print -> logger (LorenFrankLab#730)

* print -> logger * Changelog + notebook note on logger * Fix typo
CBroz1 · Dec 21, 2023 · daf671e · daf671e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Refactor restriction use in `delete_downstream_merge` #703
 - Add `cautious_delete` to Mixin class, initial implementation. #711
 - Add `deprecation_factory` to facilitate table migration. #717
+- Add Spyglass logger. #730
 
 ### Pipelines
 

diff --git a/notebooks/00_Setup.ipynb b/notebooks/00_Setup.ipynb
@@ -41,7 +41,7 @@
     "1. [Python 3.9](https://wiki.python.org/moin/BeginnersGuide/Download).\n",
     "2. [mamba](https://mamba.readthedocs.io/en/latest/installation.html) as a\n",
     "   replacement for conda. Spyglass installation is significantly faster with\n",
-    "   mamba. \n",
+    "   mamba.\n",
     "   ```bash\n",
     "   wget \"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh\"\n",
     "   bash Miniforge3-$(uname)-$(uname -m).sh\n",
@@ -133,7 +133,7 @@
     "```\n",
     "\n",
     "Members of the lab can run the `dj_config.py` helper script to generate a config\n",
-    "like the one below. \n",
+    "like the one below.\n",
     "\n",
     "```bash\n",
     "cd spyglass\n",
@@ -148,17 +148,16 @@
     "[docs](https://lorenfranklab.github.io/spyglass/0.4/installation/) for more\n",
     "information on subdirectories.\n",
     "\n",
-    "A different `output_filename` will save different files: \n",
+    "A different `output_filename` will save different files:\n",
     "\n",
     "- `dj_local_conf.json`: Recommended. Used for tutorials. A file in the current\n",
     "  directory DataJoint will automatically recognize when a Python session is\n",
     "  launched from this directory.\n",
-    "- `.datajoint_config.json` or no input: A file in the user's home directory \n",
+    "- `.datajoint_config.json` or no input: A file in the user's home directory\n",
     "  that will be referenced whenever no local version (see above) is present.\n",
     "- Anything else: A custom name that will need to be loaded (e.g.,\n",
     "  `dj.load('x')`) for each python session.\n",
     "\n",
-    "\n",
     "The config will be a `json` file like the following.\n",
     "\n",
     "```json\n",
@@ -170,6 +169,7 @@
     "    \"database.use_tls\": true,\n",
     "    \"enable_python_native_blobs\": true,\n",
     "    \"filepath_checksum_size_limit\": 1 * 1024**3,\n",
+    "    \"loglevel\": \"INFO\",\n",
     "    \"stores\": {\n",
     "        \"raw\": {\n",
     "            \"protocol\": \"file\",\n",
@@ -190,14 +190,18 @@
     "}\n",
     "```\n",
     "\n",
+    "Spyglass will use the log level present in your DataJoint config to decide the\n",
+    "appropriate logging level for this session. To change the messages you see,\n",
+    "select from one of [these options](https://docs.python.org/3/library/logging.html#levels).\n",
+    "\n",
     "If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your\n",
     "config before importing Spyglass.\n",
     "\n",
     "```python\n",
     "import datajoint as dj\n",
     "dj.load('/path/to/config')\n",
     "import spyglass\n",
-    "```"
+    "```\n"
    ]
   },
   {
@@ -226,8 +230,8 @@
     "  ```\n",
     "\n",
     "_Note_: For this demo, MySQL version won't matter. Some\n",
-    "  [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)\n",
-    "  features of Spyglass, however, expect MySQL >= 8.\n",
+    "[database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)\n",
+    "features of Spyglass, however, expect MySQL >= 8.\n",
     "\n",
     "- When run, this is referred to as a 'Docker container'\n",
     "- Next start the container with a couple additional pieces of info...\n",
@@ -277,7 +281,7 @@
    "source": [
     "### Loading the config\n",
     "\n",
-    "We can check that the paths are correctly set up by loading the config from \n",
+    "We can check that the paths are correctly set up by loading the config from\n",
     "the main Spyglass directory.\n"
    ]
   },
@@ -471,7 +475,7 @@
    "id": "13fd64af",
    "metadata": {},
    "source": [
-    "# Up Next"
+    "# Up Next\n"
    ]
   },
   {

diff --git a/notebooks/py_scripts/00_Setup.py b/notebooks/py_scripts/00_Setup.py
@@ -135,7 +135,6 @@
 # - Anything else: A custom name that will need to be loaded (e.g.,
 #   `dj.load('x')`) for each python session.
 #
-#
 # The config will be a `json` file like the following.
 #
 # ```json
@@ -147,6 +146,7 @@
 #     "database.use_tls": true,
 #     "enable_python_native_blobs": true,
 #     "filepath_checksum_size_limit": 1 * 1024**3,
+#     "loglevel": "INFO",
 #     "stores": {
 #         "raw": {
 #             "protocol": "file",
@@ -167,6 +167,10 @@
 # }
 # ```
 #
+# Spyglass will use the log level present in your DataJoint config to decide the
+# appropriate logging level for this session. To change the messages you see,
+# select from one of [these options](https://docs.python.org/3/library/logging.html#levels).
+#
 # If you see an error saying `Could not find SPYGLASS_BASE_DIR`, try loading your
 # config before importing Spyglass.
 #
@@ -175,6 +179,7 @@
 # dj.load('/path/to/config')
 # import spyglass
 # ```
+#
 
 # ### Running your own database
 #
@@ -192,8 +197,8 @@
 #   ```
 #
 # _Note_: For this demo, MySQL version won't matter. Some
-#   [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)
-#   features of Spyglass, however, expect MySQL >= 8.
+# [database management](https://lorenfranklab.github.io/spyglass/latest/misc/database_management/#mysql-version)
+# features of Spyglass, however, expect MySQL >= 8.
 #
 # - When run, this is referred to as a 'Docker container'
 # - Next start the container with a couple additional pieces of info...
@@ -244,7 +249,6 @@
 
 # +
 import os
-
 import datajoint as dj
 
 if os.path.basename(os.getcwd()) == "notebooks":
@@ -270,6 +274,7 @@
 # -
 
 # # Up Next
+#
 
 # Next, we'll try [inserting data](./01_Insert_Data.ipynb)
 #
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}"
         )