Add deprecation warning for ITPParser (#4744)

* add deprecation warning for ITPParser
* add test for no deprecation warning in itp without valid elements

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

package/CHANGELOG

@@ -112,6 +112,8 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * Element guessing in the ITPParser is deprecated and will be removed in version 3.0
+   (Issue #4698)
  * Unknown masses are set to 0.0 for current version, this will be depracated
    in version 3.0.0 and replaced by :class:`Masses`' no_value_label attribute(np.nan)
    (PR #3753)

package/MDAnalysis/topology/ITPParser.py

@@ -601,7 +601,15 @@ def parse(self, include_dir='/usr/local/gromacs/share/gromacs/top/',
         if all(e.capitalize() in SYMB2Z for e in self.elements):
             attrs.append(Elements(np.array(self.elements,
                          dtype=object), guessed=True))
-
+            warnings.warn(
+                "The elements attribute has been populated by guessing "
+                "elements from atom types. This behaviour has been "
+                "temporarily added to the ITPParser as we transition "
+                "to the new guessing API. "
+                "This behavior will be removed in release 3.0. "
+                "Please see issue #4698 for more information. ",
+                DeprecationWarning
+            )
         else:
             warnings.warn("Element information is missing, elements attribute "
                           "will not be populated. If needed these can be "

testsuite/MDAnalysisTests/topology/test_itp.py

@@ -490,3 +490,20 @@ def test_missing_elements_no_attribute():
         u = mda.Universe(ITP_atomtypes)
     with pytest.raises(AttributeError):
         _ = u.atoms.elements
+
+
+def test_elements_deprecation_warning():
+    """Test deprecation warning is present"""
+    with pytest.warns(DeprecationWarning, match="removed in release 3.0"):
+        mda.Universe(ITP_nomass)
+
+
+def test_elements_nodeprecation_warning():
+    """Test deprecation warning is not present if elements isn't guessed"""
+    with pytest.warns(UserWarning) as record:
+        mda.Universe(ITP_atomtypes)
+    assert len(record) == 2
+
+    warned = [warn.message.args[0] for warn in record]
+    assert "Element information is missing" in warned[0]
+    assert "No coordinate reader found" in warned[1]