logger.warn -> warning

src/spyglass/common/common_behav.py

@@ -197,7 +197,7 @@ def fetch1_dataframe(self):
             id_rp = [(n["id"], n["raw_position"]) for n in self.fetch_nwb()]
 
             if len(set(rp.interval for _, rp in id_rp)) > 1:
-                logger.warn("Loading DataFrame with multiple intervals.")
+                logger.warning("Loading DataFrame with multiple intervals.")
 
             df_list = [
                 pd.DataFrame(
@@ -395,7 +395,9 @@ def _no_transaction_make(self, key, verbose=True, skip_duplicates=False):
         )
 
         if videos is None:
-            logger.warn(f"No video data interface found in {nwb_file_name}\n")
+            logger.warning(
+                f"No video data interface found in {nwb_file_name}\n"
+            )
             return
         else:
             videos = videos.time_series

src/spyglass/common/common_device.py

@@ -88,7 +88,9 @@ def insert_from_nwbfile(cls, nwbf, config=None):
                 + f"{ndx_devices.keys()}"
             )
         else:
-            logger.warn("No conforming data acquisition device metadata found.")
+            logger.warning(
+                "No conforming data acquisition device metadata found."
+            )
 
     @classmethod
     def get_all_device_names(cls, nwbf, config) -> tuple:
@@ -305,7 +307,7 @@ def insert_from_nwbfile(cls, nwbf, config=None):
         if device_name_list:
             logger.info(f"Inserted camera devices {device_name_list}")
         else:
-            logger.warn("No conforming camera device metadata found.")
+            logger.warning("No conforming camera device metadata found.")
         return device_name_list
 
 
@@ -462,7 +464,7 @@ def insert_from_nwbfile(cls, nwbf, config=None):
         if all_probes_types:
             logger.info(f"Inserted probes {all_probes_types}")
         else:
-            logger.warn("No conforming probe metadata found.")
+            logger.warning("No conforming probe metadata found.")
 
         return all_probes_types
 
@@ -709,7 +711,7 @@ def create_from_nwbfile(
 
         query = ProbeType & {"probe_type": probe_type}
         if len(query) == 0:
-            logger.warn(
+            logger.warning(
                 f"No ProbeType found with probe_type '{probe_type}'. Aborting."
             )
             return
@@ -769,7 +771,7 @@ def create_from_nwbfile(
                     ]
 
         if not device_found:
-            logger.warn(
+            logger.warning(
                 "No electrodes in the NWB file were associated with a device "
                 + f"named '{nwb_device_name}'."
             )

src/spyglass/common/common_dio.py

@@ -38,7 +38,7 @@ def make(self, key):
             nwbf, "behavioral_events", pynwb.behavior.BehavioralEvents
         )
         if behav_events is None:
-            logger.warn(
+            logger.warning(
                 "No conforming behavioral events data interface found in "
                 + f"{nwb_file_name}\n"
             )

src/spyglass/common/common_session.py

@@ -152,7 +152,7 @@ def _add_data_acquisition_device_part(self, nwb_file_name, nwbf, config={}):
                 "data_acquisition_device_name": device_name
             }
             if len(query) == 0:
-                logger.warn(
+                logger.warning(
                     "Cannot link Session with DataAcquisitionDevice.\n"
                     + f"DataAcquisitionDevice does not exist: {device_name}"
                 )
@@ -180,7 +180,7 @@ def _add_experimenter_part(
             # ensure that the foreign key exists and do nothing if not
             query = LabMember & {"lab_member_name": name}
             if len(query) == 0:
-                logger.warn(
+                logger.warning(
                     "Cannot link Session with LabMember. "
                     + f"LabMember does not exist: {name}"
                 )

src/spyglass/common/common_subject.py

@@ -37,7 +37,7 @@ def insert_from_nwbfile(cls, nwbf: NWBFile, config: dict = None):
         """
         config = config or dict()
         if "Subject" not in config and nwbf.subject is None:
-            logger.warn("No subject metadata found.\n")
+            logger.warning("No subject metadata found.\n")
             return None
 
         conf = config["Subject"][0] if "Subject" in config else dict()

