We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
Add type hints to toilDestroyCluster.py
Add type hints to src/toil/utils/toilDestroyCluster.py so it can be checked under mypy during linting. 

Refers to #3568.

┆Issue is synchronized with this [Jira Task](https://ucsc-cgl.atlassian.net/browse/TOIL-905)
┆Issue Number: TOIL-905


--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `src/toil/utils/toilDestroyCluster.py`
Content:
```
1 # Copyright (C) 2015-2021 Regents of the University of California
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
4 # you may not use this file except in compliance with the License.
5 # You may obtain a copy of the License at
6 #
7 #     http://www.apache.org/licenses/LICENSE-2.0
8 #
9 # Unless required by applicable law or agreed to in writing, software
10 # distributed under the License is distributed on an "AS IS" BASIS,
11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
14 """Terminates the specified cluster and associated resources."""
15 import logging
16 from toil.common import parser_with_common_options
17 from toil.provisioners import cluster_factory
18 from toil.statsAndLogging import set_logging_from_options
19 
20 
21 logger = logging.getLogger(__name__)
22 
23 def main():
24     parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
25     options = parser.parse_args()
26     set_logging_from_options(options)
27 
28     logger.info('Destroying cluster %s', options.clusterName)
29 
30     cluster = cluster_factory(provisioner=options.provisioner,
31                               clusterName=options.clusterName,
32                               zone=options.zone)
33     cluster.destroyCluster()
34 
35     logger.info('Cluster %s is now gone.', options.clusterName)
36
```

Path: `contrib/admin/mypy-with-ignore.py`
Content:
```
1 #!/usr/bin/env python3
2 """
3 Runs mypy and ignores files that do not yet have passing type hints.
4 
5 Does not type check test files (any path including "src/toil/test").
6 """
7 import os
8 import subprocess
9 import sys
10 
11 pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))  # noqa
12 sys.path.insert(0, pkg_root)  # noqa
13 
14 from src.toil.lib.resources import glob  # type: ignore
15 
16 
17 def main():
18     all_files_to_check = []
19     for d in ['dashboard', 'docker', 'docs', 'src']:
20         all_files_to_check += glob(glob_pattern='*.py', directoryname=os.path.join(pkg_root, d))
21 
22     # TODO: Remove these paths as typing is added and mypy conflicts are addressed
23     ignore_paths = [os.path.abspath(f) for f in [
24         'docker/Dockerfile.py',
25         'docs/conf.py',
26         'docs/vendor/sphinxcontrib/fulltoc.py',
27         'docs/vendor/sphinxcontrib/__init__.py',
28         'src/toil/job.py',
29         'src/toil/leader.py',
30         'src/toil/statsAndLogging.py',
31         'src/toil/common.py',
32         'src/toil/realtimeLogger.py',
33         'src/toil/worker.py',
34         'src/toil/serviceManager.py',
35         'src/toil/toilState.py',
36         'src/toil/__init__.py',
37         'src/toil/resource.py',
38         'src/toil/deferred.py',
39         'src/toil/version.py',
40         'src/toil/wdl/utils.py',
41         'src/toil/wdl/wdl_types.py',
42         'src/toil/wdl/wdl_synthesis.py',
43         'src/toil/wdl/wdl_analysis.py',
44         'src/toil/wdl/wdl_functions.py',
45         'src/toil/wdl/toilwdl.py',
46         'src/toil/wdl/versions/draft2.py',
47         'src/toil/wdl/versions/v1.py',
48         'src/toil/wdl/versions/dev.py',
49         'src/toil/provisioners/clusterScaler.py',
50         'src/toil/provisioners/abstractProvisioner.py',
51         'src/toil/provisioners/gceProvisioner.py',
52         'src/toil/provisioners/__init__.py',
53         'src/toil/provisioners/node.py',
