Quiet mhctools logging by default

mhctools/__init__.py

@@ -1,5 +1,6 @@
 from .binding_prediction import BindingPrediction
 from .binding_prediction_collection import BindingPredictionCollection
+from .logging import set_log_level
 from .pred import (
     FIELD_BEST_DIRECTIONS,
     Kind,
@@ -87,7 +88,7 @@ def __getattr__(name):
     raise AttributeError(
         "module %r has no attribute %r" % (__name__, name))
 
-__version__ = "3.31.3"
+__version__ = "3.31.4"
 
 __all__ = [
     "Prediction",
@@ -108,6 +109,7 @@ def __getattr__(name):
     "parse_annotation_spec",
     "BindingPrediction",
     "BindingPredictionCollection",
+    "set_log_level",
     "IedbNetMHCcons",
     "IedbNetMHCpan",
     "IedbSMM",

mhctools/logging.py

@@ -11,12 +11,46 @@
 # limitations under the License.
 
 import logging
-import logging.config
-from importlib.resources import as_file, files
+
+
+_PACKAGE_LOGGER_NAME = "mhctools"
+_PACKAGE_LOGGER = logging.getLogger(_PACKAGE_LOGGER_NAME)
+if not any(isinstance(handler, logging.NullHandler)
+           for handler in _PACKAGE_LOGGER.handlers):
+    _PACKAGE_LOGGER.addHandler(logging.NullHandler())
+
+_LOG_LEVELS = {
+    "CRITICAL": logging.CRITICAL,
+    "ERROR": logging.ERROR,
+    "WARNING": logging.WARNING,
+    "WARN": logging.WARNING,
+    "INFO": logging.INFO,
+    "DEBUG": logging.DEBUG,
+    "NOTSET": logging.NOTSET,
+}
 
 
 def get_logger(name):
-    config_resource = files("mhctools").joinpath("logging.conf")
-    with as_file(config_resource) as config_path:
-        logging.config.fileConfig(str(config_path))
     return logging.getLogger(name)
+
+
+def set_log_level(level):
+    """Set the log level for mhctools loggers.
+
+    Parameters
+    ----------
+    level : str or int
+        Logging level such as ``"WARNING"``, ``"INFO"``, or ``logging.DEBUG``.
+
+    Returns
+    -------
+    logging.Logger
+        The package logger whose level was set.
+    """
+    if isinstance(level, str):
+        level_name = level.upper()
+        if level_name not in _LOG_LEVELS:
+            raise ValueError("Unknown logging level %r" % level)
+        level = _LOG_LEVELS[level_name]
+    _PACKAGE_LOGGER.setLevel(level)
+    return _PACKAGE_LOGGER

tests/test_logging.py

@@ -0,0 +1,76 @@
+import logging
+import logging.config
+
+import pytest
+
+import mhctools
+from mhctools import logging as mhctools_logging
+
+
+@pytest.fixture(autouse=True)
+def restore_mhctools_logger():
+    logger = logging.getLogger("mhctools")
+    old_level = logger.level
+    old_handlers = list(logger.handlers)
+    old_propagate = logger.propagate
+    yield
+    logger.setLevel(old_level)
+    logger.handlers[:] = old_handlers
+    logger.propagate = old_propagate
+
+
+def test_get_logger_does_not_call_fileconfig(monkeypatch):
+    def fail_fileconfig(*args, **kwargs):
+        raise AssertionError("fileConfig must not be called by mhctools")
+
+    monkeypatch.setattr(logging.config, "fileConfig", fail_fileconfig)
+
+    logger = mhctools_logging.get_logger("mhctools.test")
+
+    assert logger.name == "mhctools.test"
+
+
+def test_get_logger_does_not_reconfigure_root_logger():
+    root = logging.getLogger()
+    old_level = root.level
+    old_handlers = list(root.handlers)
+
+    mhctools_logging.get_logger("mhctools.test")
+
+    assert root.level == old_level
+    assert list(root.handlers) == old_handlers
+
+
+def test_package_logger_has_null_handler_by_default():
+    handlers = logging.getLogger("mhctools").handlers
+
+    assert any(isinstance(handler, logging.NullHandler)
+               for handler in handlers)
+
+
+def test_info_logs_are_quiet_by_default(capsys):
+    logger = mhctools_logging.get_logger("mhctools.test.quiet")
+
+    logger.info("should not print")
+
+    captured = capsys.readouterr()
+    assert captured.out == ""
+    assert captured.err == ""
+
+
+def test_set_log_level_accepts_string_levels():
+    logger = mhctools.set_log_level("WARNING")
+
+    assert logger is logging.getLogger("mhctools")
+    assert logger.level == logging.WARNING
+
+
+def test_set_log_level_accepts_numeric_levels():
+    logger = mhctools_logging.set_log_level(logging.ERROR)
+
+    assert logger.level == logging.ERROR
+
+
+def test_set_log_level_rejects_unknown_level():
+    with pytest.raises(ValueError, match="NOTALEVEL"):
+        mhctools.set_log_level("NOTALEVEL")