Add level option to setup_logging

docs/CHANGELOG.rst

@@ -2,6 +2,8 @@
 Changelog
 =========
 
+* Replace Boolean ``debug`` option in  ``setup_logging`` by more flexible integer
+  ``level`` parameter.
 
 v0.1.29 (2024-03-21)
 ------------------------------------------

src/mdacli/cli.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
 #
-# Copyright (c) 2021 Authors and contributors
+# Copyright (c) 2024 Authors and contributors
 #
 # Released under the GNU Public Licence, v2 or any higher version
 # SPDX-License-Identifier: GPL-2.0-or-later
@@ -104,13 +104,20 @@ def cli(name,
 
     args = ap.parse_args()
 
+    # Set the logging level based on the verbose argument
+    # If verbose is not an argument, default to WARNING
+    if not hasattr(args, "verbose") or not args.verbose:
+        level = logging.WARNING
+    else:
+        level = logging.INFO
+
     if args.debug:
-        args.verbose = True
+        level = logging.DEBUG
     else:
-        # Ignore all warnings if not in debug mode
+        # Ignore all warnings if not in debug mode, because MDA is noisy
         warnings.filterwarnings("ignore")
 
-    with setup_logging(logger, logfile=args.logfile, debug=args.debug):
+    with setup_logging(logger, logfile=args.logfile, level=level):
         # Execute the main client interface.
         try:
             analysis_callable = args.analysis_callable

src/mdacli/logger.py

@@ -15,7 +15,7 @@
 
 
 @contextlib.contextmanager
-def setup_logging(logobj, logfile=None, debug=False):
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
     """
     Create a logging environment for a given logobj.
 
@@ -25,19 +25,20 @@ def setup_logging(logobj, logfile=None, debug=False):
         A logging instance
     logfile : str
         Name of the log file
-    debug : bool
-        If ``True`` detailed debug logs inludcing filename and function name
-        are displayed. If ``False`` only the message logged from
-        errors, warnings and infos will be displayed.
+    level : int
+        Set the root logger level to the specified level. If for example set
+        to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
+        function name are displayed. For :py:obj:`logging.INFO only the message
+        logged from errors, warnings and infos will be displayed.
     """
     try:
-        format = '{message}'
-        if debug:
-            format = "[{levelname}] {filename}:{name}:{funcName}:{lineno}: " \
-                     + format
-            level = logging.DEBUG
+        if level == logging.DEBUG:
+            format = (
+                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+                "{message}"
+            )
         else:
-            level = logging.INFO
+            format = "{message}"
 
         logging.basicConfig(format=format,
                             handlers=[logging.StreamHandler(sys.stdout)],

tests/run_tester

@@ -0,0 +1,16 @@
+#!/usr/bin/env python3
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+#
+# Copyright (c) 2024 Authors and contributors
+#
+# Released under the GNU Public Licence, v2 or any higher version
+# SPDX-License-Identifier: GPL-2.0-or-later
+import re
+import sys
+
+from tester.__main__ import main
+
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

tests/test_cli.py

@@ -8,33 +8,38 @@
 """Test mdacli cli."""
 
 import subprocess
+import sys
+from pathlib import Path
 
 import pytest
 from MDAnalysisTests.datafiles import TPR, XTC
 
 
+tester_class = (Path('.').absolute() / 'tests/run_tester').as_posix()
+
+
 def test_required_args():
     """Test that there is a module given."""
     with pytest.raises(subprocess.CalledProcessError):
-        subprocess.check_call(['mda'])
+        subprocess.check_call(["mda"])
 
 
 def test_wrong_module():
     """Test for a non existent module."""
     with pytest.raises(subprocess.CalledProcessError):
-        subprocess.check_call(['mda', 'foo'])
+        subprocess.check_call(["mda", "foo"])
 
 
-@pytest.mark.parametrize('args', ("version", "debug", "help"))
+@pytest.mark.parametrize("args", ("version", "debug", "help"))
 def test_extra_options(args):
     """Test for a ab extra option."""
-    subprocess.check_call(['mda', '--' + args])
+    subprocess.check_call(["mda", "--" + args])
 
 
-@pytest.mark.parametrize('args', ("RMSF", "rmsf"))
+@pytest.mark.parametrize("args", ("RMSF", "rmsf"))
 def test_case_insensitive(args):
-    """Test for beeing case insensitive."""
-    subprocess.check_call(['mda', args, "-h"])
+    """Test for being case insensitive."""
+    subprocess.check_call(["mda", args, "-h"])
 