src/spyglass/common/common_task.py

@@ -33,7 +33,7 @@ def insert_from_nwbfile(cls, nwbf: pynwb.NWBFile):
         """
         tasks_mod = nwbf.processing.get("tasks")
         if tasks_mod is None:
-            logger.warn(f"No tasks processing module found in {nwbf}\n")
+            logger.warning(f"No tasks processing module found in {nwbf}\n")
             return
         for task in tasks_mod.data_interfaces.values():
             if cls.check_task_table(task):
@@ -136,7 +136,7 @@ def make(self, key):
         tasks_mod = nwbf.processing.get("tasks")
         config_tasks = config.get("Tasks", [])
         if tasks_mod is None and (not config_tasks):
-            logger.warn(
+            logger.warning(
                 f"No tasks processing module found in {nwbf} or config\n"
             )
             return
@@ -163,7 +163,7 @@ def make(self, key):
                         for camera_id in valid_camera_ids
                     ]
                 else:
-                    logger.warn(
+                    logger.warning(
                         f"No camera device found with ID {camera_ids} in NWB "
                         + f"file {nwbf}\n"
                     )
@@ -186,7 +186,7 @@ def make(self, key):
                         epoch, session_intervals
                     )
                     if target_interval is None:
-                        logger.warn("Skipping epoch.")
+                        logger.warning("Skipping epoch.")
                         continue
                     key["interval_list_name"] = target_interval
                     task_inserts.append(key.copy())
@@ -219,7 +219,7 @@ def make(self, key):
                     epoch, session_intervals
                 )
                 if target_interval is None:
-                    logger.warn("Skipping epoch.")
+                    logger.warning("Skipping epoch.")
                     continue
                 new_key["interval_list_name"] = target_interval
                 task_inserts.append(key.copy())

src/spyglass/common/prepopulate/prepopulate.py

@@ -57,7 +57,7 @@ def populate_from_yaml(yaml_path: str):
                 if k in table_cls.primary_key
             }
             if not primary_key_values:
-                logger.warn(
+                logger.warning(
                     f"Populate: No primary key provided in data {entry_dict} "
                     + f"for table {table_cls.__name__}"
                 )

src/spyglass/spikesorting/utils.py

@@ -108,7 +108,7 @@ def get_group_by_shank(
             if omit_ref_electrode_group and (
                 str(e_group) == str(ref_elec_group)
             ):
-                logger.warn(
+                logger.warning(
                     f"Omitting electrode group {e_group} from sort groups "
                     + "because contains reference."
                 )
@@ -117,7 +117,7 @@ def get_group_by_shank(
 
             # omit unitrodes if indicated
             if omit_unitrode and len(shank_elect) == 1:
-                logger.warn(
+                logger.warning(
                     f"Omitting electrode group {e_group}, shank {shank} "
                     + "from sort groups because unitrode."
                 )

src/spyglass/spikesorting/v0/sortingview.py

@@ -72,7 +72,7 @@ def make(self, key: dict):
                 LabMember.LabMemberInfo & {"lab_member_name": team_member}
             ).fetch("google_user_name")
             if len(google_user_id) != 1:
-                logger.warn(
+                logger.warning(
                     f"Google user ID for {team_member} does not exist or more than one ID detected;\
                         permission not given to {team_member}, skipping..."
                 )

src/spyglass/spikesorting/v0/sortingview_helper_fn.py

@@ -136,7 +136,7 @@ def _generate_url(
     )
 
     if initial_curation is not None:
-        logger.warn("found initial curation")
+        logger.warning("found initial curation")
         sorting_curation_uri = kcl.store_json(initial_curation)
     else:
         sorting_curation_uri = None

src/spyglass/spikesorting/v0/spikesorting_artifact.py

@@ -263,7 +263,7 @@ def _get_artifact_times(
             [[valid_timestamps[0], valid_timestamps[-1]]]
         )
         artifact_times_empty = np.asarray([])
-        logger.warn("No artifacts detected.")
+        logger.warning("No artifacts detected.")
         return recording_interval, artifact_times_empty
 
     # convert indices to intervals

src/spyglass/spikesorting/v0/spikesorting_curation.py

@@ -266,7 +266,7 @@ def save_sorting_nwb(
         AnalysisNwbfile().add(key["nwb_file_name"], analysis_file_name)
 
         if object_ids == "":
-            logger.warn(
+            logger.warning(
                 "Sorting contains no units."
                 "Created an empty analysis nwb file anyway."
             )

src/spyglass/spikesorting/v1/artifact.py

@@ -98,7 +98,7 @@ def insert_selection(cls, key: dict):
         """
         query = cls & key
         if query:
-            logger.warn("Similar row(s) already inserted.")
+            logger.warning("Similar row(s) already inserted.")
             return query.fetch(as_dict=True)
         key["artifact_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)
@@ -290,7 +290,7 @@ def _get_artifact_times(
             [[valid_timestamps[0], valid_timestamps[-1]]]
         )
         artifact_times_empty = np.asarray([])
-        logger.warn("No artifacts detected.")
+        logger.warning("No artifacts detected.")
         return recording_interval, artifact_times_empty
 