54         'src/toil/provisioners/aws/boto2Context.py',
55         'src/toil/provisioners/aws/awsProvisioner.py',
56         'src/toil/provisioners/aws/__init__.py',
57         'src/toil/batchSystems/slurm.py',
58         'src/toil/batchSystems/gridengine.py',
59         'src/toil/batchSystems/singleMachine.py',
60         'src/toil/batchSystems/abstractBatchSystem.py',
61         'src/toil/batchSystems/parasol.py',
62         'src/toil/batchSystems/kubernetes.py',
63         'src/toil/batchSystems/torque.py',
64         'src/toil/batchSystems/options.py',
65         'src/toil/batchSystems/registry.py',
66         'src/toil/batchSystems/lsf.py',
67         'src/toil/batchSystems/__init__.py',
68         'src/toil/batchSystems/abstractGridEngineBatchSystem.py',
69         'src/toil/batchSystems/lsfHelper.py',
70         'src/toil/batchSystems/htcondor.py',
71         'src/toil/batchSystems/mesos/batchSystem.py',
72         'src/toil/batchSystems/mesos/executor.py',
73         'src/toil/batchSystems/mesos/conftest.py',
74         'src/toil/batchSystems/mesos/__init__.py',
75         'src/toil/batchSystems/mesos/test/__init__.py',
76         'src/toil/cwl/conftest.py',
77         'src/toil/cwl/__init__.py',
78         'src/toil/cwl/cwltoil.py',
79         'src/toil/fileStores/cachingFileStore.py',
80         'src/toil/fileStores/abstractFileStore.py',
81         'src/toil/fileStores/nonCachingFileStore.py',
82         'src/toil/fileStores/__init__.py',
83         'src/toil/jobStores/utils.py',
84         'src/toil/jobStores/abstractJobStore.py',
85         'src/toil/jobStores/conftest.py',
86         'src/toil/jobStores/fileJobStore.py',
87         'src/toil/jobStores/__init__.py',
88         'src/toil/jobStores/googleJobStore.py',
89         'src/toil/jobStores/aws/utils.py',
90         'src/toil/jobStores/aws/jobStore.py',
91         'src/toil/jobStores/aws/__init__.py',
92         'src/toil/utils/toilDebugFile.py',
93         'src/toil/utils/toilUpdateEC2Instances.py',
94         'src/toil/utils/toilStatus.py',
95         'src/toil/utils/toilStats.py',
96         'src/toil/utils/toilSshCluster.py',
97         'src/toil/utils/toilMain.py',
98         'src/toil/utils/__init__.py',
99         'src/toil/utils/toilDestroyCluster.py',
100         'src/toil/utils/toilDebugJob.py',
101         'src/toil/utils/toilRsyncCluster.py',
102         'src/toil/utils/toilClean.py',
103         'src/toil/utils/toilLaunchCluster.py',
104         'src/toil/lib/memoize.py',
105         'src/toil/lib/throttle.py',
106         'src/toil/lib/humanize.py',
107         'src/toil/lib/compatibility.py',
108         'src/toil/lib/iterables.py',
109         'src/toil/lib/bioio.py',
110         'src/toil/lib/ec2.py',
111         # 'src/toil/lib/conversions.py',
112         'src/toil/lib/ec2nodes.py',
113         # 'src/toil/lib/misc.py',
114         'src/toil/lib/expando.py',
115         'src/toil/lib/threading.py',
116         'src/toil/lib/exceptions.py',
117         'src/toil/lib/__init__.py',
118         'src/toil/lib/generatedEC2Lists.py',
119         'src/toil/lib/retry.py',
120         'src/toil/lib/objects.py',
121         'src/toil/lib/io.py',
122         'src/toil/lib/docker.py',
123         'src/toil/lib/encryption/_nacl.py',
124         'src/toil/lib/encryption/_dummy.py',
125         'src/toil/lib/encryption/conftest.py',
126         'src/toil/lib/encryption/__init__.py',
127         'src/toil/lib/aws/utils.py',
128         'src/toil/lib/aws/__init__.py'
129     ]]
130 
131     filtered_files_to_check = []
132     for file_path in all_files_to_check:
133         if file_path not in ignore_paths and 'src/toil/test' not in file_path:
134             filtered_files_to_check.append(file_path)
135     # follow-imports type checks pypi projects we don't control, so we skip it; why is this their default?
