prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  Include a git submodule update when doing pip install
  **Is your feature request related to a problem? Please describe.**
  Currently, the installation step requires a user to run `git submodule update --init --recursive` before doing `pip install`, which can lead to broken installation if the user forgets the step.
  
  **Describe the solution you'd like**
  Ensure the [git submodule line is working correctly in the setup.py file](https://github.com/CBICA/GaNDLF/blob/f4d0f02848c894d43259c2bb0b70612db612eb53/setup.py#L95).
  
  **Describe alternatives you've considered**
  N.A.
  
  **Additional context**
  N.A.
  
  </issue>
  <code>
  [start of setup.py]
  1 #!/usr/bin/env python
  2 
  3 """The setup script."""
  4 
  5 from setuptools import setup, find_packages
  6 
  7 with open("README.md") as readme_file:
  8     readme = readme_file.read()
  9 
  10 # read version.py
  11 import sys, re
  12 
  13 try:
  14     filepath = "GANDLF/version.py"
  15     version_file = open(filepath)
  16     (__version__,) = re.findall('__version__ = "(.*)"', version_file.read())
  17 
  18 except Exception as error:
  19     __version__ = "0.0.1"
  20     sys.stderr.write("Warning: Could not open '%s' due %s\n" % (filepath, error))
  21 
  22 requirements = [
  23     "black",
  24     "numpy==1.21.0",
  25     "scipy",
  26     "SimpleITK==2.1.0",
  27     "torch>=1.7",
  28     "torchvision",
  29     "tqdm",
  30     "torchio==0.18.57",
  31     "pandas",
  32     "pylint",
  33     "scikit-learn==0.23.1",
  34     "pickle5==0.0.11",
  35     "setuptools",
  36     "seaborn",
  37     "pyyaml",
  38     "openslide-python",
  39     "scikit-image",
  40     "matplotlib",
  41     "requests>=2.25.0",
  42     "pyvips",
  43     "pytest",
  44     "coverage",
  45     "psutil",
  46     "medcam",
  47     "opencv-python",
  48     "torchmetrics",
  49     "OpenPatchMiner==0.1.6",
  50     "pydicom",
  51 ]
  52 
  53 setup(
  54     name="GANDLF",
  55     version=__version__,
  56     author="Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun Güley, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos",  # alphabetical order
  57     author_email="software@cbica.upenn.edu",
  58     python_requires=">=3.6",
  59     packages=find_packages(),
  60     scripts=[
  61         "gandlf_run",
  62         "gandlf_constructCSV",
  63         "gandlf_collectStats",
  64         "gandlf_patchMiner",
  65         "gandlf_preprocess",
  66         "gandlf_anonymizer",
  67     ],
  68     classifiers=[
  69         "Development Status :: 3 - Alpha",
  70         "Intended Audience :: Science/Research",
  71         "License :: OSI Approved :: BSD License",
  72         "Natural Language :: English",
  73         "Operating System :: OS Independent",
  74         "Programming Language :: Python :: 3.6",
  75         "Programming Language :: Python :: 3.7",
  76         "Programming Language :: Python :: 3.8",
  77         "Programming Language :: Python :: 3.9",
  78         "Topic :: Scientific/Engineering :: Medical Science Apps",
  79     ],
  80     description=(
  81         "PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging."
  82     ),
  83     install_requires=requirements,
  84     license="BSD-3-Clause License",
  85     long_description=readme,
  86     long_description_content_type="text/markdown",
  87     include_package_data=True,
  88     keywords="semantic, segmentation, regression, classification, data-augmentation, medical-imaging",
  89     zip_safe=False,
  90 )
  91 
  92 import os
  93 
  94 ## submodule update
  95 os.system("git submodule update --init --recursive")
  96 
  97 ## windows vips installation
  98 if os.name == "nt":  # proceed for windows
  99     from pathlib import Path
  100 
  101     # download and extract if main dll is absent
  102     if not Path("./vips/vips-dev-8.10/bin/libvips-42.dll").exists():
  103         print("Downloading and extracting VIPS for Windows")
  104         url = "https://github.com/libvips/libvips/releases/download/v8.10.2/vips-dev-w64-all-8.10.2.zip"
  105         zip_to_extract = "./vips.zip"
  106         import urllib.request, zipfile
  107 
  108         urllib.request.urlretrieve(url, zip_to_extract)
  109         z = zipfile.ZipFile(zip_to_extract)
  110         z.extractall("./vips")
  111         z.close()
  112         os.remove(zip_to_extract)
  113
  [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
  @@ -2,11 +2,40 @@
   
   """The setup script."""
   
