From f0a975dac289690924cf7c03c6ee18684a813f98 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Wed, 15 Dec 2021 12:56:24 -0800
Subject: [PATCH] Updates pre-commit config and adds related fixes

---
 .github/workflows/srt.yml                     |   2 +-
 .pre-commit-config.yaml                       |   8 +-
 config/cesm/machines/config_machines.xml      |   2 +-
 conftest.py                                   |   7 +-
 doc/source/users_guide/testing.rst            |   4 +-
 scripts/lib/CIME/SystemTests/ers2.py          |   2 +-
 scripts/lib/CIME/SystemTests/pgn.py           |   4 +-
 .../SystemTests/test_utils/user_nl_utils.py   |  10 +-
 scripts/lib/CIME/XML/machines.py              |  11 +-
 scripts/lib/CIME/XML/test_reporter.py         |   5 +-
 scripts/lib/CIME/provenance.py                |   8 +-
 .../CIME/tests/scripts_regression_tests.py    | 132 +++++++++++-------
 .../lib/CIME/tests/test_sys_create_newcase.py |  44 ++++--
 .../lib/CIME/tests/test_sys_test_scheduler.py |  88 +++++++++---
 scripts/lib/CIME/tests/test_sys_unittest.py   |   6 +-
 .../lib/CIME/tests/test_unit_user_nl_utils.py |  86 ++++++------
 scripts/lib/CIME/utils.py                     |   9 +-
 setup.cfg                                     |   2 +-
 src/build_scripts/buildlib.gptl               |  17 +--
 19 files changed, 286 insertions(+), 161 deletions(-)

diff --git a/.github/workflows/srt.yml b/.github/workflows/srt.yml
index a21efdd8d98..4a9bef5e5fb 100644
--- a/.github/workflows/srt.yml
+++ b/.github/workflows/srt.yml
@@ -24,7 +24,7 @@ jobs:
           python-version: 3.9
       - name: Install and run pre-commit
         uses: pre-commit/action@v2.0.3
-  
+
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a3b2b182d5d..55c25c564d7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,4 @@
-exclude: 'utils/'
+exclude: ^utils/.*$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -16,12 +16,8 @@ repos:
           - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error
         files: 'scripts/lib/CIME'
         exclude: 'scripts/lib/CIME/tests'
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-      - id: flake8
   - repo: https://github.com/psf/black
     rev: 21.10b0
     hooks:
       - id: black
-        exclude: "config"
+        files: 'scripts/lib/CIME'
diff --git a/config/cesm/machines/config_machines.xml b/config/cesm/machines/config_machines.xml
index 50a046266b7..1180f26f25a 100644
--- a/config/cesm/machines/config_machines.xml
+++ b/config/cesm/machines/config_machines.xml
@@ -543,7 +543,7 @@ This allows using a different mpirun command to launch unit tests
 <!--  Due to a bug in romio these are not working -->
         <command name="load">cray-netcdf-hdf5parallel</command>
         <command name="load">cray-hdf5-parallel</command>
-        <command name="load">cray-parallel-netcdf</command> 
+        <command name="load">cray-parallel-netcdf</command>
 <!--
         <command name="load">cray-hdf5</command>
         <command name="load">cray-netcdf</command>
diff --git a/conftest.py b/conftest.py
index 6b5f66946af..38ce216f708 100644
--- a/conftest.py
+++ b/conftest.py
@@ -20,16 +20,13 @@ def pytest_addoption(parser):
     scripts_regression_tests.setup_arguments(parser)
 
     # verbose and debug flags already exist
-    parser.addoption("--silent", action="store_true",
-                     help="Disable all logging")
+    parser.addoption("--silent", action="store_true", help="Disable all logging")
 
 
 def pytest_configure(config):
     kwargs = vars(config.option)
 
-    utils.configure_logging(kwargs['verbose'],
-                            kwargs['debug'],
-                            kwargs['silent'])
+    utils.configure_logging(kwargs["verbose"], kwargs["debug"], kwargs["silent"])
 
     scripts_regression_tests.configure_tests(**kwargs)
 
diff --git a/doc/source/users_guide/testing.rst b/doc/source/users_guide/testing.rst
index d089347c5f8..ea8c6288749 100644
--- a/doc/source/users_guide/testing.rst
+++ b/doc/source/users_guide/testing.rst
@@ -486,13 +486,13 @@ Install dependencies::
 
 Run full suite::
 
-  pytest -vvv 
+  pytest -vvv
 
 Run just unit tests::
 
   pytest -vvv scripts/lib/CIME/tests/test_unit*
 
-Run a test class:: 
+Run a test class::
 
   pytest -vvv scripts/lib/CIME/tests/test_unit_case.py
 
diff --git a/scripts/lib/CIME/SystemTests/ers2.py b/scripts/lib/CIME/SystemTests/ers2.py
index f408c708c0d..e65f703e36e 100644
--- a/scripts/lib/CIME/SystemTests/ers2.py
+++ b/scripts/lib/CIME/SystemTests/ers2.py
@@ -36,7 +36,7 @@ def _ers2_second_phase(self):
         stop_n = self._case.get_value("STOP_N")
         stop_option = self._case.get_value("STOP_OPTION")
 