136     args = ['mypy', '--follow-imports=skip'] + filtered_files_to_check
137     p = subprocess.run(args=args, stdout=subprocess.PIPE)
138     result = p.stdout.decode()
139     print(result)
140     if 'Success: no issues found' not in result:
141         exit(1)
142 
143 
144 if __name__ == '__main__':
145     main()
146
```
--- END FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

diff --git a/contrib/admin/mypy-with-ignore.py b/contrib/admin/mypy-with-ignore.py
--- a/contrib/admin/mypy-with-ignore.py
+++ b/contrib/admin/mypy-with-ignore.py
@@ -96,7 +96,6 @@
         'src/toil/utils/toilSshCluster.py',
         'src/toil/utils/toilMain.py',
         'src/toil/utils/__init__.py',
-        'src/toil/utils/toilDestroyCluster.py',
         'src/toil/utils/toilDebugJob.py',
         'src/toil/utils/toilRsyncCluster.py',
         'src/toil/utils/toilClean.py',
diff --git a/src/toil/utils/toilDestroyCluster.py b/src/toil/utils/toilDestroyCluster.py
--- a/src/toil/utils/toilDestroyCluster.py
+++ b/src/toil/utils/toilDestroyCluster.py
@@ -20,7 +20,7 @@
 
 logger = logging.getLogger(__name__)
 
-def main():
+def main() -> None:
     parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
     options = parser.parse_args()
     set_logging_from_options(options)

{"golden_diff": "diff --git a/contrib/admin/mypy-with-ignore.py b/contrib/admin/mypy-with-ignore.py\n--- a/contrib/admin/mypy-with-ignore.py\n+++ b/contrib/admin/mypy-with-ignore.py\n@@ -96,7 +96,6 @@\n         'src/toil/utils/toilSshCluster.py',\n         'src/toil/utils/toilMain.py',\n         'src/toil/utils/__init__.py',\n-        'src/toil/utils/toilDestroyCluster.py',\n         'src/toil/utils/toilDebugJob.py',\n         'src/toil/utils/toilRsyncCluster.py',\n         'src/toil/utils/toilClean.py',\ndiff --git a/src/toil/utils/toilDestroyCluster.py b/src/toil/utils/toilDestroyCluster.py\n--- a/src/toil/utils/toilDestroyCluster.py\n+++ b/src/toil/utils/toilDestroyCluster.py\n@@ -20,7 +20,7 @@\n \n logger = logging.getLogger(__name__)\n \n-def main():\n+def main() -> None:\n     parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)\n     options = parser.parse_args()\n     set_logging_from_options(options)\n", "issue": "Add type hints to toilDestroyCluster.py\nAdd type hints to src/toil/utils/toilDestroyCluster.py so it can be checked under mypy during linting. \n\nRefers to #3568.\n\n\u2506Issue is synchronized with this [Jira Task](https://ucsc-cgl.atlassian.net/browse/TOIL-905)\n\u2506Issue Number: TOIL-905\n\n", "before_files": [{"content": "# Copyright (C) 2015-2021 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\"\"\"Terminates the specified cluster and associated resources.\"\"\"\nimport logging\nfrom toil.common import parser_with_common_options\nfrom toil.provisioners import cluster_factory\nfrom toil.statsAndLogging import set_logging_from_options\n\n\nlogger = logging.getLogger(__name__)\n\ndef main():\n    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)\n    options = parser.parse_args()\n    set_logging_from_options(options)\n\n    logger.info('Destroying cluster %s', options.clusterName)\n\n    cluster = cluster_factory(provisioner=options.provisioner,\n                              clusterName=options.clusterName,\n                              zone=options.zone)\n    cluster.destroyCluster()\n\n    logger.info('Cluster %s is now gone.', options.clusterName)\n", "path": "src/toil/utils/toilDestroyCluster.py"}, {"content": "#!/usr/bin/env python3\n\"\"\"\nRuns mypy and ignores files that do not yet have passing type hints.\n\nDoes not type check test files (any path including \"src/toil/test\").