  +
  +import os
   from setuptools import setup, find_packages
  +from setuptools.command.install import install
  +from setuptools.command.develop import develop
  +from setuptools.command.egg_info import egg_info
   
   with open("README.md") as readme_file:
       readme = readme_file.read()
   
  +
  +def git_submodule_update():
  +    ## submodule update
  +    os.system("git submodule update --init --recursive")
  +
  +
  +class CustomInstallCommand(install):
  +    def run(self):
  +        install.run(self)
  +        git_submodule_update()
  +
  +
  +class CustomDevelopCommand(develop):
  +    def run(self):
  +        develop.run(self)
  +        git_submodule_update()
  +
  +
  +class CustomEggInfoCommand(egg_info):
  +    def run(self):
  +        egg_info.run(self)
  +        git_submodule_update()
  +
  +
   # read version.py
   import sys, re
   
  @@ -42,6 +71,7 @@
       "pyvips",
       "pytest",
       "coverage",
  +    "pytest-cov",
       "psutil",
       "medcam",
       "opencv-python",
  @@ -53,10 +83,15 @@
   setup(
       name="GANDLF",
       version=__version__,
  -    author="Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun Güley, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos",  # alphabetical order
  +    author="Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun Güley, Ibrahim Ethem Hamamci, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos",  # alphabetical order
       author_email="software@cbica.upenn.edu",
       python_requires=">=3.6",
       packages=find_packages(),
  +    cmdclass={  # this ensures git_submodule_update is called during install
  +        "install": CustomInstallCommand,
  +        "develop": CustomDevelopCommand,
  +        "egg_info": CustomEggInfoCommand,
  +    },
       scripts=[
           "gandlf_run",
           "gandlf_constructCSV",
  @@ -89,11 +124,6 @@
       zip_safe=False,
   )
   
  -import os
  -
  -## submodule update
  -os.system("git submodule update --init --recursive")
  -
   ## windows vips installation
   if os.name == "nt":  # proceed for windows
       from pathlib import Path
  