-        rest_n = int(stop_n/2 + 1)
+        rest_n = int(stop_n / 2 + 1)
         stop_new = rest_n
 
         self._case.set_value("REST_OPTION", stop_option)
diff --git a/scripts/lib/CIME/SystemTests/pgn.py b/scripts/lib/CIME/SystemTests/pgn.py
index 802598b29ac..457fd08f775 100644
--- a/scripts/lib/CIME/SystemTests/pgn.py
+++ b/scripts/lib/CIME/SystemTests/pgn.py
@@ -269,7 +269,9 @@ def run_phase(self):
         logger.debug("PGN_INFO: Case name is:{}".format(casename))
 
         for icond in range(NUMBER_INITIAL_CONDITIONS):
-            for iprt, (prt_name, prt_value) in enumerate(PERTURBATIONS.items()):  # pylint: disable=unused-variable
+            for iprt, (prt_name, prt_value) in enumerate(
+                PERTURBATIONS.items()
+            ):  # pylint: disable=unused-variable
                 iinst = pg._sub2instance(icond, iprt, len(PERTURBATIONS))
                 fname = os.path.join(
                     rundir,
diff --git a/scripts/lib/CIME/SystemTests/test_utils/user_nl_utils.py b/scripts/lib/CIME/SystemTests/test_utils/user_nl_utils.py
index f91b832b943..eab45921c95 100644
--- a/scripts/lib/CIME/SystemTests/test_utils/user_nl_utils.py
+++ b/scripts/lib/CIME/SystemTests/test_utils/user_nl_utils.py
@@ -5,6 +5,7 @@
 import os
 import glob
 
+
 def append_to_user_nl_files(caseroot, component, contents):
     """
     Append the string given by 'contents' to the end of each user_nl file for
@@ -30,11 +31,12 @@ def append_to_user_nl_files(caseroot, component, contents):
     files = _get_list_of_user_nl_files(caseroot, component)
 
     if len(files) == 0:
-        raise RuntimeError('No user_nl files found for component ' + component)
+        raise RuntimeError("No user_nl files found for component " + component)
 
     for one_file in files:
-        with open(one_file, 'a') as user_nl_file:
-            user_nl_file.write('\n' + contents + '\n')
+        with open(one_file, "a") as user_nl_file:
+            user_nl_file.write("\n" + contents + "\n")
+
 
 def _get_list_of_user_nl_files(path, component):
     """Get a list of all user_nl files in the current path for the component
@@ -45,7 +47,7 @@ def _get_list_of_user_nl_files(path, component):
     The list of returned files gives their full path.
     """
 
-    file_pattern = 'user_nl_' + component + '*'
+    file_pattern = "user_nl_" + component + "*"
     file_list = glob.glob(os.path.join(path, file_pattern))
 
     return file_list
diff --git a/scripts/lib/CIME/XML/machines.py b/scripts/lib/CIME/XML/machines.py
index 712c28b7e11..3e78e072571 100644
--- a/scripts/lib/CIME/XML/machines.py
+++ b/scripts/lib/CIME/XML/machines.py
@@ -194,12 +194,19 @@ def _probe_machine_name_one_guess(self, nametomatch):
                 logger.debug("machine regex string is " + regex_str)
                 # an environment variable can be used
                 if regex_str.startswith("$ENV"):
-                    machine_value = self.get_resolved_value(regex_str, allow_unresolved_envvars=True)
+                    machine_value = self.get_resolved_value(
+                        regex_str, allow_unresolved_envvars=True
+                    )
                     if not machine_value.startswith("$ENV"):
                         try:
                             match, this_machine = machine_value.split(":")
                         except ValueError:
-                            expect(False,"Bad formation of NODENAME_REGEX.  Expected envvar:value, found {}".format(regex_str))
+                            expect(
+                                False,
+                                "Bad formation of NODENAME_REGEX.  Expected envvar:value, found {}".format(
+                                    regex_str
+                                ),
+                            )
                         if match == this_machine:
                             machine = machtocheck
                             break
diff --git a/scripts/lib/CIME/XML/test_reporter.py b/scripts/lib/CIME/XML/test_reporter.py
index 692ca03fc41..fc65defda09 100644
--- a/scripts/lib/CIME/XML/test_reporter.py
+++ b/scripts/lib/CIME/XML/test_reporter.py
@@ -7,9 +7,10 @@
 import urllib.request
 from CIME.XML.standard_module_setup import *
 from CIME.XML.generic_xml import GenericXML
-from CIME.utils import expect,get_model
+from CIME.utils import expect, get_model
 import ssl
-#pylint: disable=protected-access
+
+# pylint: disable=protected-access
 ssl._create_default_https_context = ssl._create_unverified_context
 
