Merge remote-tracking branch 'upstream/main' into unique_molecules-re…

…quired

.github/workflows/CI.yml

@@ -154,7 +154,7 @@ jobs:
             PYTEST_ARGS+=" --runslow"
           fi
 
-          python -m pytest $PYTEST_ARGS $COV
+          python -m pytest --durations=20 $PYTEST_ARGS $COV
 
       - name: Run code snippets in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}

.github/workflows/beta_rc.yaml

@@ -20,7 +20,7 @@ jobs:
           - ubuntu-latest
           - macos-latest
         python-version:
-          - 3.9
+          - 3.10
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -39,12 +39,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
@@ -57,21 +51,16 @@ jobs:
           python -m pip install .
 
       - name: Install test plugins
-        run: |
-          python -m pip install utilities/test_plugins
+        run: python -m pip install utilities/test_plugins
 
       - name: Environment Information
-        run: |
-          conda info
-          conda list
+        run: micromamba info && micromamba list
 
       - name: Check links
-        run: |
-          pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
+        run: pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
 
       - name: Run mypy
-        run: |
-          mypy --namespace-packages -p "openff.toolkit"
+        run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
         run: |

devtools/conda-envs/beta_rc_env.yaml

@@ -25,7 +25,8 @@ dependencies:
   - openff-nagl-models ==0.1.0
     # Toolkit-specific
   - ambertools >=22
-  - rdkit
+    # https://github.com/rdkit/rdkit/issues/7221
+  - rdkit >=2023.09.6
   - openeye-toolkits
     # Test-only/optional/dev
   - pytest

devtools/conda-envs/rdkit-examples.yaml

@@ -27,7 +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
-  - rdkit
+    # https://github.com/rdkit/rdkit/issues/7221
+  - rdkit <2023.09.6
     # Test-only/optional/dev/typing/examples
   - pytest
   - pytest-xdist

devtools/conda-envs/rdkit.yaml

@@ -24,7 +24,8 @@ dependencies:
   - typing_extensions
     # Toolkit-specific
   - ambertools >=22
-  - rdkit
+    # https://github.com/rdkit/rdkit/issues/7221
+  - rdkit <2023.09.6
     # Test-only/optional/dev/typing
   - pytest
   - pytest-cov

devtools/conda-envs/test_env.yaml

@@ -24,7 +24,8 @@ dependencies:
   - openff-nagl-models ==0.1.0
     # Toolkit-specific
   - ambertools >=22
-  - rdkit
+    # https://github.com/rdkit/rdkit/issues/7221
+  - rdkit <2023.09.6
   - openeye-toolkits
     # Test-only/optional/dev/typing
   - pytest

openff/toolkit/_tests/test_examples.py

@@ -2,7 +2,6 @@
 Test that the examples in the repo run without errors.
 """
 
-import os
 import pathlib
 import re
 import subprocess
@@ -11,10 +10,9 @@
 
 import pytest
 
+from openff.toolkit._tests.utils import _get_readme_path
 from openff.toolkit.utils import RDKIT_AVAILABLE, get_data_file_path, temporary_cd
 
-ROOT_DIR_PATH = pathlib.Path(__file__).joinpath("../../../../").resolve()
-
 
 def run_script_file(file_path):
     """Run through the shell a python script."""
@@ -38,32 +36,37 @@ def run_script_str(script_str):
 
     """
     with tempfile.TemporaryDirectory() as tmp_dir:
-        temp_file_path = os.path.join(tmp_dir, "temp.py")
+        temp_file_path = pathlib.Path(tmp_dir, "temp.py").as_posix()
+
         # Create temporary python script.
         with open(temp_file_path, "w") as f:
             f.write(script_str)
         # Run the Python script.
         try:
             run_script_file(temp_file_path)
-        except:  # noqa
+        except Exception as error:
             script_str = textwrap.indent(script_str, "    ")
-            raise Exception(f"The following script failed:\n{script_str}")
+            raise Exception(f"The following script failed:\n{script_str}") from error
 
 
-def find_example_scripts():
+def find_example_scripts() -> list[str]:
     """Find all Python scripts, excluding Jupyter notebooks, in the examples folder.
 
