Merge branch 'main' into feat/warehouse

docs/CHANGELOG.rst

@@ -9,8 +9,8 @@ v1.9.1
 
 **Fixed:**
 
-* Fixed a bug in Protocol termination for the HybridTop and AFE Protocols
-  which would unnecessarily declare an ``UnboundLocalError``.
+* Fixed a bug in Protocol termination for the HybridTop and AFE Protocols which would unnecessarily declare an ``UnboundLocalError``.
+* Updated ``openfe_analysis`` dependency  to fix issue with RMSD analysis (`Issue 1834 <https://github.com/OpenFreeEnergy/openfe/issues/1834>`).
 
 
 

environment.yml

@@ -12,8 +12,8 @@ dependencies:
   - lomap2>=3.2.1
   - networkx
   - numpy
-  - openfe-analysis>=0.3.1
-  - openff-interchange-base
+  - openfe-analysis>=0.4.0 # min pin https://github.com/OpenFreeEnergy/openfe/issues/1834#issuecomment-3920079481, no max to check issues with new versions
+  - openff-interchange-base != 0.5.1  # https://github.com/openforcefield/openff-interchange/issues/1450
   - openff-nagl-base >=0.3.3
   - openff-nagl-models>=0.1.2
   - openff-toolkit-base >=0.16.2

news/deprecate_perses.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``. 
+This includes ``PersesAtomMapper`` and ``default_perses_scorer``.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/openfe/setup/atom_mapping/perses_mapper.py

@@ -6,6 +6,8 @@ The MCS class from Perses shamelessly wrapped and used here to match our API.
 
 """
 
+import warnings
+
 from gufe.settings.typing import AngstromQuantity
 from openff.units import Quantity, unit
 from openff.units.openmm import to_openmm
@@ -75,6 +77,10 @@ class PersesAtomMapper(LigandAtomMapper):
             can be mapped, default: 0.25*unit.angstrom
 
         """
+        warnings.warn(
+            "PersesAtomMapper is deprecated and is planned to be removed in openfe v2.0. If you have questions related to this, please open an issue at https://github.com/OpenFreeEnergy/openfe/issues.",
+            DeprecationWarning,
+        )
         self.allow_ring_breaking = allow_ring_breaking
         self.preserve_chirality = preserve_chirality
         self.use_positions = use_positions

src/openfe/setup/atom_mapping/perses_scorers.py

@@ -1,6 +1,7 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
+import warnings
 from typing import Callable
 
 from openfe.utils import requires_package
@@ -67,6 +68,11 @@ def default_perses_scorer(
     -------
         float
     """
+    warnings.warn(
+        "default_perses_scorer is deprecated and is planned to be removed in openfe v2.0. If you have questions related to this, please open an issue at https://github.com/OpenFreeEnergy/openfe/issues",
+        DeprecationWarning,
+    )
+
     score = AtomMapper(use_positions=use_positions).score_mapping(
         AtomMapping(
             old_mol=mapping.componentA.to_openff(),

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_slow.py

@@ -13,7 +13,10 @@ from openfe.protocols import openmm_afe
 
 @pytest.mark.integration  # takes too long to be a slow test ~ 4 mins locally
 @pytest.mark.flaky(reruns=3)  # pytest-rerunfailures; we can get bad minimisation
-@pytest.mark.parametrize("platform", ["CPU", "CUDA"])
+@pytest.mark.parametrize(
+    "platform",
+    [pytest.param("CPU", marks=pytest.mark.xfail(reason="see openfe issue #1670")), "CUDA"],
+)
 def test_openmm_run_engine(
     platform,
     get_available_openmm_platforms,

src/openfe/tests/setup/atom_mapping/test_perses_atommapper.py

@@ -13,8 +13,8 @@ def test_simple(atom_mapping_basic_test_files):
     # basic sanity check on the LigandAtomMapper
     mol1 = atom_mapping_basic_test_files["methylcyclohexane"]
     mol2 = atom_mapping_basic_test_files["toluene"]
-
-    mapper = PersesAtomMapper()
+    with pytest.warns(DeprecationWarning, match="PersesAtomMapper"):
+        mapper = PersesAtomMapper()
 
     mapping_gen = mapper.suggest_mappings(mol1, mol2)
 
