We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
Add type hints to misc.py
Adds type hints to src/toil/lib/encryption/misc.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-889)
┆Issue Number: TOIL-889


--- 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/lib/misc.py`
Content:
```
1 import logging
2 import os
3 import random
4 import shutil
5 import subprocess
6 import sys
7 
8 logger = logging.getLogger(__name__)
9 
10 
11 def printq(msg, quiet: bool):
12     if not quiet:
13         print(msg)
14 
15 
16 def truncExpBackoff():
17     # as recommended here https://forums.aws.amazon.com/thread.jspa?messageID=406788#406788
18     # and here https://cloud.google.com/storage/docs/xml-api/reference-status
19     yield 0
20     t = 1
21     while t < 1024:
22         # google suggests this dither
23         yield t + random.random()
24         t *= 2
25     while True:
26         yield t
27 
28 
29 class CalledProcessErrorStderr(subprocess.CalledProcessError):
30     """Version of CalledProcessError that include stderr in the error message if it is set"""
31 
32     def __str__(self):
33         if (self.returncode < 0) or (self.stderr is None):
34             return str(super())
35         else:
36             err = self.stderr if isinstance(self.stderr, str) else self.stderr.decode("ascii", errors="replace")
37             return "Command '%s' exit status %d: %s" % (self.cmd, self.returncode, err)
38 
39 
40 def call_command(cmd, *, input=None, timeout=None, useCLocale=True, env=None):
41     """Simplified calling of external commands.  This always returns
42     stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr
43     is raised.  The captured stderr is always printed, regardless of
44     if an expect occurs, so it can be logged.  At the debug log level, the
45     command and captured out are always used.  With useCLocale, C locale
46     is force to prevent failures that occurred in some batch systems
47     with UTF-8 locale.
48     """
49 
50     # using non-C locales can cause GridEngine commands, maybe other to
51     # generate errors
52     if useCLocale:
53         env = dict(os.environ) if env is None else dict(env)  # copy since modifying
54         env["LANGUAGE"] = env["LC_ALL"] = "C"
55 
56     logger.debug("run command: {}".format(" ".join(cmd)))
57     proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
58                             encoding='utf-8', errors="replace", env=env)
59     stdout, stderr = proc.communicate(input=input, timeout=timeout)
60     sys.stderr.write(stderr)
61     if proc.returncode != 0:
62         logger.debug("command failed: {}: {}".format(" ".join(cmd), stderr.rstrip()))
63         raise CalledProcessErrorStderr(proc.returncode, cmd, output=stdout, stderr=stderr)
64     logger.debug("command succeeded: {}: {}".format(" ".join(cmd), stdout.rstrip()))
65     return stdout
66
```

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/toilKill.py',
99         'src/toil/utils/__init__.py',
100         'src/toil/utils/toilDestroyCluster.py',
101         'src/toil/utils/toilDebugJob.py',
102         'src/toil/utils/toilRsyncCluster.py',
103         'src/toil/utils/toilClean.py',
104         'src/toil/utils/toilLaunchCluster.py',
105         'src/toil/lib/memoize.py',
106         'src/toil/lib/throttle.py',
107         'src/toil/lib/humanize.py',
108         'src/toil/lib/compatibility.py',
109         'src/toil/lib/iterables.py',
110         'src/toil/lib/bioio.py',
111         'src/toil/lib/ec2.py',
112         'src/toil/lib/conversions.py',
113         'src/toil/lib/ec2nodes.py',
114         'src/toil/lib/misc.py',
115         'src/toil/lib/expando.py',
116         'src/toil/lib/threading.py',
117         'src/toil/lib/exceptions.py',
118         'src/toil/lib/__init__.py',
119         'src/toil/lib/generatedEC2Lists.py',
120         'src/toil/lib/retry.py',
121         'src/toil/lib/objects.py',
122         'src/toil/lib/io.py',
123         'src/toil/lib/docker.py',
124         'src/toil/lib/encryption/_nacl.py',
125         'src/toil/lib/encryption/_dummy.py',
126         'src/toil/lib/encryption/conftest.py',
127         'src/toil/lib/encryption/__init__.py',
128         'src/toil/lib/aws/utils.py',
129         'src/toil/lib/aws/__init__.py'
130     ]]
131 
132     filtered_files_to_check = []
133     for file_path in all_files_to_check:
134         if file_path not in ignore_paths and 'src/toil/test' not in file_path:
135             filtered_files_to_check.append(file_path)
136     # follow-imports type checks pypi projects we don't control, so we skip it; why is this their default?
