Merge branch 'add_logger' of https://github.com/jverswijver/datajoint-python into remove_checksum

Author: jverswijver

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ### 0.13.6 -- TBD
 * Add - Config option to set threshold for when to stop using checksums for filepath stores. PR #1025
+* Add - unified package level logger for package
+* Update - swap various datajoint messages, warnings, ect. to use the new logger.
 
 ### 0.13.5 -- May 19, 2022
 * Update - Import ABC from collections.abc for Python 3.10 compatibility

LNX-docker-compose.yml

@@ -32,7 +32,7 @@ services:
       interval: 1s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.1.1
+    image: datajoint/nginx:v0.2.1
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

datajoint/__init__.py

@@ -52,6 +52,7 @@
     "key_hash",
 ]
 
+from .logging import logger
 from .version import __version__
 from .settings import config
 from .connection import conn, Connection

datajoint/autopopulate.py

@@ -12,7 +12,7 @@
 
 # noinspection PyExceptionInherit,PyCallingNonCallable
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 # --- helper functions for multiprocessing --
@@ -275,7 +275,7 @@ def _populate1(
                 if jobs is not None:
                     jobs.complete(self.target.table_name, self._job_key(key))
             else:
-                logger.info("Populating: " + str(key))
+                logger.debug("Populating: " + str(key))
                 self.__class__._allow_insert = True
                 try:
                     make(dict(key), **(make_kwargs or {}))

datajoint/connection.py

@@ -17,7 +17,7 @@
 from .hash import uuid_from_buffer
 from .plugin import connection_plugins
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 query_log_max_length = 300
 
 
@@ -184,7 +184,7 @@ def __init__(self, host, user, password, port=None, init_fun=None, use_tls=None)
         self.conn_info["ssl_input"] = use_tls
         self.conn_info["host_input"] = host_input
         self.init_fun = init_fun
-        print("Connecting {user}@{host}:{port}".format(**self.conn_info))
+        logger.info("Connecting {user}@{host}:{port}".format(**self.conn_info))
         self._conn = None
         self._query_cache = None
         connect_host_hook(self)
@@ -339,7 +339,7 @@ def query(
         except errors.LostConnectionError:
             if not reconnect:
                 raise
-            warnings.warn("MySQL server has gone away. Reconnecting to the server.")
+            logger.warning("MySQL server has gone away. Reconnecting to the server.")
             connect_host_hook(self)
             if self._in_transaction:
                 self.cancel_transaction()

datajoint/declare.py

@@ -75,7 +75,7 @@ def match_type(attribute_type):
         )
 
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def build_foreign_key_parser_old():
@@ -207,7 +207,7 @@ def compile_foreign_key(
         )
 
     if obsolete:
-        warnings.warn(
+        logger.warning(
             'Line "{line}" uses obsolete syntax that will no longer be supported in datajoint 0.14. '
             "For details, see issue #780 https://github.com/datajoint/datajoint-python/issues/780".format(
                 line=line

datajoint/diagram.py

@@ -2,10 +2,15 @@
 import re
 import functools
 import io
-import warnings
+import logging
 import inspect
 from .table import Table
 from .dependencies import unite_master_parts
+from .user_tables import Manual, Imported, Computed, Lookup, Part
+from .errors import DataJointError
+from .table import lookup_class_name
+
+logger = logging.getLogger(__name__.split(".")[0])
 
 try:
     from matplotlib import pyplot as plt
@@ -21,10 +26,6 @@
 except:
     diagram_active = False
 
-from .user_tables import Manual, Imported, Computed, Lookup, Part
-from .errors import DataJointError
-from .table import lookup_class_name
-
 
 user_table_classes = (Manual, Lookup, Computed, Imported, Part)
 
@@ -63,7 +64,7 @@ class Diagram:
         """
 
         def __init__(self, *args, **kwargs):
-            warnings.warn(
+            logger.warning(
                 "Please install matplotlib and pygraphviz libraries to enable the Diagram feature."
             )
 

datajoint/expression.py

@@ -17,7 +17,7 @@
 )
 from .declare import CONSTANT_LITERALS
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 class QueryExpression:

datajoint/fetch.py

@@ -1,6 +1,6 @@
 from functools import partial
 from pathlib import Path
-import warnings
+import logging
 import pandas
 import itertools
 import re
@@ -12,6 +12,8 @@
 from .settings import config
 from .utils import safe_write
 
+logger = logging.getLogger(__name__.split(".")[0])
+
 
 class key:
     """
@@ -209,7 +211,7 @@ def __call__(
                 )
 
         if limit is None and offset is not None:
-            warnings.warn(
+            logger.warning(
                 "Offset set, but no limit. Setting limit to a large number. "
                 "Consider setting a limit explicitly."
             )

datajoint/heading.py

@@ -14,7 +14,7 @@
 from .attribute_adapter import get_adapter, AttributeAdapter
 
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 default_attribute_properties = (
     dict(  # these default values are set in computed attributes