Merge branch 'main' into redirect-faq

openforcefield · Oct 1, 2024 · b3273e9 · b3273e9
2 parents 71a34e9 + 31e4c4b
commit b3273e9
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -171,4 +171,5 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
+          disable_search: true
           fail_ci_if_error: true
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -14,16 +14,12 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
-      - name: Install linters
+      - name: Install ruff
         run: |
-          pip install black isort
+          pip install ruff
 
-      - name: Run black
+      - name: Run ruffblack
         run: |
-          black --check openff
-
-      - name: Run isort
-        run: |
-          isort --check openff
+          ruff check .
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,35 +2,10 @@ ci:
   autoupdate_schedule: "quarterly"
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
 repos:
-- repo: https://github.com/psf/black
-  rev: 24.4.2
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.5
   hooks:
-  - id: black
-  - id: black-jupyter
-- repo: https://github.com/PyCQA/isort
-  rev: 5.13.2
-  hooks:
-  - id: isort
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.1.0
-  hooks:
-  - id: flake8
-    files: ^openff|(^utilities/((?!deprecated).)*$)
-    additional_dependencies: [
-        'flake8-absolute-import',
-        'flake8-no-pep420',
-        'flake8-bugbear',
-    ]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.8.5
-  hooks:
-    - id: nbqa-pyupgrade
-      args:
-        - --py39-plus
-    - id: nbqa-isort
-    - id: nbqa-flake8
-      args:
-        - '--select=F'
+    - id: ruff
 - repo: https://github.com/adamchainz/blacken-docs
   rev: 1.18.0
   hooks:

diff --git a/devtools/scripts/build_cookiecutter_json.py b/devtools/scripts/build_cookiecutter_json.py
@@ -1,6 +1,5 @@
-import sys
 import json
-
+import sys
 
 release_tag = sys.argv[1]
 python_version = sys.argv[2]

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # openff-toolkit documentation build configuration file, created by
 # sphinx-quickstart on Sun Dec  3 23:12:54 2017.
@@ -19,12 +18,12 @@
 #
 import os
 import sys
+from importlib.util import find_spec as find_import_spec
+
+import openff.toolkit
 
 sys.path.insert(0, os.path.abspath("."))
 
-import sphinx
-
-import openff.toolkit
 
 # -- General configuration ------------------------------------------------
 
@@ -128,8 +127,6 @@
 # sphinx-notfound-page
 # https://github.com/readthedocs/sphinx-notfound-page
 # Renders a 404 page with absolute links
-from importlib.util import find_spec as find_import_spec
-
 if find_import_spec("notfound"):
     extensions.append("notfound.extension")
 
@@ -292,7 +289,10 @@
         "OpenFF Toolkit Documentation",
         author,
         "openff-toolkit",
-        "A modern, extensible library for molecular mechanics force field science from the Open Force Field Consortium.",
+        (
+            "A modern, extensible library for molecular mechanics force field science from the Open Force "
+            "Field Consortium.",
+        ),
         "Miscellaneous",
     ),
 ]
diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -6,13 +6,12 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-## Upcoming Release
+## Current development
 
 ### Improved documentation and warnings
-
+- [PR #1939](https://github.com/openforcefield/openff-toolkit/pull/1939): Resolves [#1587](https://github.com/openforcefield/openff-toolkit/pull/1587) by emitting a warning when from_openeye or from_rdkit try to load a molecule with multiple disconnected components.
 - [PR #1934](https://github.com/openforcefield/openff-toolkit/pull/1934): Fold the Toolkit FAQ into the new org-level FAQ: <https://docs.openforcefield.org/faq>
 
-
 ## 0.16.4
 
 ### Bugfixes

diff --git a/docs/users/molecule_cookbook.ipynb b/docs/users/molecule_cookbook.ipynb
@@ -44,12 +44,12 @@
    "source": [
     "# Workaround for https://github.com/conda-forge/qcfractal-feedstock/issues/43\n",
     "try:\n",
-    "    import qcportal  # noqa\n",
+    "    import qcportal  # noqa: RUF100\n",
     "except ImportError:\n",
     "    pass\n",
     "import sys\n",
     "\n",
-    "ipython = get_ipython()  # noqa\n",
+    "ipython = get_ipython()  # noqa: RUF100\n",
     "\n",
     "\n",
     "def hide_traceback(\n",
@@ -1413,9 +1413,9 @@
     }
    ],
    "source": [
-    "from openmm.app.pdbfile import PDBFile\n",
+    "import openmm.app\n",
     "\n",
-    "openmm_topology = PDBFile(\"zw_l_alanine.pdb\").getTopology()\n",
+    "openmm_topology = openmm.app.PDBFile(\"zw_l_alanine.pdb\").getTopology()\n",
     "openff_topology = Topology.from_openmm(openmm_topology, unique_molecules=[zw_l_alanine])\n",
     "\n",
     "from_openmm_topology = openff_topology.molecule(0)\n",
@@ -1492,9 +1492,9 @@
     }
    ],
    "source": [
-    "from mdtraj import load_pdb\n",
+    "import mdtraj\n",
     "\n",
-    "mdtraj_topology = load_pdb(\"zw_l_alanine.pdb\").topology\n",
+    "mdtraj_topology = mdtraj.load_pdb(\"zw_l_alanine.pdb\").topology\n",
     "openff_topology = Topology.from_mdtraj(mdtraj_topology, unique_molecules=[zw_l_alanine])\n",
     "\n",
     "from_mdtraj_topology = openff_topology.molecule(0)\n",