\n\"\"\"\nimport os\nimport subprocess\nimport sys\n\npkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))  # noqa\nsys.path.insert(0, pkg_root)  # noqa\n\nfrom src.toil.lib.resources import glob  # type: ignore\n\n\ndef main():\n    all_files_to_check = []\n    for d in ['dashboard', 'docker', 'docs', 'src']:\n        all_files_to_check += glob(glob_pattern='*.py', directoryname=os.path.join(pkg_root, d))\n\n    # TODO: Remove these paths as typing is added and mypy conflicts are addressed\n    ignore_paths = [os.path.abspath(f) for f in [\n        'docker/Dockerfile.py',\n        'docs/conf.py',\n        'docs/vendor/sphinxcontrib/fulltoc.py',\n        'docs/vendor/sphinxcontrib/__init__.py',\n        'src/toil/job.py',\n        'src/toil/leader.py',\n        'src/toil/statsAndLogging.py',\n        'src/toil/common.py',\n        'src/toil/realtimeLogger.py',\n        'src/toil/worker.py',\n        'src/toil/serviceManager.py',\n        'src/toil/toilState.py',\n        'src/toil/__init__.py',\n        'src/toil/resource.py',\n        'src/toil/deferred.py',\n        'src/toil/version.py',\n        'src/toil/wdl/utils.py',\n        'src/toil/wdl/wdl_types.py',\n        'src/toil/wdl/wdl_synthesis.py',\n        'src/toil/wdl/wdl_analysis.py',\n        'src/toil/wdl/wdl_functions.py',\n        'src/toil/wdl/toilwdl.py',\n        'src/toil/wdl/versions/draft2.py',\n        'src/toil/wdl/versions/v1.py',\n        'src/toil/wdl/versions/dev.py',\n        'src/toil/provisioners/clusterScaler.py',\n        'src/toil/provisioners/abstractProvisioner.py',\n        'src/toil/provisioners/gceProvisioner.py',\n        'src/toil/provisioners/__init__.py',\n        'src/toil/provisioners/node.py',\n        'src/toil/provisioners/aws/boto2Context.py',\n        'src/toil/provisioners/aws/awsProvisioner.py',\n        'src/toil/provisioners/aws/__init__.py',\n        'src/toil/batchSystems/slurm.py',\n        'src/toil/batchSystems/gridengine.py',\n        'src/toil/batchSystems/singleMachine.py',\n        'src/toil/batchSystems/abstractBatchSystem.py',\n        'src/toil/batchSystems/parasol.py',\n        'src/toil/batchSystems/kubernetes.py',\n        'src/toil/batchSystems/torque.py',\n        'src/toil/batchSystems/options.py',\n        'src/toil/batchSystems/registry.py',\n        'src/toil/batchSystems/lsf.py',\n        'src/toil/batchSystems/__init__.py',\n        'src/toil/batchSystems/abstractGridEngineBatchSystem.py',\n        'src/toil/batchSystems/lsfHelper.py',\n        'src/toil/batchSystems/htcondor.py',\n        'src/toil/batchSystems/mesos/batchSystem.py',\n        'src/toil/batchSystems/mesos/executor.py',\n        'src/toil/batchSystems/mesos/conftest.py',\n        'src/toil/batchSystems/mesos/__init__.py',\n        'src/toil/batchSystems/mesos/test/__init__.py',\n        'src/toil/cwl/conftest.py',\n        'src/toil/cwl/__init__.py',\n        'src/toil/cwl/cwltoil.py',\n        'src/toil/fileStores/cachingFileStore.py',\n        'src/toil/fileStores/abstractFileStore.py',\n        'src/toil/fileStores/nonCachingFileStore.py',\n        'src/toil/fileStores/__init__.py',\n        'src/toil/jobStores/utils.py',\n        'src/toil/jobStores/abstractJobStore.py',\n        'src/toil/jobStores/conftest.py',\n        'src/toil/jobStores/fileJobStore.py',\n        'src/toil/jobStores/__init__.py',\n        'src/toil/jobStores/googleJobStore.py',\n        'src/toil/jobStores/aws/utils.py',\n        'src/toil/jobStores/aws/jobStore.py',\n        'src/toil/jobStores/aws/__init__.py',\n        'src/toil/utils/toilDebugFile.py',\n        'src/toil/utils/toilUpdateEC2Instances.py',\n        'src/toil/utils/toilStatus.py',\n        'src/toil/utils/toilStats.py',\n        'src/toil/utils/toilSshCluster.py',\n        'src/toil/utils/toilMain.py',\n        'src/toil/utils/__init__.py',\n        'src/toil/utils/toilDestroyCluster.py',\n        'src/toil/utils/toilDebugJob.py',\n        'src/toil/utils/toilRsyncCluster.py',\n        'src/toil/utils/toilClean.py',\n        'src/toil/utils/toilLaunchCluster.py',\n        'src/toil/lib/memoize.py',\n        'src/toil/lib/throttle.py',\n        'src/toil/lib/humanize.py',\n        'src/toil/lib/compatibility.py',\n        'src/toil/lib/iterables.py',\n        'src/toil/lib/bioio.py',\n        'src/toil/lib/ec2.py',\n        # 'src/toil/lib/conversions.py',\n        'src/toil/lib/ec2nodes.py',\n        # 