From 8ffece44e515029fbbbc6beff4efd4fd078afe7d Mon Sep 17 00:00:00 2001
From: spyke7 <dolaishreejan@gmail.com>
Date: Sat, 22 Nov 2025 00:39:53 +0530
Subject: [PATCH 1/4] Removed warnings category:UserWarning

---
 src/mdacli/libcli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mdacli/libcli.py b/src/mdacli/libcli.py
index fad9212d..ecdada19 100644
--- a/src/mdacli/libcli.py
+++ b/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])
 

From 118f44a35af75f7cd15d4f158b2ced192858b9ae Mon Sep 17 00:00:00 2001
From: spyke7 <dolaishreejan@gmail.com>
Date: Fri, 28 Nov 2025 15:58:00 +0530
Subject: [PATCH 2/4] Updated CHANGELOG and added tests

---
 docs/CHANGELOG.rst   |  6 ++++++
 tests/test_libcli.py | 45 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 97e4953b..b2237ad6 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -5,6 +5,12 @@ Changelog
 Unreleased
 ----------
 
+* Updated the ignoring warnings in libcli.py
+* Added tests for ignoring warnings
+
+v0.1.34 (2025-11-28)
+------------------------------------------
+
 * Added argcomplete for tab completion
 * Updated docs 
 
diff --git a/tests/test_libcli.py b/tests/test_libcli.py
index 0645321b..9c66710d 100644
--- a/tests/test_libcli.py
+++ b/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)]
 )

From 0c88399317c094d56b2f13b88ea64c057e6f2174 Mon Sep 17 00:00:00 2001
From: spyke7 <dolaishreejan@gmail.com>
Date: Sat, 29 Nov 2025 02:19:23 +0530
Subject: [PATCH 3/4] Skipped hbonds in __main__.py

---
 src/mdacli/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mdacli/__main__.py b/src/mdacli/__main__.py
index 07d142fb..71b3b3c0 100644
--- a/src/mdacli/__main__.py
+++ b/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,

From 3076679de167e332c53c38afe87982182ad845f9 Mon Sep 17 00:00:00 2001
From: Philip Loche <ploche@physik.fu-berlin.de>
Date: Tue, 2 Dec 2025 09:02:57 +0100
Subject: [PATCH 4/4] Format changelog

---
 docs/CHANGELOG.rst | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index b2237ad6..a7b89ead 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -5,12 +5,7 @@ Changelog
 Unreleased
 ----------
 
-* Updated the ignoring warnings in libcli.py
-* Added tests for ignoring warnings
-
-v0.1.34 (2025-11-28)
-------------------------------------------
-
+* Ignore unrelated warnings from MDAnalysis
 * Added argcomplete for tab completion
 * Updated docs