prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Add histology exception tests
  **Is your feature request related to a problem? Please describe.**
  Currently, the histology inference pipeline contains a lot of exceptions, but they aren't being tested.
  
  **Describe the solution you'd like**
  See title.
  
  **Describe alternatives you've considered**
  N.A.
  
  **Additional context**
  N.A.
  
  
  --- 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 os
  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 with open("README.md") as readme_file:
  13     readme = readme_file.read()
  14 
  15 
  16 def git_submodule_update():
  17     ## submodule update
  18     os.system("git submodule update --init --recursive")
  19 
  20 
  21 class CustomInstallCommand(install):
  22     def run(self):
  23         install.run(self)
  24         git_submodule_update()
  25 
  26 
  27 class CustomDevelopCommand(develop):
  28     def run(self):
  29         develop.run(self)
  30         git_submodule_update()
  31 
  32 
  33 class CustomEggInfoCommand(egg_info):
  34     def run(self):
  35         egg_info.run(self)
  36         git_submodule_update()
  37 
  38 
  39 # read version.py
  40 import sys, re
  41 
  42 try:
  43     filepath = "GANDLF/version.py"
  44     version_file = open(filepath)
  45     (__version__,) = re.findall('__version__ = "(.*)"', version_file.read())
  46 
  47 except Exception as error:
  48     __version__ = "0.0.1"
  49     sys.stderr.write("Warning: Could not open '%s' due %s\n" % (filepath, error))
  50 
  51 requirements = [
  52     "black",
  53     "numpy==1.22.0",
  54     "scipy",
  55     "SimpleITK!=2.0.*",
  56     "torchvision",
  57     "tqdm",
  58     "torchio==0.18.57",
  59     "pandas",
  60     "pylint",
  61     "scikit-learn>=0.23.2",
  62     "scikit-image>=0.19.1",
  63     'pickle5>=0.0.11; python_version < "3.8.0"',
  64     "setuptools",
  65     "seaborn",
  66     "pyyaml",
  67     "tiffslide",
  68     "matplotlib",
  69     "requests>=2.25.0",
  70     "pyvips",
  71     "pytest",
  72     "coverage",
  73     "pytest-cov",
  74     "psutil",
  75     "medcam",
  76     "opencv-python",
  77     "torchmetrics==0.5.1",  # newer versions have changed api for f1 invocation
  78     "OpenPatchMiner==0.1.8",
  79     "zarr==2.10.3",
  80     "pydicom",
  81     "onnx",
  82     "torchinfo==1.7.0",
  83 ]
  84 
  85 # pytorch doesn't have LTS support on OSX - https://github.com/CBICA/GaNDLF/issues/389
  86 if sys.platform == "darwin":
  87     requirements.append("torch==1.9.0")
  88 else:
  89     requirements.append("torch==1.8.2")
  90 
  91 setup(
  92     name="GANDLF",
  93     version=__version__,
  94     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
  95     author_email="software@cbica.upenn.edu",
  96     python_requires=">=3.7",
  97     packages=find_packages(),
  98     cmdclass={  # this ensures git_submodule_update is called during install
  99         "install": CustomInstallCommand,
  100         "develop": CustomDevelopCommand,
  101         "egg_info": CustomEggInfoCommand,
  102     },
  103     scripts=[
  104         "gandlf_run",
  105         "gandlf_constructCSV",
  106         "gandlf_collectStats",
  107         "gandlf_patchMiner",
  108         "gandlf_preprocess",
  109         "gandlf_anonymizer",
  110         "gandlf_verifyInstall",
  111     ],
  112     classifiers=[
  113         "Development Status :: 3 - Alpha",
  114         "Intended Audience :: Science/Research",
  115         "License :: OSI Approved :: BSD License",
  116         "Natural Language :: English",
  117         "Operating System :: OS Independent",
  118         "Programming Language :: Python :: 3.7",
  119         "Programming Language :: Python :: 3.8",
  120         "Programming Language :: Python :: 3.9",
  121         "Topic :: Scientific/Engineering :: Medical Science Apps",
  122     ],
  123     description=(
  124         "PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging."
  125     ),
  126     install_requires=requirements,
  127     license="BSD-3-Clause License",
  128     long_description=readme,
  129     long_description_content_type="text/markdown",
  130     include_package_data=True,
  131     keywords="semantic, segmentation, regression, classification, data-augmentation, medical-imaging",
  132     zip_safe=False,
  133 )
  134 
  135 ## windows vips installation
  136 if os.name == "nt":  # proceed for windows
  137     from pathlib import Path
  138 
  139     # download and extract if main dll is absent
  140     if not Path("./vips/vips-dev-8.10/bin/libvips-42.dll").exists():
  141         print("Downloading and extracting VIPS for Windows")
  142         url = "https://github.com/libvips/libvips/releases/download/v8.10.2/vips-dev-w64-all-8.10.2.zip"
  143         zip_to_extract = "./vips.zip"
  144         import urllib.request, zipfile
  145 
  146         urllib.request.urlretrieve(url, zip_to_extract)
  147         z = zipfile.ZipFile(zip_to_extract)
  148         z.extractall("./vips")
  149         z.close()
  150         os.remove(zip_to_extract)
  151
  ```
  --- 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()
  
  ```
  
