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Fix flake8 errors #59

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merged 3 commits into from
Oct 1, 2024
Merged

Fix flake8 errors #59

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6ae3ea7
ignore F401 on __init__.py files
mikemhenry Sep 30, 2024
cc04be9
fix flake8 errors
mikemhenry Sep 30, 2024
5aa6878
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 30, 2024
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2 changes: 0 additions & 2 deletions openfe_gromacs/protocols/gromacs_md/md_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,9 @@
from gufe import ChemicalSystem, SmallMoleculeComponent, settings
from openfe.protocols.openmm_utils import (
charge_generation,
settings_validation,
system_creation,
system_validation,
)
from openfe.protocols.openmm_utils.omm_settings import BasePartialChargeSettings
from openfe.utils import log_system_probe, without_oechem_backend
from openff.interchange import Interchange
from openff.toolkit.topology import Molecule as OFFMolecule
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2 changes: 0 additions & 2 deletions openfe_gromacs/tests/protocols/conftest.py
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Expand Up @@ -9,8 +9,6 @@
from rdkit import Chem
from rdkit.Geometry import Point3D

import openfe_gromacs


@pytest.fixture
def benzene_vacuum_system(benzene_modifications):
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3 changes: 2 additions & 1 deletion openfe_gromacs/tests/protocols/test_gromacs_md.py
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Expand Up @@ -45,7 +45,8 @@ def test_serialize_protocol():

def test_create_independent_repeat_ids(benzene_system):
# if we create two dags each with 3 repeats, they should give 6 repeat_ids
# this allows multiple DAGs in flight for one Transformation that don't clash on gather
# this allows multiple DAGs in flight for one Transformation that don't
# clash on gather
settings = GromacsMDProtocol.default_settings()
# Default protocol is 1 repeat, change to 3 repeats
settings.protocol_repeats = 3
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12 changes: 1 addition & 11 deletions openfe_gromacs/tests/protocols/test_md_settings.py
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@@ -1,19 +1,9 @@
# This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
import json
import pathlib
from unittest import mock

import gufe
import pytest
from openff.units import unit

import openfe_gromacs
from openfe_gromacs.protocols.gromacs_md.md_methods import (
GromacsMDProtocol,
GromacsMDProtocolResult,
GromacsMDSetupUnit,
)
from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol


def test_settings_pos_or_zero_error():
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9 changes: 9 additions & 0 deletions pyproject.toml
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Expand Up @@ -97,6 +97,15 @@ omit = [
[tool.flake8]
max-line-length = 88
extend-ignore = ['E203',]
per-file-ignores = [
'__init__.py:F401',
]
builtins = [
"nanometer",
"picosecond",
"kelvin",
"bar",
]

[tool.isort]
profile = "black"
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