From 15618e6b2f37cf9ca3fa378a2f090d194ef19e15 Mon Sep 17 00:00:00 2001
From: Christopher Sherman <sherman27@llnl.gov>
Date: Mon, 22 Jan 2024 16:01:04 -0800
Subject: [PATCH] Appyling yapf

---
 geos_ats_package/geos_ats/common_utilities.py |  2 +-
 .../geos_ats/configuration_record.py          |  4 +--
 .../geos_ats/helpers/permute_array.py         |  2 +-
 .../geos_ats/helpers/restart_check.py         | 10 +++----
 .../geos_ats/machines/batchGeosatsMoab.py     |  4 +--
 .../geos_ats/machines/bgqos_0_ASQ.py          |  6 ++--
 geos_ats_package/geos_ats/machines/darwin.py  |  2 +-
 .../geosAtsSlurmProcessorScheduled.py         |  2 +-
 geos_ats_package/geos_ats/machines/lassen.py  |  4 +--
 geos_ats_package/geos_ats/machines/nersc.py   |  2 +-
 geos_ats_package/geos_ats/machines/openmpi.py |  4 +--
 geos_ats_package/geos_ats/machines/summit.py  |  4 +--
 geos_ats_package/geos_ats/main.py             |  2 +-
 geos_ats_package/geos_ats/reporting.py        | 28 ++++++++++++-------
 geos_ats_package/geos_ats/scheduler.py        |  6 ++--
 geos_ats_package/geos_ats/suite_settings.py   |  2 +-
 geos_ats_package/geos_ats/test_case.py        |  8 +++---
 geos_ats_package/geos_ats/test_modifier.py    |  2 +-
 geos_ats_package/geos_ats/test_steps.py       |  8 +++---
 geos_ats_package/geos_ats/user_utilities.py   |  2 +-
 20 files changed, 56 insertions(+), 48 deletions(-)

diff --git a/geos_ats_package/geos_ats/common_utilities.py b/geos_ats_package/geos_ats/common_utilities.py
index 0ad4ad8..7543df1 100644
--- a/geos_ats_package/geos_ats/common_utilities.py
+++ b/geos_ats_package/geos_ats/common_utilities.py
@@ -18,7 +18,7 @@ def Error(msg):
 
 
 def Log(msg):
-    import ats    # type: ignore[import]
+    import ats  # type: ignore[import]
     testmode = False
     try:
         testmode = ats.tests.AtsTest.getOptions().get("testmode")
diff --git a/geos_ats_package/geos_ats/configuration_record.py b/geos_ats_package/geos_ats/configuration_record.py
index 8d251c5..1d0291d 100644
--- a/geos_ats_package/geos_ats/configuration_record.py
+++ b/geos_ats_package/geos_ats/configuration_record.py
@@ -90,7 +90,7 @@ def __getattr__(self, name):
 # The global config object
 config = Config()
 # Global testTimings object
-globalTestTimings = {}    # type: ignore[var-annotated]
+globalTestTimings = {}  # type: ignore[var-annotated]
 # Depth of testconfig recursion
 configDepth = 0
 
@@ -98,7 +98,7 @@ def __getattr__(self, name):
 def infoConfigShow(public, outfile=sys.stdout):
     topic = InfoTopic("config show", outfile)
     topic.startBanner()
-    import ats    # type: ignore[import]
+    import ats  # type: ignore[import]
 
     keys = sorted(config._items.keys())
     table = TextTable(3)
diff --git a/geos_ats_package/geos_ats/helpers/permute_array.py b/geos_ats_package/geos_ats/helpers/permute_array.py
index bbc9491..6f0bfcb 100644
--- a/geos_ats_package/geos_ats/helpers/permute_array.py
+++ b/geos_ats_package/geos_ats/helpers/permute_array.py
@@ -1,4 +1,4 @@
-import numpy as np    # type: ignore[import]
+import numpy as np  # type: ignore[import]
 import logging
 