137     args = ['mypy', '--follow-imports=skip'] + filtered_files_to_check
138     p = subprocess.run(args=args, stdout=subprocess.PIPE)
139     result = p.stdout.decode()
140     print(result)
141     if 'Success: no issues found' not in result:
142         exit(1)
143 
144 
145 if __name__ == '__main__':
146     main()
147
```
--- 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
@@ -111,7 +111,7 @@
         'src/toil/lib/ec2.py',
         'src/toil/lib/conversions.py',
         'src/toil/lib/ec2nodes.py',
-        'src/toil/lib/misc.py',
+        # 'src/toil/lib/misc.py',
         'src/toil/lib/expando.py',
         'src/toil/lib/threading.py',
         'src/toil/lib/exceptions.py',
diff --git a/src/toil/lib/misc.py b/src/toil/lib/misc.py
--- a/src/toil/lib/misc.py
+++ b/src/toil/lib/misc.py
@@ -4,16 +4,19 @@
 import shutil
 import subprocess
 import sys
+import typing
+
+from typing import Iterator, Union, List, Optional
 
 logger = logging.getLogger(__name__)
 
 
-def printq(msg, quiet: bool):
+def printq(msg: str, quiet: bool) -> None:
     if not quiet:
         print(msg)
 
 
-def truncExpBackoff():
+def truncExpBackoff() -> Iterator[float]:
     # as recommended here https://forums.aws.amazon.com/thread.jspa?messageID=406788#406788
     # and here https://cloud.google.com/storage/docs/xml-api/reference-status
     yield 0
@@ -29,7 +32,7 @@
 class CalledProcessErrorStderr(subprocess.CalledProcessError):
     """Version of CalledProcessError that include stderr in the error message if it is set"""
 
-    def __str__(self):
+    def __str__(self) -> str:
         if (self.returncode < 0) or (self.stderr is None):
             return str(super())
         else:
@@ -37,7 +40,8 @@
             return "Command '%s' exit status %d: %s" % (self.cmd, self.returncode, err)
 
 
-def call_command(cmd, *, input=None, timeout=None, useCLocale=True, env=None):
+def call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeout: Optional[float] = None,
+                useCLocale: bool = True, env: Optional[typing.Dict[str, str]] = None) -> Union[str, bytes]:
     """Simplified calling of external commands.  This always returns
     stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr
     is raised.  The captured stderr is always printed, regardless of

{"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@@ -111,7 +111,7 @@\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/misc.py',\n         'src/toil/lib/expando.py',\n         'src/toil/lib/threading.py',\n         'src/toil/lib/exceptions.py',\ndiff --git a/src/toil/lib/misc.py b/src/toil/lib/misc.py\n--- a/src/toil/lib/misc.py\n+++ b/src/toil/lib/misc.py\n@@ -4,16 +4,19 @@\n import shutil\n import subprocess\n import sys\n+import typing\n+\n+from typing import Iterator, Union, List, Optional\n \n logger = logging.getLogger(__name__)\n \n \n-def printq(msg, quiet: bool):\n+def printq(msg: str, quiet: bool) -> None:\n     if not quiet:\n         print(msg)\n \n \n-def truncExpBackoff():\n+def truncExpBackoff() -> Iterator[float]:\n     # as recommended here https://forums.aws.amazon.com/thread.jspa?messageID=406788#406788\n     # and here https://cloud.google.com/storage/docs/xml-api/reference-status\n     yield 0\n@@ -29,7 +32,7 @@\n class CalledProcessErrorStderr(subprocess.CalledProcessError):\n     \"\"\"Version of CalledProcessError that include stderr in the error message if it is set\"\"\"\n \n-    def __str__(self):\n+    def __str__(self) -> str:\n         if (self.returncode < 0) or (self.stderr is None):\n             return str(super())\n         else:\n@@ -37,7 +40,8 @@\n             return \"Command '%s' exit status %d: %s\" % (self.cmd, self.returncode, err)\n \n \n-def call_command(cmd, *, input=None, timeout=None, useCLocale=True, env=None):\n+def call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeout: Optional[float] = None,\n+                useCLocale: bool = True, env: Optional[typing.Dict[str, str]] = None) -> Union[str, bytes]:\n     \"\"\"Simplified calling of external commands.  This always returns\n     stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr\n     is raised.  The captured stderr is always printed, regardless of\n", "issue": "Add type hints to misc.py\nAdds type hints to src/toil/lib/encryption/misc.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-889)\n\u2506Issue Number: TOIL-889\n\n", "before_files": [{"content": "import logging\nimport os\nimport random\nimport shutil\nimport subprocess\nimport sys\n\nlogger = logging.getLogger(__name__)\n\n\ndef printq(msg, quiet: bool):\n    if not quiet:\n        print(msg)\n\n\ndef truncExpBackoff():\n    # as recommended here https://forums.aws.amazon.com/thread.jspa?messageID=406788#406788\n    # and here https://cloud.google.com/storage/docs/xml-api/reference-status\n    yield 0\n    t = 1\n    while t < 1024:\n        # google suggests this dither\n        yield t + random.random()\n        t *= 2\n    while True:\n        yield t\n\n\nclass CalledProcessErrorStderr(subprocess.CalledProcessError):\n    \"\"\"Version of CalledProcessError that include stderr in the error message if it is set\"\"\"\n\n    def __str__(self):\n        if (self.returncode < 0) or (self.stderr is None):\n            return str(super())\n        else:\n            err = self.stderr if isinstance(self.stderr, str) else self.stderr.decode(\"ascii\", errors=\"replace\")\n            return \"Command '%s' exit status %d: %s\" % (self.cmd, self.returncode, err)\n\n\ndef call_command(cmd, *, input=None, timeout=None, useCLocale=True, env=None):\n    \"\"\"Simplified calling of external commands.  