'src/toil/lib/misc.py',\n        'src/toil/lib/expando.py',\n        'src/toil/lib/threading.py',\n        'src/toil/lib/exceptions.py',\n        'src/toil/lib/__init__.py',\n        'src/toil/lib/generatedEC2Lists.py',\n        'src/toil/lib/retry.py',\n        'src/toil/lib/objects.py',\n        'src/toil/lib/io.py',\n        'src/toil/lib/docker.py',\n        'src/toil/lib/encryption/_nacl.py',\n        'src/toil/lib/encryption/_dummy.py',\n        'src/toil/lib/encryption/conftest.py',\n        'src/toil/lib/encryption/__init__.py',\n        'src/toil/lib/aws/utils.py',\n        'src/toil/lib/aws/__init__.py'\n    ]]\n\n    filtered_files_to_check = []\n    for file_path in all_files_to_check:\n        if file_path not in ignore_paths and 'src/toil/test' not in file_path:\n            filtered_files_to_check.append(file_path)\n    # follow-imports type checks pypi projects we don't control, so we skip it; why is this their default?\n    args = ['mypy', '--follow-imports=skip'] + filtered_files_to_check\n    p = subprocess.run(args=args, stdout=subprocess.PIPE)\n    result = p.stdout.decode()\n    print(result)\n    if 'Success: no issues found' not in result:\n        exit(1)\n\n\nif __name__ == '__main__':\n    main()\n", "path": "contrib/admin/mypy-with-ignore.py"}], "after_files": [{"content": "# Copyright (C) 2015-2021 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\"\"\"Terminates the specified cluster and associated resources.\"\"\"\nimport logging\nfrom toil.common import parser_with_common_options\nfrom toil.provisioners import cluster_factory\nfrom toil.statsAndLogging import set_logging_from_options\n\n\nlogger = logging.getLogger(__name__)\n\ndef main() -> None:\n    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)\n    options = parser.parse_args()\n    set_logging_from_options(options)\n\n    logger.info('Destroying cluster %s', options.clusterName)\n\n    cluster = cluster_factory(provisioner=options.provisioner,\n                              clusterName=options.clusterName,\n                              zone=options.zone)\n    cluster.destroyCluster()\n\n    logger.info('Cluster %s is now gone.', options.clusterName)\n", "path": "src/toil/utils/toilDestroyCluster.py"}, {"content": "#!/usr/bin/env python3\n\"\"\"\nRuns mypy and ignores files that do not yet have passing type hints.\n\nDoes not type check test files (any path including \"src/toil/test\").\n\"\"\"\nimport os\nimport subprocess\nimport sys\n\npkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))  # noqa\nsys.path.insert(0, pkg_root)  # noqa\n\nfrom src.toil.lib.resources import glob  # type: ignore\n\n\ndef main():\n    all_files_to_check = []\n    for d in ['dashboard', 'docker', 'docs', 'src']:\n        all_files_to_check += glob(glob_pattern='*.py', directoryname=os.path.join(pkg_root, d))\n\n    # TODO: Remove these paths as typing is added and mypy conflicts are addressed\n    ignore_paths = [os.path.abspath(f) for f in [\n        'docker/Dockerfile.py',\n        'docs/conf.py',\n        'docs/vendor/sphinxcontrib/fulltoc.py',\n        'docs/vendor/sphinxcontrib/__init__.py',\n        'src/toil/job.py',\n        'src/toil/leader.py',\n        'src/toil/statsAndLogging.py',\n        'src/toil/common.py',\n        'src/toil/realtimeLogger.py',\n        'src/toil/worker.py',\n        'src/toil/serviceManager.py',\n        'src/toil/toilState.py',\n        'src/toil/__init__.py',\n        'src/toil/resource.py',\n        'src/toil/deferred.py',\n        'src/toil/version.py',\n        'src/toil/wdl/utils.py',\n        'src/toil/wdl/wdl_types.py',\n        'src/toil/wdl/wdl_synthesis.py',\n        'src/toil/wdl/wdl_analysis.py',\n        'src/toil/wdl/wdl_functions.py',\n        'src/toil/wdl/toilwdl.py',\n        'src/toil/wdl/versions/draft2.py',\n        'src/toil/wdl/versions/v1.py',\n        'src/toil/wdl/versions/dev.py',\n        'src/toil/provisioners/clusterScaler.py',\n        'src/toil/provisioners/abstractProvisioner.py',\n        'src/toil/provisioners/gceProvisioner.py',\n        