RDKit converter inferring

.github/actions/setup-deps/action.yaml

@@ -79,7 +79,7 @@ inputs:
   pytng:
     default: 'pytng>=0.2.3'
   rdkit:
-    default: 'rdkit>=2020.03.1'
+    default: 'rdkit>=2022.09.1'
   scikit-learn:
     default: 'scikit-learn'
   seaborn:

azure-pipelines.yml

@@ -113,7 +113,7 @@ jobs:
       parmed
       pytng>=0.2.3
       tidynamics>=1.0.0
-      rdkit>=2020.03.1
+      rdkit>=2022.09.1
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - script: >-

package/CHANGELOG

@@ -17,8 +17,8 @@ The rules for this file:
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
-         yuxuanzhuang
-
+         yuxuanzhuang, cbouy
+ 
  * 2.8.0
 
 Fixes
@@ -45,6 +45,8 @@ Fixes
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
 
 Enhancements
+ * Added `TemplateInferer` and `RDKitInferer` dataclasses to the
+   `RDKitInferring` module to be used by the RDKit converter. (PR #4305)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
    (PR #4531)
  * Improved performance of PDBWriter (Issue #2785, PR #4472)
@@ -55,6 +57,9 @@ Enhancements
    DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
 
 Changes
+ * Refactored the RDKit converter code to move the inferring code in a separate
+   `RDKitInferring` module. The bond order and charges inferer has been move to
+   an `MDAnalysisInferer` dataclass in there. (PR #4305)
  * As per SPEC0 the minimum supported Python version has been raised
    to 3.10 (PR #4502)
  * MDAnalysis.analysis.hole2 is now directly imported from the mdakit
@@ -72,6 +77,8 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * The RDKit converter parameter `NoImplicit` has been deprecated in favour of
+   `implicit_hydrogens` and `inferer` parameters. (PR #4305)
  * The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
    of the waterdynamics MDAKit and will be removed in version 3.0.0 (PR #4404)
  * The MDAnalysis.analysis.psa module has been deprecated in favour of