 logger = logging.getLogger('geos_ats')
diff --git a/geos_ats_package/geos_ats/helpers/restart_check.py b/geos_ats_package/geos_ats/helpers/restart_check.py
index 261c3bf..d449e42 100644
--- a/geos_ats_package/geos_ats/helpers/restart_check.py
+++ b/geos_ats_package/geos_ats/helpers/restart_check.py
@@ -1,6 +1,6 @@
-import h5py    # type: ignore[import]
-from mpi4py import MPI    # type: ignore[import]
-import numpy as np    # type: ignore[import]
+import h5py  # type: ignore[import]
+from mpi4py import MPI  # type: ignore[import]
+import numpy as np  # type: ignore[import]
 import sys
 import os
 import re
@@ -8,10 +8,10 @@
 import logging
 from pathlib import Path
 try:
-    from geos_ats.helpers.permute_array import permuteArray    # type: ignore[import]
+    from geos_ats.helpers.permute_array import permuteArray  # type: ignore[import]
 except ImportError:
     # Fallback method to be used if geos_ats isn't found
-    from permute_array import permuteArray    # type: ignore[import]
+    from permute_array import permuteArray  # type: ignore[import]
 
 RTOL_DEFAULT = 0.0
 ATOL_DEFAULT = 0.0
diff --git a/geos_ats_package/geos_ats/machines/batchGeosatsMoab.py b/geos_ats_package/geos_ats/machines/batchGeosatsMoab.py
index bc5747d..e2bb4e7 100644
--- a/geos_ats_package/geos_ats/machines/batchGeosatsMoab.py
+++ b/geos_ats_package/geos_ats/machines/batchGeosatsMoab.py
@@ -1,9 +1,9 @@
 #BATS:batchGeosatsMoab  batchGeosatsMoab BatchGeosatsMoab -1
 
-from ats import machines, configuration, log, atsut, times, AtsTest    # type: ignore[import]
+from ats import machines, configuration, log, atsut, times, AtsTest  # type: ignore[import]
 import subprocess, sys, os, time, socket, re
 import utils  # type: ignore[import]
-from batch import BatchMachine    # type: ignore[import]
+from batch import BatchMachine  # type: ignore[import]
 import logging
 
 debug = configuration.debug
diff --git a/geos_ats_package/geos_ats/machines/bgqos_0_ASQ.py b/geos_ats_package/geos_ats/machines/bgqos_0_ASQ.py
index 6c470db..a761ea0 100644
--- a/geos_ats_package/geos_ats/machines/bgqos_0_ASQ.py
+++ b/geos_ats_package/geos_ats/machines/bgqos_0_ASQ.py
@@ -1,10 +1,10 @@
 #ATS:bgqos_0_ASQ machines.bgqos_0_ASQ bgqos_0_ASQMachine 16
 
-from ats import machines, debug, atsut    # type: ignore[import]
+from ats import machines, debug, atsut  # type: ignore[import]
 from ats import log, terminal
 from ats import configuration
-from ats.atsut import RUNNING, TIMEDOUT, SKIPPED, BATCHED, INVALID, PASSED, FAILED, CREATED, FILTERED, HALTED, EXPECTED    # type: ignore[import]
-import utils    # type: ignore[import]
+from ats.atsut import RUNNING, TIMEDOUT, SKIPPED, BATCHED, INVALID, PASSED, FAILED, CREATED, FILTERED, HALTED, EXPECTED  # type: ignore[import]
+import utils  # type: ignore[import]
 import time
 import sys
 
diff --git a/geos_ats_package/geos_ats/machines/darwin.py b/geos_ats_package/geos_ats/machines/darwin.py
index af7b8b5..952c345 100644
--- a/geos_ats_package/geos_ats/machines/darwin.py
+++ b/geos_ats_package/geos_ats/machines/darwin.py
@@ -1,6 +1,6 @@
 #ATS:darwin machines.darwin DarwinMachine 16
 
-from openmpi import OpenmpiMachine    # type: ignore[import]
+from openmpi import OpenmpiMachine  # type: ignore[import]
 
 
 class DarwinMachine(OpenmpiMachine):
diff --git a/geos_ats_package/geos_ats/machines/geosAtsSlurmProcessorScheduled.py b/geos_ats_package/geos_ats/machines/geosAtsSlurmProcessorScheduled.py
index 1770402..4ac3091 100644
--- a/geos_ats_package/geos_ats/machines/geosAtsSlurmProcessorScheduled.py
+++ b/geos_ats_package/geos_ats/machines/geosAtsSlurmProcessorScheduled.py
@@ -8,7 +8,7 @@
 