 
diff --git a/scripts/lib/CIME/provenance.py b/scripts/lib/CIME/provenance.py
index c6cb42594fe..f89f6a68c5d 100644
--- a/scripts/lib/CIME/provenance.py
+++ b/scripts/lib/CIME/provenance.py
@@ -470,6 +470,7 @@ def _save_prerun_timing_e3sm(case, lid):
             ) as fd:
                 fd.write("{}\n".format(syslog_jobid))
 
+
 def _cleanup_spio_stats(case):
     rundir = case.get_value("RUNDIR")
     for item in glob.glob(os.path.join(rundir, "io_perf_summary*")):
@@ -482,7 +483,12 @@ def _cleanup_spio_stats(case):
     try:
         os.makedirs(spio_stats_dir)
     except OSError:
-        logger.warning("{} could not be created. Scorpio I/O statistics will be stored in the run directory.".format(spio_stats_dir))
+        logger.warning(
+            "{} could not be created. Scorpio I/O statistics will be stored in the run directory.".format(
+                spio_stats_dir
+            )
+        )
+
 
 def _save_prerun_provenance_e3sm(case, lid):
     _cleanup_spio_stats(case)
diff --git a/scripts/lib/CIME/tests/scripts_regression_tests.py b/scripts/lib/CIME/tests/scripts_regression_tests.py
index 7e826cde0b0..160d2d08013 100755
--- a/scripts/lib/CIME/tests/scripts_regression_tests.py
+++ b/scripts/lib/CIME/tests/scripts_regression_tests.py
@@ -76,41 +76,74 @@ def cleanup(test_root):
 
 
 def setup_arguments(parser):
-    parser.add_argument("--fast", action="store_true",
-                        help="Skip full system tests, which saves a lot of time")
-
-    parser.add_argument("--no-batch", action="store_true",
-                        help="Do not submit jobs to batch system, run locally."
-                        " If false, will default to machine setting.")
-
-    parser.add_argument("--no-fortran-run", action="store_true",
-                        help="Do not run any fortran jobs. Implies --fast"
-                        " Used for github actions")
-
-    parser.add_argument("--no-cmake", action="store_true",
-                        help="Do not run cmake tests")
-
-    parser.add_argument("--no-teardown", action="store_true",
-                        help="Do not delete directories left behind by testing")
-
-    parser.add_argument("--machine",
-                        help="Select a specific machine setting for cime", default=None)
-
-    parser.add_argument("--compiler",
-                        help="Select a specific compiler setting for cime", default=None)
-
-    parser.add_argument( "--mpilib",
-                        help="Select a specific compiler setting for cime", default=None)
-
-    parser.add_argument( "--test-root",
-                        help="Select a specific test root for all cases created by the testing", default=None)
-
-    parser.add_argument("--timeout", type=int,
-                        help="Select a specific timeout for all tests", default=None)
-
-
-def configure_tests(timeout, no_fortran_run, fast, no_batch, no_cmake,
-                    no_teardown, machine, compiler, mpilib, test_root, **kwargs):
+    parser.add_argument(
+        "--fast",
+        action="store_true",
+        help="Skip full system tests, which saves a lot of time",
+    )
+
+    parser.add_argument(
+        "--no-batch",
+        action="store_true",
+        help="Do not submit jobs to batch system, run locally."
+        " If false, will default to machine setting.",
+    )
+
+    parser.add_argument(
+        "--no-fortran-run",
+        action="store_true",
+        help="Do not run any fortran jobs. Implies --fast" " Used for github actions",
+    )
+
+    parser.add_argument(
+        "--no-cmake", action="store_true", help="Do not run cmake tests"
+    )
+
+    parser.add_argument(
+        "--no-teardown",
+        action="store_true",
+        help="Do not delete directories left behind by testing",
+    )
+
+    parser.add_argument(
+        "--machine", help="Select a specific machine setting for cime", default=None
+    )
+
+    parser.add_argument(
+        "--compiler", help="Select a specific compiler setting for cime", default=None
+    )
+
+    parser.add_argument(
+        "--mpilib", help="Select a specific compiler setting for cime", default=None
+    )
+
+    parser.add_argument(
+        "--test-root",
+        help="Select a specific test root for all cases created by the testing",
+        default=None,
+    )
+
+    parser.add_argument(
+        "--timeout",
+        type=int,
+        help="Select a specific timeout for all tests",
+        default=None,
+    )
+
+
+def configure_tests(
+    timeout,
+    no_fortran_run,
+    fast,
+    no_batch,
+    no_cmake,
+    no_teardown,
+    machine,
+    compiler,
+    mpilib,
+    test_root,
+    **kwargs
+):
     config = CIME.utils.get_cime_config()
 
     if timeout:
@@ -177,8 +210,7 @@ def configure_tests(timeout, no_fortran_run, fast, no_batch, no_cmake,
 
 
 def _main_func(description):
-    help_str = \
-"""
+    help_str = """
 {0} [TEST] [TEST]
 OR
 {0} --help
@@ -192,25 +224,27 @@ def _main_func(description):
 
