print -> logger

CBroz1 · Dec 21, 2023 · 63eec83 · 63eec83
1 parent 237cc2d
commit 63eec83
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Showing 57 changed files with 589 additions and 486 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -48,7 +48,7 @@ dependencies = [
     "numpy<1.24",
     "ipympl",
     "tqdm",
-    "pubnub<6.4.0",
+    "pubnub<6.4.0", # TODO: remove this when sortingview is updated
     "pynwb>=2.2.0,<3",
     "hdmf>=3.4.6",
     "datajoint>=0.13.6",

diff --git a/src/spyglass/common/common_behav.py b/src/spyglass/common/common_behav.py
@@ -14,7 +14,7 @@
 from spyglass.common.common_session import Session  # noqa: F401
 from spyglass.common.common_task import TaskEpoch
 from spyglass.settings import video_dir
-from spyglass.utils.dj_mixin import SpyglassMixin
+from spyglass.utils import SpyglassMixin, logger
 from spyglass.utils.nwb_helper_fn import (
     get_all_spatial_series,
     get_data_interface,
@@ -174,7 +174,7 @@ 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:
-                print("WARNING: loading DataFrame with multiple intervals.")
+                logger.warn("Loading DataFrame with multiple intervals.")
 
             df_list = [
                 pd.DataFrame(
@@ -270,7 +270,7 @@ def make(self, key):
             "associated_files"
         ) or nwbf.processing.get("associated files")
         if associated_files is None:
-            print(
+            logger.info(
                 "Unable to import StateScriptFile: no processing module named "
                 + '"associated_files" found in {nwb_file_name}.'
             )
@@ -280,7 +280,7 @@ def make(self, key):
             if not isinstance(
                 associated_file_obj, ndx_franklab_novela.AssociatedFiles
             ):
-                print(
+                logger.info(
                     f"Data interface {associated_file_obj.name} within "
                     + '"associated_files" processing module is not '
                     + "of expected type ndx_franklab_novela.AssociatedFiles\n"
@@ -293,7 +293,7 @@ def make(self, key):
 
             epoch_list = associated_file_obj.task_epochs.split(",")
             # only insert if this is the statescript file
-            print(associated_file_obj.description)
+            logger.info(associated_file_obj.description)
             if (
                 "statescript".upper() in associated_file_obj.description.upper()
                 or "state_script".upper()
@@ -306,7 +306,7 @@ def make(self, key):
                     key["file_object_id"] = associated_file_obj.object_id
                     self.insert1(key)
             else:
-                print("not a statescript file")
+                logger.info("not a statescript file")
 
 
 @schema
@@ -347,7 +347,7 @@ def _no_transaction_make(self, key, verbose=True):
         )
 
         if videos is None:
-            print(f"No video data interface found in {nwb_file_name}\n")
+            logger.warn(f"No video data interface found in {nwb_file_name}\n")
             return
         else:
             videos = videos.time_series
@@ -388,7 +388,7 @@ def _no_transaction_make(self, key, verbose=True):
                     is_found = True
 
         if not is_found and verbose:
-            print(
+            logger.info(
                 f"No video found corresponding to file {nwb_file_name}, "
                 + f"epoch {interval_list_name}"
             )
@@ -471,7 +471,7 @@ def _no_transaction_make(self, key):
 
         # Skip populating if no pos interval list names
         if len(pos_intervals) == 0:
-            print(f"NO POS INTERVALS FOR {key}; {no_pop_msg}")
+            logger.error(f"NO POS INTERVALS FOR {key}; {no_pop_msg}")
             return
 
         valid_times = (IntervalList & key).fetch1("valid_times")
@@ -508,7 +508,7 @@ def _no_transaction_make(self, key):
 
         # Check that each pos interval was matched to only one epoch
         if len(matching_pos_intervals) != 1:
-            print(
+            logger.error(
                 f"Found {len(matching_pos_intervals)} pos intervals for {key}; "
                 + f"{no_pop_msg}\n{matching_pos_intervals}"
             )
@@ -517,7 +517,7 @@ def _no_transaction_make(self, key):
         # Insert into table
         key["position_interval_name"] = matching_pos_intervals[0]
         self.insert1(key, allow_direct_insert=True)
-        print(
+        logger.info(
             "Populated PosIntervalMap for "
             + f'{nwb_file_name}, {key["interval_list_name"]}'
         )
@@ -569,7 +569,7 @@ def convert_epoch_interval_name_to_position_interval_name(
             )
 
     if len(pos_query) == 0:
-        print(f"No position intervals found for {key}")
+        logger.info(f"No position intervals found for {key}")
         return []
 
     if len(pos_query) == 1:
@@ -596,7 +596,7 @@ def get_interval_list_name_from_epoch(nwb_file_name: str, epoch: int) -> str:
     ).fetch("interval_list_name")
 
     if len(interval_names) != 1:
-        print(
+        logger.info(
             f"Found {len(interval_names)} interval list names found for "
             + f"{nwb_file_name} epoch {epoch}"
         )

diff --git a/src/spyglass/common/common_device.py b/src/spyglass/common/common_device.py
@@ -1,10 +1,10 @@
 import datajoint as dj
 import ndx_franklab_novela
 
+from spyglass.common.errors import PopulateException
 from spyglass.utils.dj_mixin import SpyglassMixin
-
-from ..utils.nwb_helper_fn import get_nwb_file
-from .errors import PopulateException
+from spyglass.utils.logging import logger
+from spyglass.utils.nwb_helper_fn import get_nwb_file
 
 schema = dj.schema("common_device")
 