 from geos_ats.scheduler import scheduler
 from geos_ats.machine_utilities import CheckForEarlyTimeOut
-from slurmProcessorScheduled import SlurmProcessorScheduled    # type: ignore[import]
+from slurmProcessorScheduled import SlurmProcessorScheduled  # type: ignore[import]
 import subprocess
 import logging
 
diff --git a/geos_ats_package/geos_ats/machines/lassen.py b/geos_ats_package/geos_ats/machines/lassen.py
index 1bdd93b..6430ee6 100644
--- a/geos_ats_package/geos_ats/machines/lassen.py
+++ b/geos_ats_package/geos_ats/machines/lassen.py
@@ -1,11 +1,11 @@
 #ATS:SequentialMachine  SELF lassenMachine  1
 #ATS:lassen           SELF lassenMachine   1
 
-from ats import machines    # type: ignore[import]
+from ats import machines  # type: ignore[import]
 from ats import machines, debug, atsut
 from ats import log, terminal
 from ats import configuration
-from ats.atsut import RUNNING, TIMEDOUT    # type: ignore[import]
+from ats.atsut import RUNNING, TIMEDOUT  # type: ignore[import]
 from ats import AtsTest
 import os
 import subprocess
diff --git a/geos_ats_package/geos_ats/machines/nersc.py b/geos_ats_package/geos_ats/machines/nersc.py
index 1eb2443..0cd4327 100644
--- a/geos_ats_package/geos_ats/machines/nersc.py
+++ b/geos_ats_package/geos_ats/machines/nersc.py
@@ -8,7 +8,7 @@
 
 from geos_ats.scheduler import scheduler
 from geos_ats.machine_utilities import CheckForEarlyTimeOut
-from slurmProcessorScheduled import SlurmProcessorScheduled    # type: ignore[import]
+from slurmProcessorScheduled import SlurmProcessorScheduled  # type: ignore[import]
 import subprocess
 import logging
 
diff --git a/geos_ats_package/geos_ats/machines/openmpi.py b/geos_ats_package/geos_ats/machines/openmpi.py
index 842564d..6ddf0fb 100644
--- a/geos_ats_package/geos_ats/machines/openmpi.py
+++ b/geos_ats_package/geos_ats/machines/openmpi.py
@@ -1,12 +1,12 @@
 #ATS:openmpi machines.openmpi OpenmpiMachine 16
 
 import os
-import ats    # type: ignore[import]
+import ats  # type: ignore[import]
 from ats import machines
 from ats import terminal
 from ats import log
 import shlex
-from ats.atsut import RUNNING, TIMEDOUT    # type: ignore[import]
+from ats.atsut import RUNNING, TIMEDOUT  # type: ignore[import]
 from ats import AtsTest
 import logging
 
diff --git a/geos_ats_package/geos_ats/machines/summit.py b/geos_ats_package/geos_ats/machines/summit.py
index 07b2c58..1d7b751 100644
--- a/geos_ats_package/geos_ats/machines/summit.py
+++ b/geos_ats_package/geos_ats/machines/summit.py
@@ -1,11 +1,11 @@
 #ATS:SequentialMachine machines.summit summitMachine  1
 #ATS:summit            machines.summit summitMachine  1
 
-from ats import machines    # type: ignore[import]
+from ats import machines  # type: ignore[import]
 from ats import machines, debug, atsut
 from ats import log, terminal
 from ats import configuration
-from ats.atsut import RUNNING, TIMEDOUT    # type: ignore[import]
+from ats.atsut import RUNNING, TIMEDOUT  # type: ignore[import]
 from ats import AtsTest
 import os
 import subprocess
diff --git a/geos_ats_package/geos_ats/main.py b/geos_ats_package/geos_ats/main.py
index b22af5b..033d0f5 100644
--- a/geos_ats_package/geos_ats/main.py
+++ b/geos_ats_package/geos_ats/main.py
@@ -327,7 +327,7 @@ def main():
     geos_atsStartTime = time.time()
 