     Returns
     -------
     example_file_paths : list[str]
         List of full paths to python scripts to execute.
     """
-    examples_dir_path = ROOT_DIR_PATH.joinpath("examples")
+    # Count on the examples/ path being equivalently accessible as the README file
+    readme_file_path = _get_readme_path()
+
+    if readme_file_path is None:
+        return list()
+
+    examples_dir_path = pathlib.Path(_get_readme_path().parent, "examples")
 
     # Examples that require RDKit
-    rdkit_examples = {
-        examples_dir_path.joinpath("conformer_energies/conformer_energies.py"),
-    }
+    rdkit_examples = {examples_dir_path / "conformer_energies/conformer_energies.py"}
 
     example_file_paths = []
     for example_file_path in examples_dir_path.glob("*/*.py"):
@@ -75,17 +78,22 @@ def find_example_scripts():
     return example_file_paths
 
 
-def find_readme_examples():
+def find_readme_examples() -> list[str]:
     """Yield the Python scripts in the main README.md file.
 
     Returns
     -------
     readme_examples : list[str]
         The list of Python scripts included in the README.md files.
     """
-    readme_path = ROOT_DIR_PATH.joinpath("README.md")
-    with open(readme_path, "r") as f:
+    readme_file_path = _get_readme_path()
+
+    if readme_file_path is None:
+        return list()
+
+    with open(readme_file_path, "r") as f:
         readme_content = f.read()
+
     return re.findall("```python(.*?)```", readme_content, flags=re.DOTALL)
 
 

openff/toolkit/_tests/test_forcefield.py

@@ -4075,6 +4075,7 @@ def test_toolkit_registry_bad_charge_method(self):
 
 class TestSmirnoffVersionConverter:
     @requires_openeye_mol2
+    @pytest.mark.slow
     @pytest.mark.parametrize(
         ("freesolv_id", "forcefield_version", "allow_undefined_stereo"),
         generate_freesolv_parameters_assignment_cases(),

openff/toolkit/_tests/test_links.py

@@ -1,26 +1,29 @@
-import os
 import re
 from urllib.request import Request, urlopen
 
 import pytest
 
-ROOT_DIR_PATH = os.path.join(
-    os.path.dirname(os.path.realpath(__file__)), "..", "..", ".."
-)
+from openff.toolkit._tests.utils import _get_readme_path
 
 
-def find_readme_links():
+def find_readme_links() -> list[str]:
     """Yield all the links in the main README.md file.
 
     Returns
     -------
     readme_examples : list[str]
         The list of links included in the README.md file.
     """
-    readme_file_path = os.path.join(ROOT_DIR_PATH, "README.md")
-    with open(readme_file_path, "r") as f:
-        readme_content = f.read()
-    return re.findall("http[s]?://(?:[0-9a-zA-Z]|[-/.%:_])+", readme_content)
+    readme_file_path = _get_readme_path()
+
+    if readme_file_path is None:
+        return list()
+
+    else:
+        with open(readme_file_path.as_posix(), "r") as f:
+            readme_content = f.read()
+
+        return re.findall("http[s]?://(?:[0-9a-zA-Z]|[-/.%:_])+", readme_content)
 
 
 @pytest.mark.parametrize("readme_link", find_readme_links())

openff/toolkit/_tests/test_topology.py

@@ -1712,6 +1712,7 @@ def test_topology_hierarchy_iterators(
 
 @skip_if_missing("nglview")
 class TestTopologyVisaulization:
+    @pytest.mark.slow
     @requires_rdkit
     def test_visualize_basic(self):
         import nglview

openff/toolkit/_tests/utils.py

@@ -9,9 +9,11 @@
 import importlib
 import itertools
 import os
+import pathlib
 import pprint
 import textwrap
 from contextlib import contextmanager
+from typing import Union
 
 import numpy as np
 import openmm
@@ -45,6 +47,22 @@
 )
 
 
+def _get_readme_path() -> Union[pathlib.Path, None]:
+    """
+    Return a path to the README file or None if it cannot be assured to be the toolkit's README.
+    """
+    if "site-packages" in __file__:
+        # This test file is being collected from the installed package, which
+        # does not provide the README file.
+        # Note that there will likely be a mis-bundled file
+        # $CONDA_PREFIX/lib/python3.x/site-packages/README.md, but this is not
+        # the toolkit's README file!
+        return None
+
+    else:
+        return pathlib.Path(__file__).parents[3] / "README.md"
+
+
 def has_pkg(pkg_name):
     """
     Helper function to generically check if a package is installed. Intended