Actually format with ruff (#2085)

* initial implementation of NAGLChargesHandler

* have testing env use naglcharges interchange branch

* implement doi and hash fields

* add tests

* fix tests

* add docstring

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* force use of nagl for test

* fix whitespace

* Actually format with `ruff`

* Update `Atom.stereochemistry` docstring

* add doi and file_hash to nagltoolkitwrapper.assign_partial_charges, switch to use nagl_models' get_model method

* raise specific error for blank/none model_file values

* improve docstring

* test with new openff-nagl-models

* update nagl test for bad suffix error

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Run `pre-commit autoupdate && pre-commit run -a`

* update toolkit registry check to use types rather than repr

* add compatibility checks for doi and hash fields, add tests

* lint

* move imports to top of file

* thread naglcharges handler into inits for correct import paths and docs

* remove commented code

* have tests run without interchange branch

* point to nagl-models main branch for pip installs

* update expected error message in test

* revert tests to using conda packages

* revert other test envs

---------

Co-authored-by: Jeffrey Wagner <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.pre-commit-config.yaml

@@ -3,9 +3,10 @@ ci:
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.12.2
+  rev: v0.12.8
   hooks:
-    - id: ruff
+    - id: ruff-format
+    - id: ruff-check
       args: [--fix]
 - repo: https://github.com/adamchainz/blacken-docs
   rev: 1.19.1

docs/conf.py

@@ -272,9 +272,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, "openff-toolkit", "OpenFF Toolkit Documentation", [author], 1)
-]
+man_pages = [(master_doc, "openff-toolkit", "OpenFF Toolkit Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------

docs/users/molecule_cookbook.ipynb

@@ -1135,9 +1135,7 @@
     }
    ],
    "source": [
-    "inchi = Molecule.from_inchi(\n",
-    "    \"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1\"\n",
-    ")\n",
+    "inchi = Molecule.from_inchi(\"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1\")\n",
     "\n",
     "inchi.visualize()"
    ]

examples/conformer_energies/conformer_energies.ipynb

@@ -196,9 +196,7 @@
     "    simulation.context.setPositions(conformer.to_openmm())\n",
     "\n",
     "    # Keep a record of the initial energy\n",
-    "    initial_energies.append(\n",
-    "        simulation.context.getState(getEnergy=True).getPotentialEnergy()\n",
-    "    )\n",
+    "    initial_energies.append(simulation.context.getState(getEnergy=True).getPotentialEnergy())\n",
     "\n",
     "    # Perform the minimization\n",
     "    simulation.minimizeEnergy()\n",
@@ -309,7 +307,7 @@
     "    # Save the minimized conformer to file\n",
     "    working_mol.add_conformer(min_coords)\n",
     "    working_mol.to_file(\n",
-    "        f\"{molecule.name}_conf{i+1}_minimized.sdf\",\n",
+    "        f\"{molecule.name}_conf{i + 1}_minimized.sdf\",\n",
     "        file_format=\"sdf\",\n",
     "    )\n",
     "\n",
@@ -329,11 +327,7 @@
     "            minimization_rms,\n",
     "        ]\n",
     "    )\n",
-    "    print(\n",
-    "        f\"{{:5d}} / {n_confs:5d} :  {{:8.3f}} kcal/mol {{:8.3f}} kcal/mol {{:8.3f}} Å\".format(\n",
-    "            *output[-1]\n",
-    "        )\n",
-    "    )\n",
+    "    print(f\"{{:5d}} / {n_confs:5d} :  {{:8.3f}} kcal/mol {{:8.3f}} kcal/mol {{:8.3f}} Å\".format(*output[-1]))\n",
     "\n",
     "# Write the results out to CSV\n",
     "with open(f\"{molecule.name}.csv\", \"w\") as of:\n",

examples/conformer_energies/conformer_energies.py

@@ -66,9 +66,7 @@ def compute_conformer_energies_from_file(filename):
         simulation.context.setPositions(conformer.to_openmm())
 
