types and cleanups

src/toil/batchSystems/singleMachine.py

@@ -405,8 +405,14 @@ def _runDebugJob(self, jobCommand, jobID, environment):
             # We can actually run in this thread
             jobName, jobStoreLocator, jobStoreID = jobCommand.split()[1:4] # Parse command
             jobStore = Toil.resumeJobStore(jobStoreLocator)
-            toil_worker.workerScript(jobStore, jobStore.config, jobName, jobStoreID, None,
-                                     redirectOutputToLogFile=not self.debugWorker) # Call the worker
+            toil_worker.workerScript(
+                jobStore,
+                jobStore.config,
+                jobName,
+                jobStoreID,
+                None,
+                redirectOutputToLogFile=not self.debugWorker,
+            )  # Call the worker
         else:
             # Run synchronously. If starting or running the command fails, let the exception stop us.
             subprocess.check_call(jobCommand,

src/toil/leader.py

@@ -664,8 +664,8 @@ def innerLoop(self):
 
         # Consistency check the toil state
         assert self.toilState.updatedJobs == {}
-        #assert self.toilState.successorCounts == {}
-        #assert self.toilState.successorJobStoreIDToPredecessorJobs == {}
+        # assert self.toilState.successorCounts == {}
+        # assert self.toilState.successorJobStoreIDToPredecessorJobs == {}
         assert self.toilState.serviceJobStoreIDToPredecessorJob == {}
         assert self.toilState.servicesIssued == {}
         # assert self.toilState.jobsToBeScheduledWithMultiplePredecessors # These are not properly emptied yet
@@ -749,17 +749,22 @@ def issueJob(self, jobNode):
         for context in self.batchSystem.getWorkerContexts():
             # For each context manager hook the batch system wants to run in
             # the worker, serialize and send it.
-            workerCommand.append('--context')
-            workerCommand.append(base64.b64encode(pickle.dumps(context)).decode('utf-8'))
+            workerCommand.append("--context")
+            workerCommand.append(
+                base64.b64encode(pickle.dumps(context)).decode("utf-8")
+            )
 
         # add the toilState as a pickle
-        workerCommand.append('--toilState')
-        workerCommand.append(base64.b64encode(pickle.dumps(self.toilState)).decode('utf-8'))
-
-        jobNode.command = ' '.join(workerCommand)
+        workerCommand.append("--toilState")
+        workerCommand.append(
+            base64.b64encode(pickle.dumps(self.toilState)).decode("utf-8")
+        )
 
-        omp_threads = os.environ.get('OMP_NUM_THREADS') \
-            or str(max(1, int(jobNode.cores)))  # make sure OMP_NUM_THREADS is a positive integer
+        jobNode.command = " ".join(workerCommand)
+
+        omp_threads = os.environ.get("OMP_NUM_THREADS") or str(
+            max(1, int(jobNode.cores))
+        )  # make sure OMP_NUM_THREADS is a positive integer
 
         job_environment = {
             # Set the number of cores used by OpenMP applications

src/toil/test/cwl/cwlTest.py

@@ -814,11 +814,11 @@ def test_download_structure(self) -> None:
 class CWLToilOptimizeTests(ToilTest):
     def setUp(self):
         """Runs anew before each test to create farm fresh temp dirs."""
-        self.outDir = f'/tmp/toil-cwl-test-{str(uuid.uuid4())}'
+        self.outDir = f"/tmp/toil-cwl-test-{str(uuid.uuid4())}"
         os.makedirs(self.outDir)
         self.rootDir = self._projectRootPath()
-        self.jobDir = os.path.join(self.outDir, 'jobStore')
-        self.statDir = os.path.join(self.jobDir, 'stats')
+        self.jobDir = os.path.join(self.outDir, "jobStore")
+        self.statDir = os.path.join(self.jobDir, "stats")
 
     def tearDown(self):
         """Clean up outputs."""
@@ -828,36 +828,53 @@ def tearDown(self):
 
     def _tester(self, cwlfile, jobfile, expect, main_args=[]):
         from toil.cwl import cwltoil
+
         st = StringIO()
         main_args = main_args[:]
-        main_args.extend(['--logDebug','--stats','--outdir', self.outDir, '--jobStore', self.jobDir,
-                          os.path.join(self.rootDir, cwlfile), os.path.join(self.rootDir, jobfile)])
+        main_args.extend(
+            [
+                "--logDebug",
+                "--stats",
+                "--outdir",
+                self.outDir,
+                "--jobStore",
+                self.jobDir,
+                os.path.join(self.rootDir, cwlfile),
+                os.path.join(self.rootDir, jobfile),
+            ]
+        )
         cwltoil.main(main_args, stdout=st)
         out = self._extract_job_lists()
         self.assertEqual(out, expect)
 
     def _match_extract_string(self, stringin):
         import re
-        search_pattern = re.compile('^.* (\w*) kind-CWLJob/instance-.*$')
+
+        search_pattern = re.compile("^.* (\w*) kind-CWLJob/instance-.*$")
         if search_pattern.match(stringin):
-            return(search_pattern.sub(r'\1',stringin))
+            return search_pattern.sub(r"\1", stringin)
         else:
-            return(None)
+            return None
 
     def _extract_job_lists(self):
         worker_list = []
         for filename in os.listdir(self.statDir):
-            with open(os.path.join(self.statDir,filename)) as f:
+            with open(os.path.join(self.statDir, filename)) as f:
                 test_json = json.load(f)
-                if 'workers' in test_json.keys() and len(test_json['jobs']) > 0:
-                    job_list = [self._match_extract_string(x) for x in test_json['logs']['names']]
+                if "workers" in test_json.keys() and len(test_json["jobs"]) > 0:
+                    job_list = [
+                        self._match_extract_string(x)
+                        for x in test_json["logs"]["names"]
+                    ]
                     if not all(x == None for x in job_list):
                         worker_list.append(job_list)
         worker_list.sort()
-        return(worker_list)
+        return worker_list
 
     def test_biobb_fail(self):
-        self._tester('src/toil/test/cwl/md_list_reduced.cwl',
-                     'src/toil/test/cwl/md_list_reduced.json',
-                     [['genion', 'grompp', 'pdb2gmx', 'editconf', 'solvate']],
-                     main_args=[])
+        self._tester(
+            "src/toil/test/cwl/md_list_reduced.cwl",
+            "src/toil/test/cwl/md_list_reduced.json",
+            [["genion", "grompp", "pdb2gmx", "editconf", "solvate"]],
+            main_args=[],
+        )

src/toil/utils/toilDebugJob.py

@@ -46,5 +46,7 @@ def main() -> None:
 
     jobID = options.jobID[0]
     logger.debug(f"Running the following job locally: {jobID}")
-    workerScript(jobStore, config, jobID, jobID, redirectOutputToLogFile=False)
+    workerScript(
+        jobStore, config, jobID, jobID, options.toilState, redirectOutputToLogFile=False
+    )
     logger.debug(f"Finished running: {jobID}")