     \033[1;32m# Run test test_wait_for_test_all_pass from class M_TestWaitForTests \033[0m
     > {0} M_TestWaitForTests.test_wait_for_test_all_pass
-""".format(os.path.basename(sys.argv[0]))
+""".format(
+        os.path.basename(sys.argv[0])
+    )
 
-    parser = argparse.ArgumentParser(usage=help_str,
-                                     description=description,
-                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser = argparse.ArgumentParser(
+        usage=help_str,
+        description=description,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
 
     setup_arguments(parser)
 
-    parser.add_argument("--verbose", action="store_true",
-                        help="Enable verbose logging")
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose logging")
 
-    parser.add_argument("--debug", action="store_true",
-                        help="Enable debug logging")
+    parser.add_argument("--debug", action="store_true", help="Enable debug logging")
 
-    parser.add_argument("--silent", action="store_true",
-                        help="Disable all logging")
+    parser.add_argument("--silent", action="store_true", help="Disable all logging")
 
-    parser.add_argument("tests", nargs="*",
-                        help="Specific tests to run e.g. test_unit*")
+    parser.add_argument(
+        "tests", nargs="*", help="Specific tests to run e.g. test_unit*"
+    )
 
     ns, args = parser.parse_known_args()
 
diff --git a/scripts/lib/CIME/tests/test_sys_create_newcase.py b/scripts/lib/CIME/tests/test_sys_create_newcase.py
index 095e4ec0b3f..1d42fa620a6 100644
--- a/scripts/lib/CIME/tests/test_sys_create_newcase.py
+++ b/scripts/lib/CIME/tests/test_sys_create_newcase.py
@@ -162,8 +162,9 @@ def test_b_user_mods(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("%s/create_newcase %s "
-                              % (self.SCRIPT_DIR, args),from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "%s/create_newcase %s " % (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR
+        )
 
         self.assertTrue(
             os.path.isfile(
@@ -360,7 +361,9 @@ def test_f_createnewcase_with_user_compset(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("%s/create_newcase %s"%(self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "%s/create_newcase %s" % (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR
+        )
         self.run_cmd_assert_result("./case.setup", from_dir=testdir)
         self.run_cmd_assert_result("./case.build", from_dir=testdir)
 
@@ -387,12 +390,16 @@ def test_g_createnewcase_with_user_compset_and_env_mach_pes(self):
         if self.TEST_COMPILER is not None:
             args += " --compiler %s" % self.TEST_COMPILER
         if self.TEST_MPILIB is not None:
-            args +=  " --mpilib %s"%self.TEST_MPILIB
+            args += " --mpilib %s" % self.TEST_MPILIB
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("%s/create_newcase %s"%(self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR)
-        self.run_cmd_assert_result("diff env_mach_pes.xml %s"%(previous_testdir), from_dir=testdir)
+        self.run_cmd_assert_result(
+            "%s/create_newcase %s" % (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR
+        )
+        self.run_cmd_assert_result(
+            "diff env_mach_pes.xml %s" % (previous_testdir), from_dir=testdir
+        )
         # this line should cause the diff to fail (I assume no machine is going to default to 17 tasks)
         self.run_cmd_assert_result("./xmlchange NTASKS=17", from_dir=testdir)
         self.run_cmd_assert_result(
@@ -428,7 +435,9 @@ def test_h_primary_component(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("%s/create_newcase %s" % (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "%s/create_newcase %s" % (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR
+        )
         self.assertTrue(os.path.exists(testdir))
         self.assertTrue(os.path.exists(os.path.join(testdir, "case.setup")))
 
@@ -544,7 +553,10 @@ def test_j_createnewcase_user_compset_vs_alias(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("{}/create_newcase {}" .format (self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "{}/create_newcase {}".format(self.SCRIPT_DIR, args),
+            from_dir=self.SCRIPT_DIR,
+        )
         self.run_cmd_assert_result("./case.setup ", from_dir=testdir1)
         self.run_cmd_assert_result("./preview_namelists ", from_dir=testdir1)
 
