x_px, y_px, wcs)
     # If one coordinate is a NaN we exit the function and do not go further
     ra_deg, dec_deg = viewport.icrs.ra.deg, viewport.icrs.dec.deg
-    warnings.filterwarnings("default")
 
     if np.isnan(ra_deg).any() or np.isnan(dec_deg).any():
         return None
@@ -306,7 +305,7 @@ def _merge_too_small_pixels(depth_ipix_d: dict[int, tuple[np.ndarray, np.ndarray
 
     # Combine healpix pixels smaller than 1px in the plot
     if max_depth > depth_res:
-        warnings.warn(
+        logger.info(
             "This plot contains HEALPix pixels smaller than a pixel of the plot. Some values may be lost"
         )
         new_ipix_d = {}
@@ -592,7 +591,7 @@ def initialize_wcs_axes(
                 wcs = ax.wcs
                 return fig, ax, wcs
             # Plot onto new axes on new figure if current axes is not correct type
-            warnings.warn("Current axes is not of correct type WCSAxes. A new figure and axes will be used.")
+            logger.warning("Current axes is not of correct type WCSAxes. A new figure and axes will be used.")
             fig = plt.figure(**kwargs)
         if wcs is None:
             # Initialize wcs with params if no WCS provided

src/hats/io/validation.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-import warnings
+import logging
 from pathlib import Path
 
 import numpy as np
@@ -18,6 +18,8 @@
 from hats.pixel_math.healpix_pixel import INVALID_PIXEL
 from hats.pixel_math.healpix_pixel_function import sort_pixels
 
+logger = logging.getLogger(__name__)
+
 
 # pylint: disable=too-many-statements,too-many-locals
 def is_valid_catalog(
@@ -63,7 +65,7 @@ def handle_error(msg):
         if verbose:
             print(msg)
         else:
-            warnings.warn(msg)
+            logger.warning(msg)
         is_valid = False
 
     if not is_catalog_info_valid(pointer):

src/hats/loaders/read_hats.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-import warnings
+import logging
 from pathlib import Path
 
 import numpy as np
@@ -26,6 +26,8 @@
     CatalogType.MAP: MapCatalog,
 }
 
+logger = logging.getLogger(__name__)
+
 
 def read_hats(catalog_path: str | Path | UPath) -> Dataset:
     """Reads a HATS Catalog from a HATS directory
@@ -88,7 +90,7 @@ def _read_schema_from_metadata(catalog_base_dir: str | Path | UPath) -> pa.Schem
     metadata_file = paths.get_parquet_metadata_pointer(catalog_base_dir)
     metadata_exists = file_io.does_file_or_directory_exist(metadata_file)
     if not (common_metadata_exists or metadata_exists):
-        warnings.warn(
+        logger.warning(
             "_common_metadata or _metadata files not found for this catalog."
             "The arrow schema will not be set."
         )