We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
PyTorch security vulnerability
See https://github.com/advisories/GHSA-47fc-vmwq-366v

Need to upgrade to PyTorch 1.13.1

--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `setup.py`
Content:
```
1 #!/usr/bin/env python
2 
3 """The setup script."""
4 
5 
6 import sys, re
7 from setuptools import setup, find_packages
8 from setuptools.command.install import install
9 from setuptools.command.develop import develop
10 from setuptools.command.egg_info import egg_info
11 
12 try:
13     with open("README.md") as readme_file:
14         readme = readme_file.read()
15 except Exception as error:
16     readme = "No README information found."
17     sys.stderr.write("Warning: Could not open '%s' due %s\n" % ("README.md", error))
18 
19 
20 class CustomInstallCommand(install):
21     def run(self):
22         install.run(self)
23 
24 
25 class CustomDevelopCommand(develop):
26     def run(self):
27         develop.run(self)
28 
29 
30 class CustomEggInfoCommand(egg_info):
31     def run(self):
32         egg_info.run(self)
33 
34 
35 try:
36     filepath = "GANDLF/version.py"
37     version_file = open(filepath)
38     (__version__,) = re.findall('__version__ = "(.*)"', version_file.read())
39 
40 except Exception as error:
41     __version__ = "0.0.1"
42     sys.stderr.write("Warning: Could not open '%s' due %s\n" % (filepath, error))
43 
44 requirements = [
45     "black",
46     "numpy==1.22.0",
47     "scipy",
48     "SimpleITK!=2.0.*",
49     "SimpleITK!=2.2.1",  # https://github.com/mlcommons/GaNDLF/issues/536
50     "torchvision",
51     "tqdm",
52     "torchio==0.18.75",
53     "pandas",
54     "scikit-learn>=0.23.2",
55     "scikit-image>=0.19.1",
56     "setuptools",
57     "seaborn",
58     "pyyaml",
59     "tiffslide",
60     "matplotlib",
61     "requests>=2.25.0",
62     "pytest",
63     "coverage",
64     "pytest-cov",
65     "psutil",
66     "medcam",
67     "opencv-python",
68     "torchmetrics==0.5.1",  # newer versions have changed api for f1 invocation
69     "OpenPatchMiner==0.1.8",
70     "zarr==2.10.3",
71     "pydicom",
72     "onnx",
73     "torchinfo==1.7.0",
74     "segmentation-models-pytorch==0.3.0",
75     "ACSConv==0.1.1",
76     "docker",
77     "dicom-anonymizer",
78     "twine",
79     "zarr",
80     "keyring",
81 ]
82 
83 # pytorch doesn't have LTS support on OSX - https://github.com/mlcommons/GaNDLF/issues/389
84 if sys.platform == "darwin":
85     requirements.append("torch==1.11.0")
86 else:
87     requirements.append("torch==1.11.0")
88 
89 if __name__ == "__main__":
90     setup(
91         name="GANDLF",
92         version=__version__,
93         author="MLCommons",
94         author_email="gandlf@mlcommons.org",
95         python_requires=">=3.8",
96         packages=find_packages(),
97         cmdclass={
98             "install": CustomInstallCommand,
99             "develop": CustomDevelopCommand,
100             "egg_info": CustomEggInfoCommand,
101         },
102         scripts=[
103             "gandlf_run",
104             "gandlf_constructCSV",
105             "gandlf_collectStats",
106             "gandlf_patchMiner",
107             "gandlf_preprocess",
108             "gandlf_anonymizer",
109             "gandlf_verifyInstall",
110             "gandlf_configGenerator",
111             "gandlf_recoverConfig",
112             "gandlf_deploy",
113         ],
114         classifiers=[
115             "Development Status :: 3 - Alpha",
116             "Intended Audience :: Science/Research",
117             "License :: OSI Approved :: Apache Software License",
118             "Natural Language :: English",
119             "Operating System :: OS Independent",
120             "Programming Language :: Python :: 3.8",
121             "Programming Language :: Python :: 3.9",
122             "Programming Language :: Python :: 3.10",
123             "Topic :: Scientific/Engineering :: Medical Science Apps",
124         ],
125         description=(
126             "PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging."
