Add centralized logger.

Author: jverswijver

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 --

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
 
 
@@ -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

@@ -2,11 +2,13 @@
 import re
 import functools
 import io
-import warnings
+import logging
 import inspect
 from .table import Table
 from .dependencies import unite_master_parts
 
+logger = logging.getLogger(__name__.split(".")[0])
+
 try:
     from matplotlib import pyplot as plt
 
@@ -63,7 +65,7 @@ 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

datajoint/logging.py

@@ -0,0 +1,57 @@
+import logging
+import os
+import sys
+import io
+
+logger = logging.getLogger(__name__.split(".")[0])
+
+log_level = os.environ.get("DJ_LOG_LEVEL", "warning").upper()
+
+log_format = logging.Formatter(
+    "[%(asctime)s][%(funcName)s][%(levelname)s]: %(message)s"
+)
+
+stream_handler = logging.StreamHandler()  # default handler
+stream_handler.setFormatter(log_format)
+
+logger.setLevel(level=log_level)
+logger.handlers = [stream_handler]
+
+
+def excepthook(exc_type, exc_value, exc_traceback):
+    if issubclass(exc_type, KeyboardInterrupt):
+        sys.__excepthook__(exc_type, exc_value, exc_traceback)
+        return
+
+    if logger.getEffectiveLevel() == 10:
+        logger.debug(
+            "Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)
+        )
+    else:
+        logger.error(f"Uncaught exception: {exc_value}")
+
+
+sys.excepthook = excepthook
+
+
+# https://github.com/tqdm/tqdm/issues/313#issuecomment-267959111
+class TqdmToLogger(io.StringIO):
+    """
+    Output stream for TQDM which will output to logger module instead of
+    the StdOut.
+    """
+
+    logger = None
+    level = None
+    buf = ""
+
+    def __init__(self, logger, level=None):
+        super(TqdmToLogger, self).__init__()
+        self.logger = logger
+        self.level = level or logging.INFO
+
+    def write(self, buf):
+        self.buf = buf.strip("\r\n\t ")
+
+    def flush(self):
+        self.logger.log(self.level, self.buf)

datajoint/plugin.py

@@ -3,6 +3,9 @@
 from pathlib import Path
 from cryptography.exceptions import InvalidSignature
 from otumat import hash_pkg, verify
+import logging
+
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def _update_error_stack(plugin_name):
@@ -15,10 +18,10 @@ def _update_error_stack(plugin_name):
         signature = plugin_meta.get_metadata("{}.sig".format(plugin_name))
         pubkey_path = str(Path(base_meta.egg_info, "{}.pub".format(base_name)))
         verify(pubkey_path=pubkey_path, data=data, signature=signature)
-        print("DataJoint verified plugin `{}` detected.".format(plugin_name))
+        logger.info("DataJoint verified plugin `{}` detected.".format(plugin_name))
         return True
     except (FileNotFoundError, InvalidSignature):
-        print("Unverified plugin `{}` detected.".format(plugin_name))
+        logger.warning("Unverified plugin `{}` detected.".format(plugin_name))
         return False