 
 @pytest.mark.parametrize('args', ("RMSF", "rmsf"))
@@ -48,4 +53,54 @@ def test_running_analysis(tmpdir):
     """Test running a complete analysis."""
     with tmpdir.as_cwd():
         subprocess.check_call(
-            ['mda', "rmsf", "-s", TPR, "-f", XTC, "-atomgroup", "all"])
+            ["mda", "rmsf", "-s", TPR, "-f", XTC, "-atomgroup", "all"]
+        )
+
+
+def test_verbosity_level_warning(caplog):
+    """Test the log level warning."""
+    # This should only print warning messages
+    output = subprocess.check_output(
+        [sys.executable, tester_class,
+         "tester", "-s", TPR, "-f", XTC, "-atomgroup", "all"],
+        text=True,
+    )
+    assert "This is a warning" in output
+    # Cross-check that info and debug messages are not printed
+    assert "This is a debug message" not in output
+    assert "This is an info message" not in output
+
+
+def test_verbosity_level_info(caplog):
+    """Test the log level info."""
+    # This should only print warning and info messages
+    output = subprocess.check_output(
+        [
+            sys.executable, tester_class,
+            "tester", "-s", TPR, "-f", XTC,
+            "-atomgroup", "all",
+            "-v",
+        ],
+        text=True,
+    )
+    assert "This is an info message" in output
+    assert "This is a warning" in output
+    # Cross-check that debug messages are not printed
+    assert "This is a debug message" not in output
+
+
+def test_verbosity_level_debug(caplog):
+    """Test the log level debug."""
+    # This should print all messages
+    output = subprocess.check_output(
+        [
+            sys.executable, tester_class, "--debug",
+            "tester", "-s", TPR, "-f", XTC,
+            "-atomgroup", "all",
+            "-v",
+        ],
+        text=True,
+    )
+    assert "This is an info message" in output
+    assert "This is a warning" in output
+    assert "This is a debug message" in output

tests/test_logger.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
 #
-# Copyright (c) 2021 Authors and contributors
+# Copyright (c) 2024 Authors and contributors
 #
 # Released under the GNU Public Licence, v2 or any higher version
 # SPDX-License-Identifier: GPL-2.0-or-later
@@ -20,7 +20,7 @@ def test_default_log(self, caplog):
         logger = logging.getLogger("test")
         with mdacli.logger.setup_logging(logger,
                                          logfile=None,
-                                         debug=False):
+                                         level=logging.INFO):
             logger.info("foo")
             assert "foo" in caplog.text
 
@@ -33,7 +33,7 @@ def test_info_log(self, tmpdir, caplog):
             # is created by the function.
             with mdacli.logger.setup_logging(logger,
                                              logfile="logfile",
-                                             debug=False):
+                                             level=logging.INFO):
                 logger.info("foo")
                 assert "foo" in caplog.text
             with open("logfile.log", "r") as f:
@@ -48,7 +48,7 @@ def test_debug_log(self, tmpdir, caplog):
         with tmpdir.as_cwd():
             with mdacli.logger.setup_logging(logger,
                                              logfile="logfile",
-                                             debug=True):
+                                             level=logging.DEBUG):
                 logger.info("foo")
                 assert "test:test_logger.py:52 foo\n" in caplog.text
 

tests/tester/__init__.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+#
+# Copyright (c) 2024 Authors and contributors
+#
+# Released under the GNU Public Licence, v2 or any higher version
+# SPDX-License-Identifier: GPL-2.0-or-later
+"""Make the tester module available to mdacli."""
+
+from .tester_class import Tester  # noqa

tests/tester/__main__.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+#
+# Copyright (c) 2024 Authors and contributors
+# (see the AUTHORS.rst file for the full list of names)
+#
+# Released under the GNU Public Licence, v3 or any higher version
+# SPDX-License-Identifier: GPL-3.0-or-later
+"""Test module for mdacli."""
+
+from MDAnalysis.analysis.base import AnalysisBase
+
+from mdacli import cli
+
+
+def main():
+    """Execute main CLI entry point."""
+    cli(
+        name="Tester",
+        module_list=["tester"],
+        base_class=AnalysisBase,
+        version=0.0,
+        description="test",
+        ignore_warnings=True,
+    )
+
+
+if __name__ == "__main__":
+    main()

tests/tester/tester_class.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+#
+# Copyright (c) 2024 Authors and contributors
+#
+# Released under the GNU Public Licence, v2 or any higher version
+# SPDX-License-Identifier: GPL-2.0-or-later
+"""Mock module for mdacli to test logging."""
+
+import logging
+
+from MDAnalysis.analysis.base import AnalysisBase
+
+
+logger = logging.getLogger(__name__)
+
+
+class Tester(AnalysisBase):
+    """Mock class for mdacli. Implements only the minimum requirements.
+
+    Currently only logs messages at different levels to check the verbosity and
+    debug flags in the CLI.
+
+    Parameters
+    ----------
+    atomgroup : AtomGroup or Universe
+    """
+
+    def __init__(self, atomgroup, **kwargs):
+        """Initialise the Tester class."""
+        super(Tester, self).__init__(atomgroup.universe.trajectory, **kwargs)
+        logger.info("This is an info message")
+        logger.warn("This is a warning")
+        logger.debug("This is a debug message")
+
+    def _prepare(self):
+        """Prepare the analysis."""
+        pass
+
+    def _single_frame(self):
+        """Analyse a single frame."""
+        pass
+
+    def _conclude(self):
+        """Conclude the analysis."""
+        pass