'src/toil/provisioners/__init__.py',\n        'src/toil/provisioners/node.py',\n        'src/toil/provisioners/aws/boto2Context.py',\n        'src/toil/provisioners/aws/awsProvisioner.py',\n        'src/toil/provisioners/aws/__init__.py',\n        'src/toil/batchSystems/slurm.py',\n        'src/toil/batchSystems/gridengine.py',\n        'src/toil/batchSystems/singleMachine.py',\n        'src/toil/batchSystems/abstractBatchSystem.py',\n        'src/toil/batchSystems/parasol.py',\n        'src/toil/batchSystems/kubernetes.py',\n        'src/toil/batchSystems/torque.py',\n        'src/toil/batchSystems/options.py',\n        'src/toil/batchSystems/registry.py',\n        'src/toil/batchSystems/lsf.py',\n        'src/toil/batchSystems/__init__.py',\n        'src/toil/batchSystems/abstractGridEngineBatchSystem.py',\n        'src/toil/batchSystems/lsfHelper.py',\n        'src/toil/batchSystems/htcondor.py',\n        'src/toil/batchSystems/mesos/batchSystem.py',\n        'src/toil/batchSystems/mesos/executor.py',\n        'src/toil/batchSystems/mesos/conftest.py',\n        'src/toil/batchSystems/mesos/__init__.py',\n        'src/toil/batchSystems/mesos/test/__init__.py',\n        'src/toil/cwl/conftest.py',\n        'src/toil/cwl/__init__.py',\n        'src/toil/cwl/cwltoil.py',\n        'src/toil/fileStores/cachingFileStore.py',\n        'src/toil/fileStores/abstractFileStore.py',\n        'src/toil/fileStores/nonCachingFileStore.py',\n        'src/toil/fileStores/__init__.py',\n        'src/toil/jobStores/utils.py',\n        'src/toil/jobStores/abstractJobStore.py',\n        'src/toil/jobStores/conftest.py',\n        'src/toil/jobStores/fileJobStore.py',\n        'src/toil/jobStores/__init__.py',\n        'src/toil/jobStores/googleJobStore.py',\n        'src/toil/jobStores/aws/utils.py',\n        'src/toil/jobStores/aws/jobStore.py',\n        'src/toil/jobStores/aws/__init__.py',\n        'src/toil/utils/toilDebugFile.py',\n        'src/toil/utils/toilUpdateEC2Instances.py',\n        'src/toil/utils/toilStatus.py',\n        'src/toil/utils/toilStats.py',\n        'src/toil/utils/toilSshCluster.py',\n        'src/toil/utils/toilMain.py',\n        'src/toil/utils/__init__.py',\n        'src/toil/utils/toilDebugJob.py',\n        'src/toil/utils/toilRsyncCluster.py',\n        'src/toil/utils/toilClean.py',\n        'src/toil/utils/toilLaunchCluster.py',\n        'src/toil/lib/memoize.py',\n        'src/toil/lib/throttle.py',\n        'src/toil/lib/humanize.py',\n        'src/toil/lib/compatibility.py',\n        'src/toil/lib/iterables.py',\n        'src/toil/lib/bioio.py',\n        'src/toil/lib/ec2.py',\n        # 'src/toil/lib/conversions.py',\n        'src/toil/lib/ec2nodes.py',\n        # 'src/toil/lib/misc.py',\n        'src/toil/lib/expando.py',\n        'src/toil/lib/threading.py',\n        'src/toil/lib/exceptions.py',\n        'src/toil/lib/__init__.py',\n        'src/toil/lib/generatedEC2Lists.py',\n        'src/toil/lib/retry.py',\n        'src/toil/lib/objects.py',\n        'src/toil/lib/io.py',\n        'src/toil/lib/docker.py',\n        'src/toil/lib/encryption/_nacl.py',\n        'src/toil/lib/encryption/_dummy.py',\n        'src/toil/lib/encryption/conftest.py',\n        'src/toil/lib/encryption/__init__.py',\n        'src/toil/lib/aws/utils.py',\n        'src/toil/lib/aws/__init__.py'\n    ]]\n\n    filtered_files_to_check = []\n    for file_path in all_files_to_check:\n        if file_path not in ignore_paths and 'src/toil/test' not in file_path:\n            filtered_files_to_check.append(file_path)\n    # follow-imports type checks pypi projects we don't control, so we skip it; why is this their default?\n    args = ['mypy', '--follow-imports=skip'] + filtered_files_to_check\n    p = subprocess.run(args=args, stdout=subprocess.PIPE)\n    result = p.stdout.decode()\n    print(result)\n    if 'Success: no issues found' not in result:\n        exit(1)\n\n\nif __name__ == '__main__':\n    main()\n", "path": "contrib/admin/mypy-with-ignore.py"}]}