@@ -582,7 +594,10 @@ def test_j_createnewcase_user_compset_vs_alias(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-        self.run_cmd_assert_result("{}/create_newcase {}".format(self.SCRIPT_DIR, args), from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "{}/create_newcase {}".format(self.SCRIPT_DIR, args),
+            from_dir=self.SCRIPT_DIR,
+        )
         self.run_cmd_assert_result("./case.setup ", from_dir=testdir2)
         self.run_cmd_assert_result("./preview_namelists ", from_dir=testdir2)
 
@@ -693,8 +708,9 @@ def test_ka_createnewcase_extra_machines_dir(self):
             args += " --res f19_g17 "
         else:
             args += " --res f19_g16 "
-        self.run_cmd_assert_result("./create_newcase {}".format(args),
-                              from_dir=self.SCRIPT_DIR)
+        self.run_cmd_assert_result(
+            "./create_newcase {}".format(args), from_dir=self.SCRIPT_DIR
+        )
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
@@ -784,9 +800,9 @@ def test_n_createnewcase_bad_compset(self):
 
         args += f" --machine {self.MACHINE.get_machine_name()}"
 
-
-        self.run_cmd_assert_result("./create_newcase %s"%(args),
-                              from_dir=self.SCRIPT_DIR, expected_stat=1)
+        self.run_cmd_assert_result(
+            "./create_newcase %s" % (args), from_dir=self.SCRIPT_DIR, expected_stat=1
+        )
         self.assertFalse(os.path.exists(testdir))
 
     @classmethod
diff --git a/scripts/lib/CIME/tests/test_sys_test_scheduler.py b/scripts/lib/CIME/tests/test_sys_test_scheduler.py
index 90419168388..977cce26f20 100755
--- a/scripts/lib/CIME/tests/test_sys_test_scheduler.py
+++ b/scripts/lib/CIME/tests/test_sys_test_scheduler.py
@@ -52,8 +52,14 @@ def test_a_phases(self):
             self._compiler,
         )
         self.assertEqual(len(tests), 3)
-        ct = test_scheduler.TestScheduler(tests, test_root=self._testroot, output_root=self._testroot,
-                           compiler=self._compiler, mpilib=self.TEST_MPILIB, machine_name=self.MACHINE.get_machine_name())
+        ct = test_scheduler.TestScheduler(
+            tests,
+            test_root=self._testroot,
+            output_root=self._testroot,
+            compiler=self._compiler,
+            mpilib=self.TEST_MPILIB,
+            machine_name=self.MACHINE.get_machine_name(),
+        )
 
         build_fail_test = [item for item in tests if "TESTBUILDFAIL" in item][0]
         run_fail_test = [item for item in tests if "TESTRUNFAIL" in item][0]
@@ -143,10 +149,20 @@ def test_a_phases(self):
                     self.assertTrue(ct._work_remains(test))
 
     def test_b_full(self):
-        tests = get_tests.get_full_test_names(["cime_test_only"], self._machine, self._compiler)
-        test_id="%s-%s" % (self._baseline_name, utils.get_timestamp())
-        ct = test_scheduler.TestScheduler(tests, test_id=test_id, no_batch=self.NO_BATCH, test_root=self._testroot,
-                           output_root=self._testroot,compiler=self._compiler, mpilib=self.TEST_MPILIB, machine_name=self.MACHINE.get_machine_name())
+        tests = get_tests.get_full_test_names(
+            ["cime_test_only"], self._machine, self._compiler
+        )
+        test_id = "%s-%s" % (self._baseline_name, utils.get_timestamp())
+        ct = test_scheduler.TestScheduler(
+            tests,
+            test_id=test_id,
+            no_batch=self.NO_BATCH,
+            test_root=self._testroot,
+            output_root=self._testroot,
+            compiler=self._compiler,
+            mpilib=self.TEST_MPILIB,
+            machine_name=self.MACHINE.get_machine_name(),
+        )
 
         build_fail_test = [item for item in tests if "TESTBUILDFAIL_" in item][0]
         build_fail_exc_test = [item for item in tests if "TESTBUILDFAILEXC" in item][0]
@@ -262,11 +278,26 @@ def test_b_full(self):
                     )
 
     def test_c_use_existing(self):
-        tests = get_tests.get_full_test_names(["TESTBUILDFAIL_P1.f19_g16_rx1.A", "TESTRUNFAIL_P1.f19_g16_rx1.A", "TESTRUNPASS_P1.f19_g16_rx1.A"],
-                                                      self._machine, self._compiler)
-        test_id="%s-%s" % (self._baseline_name, utils.get_timestamp())
-        ct = test_scheduler.TestScheduler(tests, test_id=test_id, no_batch=self.NO_BATCH, test_root=self._testroot,
-                           output_root=self._testroot,compiler=self._compiler, mpilib=self.TEST_MPILIB, machine_name=self.MACHINE.get_machine_name())
+        tests = get_tests.get_full_test_names(
+            [
+                "TESTBUILDFAIL_P1.f19_g16_rx1.A",
+                "TESTRUNFAIL_P1.f19_g16_rx1.A",
+                "TESTRUNPASS_P1.f19_g16_rx1.A",
+            ],
+            self._machine,
+            self._compiler,
+        )
+        test_id = "%s-%s" % (self._baseline_name, utils.get_timestamp())
+        ct = test_scheduler.TestScheduler(
+            tests,
+            test_id=test_id,
+            no_batch=self.NO_BATCH,
+            test_root=self._testroot,
+            output_root=self._testroot,
+            compiler=self._compiler,
+            mpilib=self.TEST_MPILIB,
+            machine_name=self.MACHINE.get_machine_name(),
+        )
 