127         ),
128         install_requires=requirements,
129         license="Apache-2.0",
130         long_description=readme,
131         long_description_content_type="text/markdown",
132         include_package_data=True,
133         keywords="semantic, segmentation, regression, classification, data-augmentation, medical-imaging, clinical-workflows, deep-learning, pytorch",
134         zip_safe=False,
135     )
136
```
--- 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/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -42,6 +42,7 @@
     sys.stderr.write("Warning: Could not open '%s' due %s\n" % (filepath, error))
 
 requirements = [
+    "torch==1.13.1",
     "black",
     "numpy==1.22.0",
     "scipy",
@@ -80,12 +81,6 @@
     "keyring",
 ]
 
-# pytorch doesn't have LTS support on OSX - https://github.com/mlcommons/GaNDLF/issues/389
-if sys.platform == "darwin":
-    requirements.append("torch==1.11.0")
-else:
-    requirements.append("torch==1.11.0")
-
 if __name__ == "__main__":
     setup(
         name="GANDLF",

{"golden_diff": "diff --git a/setup.py b/setup.py\n--- a/setup.py\n+++ b/setup.py\n@@ -42,6 +42,7 @@\n     sys.stderr.write(\"Warning: Could not open '%s' due %s\\n\" % (filepath, error))\n \n requirements = [\n+    \"torch==1.13.1\",\n     \"black\",\n     \"numpy==1.22.0\",\n     \"scipy\",\n@@ -80,12 +81,6 @@\n     \"keyring\",\n ]\n \n-# pytorch doesn't have LTS support on OSX - https://github.com/mlcommons/GaNDLF/issues/389\n-if sys.platform == \"darwin\":\n-    requirements.append(\"torch==1.11.0\")\n-else:\n-    requirements.append(\"torch==1.11.0\")\n-\n if __name__ == \"__main__\":\n     setup(\n         name=\"GANDLF\",\n", "issue": "PyTorch security vulnerability\nSee https://github.com/advisories/GHSA-47fc-vmwq-366v\r\n\r\nNeed to upgrade to PyTorch 1.13.1\n", "before_files": [{"content": "#!/usr/bin/env python\n\n\"\"\"The setup script.\"\"\"\n\n\nimport sys, re\nfrom setuptools import setup, find_packages\nfrom setuptools.command.install import install\nfrom setuptools.command.develop import develop\nfrom setuptools.command.egg_info import egg_info\n\ntry:\n    with open(\"README.md\") as readme_file:\n        readme = readme_file.read()\nexcept Exception as error:\n    readme = \"No README information found.\"\n    sys.stderr.write(\"Warning: Could not open '%s' due %s\\n\" % (\"README.md\", error))\n\n\nclass CustomInstallCommand(install):\n    def run(self):\n        install.run(self)\n\n\nclass CustomDevelopCommand(develop):\n    def run(self):\n        develop.run(self)\n\n\nclass CustomEggInfoCommand(egg_info):\n    def run(self):\n        egg_info.run(self)\n\n\ntry:\n    filepath = \"GANDLF/version.py\"\n    version_file = open(filepath)\n    (__version__,) = re.findall('__version__ = \"(.*)\"', version_file.read())\n\nexcept Exception as error:\n    __version__ = \"0.0.1\"\n    sys.stderr.write(\"Warning: Could not open '%s' due %s\\n\" % (filepath, error))\n\nrequirements = [\n    \"black\",\n    \"numpy==1.22.0\",\n    \"scipy\",\n    \"SimpleITK!=2.0.*\",\n    \"SimpleITK!