prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  PyTorch security vulnerability
  See https://github.com/advisories/GHSA-47fc-vmwq-366v
  
  Need to upgrade to PyTorch 1.13.1
  
  </issue>
  <code>
  [start of setup.py]
  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 of setup.py]
  </code>
  
  I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply. Please respond with a single patch file in the following format.
  <patch>
  diff --git a/file.py b/file.py
  --- a/file.py
  +++ b/file.py
  @@ -1,27 +1,35 @@
   def euclidean(a, b):
  -    while b:
  -        a, b = b, a % b
  -    return a
  +    if b == 0:
  +        return a
  +    return euclidean(b, a % b)
   
   
   def bresenham(x0, y0, x1, y1):
       points = []
       dx = abs(x1 - x0)
       dy = abs(y1 - y0)
  -    sx = 1 if x0 < x1 else -1
  -    sy = 1 if y0 < y1 else -1
  -    err = dx - dy
  +    x, y = x0, y0
  +    sx = -1 if x0 > x1 else 1
  +    sy = -1 if y0 > y1 else 1
   
  -    while True:
  -        points.append((x0, y0))
  -        if x0 == x1 and y0 == y1:
  -            break
  -        e2 = 2 * err
  -        if e2 > -dy:
  -            err -= dy
  -            x0 += sx
  -        if e2 < dx:
  -            err += dx
  -            y0 += sy
  +    if dx > dy:
  +        err = dx / 2.0
  +        while x != x1:
  +            points.append((x, y))
  +            err -= dy
  +            if err < 0:
  +                y += sy
  +                err += dx
  +            x += sx
  +    else:
  +        err = dy / 2.0
  +        while y != y1:
  +            points.append((x, y))
  +            err -= dx
  +            if err < 0:
  +                x += sx
  +                err += dy
  +            y += sy
  +
  +    points.append((x, y))
       return points
  
  </patch>
golden_diff: 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",
  
verification_info: {"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"}]}