diff --git a/docs/users/pdb_cookbook/index.ipynb b/docs/users/pdb_cookbook/index.ipynb
@@ -67,10 +67,11 @@
    "outputs": [],
    "source": [
     "import sys\n",
+    "import warnings\n",
     "\n",
     "from openff.toolkit import Molecule, Topology\n",
     "\n",
-    "ipython = get_ipython()  # noqa\n",
+    "ipython = get_ipython()\n",
     "\n",
     "\n",
     "def hide_traceback(\n",
@@ -93,8 +94,6 @@
     "ipython.showtraceback = hide_traceback\n",
     "\n",
     "# Hide NumPy warnings\n",
-    "import warnings\n",
-    "\n",
     "warnings.filterwarnings(\n",
     "    \"ignore\",\n",
     "    r\"The value of the smallest subnormal for \",\n",

diff --git a/examples/conformer_energies/conformer_energies.py b/examples/conformer_energies/conformer_energies.py
@@ -144,7 +144,11 @@ def compute_conformer_energies_from_file(filename):
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
-        description="Perform energy minimization on a molecule, potentially with many conformers. For each conformer, this script will provide the initial energy, minimized energy, and RMSD between the initial and minimized structure (both as STDOUT and a csv file). The minimized conformers will be written out to SDF."
+        description=(
+            "Perform energy minimization on a molecule, potentially with many conformers. For each conformer, this "
+            "script will provide the initial energy, minimized energy, and RMSD between the initial and minimized "
+            "structure (both as STDOUT and a csv file). The minimized conformers will be written out to SDF."
+        ),
     )
     parser.add_argument(
         "-f", "--filename", help="Name of an input file containing conformers"

diff --git a/...eters_with_openmmforcefields/swap_existing_ligand_parameters_with_openmmforcefields.ipynb b/...eters_with_openmmforcefields/swap_existing_ligand_parameters_with_openmmforcefields.ipynb
@@ -136,7 +136,8 @@
     }
    ],
    "source": [
-    "# Create a parameterized OpenMM System from the PDB topology without bond constraints so we can convert to other packages\n",
+    "# Create a parameterized OpenMM System from the PDB topology without bond constraints\n",
+    "# so we can convert to other packages\n",
     "system = forcefield.createSystem(\n",
     "    pdbfile.topology,\n",
     "    nonbondedMethod=app.PME,\n",

diff --git a/...ples/external/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb b/...ples/external/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
@@ -19,7 +19,10 @@
    "source": [
     "# Retrieve protein and ligand files for BRD4 and a docked inhibitor from the benchmark systems GitHub repository\n",
     "# https://github.com/MobleyLab/benchmarksets\n",
+    "import parmed\n",
     "import requests\n",
+    "from openmm import XmlSerializer, app, unit\n",
+    "from openmm.app import HBonds, NoCutoff, PDBFile\n",
     "\n",
     "repo_url = (\n",
     "    \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
@@ -92,16 +95,6 @@
     "</div>"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from openmm import XmlSerializer, app, unit\n",
-    "from openmm.app import HBonds, NoCutoff, PDBFile"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -120,8 +113,6 @@
     "ligand_pdbfile = PDBFile(\"ligand.pdb\")\n",
     "\n",
     "# Convert OpenMM System object containing ligand parameters into a ParmEd Structure.\n",
-    "import parmed\n",
-    "\n",
     "ligand_structure = parmed.openmm.load_topology(\n",
     "    ligand_pdbfile.topology, ligand_system, xyz=ligand_pdbfile.positions\n",
     ")"