=2.2.1\",  # https://github.com/mlcommons/GaNDLF/issues/536\n    \"torchvision\",\n    \"tqdm\",\n    \"torchio==0.18.75\",\n    \"pandas\",\n    \"scikit-learn>=0.23.2\",\n    \"scikit-image>=0.19.1\",\n    \"setuptools\",\n    \"seaborn\",\n    \"pyyaml\",\n    \"tiffslide\",\n    \"matplotlib\",\n    \"requests>=2.25.0\",\n    \"pytest\",\n    \"coverage\",\n    \"pytest-cov\",\n    \"psutil\",\n    \"medcam\",\n    \"opencv-python\",\n    \"torchmetrics==0.5.1\",  # newer versions have changed api for f1 invocation\n    \"OpenPatchMiner==0.1.8\",\n    \"zarr==2.10.3\",\n    \"pydicom\",\n    \"onnx\",\n    \"torchinfo==1.7.0\",\n    \"segmentation-models-pytorch==0.3.0\",\n    \"ACSConv==0.1.1\",\n    \"docker\",\n    \"dicom-anonymizer\",\n    \"twine\",\n    \"zarr\",\n    \"keyring\",\n]\n\n# pytorch doesn't have LTS support on OSX - https://github.com/mlcommons/GaNDLF/issues/389\nif sys.platform == \"darwin\":\n    requirements.append(\"torch==1.11.0\")\nelse:\n    requirements.append(\"torch==1.11.0\")\n\nif __name__ == \"__main__\":\n    setup(\n        name=\"GANDLF\",\n        version=__version__,\n        author=\"MLCommons\",\n        author_email=\"gandlf@mlcommons.org\",\n        python_requires=\">=3.8\",\n        packages=find_packages(),\n        cmdclass={\n            \"install\": CustomInstallCommand,\n            \"develop\": CustomDevelopCommand,\n            \"egg_info\": CustomEggInfoCommand,\n        },\n        scripts=[\n            \"gandlf_run\",\n            \"gandlf_constructCSV\",\n            \"gandlf_collectStats\",\n            \"gandlf_patchMiner\",\n            \"gandlf_preprocess\",\n            \"gandlf_anonymizer\",\n            \"gandlf_verifyInstall\",\n            \"gandlf_configGenerator\",\n            \"gandlf_recoverConfig\",\n            \"gandlf_deploy\",\n        ],\n        classifiers=[\n            \"Development Status :: 3 - Alpha\",\n            \"Intended Audience :: Science/Research\",\n            \"License :: OSI Approved :: Apache Software License\",\n            \"Natural Language :: English\",\n            \"Operating System :: OS Independent\",\n            \"Programming Language :: Python :: 3.8\",\n            \"Programming Language :: Python :: 3.9\",\n            \"Programming Language :: Python :: 3.10\",\n            \"Topic :: Scientific/Engineering :: Medical Science Apps\",\n        ],\n        description=(\n            \"PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.\"\n        ),\n        install_requires=requirements,\n        license=\"Apache-2.0\",\n        long_description=readme,\n        long_description_content_type=\"text/markdown\",\n        include_package_data=True,\n        keywords=\"semantic, segmentation, regression, classification, data-augmentation, medical-imaging, clinical-workflows, deep-learning, pytorch\",\n        zip_safe=False,\n    )\n", "path": "setup.py"}], "after_files": [{"content": "#!/usr/bin/env python\n\n\"\"\"The setup script.\"\"\"\n\n\nimport sys, re\nfrom setuptools import setup, find_packages\nfrom setuptools.command.install import install\nfrom setuptools.command.develop import develop\nfrom setuptools.command.egg_info import egg_info\n\ntry:\n    with open(\"README.md\") as readme_file:\n        readme = readme_file.read()\nexcept Exception as error:\n    readme = \"No README information found.