define skip_if_no_openbabel decorator once and reuse

custodian/ansible/actions.py

@@ -231,8 +231,8 @@ def file_create(filename, settings, directory):
             raise ValueError("Settings must only contain one item with key 'content'.")
         for k, v in settings.items():
             if k == "content":
-                with open(filename, "w") as f:
-                    f.write(v)
+                with open(filename, "w") as file:
+                    file.write(v)
 
     @staticmethod
     def file_move(filename, settings, directory):

custodian/cp2k/utils.py

@@ -176,8 +176,8 @@ def can_use_ot(output, ci, minimum_band_gap=0.1):
 
 def tail(filename, n=10):
     """Returns the last n lines of a file as a list (including empty lines)."""
-    with open(filename) as f:
-        t = deque(f, n)
+    with open(filename) as file:
+        t = deque(file, n)
         if t:
             return t
         return [""] * n

custodian/custodian.py

@@ -215,7 +215,7 @@ def _load_checkpoint(directory):
             chkpt = sorted(chkpts, key=lambda c: int(c.split(".")[-3]))[0]
             restart = int(chkpt.split(".")[-3])
             logger.info(f"Loading from checkpoint file {chkpt}...")
-            with tarfile.open(chkpt) as t:
+            with tarfile.open(chkpt) as file:
 
                 def is_within_directory(directory, target):
                     abs_directory = os.path.abspath(directory)
@@ -233,7 +233,7 @@ def safe_extract(tar, path=directory, members=None, *, numeric_owner=False):
 
                     tar.extractall(path, members, numeric_owner=numeric_owner)
 
-                safe_extract(t, directory)
+                safe_extract(file, directory)
             # Log the corrections to a json file.
             run_log = loadfn(os.path.join(directory, Custodian.LOG_FILE), cls=MontyDecoder)
 
@@ -249,8 +249,8 @@ def _save_checkpoint(directory, index):
         try:
             Custodian._delete_checkpoints(directory)
             n = os.path.join(directory, f"custodian.chk.{index}.tar.gz")
-            with tarfile.open(n, mode="w:gz", compresslevel=3) as f:
-                f.add(directory, arcname=".")
+            with tarfile.open(n, mode="w:gz", compresslevel=3) as file:
+                file.add(directory, arcname=".")
             logger.info(f"Checkpoint written to {n}")
         except Exception:
             logger.info("Checkpointing failed")

custodian/feff/handlers.py

@@ -56,8 +56,8 @@ def _notconverge_check(self, directory):
         # Process the output file and get converge information
         not_converge_pattern = re.compile("Convergence not reached.*")
         converge_pattern = re.compile("Convergence reached.*")
-        with open(os.path.join(directory, self.output_filename)) as f:
-            for line in f:
+        with open(os.path.join(directory, self.output_filename)) as file:
+            for line in file:
                 if len(not_converge_pattern.findall(line)) > 0:
                     return True
 

custodian/lobster/handlers.py

@@ -33,8 +33,8 @@ def check(self, directory: str = "./") -> bool:
         """
         # checks if correct number of bands is available
         try:
-            with open(os.path.join(directory, self.output_filename)) as f:
-                data = f.read()
+            with open(os.path.join(directory, self.output_filename)) as file:
+                data = file.read()
             return "You are employing too few bands in your PAW calculation." in data
         except OSError:
             return False

custodian/qchem/jobs.py

@@ -191,8 +191,8 @@ def run(self, directory: str | Path = "./"):
         if os.path.exists(os.path.join(os.environ["QCSCRATCH"], "53.0")):
             os.makedirs(local_scratch, exist_ok=True)
             shutil.move(os.path.join(os.environ["QCSCRATCH"], "53.0"), local_scratch)
-        with open(self.qclog_file, "w") as qclog:
-            return subprocess.Popen(self.current_command, cwd=directory, stdout=qclog, shell=True)  # pylint: disable=R1732
+        with open(self.qclog_file, "w") as qc_log:
+            return subprocess.Popen(self.current_command, cwd=directory, stdout=qc_log, shell=True)  # pylint: disable=R1732
 
     @classmethod
     def opt_with_frequency_flattener(

custodian/vasp/handlers.py

@@ -709,8 +709,8 @@ def __init__(self, output_filename: str = "std_err.txt"):
     def check(self, directory="./"):
         """Check for error."""
         self.errors = set()
-        with open(os.path.join(directory, self.output_filename)) as f:
-            for line in f:
+        with open(os.path.join(directory, self.output_filename)) as file:
+            for line in file:
                 line = line.strip()
                 for err, msgs in LrfCommutatorHandler.error_msgs.items():
                     for msg in msgs:
@@ -825,8 +825,8 @@ def check(self, directory="./"):
         """Check for error."""
         incar = Incar.from_file(os.path.join(directory, "INCAR"))
         self.errors = set()
-        with open(os.path.join(directory, self.output_filename)) as f:
-            for line in f:
+        with open(os.path.join(directory, self.output_filename)) as file:
+            for line in file:
                 line = line.strip()
                 for err, msgs in AliasingErrorHandler.error_msgs.items():
                     for msg in msgs:
@@ -1009,8 +1009,8 @@ def check(self, directory="./"):
                 return False
         except Exception:
             pass
-        with open(os.path.join(directory, self.output_filename)) as f:
-            for line in f:
+        with open(os.path.join(directory, self.output_filename)) as file:
+            for line in file:
                 line = line.strip()
                 if line.find(msg) != -1:
                     return True

