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ruff: address pycodestyle changes (#1668)

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* apply E741: ambiguous variable name check

* apply E713: 'not in' fixes

* address E721 with isintance() checks

* fix bare excepts

* precommit
This commit is contained in:
Alyssa Travitz
2025-11-11 11:34:29 -07:00
committed by GitHub
parent 18f211db97
commit b693d37c8a
12 changed files with 27 additions and 26 deletions
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4
openfe/__init__.py
View File

@@ -3,11 +3,11 @@ import logging
def _mute_timeseries(record):
return not "Warning on use of the timeseries module:" in record.msg
return "Warning on use of the timeseries module:" not in record.msg
def _mute_jax(record):
return not "****** PyMBAR will use 64-bit JAX! *******" in record.msg
return "****** PyMBAR will use 64-bit JAX! *******" not in record.msg
_mbar_log = logging.getLogger("pymbar.timeseries")

2
openfe/protocols/openmm_afe/equil_binding_afe_method.py
View File

@@ -727,7 +727,7 @@ class AbsoluteBindingProtocol(gufe.Protocol):
lambda_components = [lambda_vdw, lambda_elec, lambda_restraints]
it = iter(lambda_components)
the_len = len(next(it))
if not all(len(l) == the_len for l in it):
if not all(len(lambda_comp) == the_len for lambda_comp in it):
errmsg = (
"Components elec, vdw, and restraints must have equal amount"
f" of lambda windows. Got {len(lambda_elec)} elec lambda"

2
openfe/protocols/openmm_afe/equil_solvation_afe_method.py
View File

@@ -619,7 +619,7 @@ class AbsoluteSolvationProtocol(gufe.Protocol):
lambda_components = [lambda_vdw, lambda_elec, lambda_restraints]
it = iter(lambda_components)
the_len = len(next(it))
if not all(len(l) == the_len for l in it):
if not all(len(lambda_comp) == the_len for lambda_comp in it):
errmsg = (
"Components elec, vdw, and restraints must have equal amount"
f" of lambda windows. Got {len(lambda_elec)} elec lambda"

4
openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py
View File

@@ -103,9 +103,9 @@ class LambdaProtocol(object):
else:
self.lambda_schedule = np.linspace(0., 1., windows)
if type(self.functions) == dict:
if isinstance(self.functions, dict):
self.type = 'user-defined'
elif type(self.functions) == str:
elif isinstance(self.functions, str):
self.functions = None # will be set later
self.type = functions

6
openfe/setup/ligand_network_planning.py
View File

@@ -406,8 +406,8 @@ def load_orion_network(
with open(network_file, "r") as f:
network_lines = [
l.strip().split(" ") for l in f
if not l.startswith("#")
line.strip().split(" ") for line in f
if not line.startswith("#")
] # fmt: skip
names = []
@@ -451,7 +451,7 @@ def load_fepplus_network(
"""
with open(network_file, "r") as f:
network_lines = [l.split() for l in f.readlines()]
network_lines = [line.split() for line in f.readlines()]
names = []
for entry in network_lines:

3
openfe/tests/conftest.py
View File

@@ -2,6 +2,7 @@
# For details, see https://github.com/OpenFreeEnergy/openfe
import os
import pathlib
import urllib.error
import urllib.request
from importlib import resources
@@ -361,7 +362,7 @@ def am1bcc_ref_charges():
try:
urllib.request.urlopen("https://www.google.com")
except: # -no-cov-
except urllib.error.URLError: # -no-cov-
HAS_INTERNET = False
else:
HAS_INTERNET = True

