Fixed logging.*(…, deep="…")

Fixes scverse#746

scanpy/_settings.py

@@ -3,6 +3,7 @@
 from enum import IntEnum
 from pathlib import Path
 from time import time
+from logging import getLevelName
 from typing import Tuple, Union, Any, List, Iterable, TextIO, Optional
 
 from . import logging
@@ -15,7 +16,6 @@
     'hint': 'HINT',
     'debug': 'DEBUG',
 }
-verbosity_names = list(_VERBOSITY_TO_LOGLEVEL.keys())
 # Python 3.7 ensures iteration order
 for v, level in enumerate(list(_VERBOSITY_TO_LOGLEVEL.values())):
     _VERBOSITY_TO_LOGLEVEL[v] = level
@@ -28,6 +28,11 @@ class Verbosity(IntEnum):
     hint = 3
     debug = 4
 
+    @property
+    def level(self) -> int:
+        # getLevelName(str) returns the int level…
+        return getLevelName(_VERBOSITY_TO_LOGLEVEL[self])
+
 
 def _type_check(var: Any, varname: str, types: Union[type, Tuple[type, ...]]):
     if isinstance(var, types):

scanpy/logging.py

@@ -28,11 +28,12 @@ def log(
         time: datetime = None,
         deep: Optional[str] = None,
     ) -> datetime:
+        from . import settings
         now = datetime.now(timezone.utc)
         time_passed: timedelta = None if time is None else now - time
         extra = {
             **(extra or {}),
-            'deep': deep,
+            'deep': deep if settings.verbosity.level < level else None,
             'time_passed': time_passed
         }
         super().log(level, msg, extra=extra)
@@ -98,6 +99,8 @@ def format(self, record: logging.LogRecord):
                 record.msg = record.msg.replace('{time_passed}', str(record.time_passed))
             else:
                 self._style._fmt += ' ({time_passed})'
+        if record.deep:
+            record.msg = f'{record.msg}: {record.deep}'
         result = logging.Formatter.format(self, record)
         self._style._fmt = format_orig
         return result

scanpy/tests/test_logging.py

@@ -34,6 +34,20 @@ def test_formats(capsys, logging_state):
     assert capsys.readouterr().err == '    4\n'
 
 
+def test_deep(capsys, logging_state):
+    s.logfile = sys.stderr
+    s.verbosity = Verbosity.hint
+    l.hint('0')
+    assert capsys.readouterr().err == '--> 0\n'
+    l.hint('1', deep='1!')
+    assert capsys.readouterr().err == '--> 1\n'
+    s.verbosity = Verbosity.debug
+    l.hint('2')
+    assert capsys.readouterr().err == '--> 2\n'
+    l.hint('3', deep='3!')
+    assert capsys.readouterr().err == '--> 3: 3!\n'
+
+
 def test_logfile(tmp_path, logging_state):
     s.verbosity = Verbosity.hint