         build_fail_test = [item for item in tests if "TESTBUILDFAIL" in item][0]
         run_fail_test = [item for item in tests if "TESTRUNFAIL" in item][0]
@@ -327,9 +358,17 @@ def test_c_use_existing(self):
 
         os.environ["TESTBUILDFAIL_PASS"] = "True"
         os.environ["TESTRUNFAIL_PASS"] = "True"
-        ct2 = test_scheduler.TestScheduler(tests, test_id=test_id, no_batch=self.NO_BATCH, use_existing=True,
-                            test_root=self._testroot,output_root=self._testroot,compiler=self._compiler,
-                            mpilib=self.TEST_MPILIB, machine_name=self.MACHINE.get_machine_name())
+        ct2 = test_scheduler.TestScheduler(
+            tests,
+            test_id=test_id,
+            no_batch=self.NO_BATCH,
+            use_existing=True,
+            test_root=self._testroot,
+            output_root=self._testroot,
+            compiler=self._compiler,
+            mpilib=self.TEST_MPILIB,
+            machine_name=self.MACHINE.get_machine_name(),
+        )
 
         log_lvl = logging.getLogger().getEffectiveLevel()
         logging.disable(logging.CRITICAL)
@@ -361,9 +400,17 @@ def test_c_use_existing(self):
 
         # test that passed tests are not re-run
 
-        ct2 = test_scheduler.TestScheduler(tests, test_id=test_id, no_batch=self.NO_BATCH, use_existing=True,
-                            test_root=self._testroot,output_root=self._testroot,compiler=self._compiler,
-                            mpilib=self.TEST_MPILIB, machine_name=self.MACHINE.get_machine_name())
+        ct2 = test_scheduler.TestScheduler(
+            tests,
+            test_id=test_id,
+            no_batch=self.NO_BATCH,
+            use_existing=True,
+            test_root=self._testroot,
+            output_root=self._testroot,
+            compiler=self._compiler,
+            mpilib=self.TEST_MPILIB,
+            machine_name=self.MACHINE.get_machine_name(),
+        )
 
         log_lvl = logging.getLogger().getEffectiveLevel()
         logging.disable(logging.CRITICAL)
@@ -391,7 +438,12 @@ def test_c_use_existing(self):
             )
 
     def test_d_retry(self):
-        args = ["TESTBUILDFAIL_P1.f19_g16_rx1.A", "TESTRUNFAILRESET_P1.f19_g16_rx1.A", "TESTRUNPASS_P1.f19_g16_rx1.A", "--retry=1"]
+        args = [
+            "TESTBUILDFAIL_P1.f19_g16_rx1.A",
+            "TESTRUNFAILRESET_P1.f19_g16_rx1.A",
+            "TESTRUNPASS_P1.f19_g16_rx1.A",
+            "--retry=1",
+        ]
 
         self._create_test(args)
 
diff --git a/scripts/lib/CIME/tests/test_sys_unittest.py b/scripts/lib/CIME/tests/test_sys_unittest.py
index 4fa51780ad6..e95695093b8 100644
--- a/scripts/lib/CIME/tests/test_sys_unittest.py
+++ b/scripts/lib/CIME/tests/test_sys_unittest.py
@@ -80,7 +80,11 @@ def test_b_cime_f90_unit_tests(self):
 
     @classmethod
     def tearDownClass(cls):
-        do_teardown = len(cls._do_teardown) > 0 and sys.exc_info() == (None, None, None) and not cls.NO_TEARDOWN
+        do_teardown = (
+            len(cls._do_teardown) > 0
+            and sys.exc_info() == (None, None, None)
+            and not cls.NO_TEARDOWN
+        )
         del os.environ["CIME_NO_CMAKE_MACRO"]
 
         teardown_root = True
diff --git a/scripts/lib/CIME/tests/test_unit_user_nl_utils.py b/scripts/lib/CIME/tests/test_unit_user_nl_utils.py
index ceebde32ec6..fcd6e067f0b 100755
--- a/scripts/lib/CIME/tests/test_unit_user_nl_utils.py
+++ b/scripts/lib/CIME/tests/test_unit_user_nl_utils.py
@@ -7,6 +7,7 @@
 from CIME.SystemTests.test_utils import user_nl_utils
 import six
 
+
 class TestUserNLCopier(unittest.TestCase):
 
     # ========================================================================
@@ -19,7 +20,7 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._caseroot, ignore_errors=True)
 
-    def write_user_nl_file(self, component, contents, suffix=''):
+    def write_user_nl_file(self, component, contents, suffix=""):
         """Write contents to a user_nl file in the case directory. Returns the
         basename (i.e., not the full path) of the file that is created.
 
