Update RDKit versions used in tests (#1942)

* Test new RDKit constraint * Fix merge * Work around another bug ... ? * Updates for RDKit changes * Don't trust RDKit stubs * Cleanup, shuffle dependencies * Ignore mypy errors in (skipped) RDKit wrapper * un-xfail mols that now pass in to_from_rdkit tests due to stereo handling updates in rdkit * test configuration housekeeping * update releasehistory --------- Co-authored-by: Jeffrey Wagner <[email protected]>
openforcefield · Oct 4, 2024 · 6aa989e · 6aa989e
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -139,8 +139,12 @@ jobs:
         run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
 
       - name: Run mypy
-        # subtle differences in Python/mypy versions, just keep it passing on one
-        if: ${{ matrix.rdkit == true && matrix.openeye && matrix.python-version == 3.10 }}
+        # Subtle differences in Python/mypy versions, just keep it passing on one.
+        # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs
+        # in stubs and there are other subtleties (in the source code and builds) that reduce the number
+        # of available builds.
+        # See ex https://github.com/rdkit/rdkit/issues/7221
+        if: ${{ matrix.rdkit == false && matrix.openeye && matrix.python-version == 3.10 }}
         run: mypy -p "openff.toolkit"
 
       - name: Run unit tests

diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
@@ -40,3 +40,13 @@ dependencies:
   - mdtraj
   - nglview
   - parmed =3
+  - mypy
+  - typing_extensions
+  - pip:
+    - types-setuptools
+    - types-toml
+    - types-PyYAML
+    - types-networkx
+    - types-xmltodict
+    - types-cachetools
+    - mongo-types
diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml
@@ -27,8 +27,8 @@ dependencies:
   # AmberTools 23 brings in ParmEd 4, which doesn't yet work with examples
   # https://github.com/openforcefield/openff-toolkit/issues/1532
   - ambertools =22.4
-    # https://github.com/rdkit/rdkit/issues/7221
-  - rdkit <2023.09.6
+    # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
+  - rdkit !=2024.03.6,!=2024.03.5
     # Test-only/optional/dev/typing/examples
   - pytest
   - pytest-xdist

diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml
@@ -24,8 +24,8 @@ dependencies:
   - typing_extensions
     # Toolkit-specific
   - ambertools >=22
-    # https://github.com/rdkit/rdkit/issues/7221
-  - rdkit <2023.09.6
+    # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
+  - rdkit !=2024.03.6,!=2024.03.5
     # Test-only/optional/dev/typing
   - pytest
   - pytest-cov

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -5,7 +5,7 @@ channels:
 dependencies:
     # Base depends
   - python
-  - pip
+  - pydantic =1
   - packaging
   - numpy
   - networkx
@@ -24,8 +24,12 @@ dependencies:
   - openff-nagl-models ==0.3.0
     # Toolkit-specific
   - ambertools >=22
+    # rdkit 2024.03.6 and 2024.09.1 packages fail when run natively on osx-arm64 macs
+    # https://github.com/rdkit/rdkit/issues/7583
+    # and a bad stub (causing mypy failure only)
     # https://github.com/rdkit/rdkit/issues/7221
-  - rdkit <2023.09.6
+  - rdkit !=2024.03.6,!=2024.09.1
+
   - openeye-toolkits
     # Test-only/optional/dev/typing
   - pytest
@@ -47,7 +51,6 @@ dependencies:
   - nomkl
   - mypy
   - typing_extensions
-  - pydantic =1
   - pip:
     - types-setuptools
     - types-toml

diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -18,6 +18,10 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Improved documentation and warnings
 
+### Tests updated
+- [PR #1942](https://github.com/openforcefield/openff-toolkit/pull/1942): Update tests for newer versions of RDKit, while stepping around recent RDKit conda-forge packages that fail when run natively on osx-arm64.
+
+
 ## 0.16.5
 
 ### Improved documentation and warnings

diff --git a/openff/toolkit/_tests/test_molecule.py b/openff/toolkit/_tests/test_molecule.py
@@ -251,7 +251,7 @@ def mini_drug_bank(xfail_mols=None, wip_mols=None):
     "DrugBank_6531",
 }
 
-# All the molecules that raise UndefinedStereochemistryError when read by OETK().
+# All the molecules that raise UndefinedStereochemistryError when read by RDKTKW().
 # Note that this list is different from that for OEMol,
 # since the toolkits have different definitions of "stereogenic"
 rdkit_drugbank_undefined_stereo_mols = {
@@ -261,8 +261,6 @@ def mini_drug_bank(xfail_mols=None, wip_mols=None):
     "DrugBank_3930",
     "DrugBank_5043",
     "DrugBank_5418",
-    "DrugBank_7124",
-    "DrugBank_6865",
 }
 
 

diff --git a/openff/toolkit/_tests/test_toolkits.py b/openff/toolkit/_tests/test_toolkits.py
@@ -193,8 +193,6 @@ def get_mini_drug_bank(toolkit_class, xfail_mols=None):
     "DrugBank_1962",
     "DrugBank_5043",
     "DrugBank_2519",
-    "DrugBank_7124",
-    "DrugBank_6865",
 ]
 
 openeye_iupac_bad_stereo = [

diff --git a/openff/toolkit/utils/rdkit_wrapper.py b/openff/toolkit/utils/rdkit_wrapper.py
@@ -1,3 +1,4 @@
+# mypy: ignore-errors
 """
 Wrapper class providing a minimal consistent interface to the `RDKit <http://www.rdkit.org/>`.
 """