diff --git a/examples/forcefield_modification/forcefield_modification.ipynb b/examples/forcefield_modification/forcefield_modification.ipynb
@@ -1574,8 +1574,8 @@
     }
    ],
    "source": [
-    "fluorine = [atom for atom in ligand.atoms if atom.symbol == \"F\"][0]\n",
-    "carbon = [neighbor_atom for neighbor_atom in fluorine.bonded_atoms][0]\n",
+    "fluorine = next(atom for atom in ligand.atoms if atom.symbol == \"F\")\n",
+    "carbon = next(iter(fluorine.bonded_atoms))\n",
     "fluorine_carbon_bond_indices = (\n",
     "    fluorine.molecule_atom_index,\n",
     "    carbon.molecule_atom_index,\n",

diff --git a/examples/virtual_sites/vsite_showcase.ipynb b/examples/virtual_sites/vsite_showcase.ipynb
@@ -795,7 +795,7 @@
     "_energy_difference = from_openmm(energy_difference)\n",
     "\n",
     "print(\n",
-    "    f\"Results for: OpenFF – OpenMM comparison (per molecule) \\n\"\n",
+    "    f\"Results for: OpenFF – OpenMM comparison (per molecule) \\n\"  # noqa: RUF001\n",
     "    f\"Energy difference ({_energy_difference.units}):\\n\\t\"\n",
     "    f\"{_energy_difference.m:0.3e}\\n\"\n",
     "    f\"Coordinates difference ({coordinate_difference.units}, norm):\\n\\t\"\n",

diff --git a/examples/visualization/visualization.ipynb b/examples/visualization/visualization.ipynb
@@ -66,7 +66,8 @@
    },
    "outputs": [],
    "source": [
-    "from openff.toolkit import Molecule, Topology"
+    "from openff.toolkit import Molecule, Topology\n",
+    "from openff.toolkit.utils import get_data_file_path"
    ]
   },
   {
@@ -225,7 +226,7 @@
     }
    ],
    "source": [
-    "display(m)  # noqa"
+    "display(m)"
    ]
   },
   {
@@ -733,7 +734,6 @@
    },
    "outputs": [],
    "source": [
-    "from openff.toolkit.utils.utils import get_data_file_path\n",
     "\n",
     "topology = Topology.from_pdb(\n",
     "    get_data_file_path(\"systems/test_systems/T4_lysozyme_water_ions.pdb\")\n",

diff --git a/openff/toolkit/_tests/_stale_tests.py b/openff/toolkit/_tests/_stale_tests.py
@@ -114,9 +114,7 @@ def test_electrostatics_options(self):
         # Change electrostatics method
         forcefield.forces["Electrostatics"].method = method
         f = partial(check_system_creation_from_molecule, forcefield, molecule)
-        f.description = "Testing {} parameter assignment using molecule {}".format(
-            offxml_file_path, molecule.name
-        )
+        f.description = f"Testing {offxml_file_path} parameter assignment using molecule {molecule.name}"
         # yield f
     # TODO: Implement a similar test, where we compare OpenMM energy evals from an
     #       AMBER-parameterized system to OFF-parameterized systems

diff --git a/openff/toolkit/_tests/create_molecules.py b/openff/toolkit/_tests/create_molecules.py
@@ -419,8 +419,8 @@ def propane_from_smiles_w_vsites():
 def tip5_water():
     # Make a TIP5 water
     molecule = Molecule.from_smiles("[H][O][H]")
-    O1 = [atom for atom in molecule.atoms if atom.atomic_number == 8][0]
-    H1, H2 = [atom for atom in O1.bonded_atoms if atom.atomic_number == 1]
+    O1 = next(atom for atom in molecule.atoms if atom.atomic_number == 8)
+    H1, H2 = (atom for atom in O1.bonded_atoms if atom.atomic_number == 1)
     molecule.add_divalent_lone_pair_virtual_site(
         (H1, O1, H2),
         0.7 * unit.angstrom,

diff --git a/openff/toolkit/_tests/test_energies.py b/openff/toolkit/_tests/test_energies.py
@@ -26,7 +26,7 @@ def test_reference(constrained, mol):
     by version 0.8.0 of the toolkit"""
     # TODO: Also test periodic vs. vacuum
     with open(
-        get_data_file_path("reference_energies/reference_after_1007.json"), "r"
+        get_data_file_path("reference_energies/reference_after_1007.json")
     ) as fi:
         reference = json.loads(fi.read())
 

diff --git a/openff/toolkit/_tests/test_examples.py b/openff/toolkit/_tests/test_examples.py
@@ -91,7 +91,7 @@ def find_readme_examples() -> list[str]:
     if readme_file_path is None:
         return list()
 
-    with open(readme_file_path, "r") as f:
+    with open(readme_file_path) as f:
         readme_content = f.read()
 
     return re.findall("```python(.*?)```", readme_content, flags=re.DOTALL)