This always returns\n    stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr\n    is raised.  The captured stderr is always printed, regardless of\n    if an expect occurs, so it can be logged.  At the debug log level, the\n    command and captured out are always used.  With useCLocale, C locale\n    is force to prevent failures that occurred in some batch systems\n    with UTF-8 locale.\n    \"\"\"\n\n    # using non-C locales can cause GridEngine commands, maybe other to\n    # generate errors\n    if useCLocale:\n        env = dict(os.environ) if env is None else dict(env)  # copy since modifying\n        env[\"LANGUAGE\"] = env[\"LC_ALL\"] = \"C\"\n\n    logger.debug(\"run command: {}\".format(\" \".join(cmd)))\n    proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE,\n                            encoding='utf-8', errors=\"replace\", env=env)\n    stdout, stderr = proc.communicate(input=input, timeout=timeout)\n    sys.stderr.write(stderr)\n    if proc.returncode != 0:\n        logger.debug(\"command failed: {}: {}\".format(\" \".join(cmd), stderr.rstrip()))\n        raise CalledProcessErrorStderr(proc.returncode, cmd, output=stdout, stderr=stderr)\n    logger.debug(\"command succeeded: {}: {}\".format(\" \".join(cmd), stdout.rstrip()))\n    return stdout\n", "path": "src/toil/lib/misc.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/toilKill.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": "import logging\nimport os\nimport random\nimport shutil\nimport subprocess\nimport sys\nimport typing\n\nfrom typing import Iterator, Union, List, Optional\n\nlogger = logging.getLogger(__name__)\n\n\ndef printq(msg: str, quiet: bool) -> None:\n    if not quiet:\n        print(msg)\n\n\ndef truncExpBackoff() -> Iterator[float]:\n    # as recommended here https://forums.aws.amazon.com/thread.jspa?messageID=406788#406788\n    # and here https://cloud.google.com/storage/docs/xml-api/reference-status\n    yield 0\n    t = 1\n    while t < 1024:\n        # google suggests this dither\n        yield t + random.random()\n        t *= 2\n    while True:\n        yield t\n\n\nclass CalledProcessErrorStderr(subprocess.CalledProcessError):\n    \"\"\"Version of CalledProcessError that include stderr in the error message if it is set\"\"\"\n\n    def __str__(self) -> str:\n        if (self.returncode < 0) or (self.stderr is None):\n            return str(super())\n        else:\n            err = self.stderr if isinstance(self.stderr, str) else self.stderr.decode(\"ascii\", errors=\"replace\")\n            return \"Command '%s' exit status %d: %s\" % (self.cmd, self.returncode, err)\n\n\ndef call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeout: Optional[float] = None,\n                useCLocale: bool = True, env: Optional[typing.Dict[str, str]] = None) -> Union[str, bytes]:\n    \"\"\"Simplified calling of external commands.  This always returns\n    stdout and uses utf- encode8.  If process fails, CalledProcessErrorStderr\n    is raised.  The captured stderr is always printed, regardless of\n    if an expect occurs, so it can be logged.  At the debug log level, the\n    command and captured out are always used.  With useCLocale, C locale\n    is force to prevent failures that occurred in some batch systems\n    with UTF-8 locale.\n    \"\"\"\n\n    # using non-C locales can cause GridEngine commands, maybe other to\n    # generate errors\n    if useCLocale:\n        env = dict(os.environ) if env is None else dict(env)  # copy since modifying\n        env[\"LANGUAGE\"] = env[\"LC_ALL\"] = \"C\"\n\n    logger.debug(\"run command: {}\".format(\" \".join(cmd)))\n    proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE,\n                            encoding='utf-8', errors=\"replace\", env=env)\n    stdout, stderr = proc.communicate(input=input, timeout=timeout)\n    sys.stderr.write(stderr)\n    if proc.returncode != 0:\n        logger.debug(\"command failed: {}: {}\".format(\" \".join(cmd), stderr.rstrip()))\n        raise CalledProcessErrorStderr(proc.returncode, cmd, output=stdout, stderr=stderr)\n    logger.debug(\"command succeeded: {}: {}\".format(\" \".join(cmd), stdout.rstrip()))\n    return stdout\n", "path": "src/toil/lib/misc.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/toilKill.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"}]}