         # Keep a record of the initial energy
-        initial_energies.append(
-            simulation.context.getState(getEnergy=True).getPotentialEnergy()
-        )
+        initial_energies.append(simulation.context.getState(getEnergy=True).getPotentialEnergy())
 
         # Perform the minimization
         simulation.minimizeEnergy()
@@ -109,7 +107,7 @@ def compute_conformer_energies_from_file(filename):
         # Save the minimized conformer to file
         working_mol.add_conformer(min_coords)
         working_mol.to_file(
-            f"{molecule.name}_conf{i+1}_minimized.sdf",
+            f"{molecule.name}_conf{i + 1}_minimized.sdf",
             file_format="sdf",
         )
 
@@ -129,11 +127,7 @@ def compute_conformer_energies_from_file(filename):
                 minimization_rms,
             ]
         )
-        print(
-            f"{{:5d}} / {n_confs:5d} :  {{:8.3f}} kcal/mol {{:8.3f}} kcal/mol {{:8.3f}} Å".format(
-                *output[-1]
-            )
-        )
+        print(f"{{:5d}} / {n_confs:5d} :  {{:8.3f}} kcal/mol {{:8.3f}} kcal/mol {{:8.3f}} Å".format(*output[-1]))
 
     # Write the results out to CSV
     with open(f"{molecule.name}.csv", "w") as of:
@@ -150,9 +144,7 @@ def compute_conformer_energies_from_file(filename):
             "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"
-    )
+    parser.add_argument("-f", "--filename", help="Name of an input file containing conformers")
     args = parser.parse_args()
 
     compute_conformer_energies_from_file(args.filename)

examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb

@@ -143,9 +143,7 @@
     "            atomstr = \"\"\n",
     "            for idx in atom_indices:\n",
     "                atomstr += f\"{idx:>3}\"\n",
-    "            print(\n",
-    "                f\"atoms: {atomstr}  parameter_id: {parameter.id}  smirks {parameter.smirks}\"\n",
-    "            )"
+    "            print(f\"atoms: {atomstr}  parameter_id: {parameter.id}  smirks {parameter.smirks}\")"
    ]
   },
   {

examples/toolkit_showcase/toolkit_showcase.ipynb

@@ -327,9 +327,7 @@
    "outputs": [],
    "source": [
     "fixer = PDBFixer(receptor_path)\n",
-    "fixer.addSolvent(\n",
-    "    padding=1.0 * openmm_unit.nanometer, ionicStrength=0.15 * openmm_unit.molar\n",
-    ")\n",
+    "fixer.addSolvent(padding=1.0 * openmm_unit.nanometer, ionicStrength=0.15 * openmm_unit.molar)\n",
     "\n",
     "with open(\"receptor_solvated.pdb\", \"w\") as f:\n",
     "    openmm.app.PDBFile.writeFile(fixer.topology, fixer.positions, f)\n",
@@ -390,9 +388,7 @@
     "\n",
     "        # np.linalg.norm doesn't work on Pint quantities 😢\n",
     "        working_unit = unit.nanometer\n",
-    "        distance_matrix = (\n",
-    "            np.linalg.norm(diff_matrix.m_as(working_unit), axis=-1) * working_unit\n",
-    "        )\n",
+    "        distance_matrix = np.linalg.norm(diff_matrix.m_as(working_unit), axis=-1) * working_unit\n",
     "\n",
     "        if distance_matrix.min() > radius:\n",
     "            # This molecule is not clashing, so add it to the topology\n",

examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb

@@ -21,9 +21,7 @@
     "# https://github.com/MobleyLab/benchmarksets\n",
     "import requests\n",
     "\n",
-    "repo_url = (\n",
-    "    \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
-    ")\n",
+    "repo_url = \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",
     "sources = {\n",
     "    \"receptor.pdb\": repo_url + \"BRD4/pdb/BRD4.pdb\",\n",
     "    \"ligand.pdb\": repo_url + \"BRD4/pdb/ligand-1.pdb\",\n",