custodian/vasp/jobs.py

@@ -707,8 +707,8 @@ def terminate(self, directory="./"):
                     if (vasprun_path in open_paths) and psutil.pid_exists(proc.pid):
                         proc.kill()
                         return
-            except (psutil.NoSuchProcess, psutil.AccessDenied) as e:
-                logger.warning(f"Exception {e} encountered while killing VASP.")
+            except (psutil.NoSuchProcess, psutil.AccessDenied) as exc:
+                logger.warning(f"Exception {exc} encountered while killing VASP.")
                 continue
 
         logger.warning(

tasks.py

@@ -27,14 +27,14 @@ def make_doc(ctx):
         ctx.run("cp markdown/custodian*.md .")
         ctx.run("rm custodian*tests*.md", warn=True)
         for fn in glob("custodian*.md"):
-            with open(fn) as f:
-                lines = [line.rstrip() for line in f if "Submodules" not in line]
+            with open(fn) as file:
+                lines = [line.rstrip() for line in file if "Submodules" not in line]
             if fn == "custodian.md":
                 preamble = ["---", "layout: default", "title: API Documentation", "nav_order: 6", "---", ""]
             else:
                 preamble = ["---", "layout: default", "title: " + fn, "nav_exclude: true", "---", ""]
-            with open(fn, "w") as f:
-                f.write("\n".join(preamble + lines))
+            with open(fn, "w") as file:
+                file.write("\n".join(preamble + lines))
         ctx.run("rm -r markdown doctrees", warn=True)
 
 
@@ -117,16 +117,16 @@ def update_changelog(ctx, version=None, sim=False):
                 pass
         else:
             misc.append("- " + line)
-    with open("docs/changelog.md") as f:
-        contents = f.read()
+    with open("docs/changelog.md") as file:
+        contents = file.read()
     head = "# Change Log"
     i = contents.find(head)
     i += len(head)
 
     contents = contents[0:i] + f"\n\n## {NEW_VER}\n" + "\n".join(lines) + contents[i:]
     if not sim:
-        with open("docs/changelog.md", "w") as f:
-            f.write(contents)
+        with open("docs/changelog.md", "w") as file:
+            file.write(contents)
         ctx.run("open docs/changelog.md")
     else:
         print(contents)

tests/qchem/test_handlers.py

@@ -26,9 +26,10 @@
 TEST_DIR = f"{TEST_FILES}/qchem/new_test_files"
 SCR_DIR = f"{TEST_DIR}/scratch"
 CWD = os.getcwd()
+skip_if_no_openbabel = unittest.skipIf(ob is None, "openbabel not installed")
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class QChemErrorHandlerTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)

tests/qchem/test_job_handler_interaction.py

@@ -25,9 +25,10 @@
 TEST_DIR = f"{TEST_FILES}/qchem/new_test_files"
 SCR_DIR = f"{TEST_DIR}/scratch"
 CWD = os.getcwd()
+skip_if_no_openbabel = unittest.skipIf(ob is None, "openbabel not installed")
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class FFOptJobHandlerInteraction(TestCase):
     def _check_equivalent_inputs(self, input1, input2):
         QCinput1 = QCInput.from_file(input1)

tests/qchem/test_jobs.py

@@ -27,9 +27,10 @@
 TEST_DIR = f"{TEST_FILES}/qchem/new_test_files"
 SCR_DIR = f"{TEST_DIR}/scratch"
 CWD = os.getcwd()
+skip_if_no_openbabel = unittest.skipIf(ob is None, "openbabel not installed")
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class QCJobTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -88,7 +89,7 @@ def test_save_scratch(self):
             assert os.environ["QCLOCALSCR"] == "/tmp/scratch"
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFComplexUnlinkedTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -151,7 +152,7 @@ def test_OptFF(self):
         )
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTestComplexLinkedChangeNsegTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -236,7 +237,7 @@ def test_OptFF(self):
         )
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -317,7 +318,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest1(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -347,7 +348,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest2(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -397,7 +398,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTestSwitching(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -509,7 +510,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest6004(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -619,7 +620,7 @@ def test_OptFF(self):
         )
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest5952(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -669,7 +670,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFTest5690(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -781,7 +782,7 @@ def test_OptFF(self):
             next(job)
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFSmallNegFreqTest(TestCase):
     def setUp(self):
         os.makedirs(f"{SCR_DIR}/scratch", exist_ok=True)
@@ -917,7 +918,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class OptFFSingleFreqFragsTest(TestCase):
     def setUp(self):
         os.makedirs(f"{SCR_DIR}/scratch", exist_ok=True)
@@ -973,7 +974,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class TSFFTest(TestCase):
     def setUp(self):
         os.makedirs(SCR_DIR)
@@ -1024,7 +1025,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class TSFFFreqfirstTest(TestCase):
     def setUp(self):
         os.makedirs(f"{SCR_DIR}/scratch", exist_ok=True)
@@ -1096,7 +1097,7 @@ def test_OptFF(self):
             job.__next__()
 
 
-@unittest.skipIf(ob is None, "openbabel not installed")
+@skip_if_no_openbabel
 class TSFFFreqFirstMultipleCyclesTest(TestCase):
     def setUp(self):
         os.makedirs(f"{SCR_DIR}/scratch", exist_ok=True)

tests/vasp/test_handlers.py

@@ -933,8 +933,8 @@ def test_check_and_correct(self):
 
         # Test that the STOPCAR is written correctly.
         handler.correct()
-        with open("STOPCAR") as f:
-            content = f.read()
+        with open("STOPCAR") as file:
+            content = file.read()
             assert content == "LSTOP = .TRUE."
         os.remove("STOPCAR")
 
@@ -945,8 +945,8 @@ def test_check_and_correct(self):
         assert handler.check()
 
         handler.correct()
-        with open("STOPCAR") as f:
-            content = f.read()
+        with open("STOPCAR") as file:
+            content = file.read()
             assert content == "LABORT = .TRUE."
         os.remove("STOPCAR")