@@ -29,9 +30,9 @@ def write_user_nl_file(self, component, contents, suffix=''):
         If the suffix is '_0001', the file name will be user_nl_foo_0001
         """
 
-        filename = 'user_nl_' + component + suffix
+        filename = "user_nl_" + component + suffix
 
-        with open(os.path.join(self._caseroot, filename), 'w') as user_nl_file:
+        with open(os.path.join(self._caseroot, filename), "w") as user_nl_file:
             user_nl_file.write(contents)
 
         return filename
@@ -41,7 +42,7 @@ def assertFileContentsEqual(self, expected, filepath, msg=None):
         the string given by 'expected'. 'msg' gives an optional message to be
         printed if the assertion fails."""
 
-        with open(filepath, 'r') as myfile:
+        with open(filepath, "r") as myfile:
             contents = myfile.read()
 
         self.assertEqual(expected, contents, msg=msg)
@@ -52,68 +53,75 @@ def assertFileContentsEqual(self, expected, filepath, msg=None):
 
     def test_append(self):
         # Define some variables
-        component = 'foo'
+        component = "foo"
         # deliberately exclude new line from file contents, to make sure that's
         # handled correctly
-        orig_contents = 'bar = 42'
-        contents_to_append = 'baz = 101'
+        orig_contents = "bar = 42"
+        contents_to_append = "baz = 101"
 
         # Setup
         filename = self.write_user_nl_file(component, orig_contents)
 
         # Exercise
-        user_nl_utils.append_to_user_nl_files(caseroot = self._caseroot,
-                                              component = component,
-                                              contents = contents_to_append)
+        user_nl_utils.append_to_user_nl_files(
+            caseroot=self._caseroot, component=component, contents=contents_to_append
+        )
 
         # Verify
-        expected_contents = orig_contents + '\n' + contents_to_append + '\n'
-        self.assertFileContentsEqual(expected_contents,
-                                     os.path.join(self._caseroot, filename))
+        expected_contents = orig_contents + "\n" + contents_to_append + "\n"
+        self.assertFileContentsEqual(
+            expected_contents, os.path.join(self._caseroot, filename)
+        )
 
     def test_append_multiple_files(self):
         # Simulates a multi-instance test
-        component = 'foo'
-        orig_contents1 = 'bar = 42'
-        orig_contents2 = 'bar = 17'
-        contents_to_append = 'baz = 101'
+        component = "foo"
+        orig_contents1 = "bar = 42"
+        orig_contents2 = "bar = 17"
+        contents_to_append = "baz = 101"
 
         # Setup
-        filename1 = self.write_user_nl_file(component, orig_contents1, suffix='_0001')
-        filename2 = self.write_user_nl_file(component, orig_contents2, suffix='_0002')
+        filename1 = self.write_user_nl_file(component, orig_contents1, suffix="_0001")
+        filename2 = self.write_user_nl_file(component, orig_contents2, suffix="_0002")
 
         # Exercise
-        user_nl_utils.append_to_user_nl_files(caseroot = self._caseroot,
-                                              component = component,
-                                              contents = contents_to_append)
+        user_nl_utils.append_to_user_nl_files(
+            caseroot=self._caseroot, component=component, contents=contents_to_append
+        )
 
         # Verify
-        expected_contents1 = orig_contents1 + '\n' + contents_to_append + '\n'
-        expected_contents2 = orig_contents2 + '\n' + contents_to_append + '\n'
-        self.assertFileContentsEqual(expected_contents1,
-                                     os.path.join(self._caseroot, filename1))
-        self.assertFileContentsEqual(expected_contents2,
-                                     os.path.join(self._caseroot, filename2))
-
+        expected_contents1 = orig_contents1 + "\n" + contents_to_append + "\n"
+        expected_contents2 = orig_contents2 + "\n" + contents_to_append + "\n"
+        self.assertFileContentsEqual(
+            expected_contents1, os.path.join(self._caseroot, filename1)
+        )
+        self.assertFileContentsEqual(
+            expected_contents2, os.path.join(self._caseroot, filename2)
+        )
 
     def test_append_without_files_raises_exception(self):
         # This test verifies that you get an exception if you call
         # append_to_user_nl_files when there are no user_nl files of interest
 
