ruff: address pycodestyle changes (#1668)

* apply E741: ambiguous variable name check

* apply E713: 'not in' fixes

* address E721 with isintance() checks

* fix bare excepts

* precommit

openfe/__init__.py

@@ -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")

openfe/protocols/openmm_afe/equil_binding_afe_method.py

@@ -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"

openfe/protocols/openmm_afe/equil_solvation_afe_method.py

@@ -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"

openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py

@@ -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
 

openfe/setup/ligand_network_planning.py

@@ -406,8 +406,8 @@ def load_orion_network(
 
     with open(network_file, "r") as f:
         network_lines = [
-            l.strip().split(" ") for l in f
+            line.strip().split(" ") for line in f
-            if not l.startswith("#")
+            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:

openfe/tests/conftest.py

@@ -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

openfe/tests/setup/test_network_planning.py

@@ -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",
             )

openfe/utils/logging_filter.py

@@ -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

openfe/utils/system_probe.py

@@ -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']}'")

openfecli/tests/conftest.py

@@ -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

openfecli/utils.py

@@ -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
+        _logger.parent is not None  # not the root logger
-        and l.level == logging.NOTSET  # level not already set
+        and _logger.level == logging.NOTSET  # level not already set
-        and l.propagate  # configured to use parent when not 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
 

pyproject.toml

@@ -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)
+  "E501", # line length too long, resolve this for comments
-  "E731", # lambda expressions (TODO: we should fix these)
   "F401", # unused imports (TODO: we should fix these)
   "F811",
   "F841",