examples/virtual_sites/vsite_showcase.ipynb

@@ -500,10 +500,7 @@
     "    state = sim.context.getState(getEnergy=True, getPositions=True)\n",
     "    ene = state.getPotentialEnergy()\n",
     "    pos = openmm.unit.Quantity(\n",
-    "        [\n",
-    "            list(xyz)\n",
-    "            for xyz in state.getPositions().value_in_unit(openmm.unit.nanometer)\n",
-    "        ],\n",
+    "        [list(xyz) for xyz in state.getPositions().value_in_unit(openmm.unit.nanometer)],\n",
     "        openmm.unit.nanometer,\n",
     "    )\n",
     "\n",
@@ -628,12 +625,8 @@
     "    # First, get an OpenMM Topology and atom positions with no virtual sites\n",
     "    _topology: openmm.app.Topology = Topology.from_molecules(water).to_openmm()\n",
     "\n",
-    "    atom_positions_unitless = numpy.vstack(\n",
-    "        [mol.conformers[0].m_as(unit.nanometer) for mol in water]\n",
-    "    )\n",
-    "    atom_positions = openmm.unit.Quantity(\n",
-    "        atom_positions_unitless, openmm.unit.nanometer\n",
-    "    )\n",
+    "    atom_positions_unitless = numpy.vstack([mol.conformers[0].m_as(unit.nanometer) for mol in water])\n",
+    "    atom_positions = openmm.unit.Quantity(atom_positions_unitless, openmm.unit.nanometer)\n",
     "\n",
     "    # Use OpenMM's Modeller to add virtual particles as perscribed by the force field\n",
     "    modeller = openmm.app.Modeller(_topology, atom_positions)\n",
@@ -642,16 +635,12 @@
     "    # This topology includes virtual particles, so we can use it to create a System\n",
     "    topology = modeller.getTopology()\n",
     "\n",
-    "    system: openmm.System = openmm_force_field.createSystem(\n",
-    "        topology, nonbondedMethod=openmm.app.NoCutoff\n",
-    "    )\n",
+    "    system: openmm.System = openmm_force_field.createSystem(topology, nonbondedMethod=openmm.app.NoCutoff)\n",
     "\n",
     "    # Add positions of virtual particles now that the topology includes them\n",
     "    particle_positions = modeller.getPositions()\n",
     "\n",
-    "    return _evaluate_positions_and_energy(\n",
-    "        topology, system, particle_positions, minimize=minimize\n",
-    "    )"
+    "    return _evaluate_positions_and_energy(topology, system, particle_positions, minimize=minimize)"
    ]
   },
   {
@@ -802,12 +791,10 @@
     "    f\"{coordinate_difference.m:0.3e}\\n\"\n",
     ")\n",
     "\n",
-    "assert coordinate_difference < Quantity(\n",
-    "    1e-6, unit.angstrom\n",
-    "), f\"Coordinates differ by a norm of {coordinate_difference}\"\n",
-    "assert (\n",
-    "    energy_difference < 1e-4 * openmm.unit.kilojoule_per_mole\n",
-    "), f\"Energies differ by {energy_difference}\""
+    "assert coordinate_difference < Quantity(1e-6, unit.angstrom), (\n",
+    "    f\"Coordinates differ by a norm of {coordinate_difference}\"\n",
+    ")\n",
+    "assert energy_difference < 1e-4 * openmm.unit.kilojoule_per_mole, f\"Energies differ by {energy_difference}\""
    ]
   },
   {

examples/visualization/visualization.ipynb

@@ -734,10 +734,7 @@
    },
    "outputs": [],
    "source": [
-    "\n",
-    "topology = Topology.from_pdb(\n",
-    "    get_data_file_path(\"systems/test_systems/T4_lysozyme_water_ions.pdb\")\n",
-    ")"
+    "topology = Topology.from_pdb(get_data_file_path(\"systems/test_systems/T4_lysozyme_water_ions.pdb\"))"
    ]
   },
   {