@@ -14,7 +14,6 @@ class DataAcquisitionDeviceSystem(SpyglassMixin, dj.Manual):
     definition = """
     # Known data acquisition device system names.
     data_acquisition_device_system: varchar(80)
-    ---
     """
 
 
@@ -23,7 +22,6 @@ class DataAcquisitionDeviceAmplifier(SpyglassMixin, dj.Manual):
     definition = """
     # Known data acquisition device amplifier names.
     data_acquisition_device_amplifier: varchar(80)
-    ---
     """
 
 
@@ -84,12 +82,12 @@ def insert_from_nwbfile(cls, nwbf, config):
             cls._add_device(new_device_dict)
 
         if ndx_devices:
-            print(
+            logger.info(
                 "Inserted or referenced data acquisition device(s): "
                 + f"{ndx_devices.keys()}"
             )
         else:
-            print("No conforming data acquisition device metadata found.")
+            logger.warn("No conforming data acquisition device metadata found.")
 
     @classmethod
     def get_all_device_names(cls, nwbf, config) -> tuple:
@@ -158,7 +156,7 @@ def _add_device(cls, new_device_dict):
         ).tolist()
         if name not in all_values:
             # no entry with the same name exists, prompt user to add a new entry
-            print(
+            logger.info(
                 f"\nData acquisition device '{name}' was not found in the "
                 f"database. The current values are: {all_values}. "
                 "Please ensure that the device you want to add does not already"
@@ -216,7 +214,7 @@ def _add_system(cls, system):
             "data_acquisition_device_system"
         ).tolist()
         if system not in all_values:
-            print(
+            logger.info(
                 f"\nData acquisition device system '{system}' was not found in"
                 f" the database. The current values are: {all_values}. "
                 "Please ensure that the system you want to add does not already"
@@ -267,7 +265,7 @@ def _add_amplifier(cls, amplifier):
             "data_acquisition_device_amplifier"
         ).tolist()
         if amplifier not in all_values:
-            print(
+            logger.info(
                 f"\nData acquisition device amplifier '{amplifier}' was not "
                 f"found in the database. The current values are: {all_values}. "
                 "Please ensure that the amplifier you want to add does not "
@@ -337,9 +335,9 @@ def insert_from_nwbfile(cls, nwbf):
                 cls.insert1(device_dict, skip_duplicates=True)
                 device_name_list.append(device_dict["camera_name"])
         if device_name_list:
-            print(f"Inserted camera devices {device_name_list}")
+            logger.info(f"Inserted camera devices {device_name_list}")
         else:
-            print("No conforming camera device metadata found.")
+            logger.warn("No conforming camera device metadata found.")
         return device_name_list
 
 
@@ -442,7 +440,7 @@ def insert_from_nwbfile(cls, nwbf, config):
             # the ones in the database
             query = Probe & {"probe_id": new_probe_dict["probe_id"]}
             if len(query) > 0:
-                print(
+                logger.info(
                     f"Probe ID '{new_probe_dict['probe_id']}' already exists in"
                     " the database. Spyglass will use that and not create a new"
                     " Probe, Shanks, or Electrodes."
@@ -457,9 +455,9 @@ def insert_from_nwbfile(cls, nwbf, config):
                 cls.Electrode.insert1(electrode, skip_duplicates=True)
 
         if all_probes_types:
-            print(f"Inserted probes {all_probes_types}")
+            logger.info(f"Inserted probes {all_probes_types}")
         else:
-            print("No conforming probe metadata found.")
+            logger.warn("No conforming probe metadata found.")
 
         return all_probes_types
 
@@ -579,7 +577,7 @@ def _add_probe_type(cls, new_probe_type_dict):
         probe_type = new_probe_type_dict["probe_type"]
         all_values = ProbeType.fetch("probe_type").tolist()
         if probe_type not in all_values:
-            print(
+            logger.info(
                 f"\nProbe type '{probe_type}' was not found in the database. "
                 f"The current values are: {all_values}. "
                 "Please ensure that the probe type you want to add does not "
@@ -663,7 +661,7 @@ def create_from_nwbfile(
 
         query = ProbeType & {"probe_type": probe_type}
         if len(query) == 0:
-            print(
+            logger.warn(
                 f"No ProbeType found with probe_type '{probe_type}'. Aborting."
             )
             return
@@ -727,7 +725,7 @@ def create_from_nwbfile(
                     ]
 
         if not device_found:
-            print(
+            logger.warn(
                 "No electrodes in the NWB file were associated with a device "
                 + f"named '{nwb_device_name}'."
             )

diff --git a/src/spyglass/common/common_dio.py b/src/spyglass/common/common_dio.py
@@ -4,13 +4,12 @@
 import pandas as pd
 import pynwb
 
-from spyglass.utils.dj_mixin import SpyglassMixin
-
-from ..utils.nwb_helper_fn import get_data_interface, get_nwb_file
-from .common_ephys import Raw
-from .common_interval import IntervalList
-from .common_nwbfile import Nwbfile
-from .common_session import Session  # noqa: F401
+from spyglass.common.common_ephys import Raw
+from spyglass.common.common_interval import IntervalList
+from spyglass.common.common_nwbfile import Nwbfile
+from spyglass.common.common_session import Session  # noqa: F401
+from spyglass.utils import SpyglassMixin, logger
+from spyglass.utils.nwb_helper_fn import get_data_interface, get_nwb_file
 
 schema = dj.schema("common_dio")
 
@@ -36,7 +35,7 @@ def make(self, key):
             nwbf, "behavioral_events", pynwb.behavior.BehavioralEvents
         )
         if behav_events is None:
-            print(
+            logger.warn(
                 "No conforming behavioral events data interface found in "
                 + f"{nwb_file_name}\n"
             )