     # Note: the sys.argv is read here by default
-    import ats    # type: ignore[import]
+    import ats  # type: ignore[import]
     ats.manager.init()
     logger.debug('Copying options to the geos_ats config record file')
     config.copy_values(ats.manager.machine)
diff --git a/geos_ats_package/geos_ats/reporting.py b/geos_ats_package/geos_ats/reporting.py
index 633f5dd..1b35a0e 100644
--- a/geos_ats_package/geos_ats/reporting.py
+++ b/geos_ats_package/geos_ats/reporting.py
@@ -7,15 +7,13 @@
 import glob
 import logging
 from ats.times import hms
-from ats import (PASSED, FAILED, TIMEDOUT, EXPECTED, BATCHED, FILTERED,
-                 SKIPPED, CREATED, RUNNING, HALTED, LSFERROR)
+from ats import (PASSED, FAILED, TIMEDOUT, EXPECTED, BATCHED, FILTERED, SKIPPED, CREATED, RUNNING, HALTED, LSFERROR)
 
 # Get the active logger instance
 logger = logging.getLogger('geos_ats')
 
 # Status value in priority order
-STATUS = (EXPECTED, CREATED, BATCHED, FILTERED, SKIPPED, RUNNING,
-          PASSED, TIMEDOUT, HALTED, LSFERROR, FAILED)
+STATUS = (EXPECTED, CREATED, BATCHED, FILTERED, SKIPPED, RUNNING, PASSED, TIMEDOUT, HALTED, LSFERROR, FAILED)
 
 COLORS = {}
 COLORS[EXPECTED.name] = "black"
@@ -47,15 +45,27 @@ def __init__(self, test_steps):
 
         for t in test_steps:
             # Parse the test step name
-            step_name = t.name[t.name.find('(')+1:t.name.rfind('_')]
+            step_name = t.name[t.name.find('(') + 1:t.name.rfind('_')]
             test_name = step_name[:step_name.rfind('_')]
             test_id = t.group.number
             group_name = test_name[:test_name.rfind('_')]
 
             # Save data
             if test_name not in self.test_results:
-                self.test_results[test_name] = {'steps': {}, 'status': EXPECTED, 'id': test_id, 'elapsed': 0.0, 'current_step': ' ', 'resources': t.np}
-            self.test_results[test_name]['steps'][t.name] = {'status': t.status, 'log': t.outname, 'output': t.step_outputs, 'number': t.groupSerialNumber}
+                self.test_results[test_name] = {
+                    'steps': {},
+                    'status': EXPECTED,
+                    'id': test_id,
+                    'elapsed': 0.0,
+                    'current_step': ' ',
+                    'resources': t.np
+                }
+            self.test_results[test_name]['steps'][t.name] = {
+                'status': t.status,
+                'log': t.outname,
+                'output': t.step_outputs,
+                'number': t.groupSerialNumber
+            }
 
             # Check elapsed time
             elapsed = 0.0
@@ -207,9 +217,7 @@ def writeHeader(self, sp, refresh):
             username = os.getenv("USER")
 
         header += "<h1>GEOS ATS Report</h1>\n<h2>Configuration</h2>\n"
-        table = [['Test Results', gentime],
-                 ['User', username],
-                 ['Platform', platform]]
+        table = [['Test Results', gentime], ['User', username], ['Platform', platform]]
         header += tabulate(table, tablefmt='html')
         header += '\n'
         sp.write(header)
diff --git a/geos_ats_package/geos_ats/scheduler.py b/geos_ats_package/geos_ats/scheduler.py
index 108deab..b7cf544 100644
--- a/geos_ats_package/geos_ats/scheduler.py
+++ b/geos_ats_package/geos_ats/scheduler.py
@@ -4,9 +4,9 @@
 import time
 from geos_ats.configuration_record import config
 from geos_ats.common_utilities import Log
-from ats.log import log    # type: ignore[import]
-from ats.atsut import PASSED, FAILED, CREATED, EXPECTED, TIMEDOUT    # type: ignore[import]
-from ats.schedulers import StandardScheduler    # type: ignore[import]
+from ats.log import log  # type: ignore[import]
+from ats.atsut import PASSED, FAILED, CREATED, EXPECTED, TIMEDOUT  # type: ignore[import]
+from ats.schedulers import StandardScheduler  # type: ignore[import]
 
 
 class GeosAtsScheduler(StandardScheduler):
diff --git a/geos_ats_package/geos_ats/suite_settings.py b/geos_ats_package/geos_ats/suite_settings.py
index 824079f..594bc51 100644
--- a/geos_ats_package/geos_ats/suite_settings.py
+++ b/geos_ats_package/geos_ats/suite_settings.py
@@ -3,7 +3,7 @@
 