     # convert indices to intervals

src/spyglass/spikesorting/v1/figurl_curation.py

@@ -51,7 +51,7 @@ def insert_selection(cls, key: dict):
         if "figurl_curation_id" in key:
             query = cls & {"figurl_curation_id": key["figurl_curation_id"]}
             if query:
-                logger.warn("Similar row(s) already inserted.")
+                logger.warning("Similar row(s) already inserted.")
                 return query.fetch(as_dict=True)
         key["figurl_curation_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)

src/spyglass/spikesorting/v1/metric_curation.py

@@ -190,7 +190,7 @@ def insert_selection(cls, key: dict):
             key for the inserted row
         """
         if cls & key:
-            logger.warn("This row has already been inserted.")
+            logger.warning("This row has already been inserted.")
             return (cls & key).fetch1()
         key["metric_curation_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)

src/spyglass/spikesorting/v1/recording.py

@@ -154,7 +154,7 @@ def insert_selection(cls, key: dict):
         """
         query = cls & key
         if query:
-            logger.warn("Similar row(s) already inserted.")
+            logger.warning("Similar row(s) already inserted.")
             return query.fetch(as_dict=True)
         key["recording_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)

src/spyglass/utils/dj_helper_fn.py

@@ -124,7 +124,7 @@ def _subclass_factory(
 
     # Define the __call__ method for the new class
     def init_override(self, *args, **kwargs):
-        logger.warn(
+        logger.warning(
             "Deprecation: this class has been moved out of "
             + f"{old_module}\n"
             + f"\t{old_name} -> {new_module}.{new_class.__name__}"

src/spyglass/utils/dj_merge_tables.py

@@ -66,14 +66,14 @@ def __init__(self):
         self._reserved_sk = RESERVED_SECONDARY_KEY
         if not self.is_declared:
             if not is_merge_table(self):  # Check definition
-                logger.warn(
+                logger.warning(
                     "Merge table with non-default definition\n"
                     + f"Expected:\n{MERGE_DEFINITION.strip()}\n"
                     + f"Actual  :\n{self.definition.strip()}"
                 )
             for part in self.parts(as_objects=True):
                 if part.primary_key != self.primary_key:
-                    logger.warn(  # PK is only 'merge_id' in parts, no others
+                    logger.warning(  # PK is only 'merge_id' in parts, no others
                         f"Unexpected primary key in {part.table_name}"
                         + f"\n\tExpected: {self.primary_key}"
                         + f"\n\tActual  : {part.primary_key}"
@@ -721,7 +721,7 @@ def _normalize_source(
                 raise ValueError(f"Unable to find source for {source}")
             source = fetched_source[0]
             if len(fetched_source) > 1:
-                logger.warn(f"Multiple sources. Selecting first: {source}.")
+                logger.warning(f"Multiple sources. Selecting first: {source}.")
         if isinstance(source, dj.Table):
             source = self._part_name(source)
         if isinstance(source, dict):
@@ -814,7 +814,7 @@ def merge_fetch(
             try:
                 results.extend(part.fetch(*attrs, **kwargs))
             except DataJointError as e:
-                logger.warn(
+                logger.warning(
                     f"{e.args[0]} Skipping "
                     + to_camel_case(part.table_name.split("__")[-1])
                 )

src/spyglass/utils/dj_mixin.py

@@ -368,15 +368,15 @@ def _check_delete_permission(self) -> None:
             not self._session_connection  # Table has no session
             or self._member_pk in self.heading.names  # Table has experimenter
         ):
-            logger.warn(  # Permit delete if no session connection
+            logger.warning(  # Permit delete if no session connection
                 "Could not find lab team associated with "
                 + f"{self.__class__.__name__}."
                 + "\nBe careful not to delete others' data."
             )
             return
 
         if not (sess_summary := self._get_exp_summary()):
-            logger.warn(
+            logger.warning(
                 f"Could not find a connection from {self.camel_name} "
                 + "to Session.\n Be careful not to delete others' data."
             )

src/spyglass/utils/nwb_helper_fn.py

@@ -364,7 +364,7 @@ def get_valid_intervals(
 
     if total_time < min_valid_len:
         half_total_time = total_time / 2
-        logger.warn(f"Setting minimum valid interval to {half_total_time}")
+        logger.warning(f"Setting minimum valid interval to {half_total_time}")
         min_valid_len = half_total_time
 
     # get rid of NaN elements

tests/conftest.py

@@ -419,7 +419,6 @@ def video_keys(common, base_dir):
     for file in DOWNLOADS.file_downloads:
         if file.endswith(".h264"):
             DOWNLOADS.wait_for(file)
-    DOWNLOADS.rename_files()
 
     return common.VideoFile().fetch(as_dict=True)