\"\n    sys.stderr.write(\"Warning: Could not open '%s' due %s\\n\" % (\"README.md\", error))\n\n\nclass CustomInstallCommand(install):\n    def run(self):\n        install.run(self)\n\n\nclass CustomDevelopCommand(develop):\n    def run(self):\n        develop.run(self)\n\n\nclass CustomEggInfoCommand(egg_info):\n    def run(self):\n        egg_info.run(self)\n\n\ntry:\n    filepath = \"GANDLF/version.py\"\n    version_file = open(filepath)\n    (__version__,) = re.findall('__version__ = \"(.*)\"', version_file.read())\n\nexcept Exception as error:\n    __version__ = \"0.0.1\"\n    sys.stderr.write(\"Warning: Could not open '%s' due %s\\n\" % (filepath, error))\n\nrequirements = [\n    \"torch==1.13.1\",\n    \"black\",\n    \"numpy==1.22.0\",\n    \"scipy\",\n    \"SimpleITK!=2.0.*\",\n    \"SimpleITK!=2.2.1\",  # https://github.com/mlcommons/GaNDLF/issues/536\n    \"torchvision\",\n    \"tqdm\",\n    \"torchio==0.18.75\",\n    \"pandas\",\n    \"scikit-learn>=0.23.2\",\n    \"scikit-image>=0.19.1\",\n    \"setuptools\",\n    \"seaborn\",\n    \"pyyaml\",\n    \"tiffslide\",\n    \"matplotlib\",\n    \"requests>=2.25.0\",\n    \"pytest\",\n    \"coverage\",\n    \"pytest-cov\",\n    \"psutil\",\n    \"medcam\",\n    \"opencv-python\",\n    \"torchmetrics==0.5.1\",  # newer versions have changed api for f1 invocation\n    \"OpenPatchMiner==0.1.8\",\n    \"zarr==2.10.3\",\n    \"pydicom\",\n    \"onnx\",\n    \"torchinfo==1.7.0\",\n    \"segmentation-models-pytorch==0.3.0\",\n    \"ACSConv==0.1.1\",\n    \"docker\",\n    \"dicom-anonymizer\",\n    \"twine\",\n    \"zarr\",\n    \"keyring\",\n]\n\nif __name__ == \"__main__\":\n    setup(\n        name=\"GANDLF\",\n        version=__version__,\n        author=\"MLCommons\",\n        author_email=\"gandlf@mlcommons.org\",\n        python_requires=\">=3.8\",\n        packages=find_packages(),\n        cmdclass={\n            \"install\": CustomInstallCommand,\n            \"develop\": CustomDevelopCommand,\n            \"egg_info\": CustomEggInfoCommand,\n        },\n        scripts=[\n            \"gandlf_run\",\n            \"gandlf_constructCSV\",\n            \"gandlf_collectStats\",\n            \"gandlf_patchMiner\",\n            \"gandlf_preprocess\",\n            \"gandlf_anonymizer\",\n            \"gandlf_verifyInstall\",\n            \"gandlf_configGenerator\",\n            \"gandlf_recoverConfig\",\n            \"gandlf_deploy\",\n        ],\n        classifiers=[\n            \"Development Status :: 3 - Alpha\",\n            \"Intended Audience :: Science/Research\",\n            \"License :: OSI Approved :: Apache Software License\",\n            \"Natural Language :: English\",\n            \"Operating System :: OS Independent\",\n            \"Programming Language :: Python :: 3.8\",\n            \"Programming Language :: Python :: 3.9\",\n            \"Programming Language :: Python :: 3.10\",\n            \"Topic :: Scientific/Engineering :: Medical Science Apps\",\n        ],\n        description=(\n            \"PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.\"\n        ),\n        install_requires=requirements,\n        license=\"Apache-2.0\",\n        long_description=readme,\n        long_description_content_type=\"text/markdown\",\n        include_package_data=True,\n        keywords=\"semantic, segmentation, regression, classification, data-augmentation, medical-imaging, clinical-workflows, deep-learning, pytorch\",\n        zip_safe=False,\n    )\n", "path": "setup.py"}]}