         # Define some variables
-        component_exists = 'foo'
-        component_for_append = 'bar'
+        component_exists = "foo"
+        component_for_append = "bar"
 
         # Setup
         # Create file in caseroot for component_exists, but not for component_for_append
-        self.write_user_nl_file(component_exists, 'irrelevant contents')
+        self.write_user_nl_file(component_exists, "irrelevant contents")
 
         # Exercise & verify
-        six.assertRaisesRegex(self, RuntimeError, "No user_nl files found",
-                                user_nl_utils.append_to_user_nl_files,
-                                caseroot = self._caseroot,
-                                component = component_for_append,
-                                contents = 'irrelevant contents to append')
-
-if __name__ == '__main__':
+        six.assertRaisesRegex(
+            self,
+            RuntimeError,
+            "No user_nl files found",
+            user_nl_utils.append_to_user_nl_files,
+            caseroot=self._caseroot,
+            component=component_for_append,
+            contents="irrelevant contents to append",
+        )
+
+
+if __name__ == "__main__":
     unittest.main()
diff --git a/scripts/lib/CIME/utils.py b/scripts/lib/CIME/utils.py
index c92d8e6550e..992c2339d7b 100644
--- a/scripts/lib/CIME/utils.py
+++ b/scripts/lib/CIME/utils.py
@@ -156,7 +156,8 @@ def expect(condition, error_msg, exc_type=CIMEError, error_prefix="ERROR:"):
     if not condition:
         if logger.isEnabledFor(logging.DEBUG):
             import pdb
-            pdb.set_trace() # pylint: disable=forgotten-debug-statement
+
+            pdb.set_trace()  # pylint: disable=forgotten-debug-statement
 
         msg = error_prefix + " " + error_msg
         raise exc_type(msg)
@@ -1502,12 +1503,13 @@ def filter(self, record):
         # non-zero return means we log this message
         return 1 if record.levelno < self.max_level else 0
 
+
 def configure_logging(verbose, debug, silent):
     root_logger = logging.getLogger()
 
     verbose_formatter = logging.Formatter(
-        fmt='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
-        datefmt='%m-%d %H:%M')
+        fmt="%(asctime)s %(name)-12s %(levelname)-8s %(message)s", datefmt="%m-%d %H:%M"
+    )
 
     # Change info to go to stdout. This handle applies to INFO exclusively
     stdout_stream_handler = logging.StreamHandler(stream=sys.stdout)
@@ -1541,6 +1543,7 @@ def configure_logging(verbose, debug, silent):
     else:
         root_logger.setLevel(logging.INFO)
 
+
 def parse_args_and_handle_standard_logging_options(args, parser=None):
     """
     Guide to logging in CIME.
diff --git a/setup.cfg b/setup.cfg
index 185f292e02d..67b0aa86e0c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,7 +2,7 @@
 junit_family=xunit2
 addopts = --cov=CIME --cov-report term-missing --cov-report html:test_coverage/html --cov-report xml:test_coverage/coverage.xml -s
 python_files = test_*.py
-testpaths = 
+testpaths =
     scripts/lib/CIME/tests
 
 [coverage:report]
diff --git a/src/build_scripts/buildlib.gptl b/src/build_scripts/buildlib.gptl
index 3537957c3f9..14d84ef2329 100755
--- a/src/build_scripts/buildlib.gptl
+++ b/src/build_scripts/buildlib.gptl
@@ -52,16 +52,13 @@ def buildlib(bldroot, installpath, case):
     comp_interface = case.get_value("COMP_INTERFACE")
 
     gptl_dir = os.path.join(case.get_value("CIMEROOT"), "src", "share", "timing")
-    gmake_opts = (
-        "-f {gptl}/Makefile install -C {bldroot} MACFILE={macfile} COMP_NAME=gptl GPTL_DIR={gptl} GPTL_LIBDIR={bldroot}"
-        " SHAREDPATH={install} COMP_INTERFACE={comp_interface} {stdargs} ".format(
-            gptl=gptl_dir,
-            bldroot=bldroot,
-            macfile=os.path.join(caseroot, "Macros.make"),
-            install=installpath,
-            comp_interface=comp_interface,
-            stdargs=get_standard_makefile_args(case, shared_lib=True),
-        )
+    gmake_opts = "-f {gptl}/Makefile install -C {bldroot} MACFILE={macfile} COMP_NAME=gptl GPTL_DIR={gptl} GPTL_LIBDIR={bldroot}" " SHAREDPATH={install} COMP_INTERFACE={comp_interface} {stdargs} ".format(
+        gptl=gptl_dir,
+        bldroot=bldroot,
+        macfile=os.path.join(caseroot, "Macros.make"),
+        install=installpath,
+        comp_interface=comp_interface,
+        stdargs=get_standard_makefile_args(case, shared_lib=True),
     )
 
     gmake_cmd = case.get_value("GMAKE")