@@ -31,8 +31,8 @@ def test_generator_length(atom_mapping_basic_test_files):
     # generator stops correctly
     mol1 = atom_mapping_basic_test_files["methylcyclohexane"]
     mol2 = atom_mapping_basic_test_files["toluene"]
-
-    mapper = PersesAtomMapper()
+    with pytest.warns(DeprecationWarning, match="PersesAtomMapper"):
+        mapper = PersesAtomMapper()
 
     mapping_gen = mapper.suggest_mappings(mol1, mol2)
 
@@ -45,7 +45,8 @@ def test_generator_length(atom_mapping_basic_test_files):
 @skip_if_missing("perses")
 def test_empty_atommappings(mol_pair_to_shock_perses_mapper):
     mol1, mol2 = mol_pair_to_shock_perses_mapper
-    mapper = PersesAtomMapper()
+    with pytest.warns(DeprecationWarning, match="PersesAtomMapper"):
+        mapper = PersesAtomMapper()
 
     mapping_gen = mapper.suggest_mappings(mol1, mol2)
 
@@ -59,11 +60,12 @@ def test_empty_atommappings(mol_pair_to_shock_perses_mapper):
 @skip_if_missing("openeye")
 @skip_if_missing("perses")
 def test_dict_round_trip():
-    # use some none defaults
-    mapper1 = PersesAtomMapper(
-        allow_ring_breaking=False,
-        preserve_chirality=False,
-        coordinate_tolerance=0.01 * unit.nanometer,
-    )
-    mapper2 = PersesAtomMapper.from_dict(mapper1.to_dict())
+    with pytest.warns(DeprecationWarning, match="PersesAtomMapper"):
+        # use some none defaults
+        mapper1 = PersesAtomMapper(
+            allow_ring_breaking=False,
+            preserve_chirality=False,
+            coordinate_tolerance=0.01 * unit.nanometer,
+        )
+        mapper2 = PersesAtomMapper.from_dict(mapper1.to_dict())
     assert mapper2.to_dict() == mapper1.to_dict()

src/openfe/tests/setup/atom_mapping/test_perses_scorers.py

@@ -18,7 +18,8 @@ USING_OLD_OFF = False
 @pytest.mark.xfail(not USING_OLD_OFF, reason="perses #1108")
 def test_perses_normalization_not_using_positions(gufe_atom_mapping_matrix):
     # now run the openfe equivalent with the same ligand atom _mappings
-    scorer = perses_scorers.default_perses_scorer
+    with pytest.warns(DeprecationWarning, match="default_perses_scorer"):
+        scorer = perses_scorers.default_perses_scorer
     molecule_row = np.max(list(gufe_atom_mapping_matrix.keys())) + 1
     norm_scores = np.zeros([molecule_row, molecule_row])
 
@@ -41,7 +42,8 @@ def test_perses_normalization_not_using_positions(gufe_atom_mapping_matrix):
 @skip_if_missing("perses")
 @pytest.mark.xfail(not USING_OLD_OFF, reason="perses #1108")
 def test_perses_not_implemented_position_using(gufe_atom_mapping_matrix):
-    scorer = perses_scorers.default_perses_scorer
+    with pytest.warns(DeprecationWarning, match="default_perses_scorer"):
+        scorer = perses_scorers.default_perses_scorer
 
     first_key = list(gufe_atom_mapping_matrix.keys())[0]
     match_re = "normalizing using positions is not currently implemented"
@@ -76,7 +78,8 @@ def test_perses_regression(gufe_atom_mapping_matrix):
     assert matrix.shape == (8, 8)
 
     # now run the openfe equivalent with the same ligand atom _mappings
-    scorer = perses_scorers.default_perses_scorer
+    with pytest.warns(DeprecationWarning, match="default_perses_scorer"):
+        scorer = perses_scorers.default_perses_scorer
     scores = np.zeros_like(matrix)
     for (i, j), ligand_atom_mapping in gufe_atom_mapping_matrix.items():
         score = scorer(