8
openfe/tests/setup/test_network_planning.py
View File

@@ -691,7 +691,7 @@ def test_network_from_external(file_fixture, loader, request, benzene_modificati
network_file = request.getfixturevalue(file_fixture)
network = loader(
ligands=[l for l in benzene_modifications.values()],
ligands=[lig for lig in benzene_modifications.values()],
mapper=openfe.LomapAtomMapper(),
network_file=network_file,
)
@@ -721,7 +721,7 @@ def test_network_from_external(file_fixture, loader, request, benzene_modificati
)
def test_network_from_external_unknown_edge(file_fixture, loader, request, benzene_modifications):
network_file = request.getfixturevalue(file_fixture)
ligands = [l for l in benzene_modifications.values() if l.name != "phenol"]
ligands = [lig for lig in benzene_modifications.values() if lig.name != "phenol"]
with pytest.raises(KeyError, match="Invalid name"):
_ = loader(
@@ -750,7 +750,7 @@ def test_bad_orion_network(benzene_modifications, tmpdir):
with pytest.raises(KeyError, match="line does not match"):
_ = openfe.setup.ligand_network_planning.load_orion_network(
ligands=[l for l in benzene_modifications.values()],
ligands=[lig for lig in benzene_modifications.values()],
mapper=openfe.LomapAtomMapper(),
network_file="bad_orion_net.dat",
)
@@ -773,7 +773,7 @@ def test_bad_edges_network(benzene_modifications, tmpdir):
with pytest.raises(KeyError, match="line does not match"):
_ = openfe.setup.ligand_network_planning.load_fepplus_network(
ligands=[l for l in benzene_modifications.values()],
ligands=[lig for lig in benzene_modifications.values()],
mapper=openfe.LomapAtomMapper(),
network_file="bad_edges.edges",
)

2
openfe/utils/logging_filter.py
View File

@@ -17,4 +17,4 @@ class MsgIncludesStringFilter:
self.string = string
def filter(self, record):
return not self.string in record.msg
return self.string not in record.msg

2
openfe/utils/system_probe.py
View File

@@ -513,7 +513,7 @@ def log_system_probe(level=logging.DEBUG, paths: Optional[Iterable[os.PathLike]]
gpu = logging.getLogger(basename + ".gpu")
hostname = logging.getLogger(basename + ".hostname")
loggers = [base, gpu, hostname]
if any(l.isEnabledFor(level) for l in loggers):
if any(logger.isEnabledFor(level) for logger in loggers):
sysinfo = _probe_system(pl_paths)["system information"]
base.log(level, "SYSTEM CONFIG DETAILS:")
hostname.log(level, f"hostname: '{sysinfo['hostname']}'")

3
openfecli/tests/conftest.py
View File

@@ -1,8 +1,9 @@
import urllib.error
import urllib.request
try:
urllib.request.urlopen("https://www.google.com")
except: # -no-cov-
except urllib.error.URLError: # -no-cov-
HAS_INTERNET = False
else:
HAS_INTERNET = True

12
openfecli/utils.py
View File

@@ -58,15 +58,15 @@ def _should_configure_logger(logger: logging.Logger):
return False
# walk up the logging tree to see if any parent loggers are not default
l = logger
_logger = logger
while (
l.parent is not None # not the root logger
and l.level == logging.NOTSET # level not already set
and l.propagate # configured to use parent when not set
_logger.parent is not None # not the root logger
and _logger.level == logging.NOTSET # level not already set
and _logger.propagate # configured to use parent when not set
):
l = l.parent
_logger = _logger.parent
is_default = (l == logging.root and l.level == logging.WARNING) # fmt: skip
is_default = (_logger == logging.root and _logger.level == logging.WARNING) # fmt: skip
return is_default

5
pyproject.toml
View File

@@ -52,17 +52,16 @@ line-length = 100
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
lint.select = [
"E", # pycodestyle errors
"F", # Pyflakes
"I", # isort
"W", # pycodestyle warnings
# "E", # pycodestyle errors
# "C901" # mccabe complexity TODO: add this back in
# "UP", # TODO: add this in
]
lint.ignore = [
"E402", # module-level import not at top (conflicts w/ isort)
"E722", # bare excepts (TODO: we should fix these in a follow-up PR)
"E731", # lambda expressions (TODO: we should fix these)
"E501", # line length too long, resolve this for comments
"F401", # unused imports (TODO: we should fix these)
"F811",
"F841",