fix undeclared logger in atomate/vasp/analysis/linear_response.py, fix ambiguous file names, flake8 ignore E203, W503

Author: janosh

atomate/utils/fileio.py

@@ -131,7 +131,7 @@ def abspath(self, path):
         else:
             command = f". ./.bashrc; readlink -f {path}"
             stdin, stdout, stderr = self.ssh.exec_command(command)
-            full_path = [l.split("\n")[0] for l in stdout]
+            full_path = [line.split("\n")[0] for line in stdout]
             return full_path[0]
 
     def glob(self, path):
@@ -146,4 +146,4 @@ def glob(self, path):
         else:
             command = f". ./.bashrc; for i in $(ls {path}); do readlink -f $i; done"
             stdin, stdout, stderr = self.ssh.exec_command(command)
-            return [l.split("\n")[0] for l in stdout]
+            return [line.split("\n")[0] for line in stdout]

atomate/vasp/analysis/linear_response.py

@@ -1,6 +1,10 @@
 import numpy as np
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer
 
+from atomate.utils.utils import get_logger
+
+logger = get_logger(__name__)
+
 
 def procure_response_dict(
     struct_final,

atomate/vasp/firetasks/approx_neb_tasks.py

@@ -67,7 +67,7 @@ def run_task(self, fw_spec):
             {"task_id": t_id, "approx_neb.calc_type": "host"},
             {"$push": {"approx_neb.wf_uuids": wf_uuid}},
         )
-        if host_tasks_doc == None:
+        if host_tasks_doc is None:
             raise ValueError(f"Error updating approx neb host with task_id: {t_id}")
 
         # Initialize and store select host task doc fields in approx_neb_doc
@@ -818,7 +818,7 @@ def run_task(self, fw_spec):
                 },
             },
         )
-        if task_doc == None:
+        if task_doc is None:
             raise ValueError(f"Error updating approx neb image with task_id: {t_id}")
 
         # Store info in approx_neb collection for record keeping

setup.cfg

@@ -12,6 +12,9 @@ release = register sdist upload
 
 [flake8]
 max-line-length = 125
+# E203 whitespace before ':'
+# W503 line break before binary operator
+ignore = E203, W503
 per-file-ignores =
   # F401: imported but unused
   __init__.py: F401