Removed warnings only for warnings with category : UserWarning

docs/CHANGELOG.rst

@@ -5,6 +5,7 @@ Changelog
 Unreleased
 ----------
 
+* Ignore unrelated warnings from MDAnalysis
 * Added argcomplete for tab completion
 * Updated docs 
 

src/mdacli/__main__.py

@@ -40,7 +40,7 @@ def main():
 
     mdacli.cli(
         name="MDAnalysis",
-        module_list=[f"MDAnalysis.analysis.{m}" for m in __all__],
+        module_list=[f"MDAnalysis.analysis.{m}" for m in __all__ if m != "hbonds"],
         version=mdacli.__version__,
         description=__doc__,
         skip_modules=skip_mods,

src/mdacli/libcli.py

@@ -127,7 +127,7 @@ def find_cls_members(cls, modules, ignore_warnings=False):
         Flag to ignore warnings
     """
     with warnings.catch_warnings():
-        if not ignore_warnings:
+        if ignore_warnings:
             warnings.simplefilter("ignore")
         return find_classes_in_modules(cls, *[m for m in modules])
 

tests/test_libcli.py

@@ -10,6 +10,7 @@
 import logging
 import os
 import sys
+import warnings
 from io import StringIO
 from json.decoder import JSONDecodeError
 from pathlib import Path
@@ -125,6 +126,50 @@ def test_find_cls_members_single(cls):
     assert members[1] is InterRDF_s
 
 
+def test_find_cls_members_ignore_warnings_true():
+    """Test that warnings are suppressed when ignore_warnings=True."""
+    with patch("mdacli.libcli.find_classes_in_modules") as mocked:
+
+        def warn_func(*_args, **_kwargs):
+            warnings.warn("warning", DeprecationWarning, stacklevel=2)
+            return ["OK"]
+
+        mocked.side_effect = warn_func
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")
+
+            members = find_cls_members(
+                AnalysisBase,
+                modules=["dummy.mod"],
+                ignore_warnings=True,
+            )
+
+        assert members == ["OK"]
+
+
+def test_find_cls_members_ignore_warnings_false():
+    """Test that warnings are emitted when ignore_warnings=False."""
+    with patch("mdacli.libcli.find_classes_in_modules") as mocked:
+
+        def warn_func(*_args, **_kwargs):
+            warnings.warn(
+                "This module was moved to ...", DeprecationWarning, stacklevel=2
+            )
+            return ["OK"]
+
+        mocked.side_effect = warn_func
+
+        with pytest.warns(DeprecationWarning, match="moved to"):
+            members = find_cls_members(
+                AnalysisBase,
+                modules=["dummy.mod"],
+                ignore_warnings=False,
+            )
+
+        assert members == ["OK"]
+
+
 @pytest.mark.parametrize(
     "cls", [AnalysisBase, [AnalysisBase, AnalysisBase], (AnalysisBase, AnalysisBase)]
 )