re-enable gaff (#334)

* re-enable gaff * run espaloma and gaff tests * gaff has two fs michael * Use 8.1.2rc1 * Update linters * Remove Espaloma tests * Apply suggestions from code review Co-authored-by: Iván Pulido <[email protected]> * Use Intel macOS runners * check if older macos works * test all the macos versions * see if rdkit is the issue * Drop macOS 13 * Typo/fix * Update dependencies --------- Co-authored-by: Matthew W. Thompson <[email protected]> Co-authored-by: Iván Pulido <[email protected]>
openmm · Jul 19, 2024 · 38eb754 · 38eb754
1 parent b3fae57
commit 38eb754
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-12, macos-latest]
         python-version: ["3.10", "3.11", "3.12"]
         amber-conversion: [false]
         charmm-conversion: [false]
@@ -57,7 +57,7 @@ jobs:
 
     - name: Test Installed Package
       run: |
-        pytest -v -n logical --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
+        pytest -v -n logical --rungaff --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
           openmmforcefields/tests/
 
         # add --rungaff / --runespaloma to run those tests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ ci:
   autoupdate_schedule: "quarterly"
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.5.1
   hooks:
     - id: ruff
       args: ["--fix", "--unsafe-fixes"]

diff --git a/README.md b/README.md
@@ -410,6 +410,10 @@ See the corresponding directories for information on how to use the provided con
 
 # [Changelog](https://github.com/openmm/openmmforcefields/releases)
 
+## 0.14.0 Bring back GAFFTemplateGenerator
+
+This release effectively reverts the changes in 0.13.0. This release is **only** compatible with OpenMM 8.1.2. No other changes were made.
+
 ## 0.13.0 Temporarily remove GAFFTemplateGenerator
 
 This release temporarily removes GAFFTemplateGenerator because of packaging incompatibilities with

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -1,37 +1,18 @@
 name: openmmforcefields-test
-
 channels:
   - conda-forge
-
 dependencies:
-    # Base depends
   - python
   - pip
-
-    # Testing
   - pytest
   - pytest-cov
   - pytest-xdist
   - pytest-randomly
-
-    # Requirements for converted force field installer
-  - openmm >=7.6.0
-
+  - openmm >=8.1.2,<9
   - openff-toolkit >=0.11
-
-    # Requirements for conversion tools
   - pyyaml
   - ambertools >=22,<24
   - lxml
   - networkx
-
-    # JSON caching of residue templates
   - tinydb
-
-    # Validating URLs
   - validators
-
-    #
-    # Espaloma requirements below
-    #
-  # espaloma >=0.3.1
diff --git a/openmmforcefields/generators/system_generators.py b/openmmforcefields/generators/system_generators.py
@@ -247,7 +247,6 @@ def __init__(
         # Create and cache a residue template generator
         from openmmforcefields.generators.template_generators import (
             SmallMoleculeTemplateGenerator,
-            GAFFNotSupportedError,
         )
 
         self.template_generator = None
@@ -261,17 +260,10 @@ def __init__(
                         template_generator_kwargs=self.template_generator_kwargs,
                     )
                     break
-                except (ValueError, GAFFNotSupportedError) as e:
+                except (ValueError,) as e:
                     _logger.debug(f"  {template_generator_cls.__name__} cannot load {small_molecule_forcefield}")
                     _logger.debug(e)
             if self.template_generator is None:
-                if small_molecule_forcefield.startswith("gaff"):
-                    raise GAFFNotSupportedError(
-                        "This release (0.13.x) of openmmforcefields temporarily drops GAFF support and "
-                        "thereby the GAFFTemplateGenerator class. Support will be re-introduced in "
-                        "future releases (0.14.x). To use this class, install version 0.12.0 or older."
-                    )
-
                 msg = (
                     "No registered small molecule template generators could load force field "
                     f"'{small_molecule_forcefield}'\n"

diff --git a/openmmforcefields/generators/template_generators.py b/openmmforcefields/generators/template_generators.py
@@ -27,10 +27,6 @@ class ForceException(Exception):
     """Exception for forces"""
 
 
-class GAFFNotSupportedError(Exception):
-    """Exception for missing GAFF support"""
-
-
 class SmallMoleculeTemplateGenerator:
     """
     Abstract base class for small molecule template generation for OpenMM ForceField.
@@ -507,11 +503,6 @@ def __init__(self, molecules=None, forcefield=None, cache=None, **kwargs):
 
         Newly parameterized molecules will be written to the cache, saving time next time!
         """
-        raise GAFFNotSupportedError(
-            "This release (0.13.x) of openmmforcefields temporarily drops GAFF support and "
-            "thereby the GAFFTemplateGenerator class. Support will be re-introduced in "
-            "future releases (0.14.x). To use this class, install version 0.12.0 or older."
-        )
 
         # Initialize molecules and cache
         super().__init__(molecules=molecules, cache=cache)