verification_info: {"golden_diff": "diff --git a/setup.py b/setup.py\n--- a/setup.py\n+++ b/setup.py\n@@ -2,11 +2,40 @@\n \n \"\"\"The setup script.\"\"\"\n \n+\n+import os\n from setuptools import setup, find_packages\n+from setuptools.command.install import install\n+from setuptools.command.develop import develop\n+from setuptools.command.egg_info import egg_info\n \n with open(\"README.md\") as readme_file:\n     readme = readme_file.read()\n \n+\n+def git_submodule_update():\n+    ## submodule update\n+    os.system(\"git submodule update --init --recursive\")\n+\n+\n+class CustomInstallCommand(install):\n+    def run(self):\n+        install.run(self)\n+        git_submodule_update()\n+\n+\n+class CustomDevelopCommand(develop):\n+    def run(self):\n+        develop.run(self)\n+        git_submodule_update()\n+\n+\n+class CustomEggInfoCommand(egg_info):\n+    def run(self):\n+        egg_info.run(self)\n+        git_submodule_update()\n+\n+\n # read version.py\n import sys, re\n \n@@ -42,6 +71,7 @@\n     \"pyvips\",\n     \"pytest\",\n     \"coverage\",\n+    \"pytest-cov\",\n     \"psutil\",\n     \"medcam\",\n     \"opencv-python\",\n@@ -53,10 +83,15 @@\n setup(\n     name=\"GANDLF\",\n     version=__version__,\n-    author=\"Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun G\u00fcley, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos\",  # alphabetical order\n+    author=\"Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun G\u00fcley, Ibrahim Ethem Hamamci, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos\",  # alphabetical order\n     author_email=\"software@cbica.upenn.edu\",\n     python_requires=\">=3.6\",\n     packages=find_packages(),\n+    cmdclass={  # this ensures git_submodule_update is called during install\n+        \"install\": CustomInstallCommand,\n+        \"develop\": CustomDevelopCommand,\n+        \"egg_info\": CustomEggInfoCommand,\n+    },\n     scripts=[\n         \"gandlf_run\",\n         \"gandlf_constructCSV\",\n@@ -89,11 +124,6 @@\n     zip_safe=False,\n )\n \n-import os\n-\n-## submodule update\n-os.system(\"git submodule update --init --recursive\")\n-\n ## windows vips installation\n if os.name == \"nt\":  # proceed for windows\n     from pathlib import Path\n", "issue": "Include a git submodule update when doing pip install\n**Is your feature request related to a problem? Please describe.**\r\nCurrently, the installation step requires a user to run `git submodule update --init --recursive` before doing `pip install`, which can lead to broken installation if the user forgets the step.\r\n\r\n**Describe the solution you'd like**\r\nEnsure the [git submodule line is working correctly in the setup.py file](https://github.com/CBICA/GaNDLF/blob/f4d0f02848c894d43259c2bb0b70612db612eb53/setup.py#L95).\r\n\r\n**Describe alternatives you've considered**\r\nN.A.\r\n\r\n**Additional context**\r\nN.A.\n", "before_files": [{"content": "#!/usr/bin/env python\n\n\"\"\"The setup script.\"\"\"\n\nfrom setuptools import setup, find_packages\n\nwith open(\"README.md\") as readme_file:\n    readme = readme_file.read()\n\n# read version.py\nimport sys, re\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==1.21.0\",\n    \"scipy\",\n    \"SimpleITK==2.1.0\",\n    \"torch>=1.7\",\n    \"torchvision\",\n    \"tqdm\",\n    \"torchio==0.18.57\",\n    \"pandas\",\n    \"pylint\",\n    \"scikit-learn==0.23.1\",\n    \"pickle5==0.0.11\",\n    \"setuptools\",\n    \"seaborn\",\n    \"pyyaml\",\n    \"openslide-python\",\n    \"scikit-image\",\n    \"matplotlib\",\n    \"requests>=2.25.0\",\n    \"pyvips\",\n    \"pytest\",\n    \"coverage\",\n    \"psutil\",\n    \"medcam\",\n    \"opencv-python\",\n    \"torchmetrics\",\n    \"OpenPatchMiner==0.1.6\",\n    \"pydicom\",\n]\n\nsetup(\n    name=\"GANDLF\",\n    version=__version__,\n    author=\"Jose Agraz, Vinayak Ahluwalia, Bhakti Baheti, Spyridon Bakas, Ujjwal Baid, Megh Bhalerao, Brandon Edwards, Karol Gotkowski, Caleb Grenko, Orhun G\u00fcley, Sarthak Pati, Micah Sheller, Juliia Skobleva, Siddhesh Thakur, Spiros Thermos\",  # alphabetical order\n    author_email=\"software@cbica.upenn.edu\",\n    python_requires=\">=3.6\",\n    packages=find_packages(),\n    scripts=[\n        \"gandlf_run\",\n        \"gandlf_constructCSV\",\n        \"gandlf_collectStats\",\n        \"gandlf_patchMiner\",\n        \"gandlf_preprocess\",\n        \"gandlf_anonymizer\",\n    ],\n    classifiers=[\n        \"Development Status :: 3 - Alpha\",\n        \"Intended Audience :: Science/Research\",\n        \"License :: OSI Approved :: BSD License\",\n        \"Natural Language :: English\",\n        \"Operating System :: OS Independent\",\n        \"Programming Language :: Python :: 3.6\",\n        \"Programming Language :: Python :: 3.7\",\n        \"Programming Language :: Python :: 3.8\",\n        \"Programming Language :: Python :: 3.9\",\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=\"BSD-3-Clause License\",\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\",\n    zip_safe=False,\n)\n\nimport os\n\n## submodule update\nos.system(\"git submodule update --init --recursive\")\n\n## windows vips installation\nif os.name == \"nt\":  # proceed for windows\n    from pathlib import Path\n\n    # download and extract if main dll is absent\n    if not Path(\"./vips/vips-dev-8.10/bin/libvips-42.dll\").exists():\n        print(\"Downloading and extracting VIPS for Windows\")\n        url = \"https://github.com/libvips/libvips/releases/download/v8.10.2/vips-dev-w64-all-8.10.2.zip\"\n        zip_to_extract = \"./vips.zip\"\n        import urllib.request, zipfile\n\n        urllib.request.urlretrieve(url, zip_to_extract)\n        z = zipfile.ZipFile(zip_to_extract)\n        z.extractall(\"./vips\")\n        z.close()\n        os.remove(zip_to_extract)\n", "path": "setup.py"}]}