 testLabels = [
     "geos",
-    "auto",    # label used when the tests were automatically converted.  Will be deprecated.
+    "auto",  # label used when the tests were automatically converted.  Will be deprecated.
 ]
 
 testOwners = [("corbett5", "Ben Corbett")]
diff --git a/geos_ats_package/geos_ats/test_case.py b/geos_ats_package/geos_ats/test_case.py
index a7a751a..2a43658 100644
--- a/geos_ats_package/geos_ats/test_case.py
+++ b/geos_ats_package/geos_ats/test_case.py
@@ -1,4 +1,4 @@
-import ats    # type: ignore[import]
+import ats  # type: ignore[import]
 import os
 import shutil
 import logging
@@ -33,8 +33,8 @@ def __init__(self, enabled=True, duration="1h", ppn=0, altname=None):
             logger.error(e)
             Error("bad time specification: %s" % duration)
 
-        self.ppn = ppn    # processor per node
-        self.altname = altname    # alternate name to use when launcing the batch job
+        self.ppn = ppn  # processor per node
+        self.altname = altname  # alternate name to use when launcing the batch job
 
 
 class TestCase(object):
@@ -263,7 +263,7 @@ def _remove(path):
                         else:
                             os.remove(p)
                     except OSError:
-                        pass    # so that two simultaneous clean operations don't fail
+                        pass  # so that two simultaneous clean operations don't fail
 
         # clean
         self.testClean()
diff --git a/geos_ats_package/geos_ats/test_modifier.py b/geos_ats_package/geos_ats/test_modifier.py
index c6d7cb2..b625be4 100644
--- a/geos_ats_package/geos_ats/test_modifier.py
+++ b/geos_ats_package/geos_ats/test_modifier.py
@@ -1,4 +1,4 @@
-import ats    # type: ignore[import]
+import ats  # type: ignore[import]
 from geos_ats import common_utilities
 from geos_ats.configuration_record import config
 from geos_ats import test_steps
diff --git a/geos_ats_package/geos_ats/test_steps.py b/geos_ats_package/geos_ats/test_steps.py
index b1aa190..3f471de 100644
--- a/geos_ats_package/geos_ats/test_steps.py
+++ b/geos_ats_package/geos_ats/test_steps.py
@@ -1,5 +1,5 @@
 import os
-import ats    # type: ignore[import]
+import ats  # type: ignore[import]
 import glob
 import shutil
 import sys
@@ -265,7 +265,7 @@ def _remove(self, paths, noclean):
                         else:
                             os.remove(p)
                     except OSError as e:
-                        logger.debug(e)    # so that two simultaneous clean operations don't fail
+                        logger.debug(e)  # so that two simultaneous clean operations don't fail
 
     def getCheckOption(self):
         return ats.tests.AtsTest.getOptions().get("checkoption")
@@ -388,8 +388,8 @@ class geos(TestStepBase):
     params = TestStepBase.defaultParams + (
         TestStepBase.commonParams["name"], TestStepBase.commonParams["deck"], TestStepBase.commonParams["np"],
         TestStepBase.commonParams["ngpu"], TestStepBase.commonParams["check"],
-        TestStepBase.commonParams["test_directory"], TestStepBase.commonParams["baseline_directory"], TestStepBase.commonParams["output_directory"],
-        TestParam("restart_file", "The name of the restart file."),
+        TestStepBase.commonParams["test_directory"], TestStepBase.commonParams["baseline_directory"],
+        TestStepBase.commonParams["output_directory"], TestParam("restart_file", "The name of the restart file."),
         TestParam("x_partitions", "The number of partitions in the x direction."),
         TestParam("y_partitions", "The number of partitions in the y direction."),
         TestParam("z_partitions",
diff --git a/geos_ats_package/geos_ats/user_utilities.py b/geos_ats_package/geos_ats/user_utilities.py
index 775e3a1..24ebd89 100644
--- a/geos_ats_package/geos_ats/user_utilities.py
+++ b/geos_ats_package/geos_ats/user_utilities.py
@@ -1,4 +1,4 @@
-import ats    # type: ignore[import]
+import ats  # type: ignore[import]
 import os