golden_diff: diff --git a/setup.py b/setup.py
  --- a/setup.py
  +++ b/setup.py
  @@ -67,7 +67,7 @@
       "tiffslide",
       "matplotlib",
       "requests>=2.25.0",
  -    "pyvips",
  +    "pyvips==2.2.1",
       "pytest",
       "coverage",
       "pytest-cov",
  
verification_info: {"golden_diff": "diff --git a/setup.py b/setup.py\n--- a/setup.py\n+++ b/setup.py\n@@ -67,7 +67,7 @@\n     \"tiffslide\",\n     \"matplotlib\",\n     \"requests>=2.25.0\",\n-    \"pyvips\",\n+    \"pyvips==2.2.1\",\n     \"pytest\",\n     \"coverage\",\n     \"pytest-cov\",\n", "issue": "Add histology exception tests\n**Is your feature request related to a problem? Please describe.**\r\nCurrently, the histology inference pipeline contains a lot of exceptions, but they aren't being tested.\r\n\r\n**Describe the solution you'd like**\r\nSee title.\r\n\r\n**Describe alternatives you've considered**\r\nN.A.\r\n\r\n**Additional context**\r\nN.A.\r\n\n", "before_files": [{"content": "#!/usr/bin/env python\n\n\"\"\"The setup script.\"\"\"\n\n\nimport os\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\nwith open(\"README.md\") as readme_file:\n    readme = readme_file.read()\n\n\ndef git_submodule_update():\n    ## submodule update\n    os.system(\"git submodule update --init --recursive\")\n\n\nclass CustomInstallCommand(install):\n    def run(self):\n        install.run(self)\n        git_submodule_update()\n\n\nclass CustomDevelopCommand(develop):\n    def run(self):\n        develop.run(self)\n        git_submodule_update()\n\n\nclass CustomEggInfoCommand(egg_info):\n    def run(self):\n        egg_info.run(self)\n        git_submodule_update()\n\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==1.22.0\",\n    \"scipy\",\n    \"SimpleITK!=2.0.*\",\n    \"torchvision\",\n    \"tqdm\",\n    \"torchio==0.18.57\",\n    \"pandas\",\n    \"pylint\",\n    \"scikit-learn>=0.23.2\",\n    \"scikit-image>=0.19.1\",\n    'pickle5>=0.0.11; python_version < \"3.8.0\"',\n    \"setuptools\",\n    \"seaborn\",\n    \"pyyaml\",\n    \"tiffslide\",\n    \"matplotlib\",\n    \"requests>=2.25.0\",\n    \"pyvips\",\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]\n\n# pytorch doesn't have LTS support on OSX - https://github.com/CBICA/GaNDLF/issues/389\nif sys.platform == \"darwin\":\n    requirements.append(\"torch==1.9.0\")\nelse:\n    requirements.append(\"torch==1.8.2\")\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, 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=\">=3.7\",\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        \"gandlf_collectStats\",\n        \"gandlf_patchMiner\",\n        \"gandlf_preprocess\",\n        \"gandlf_anonymizer\",\n        \"gandlf_verifyInstall\",\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 :: 3.7\",\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\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"}], "after_files": [{"content": "#!/usr/bin/env python\n\n\"\"\"The setup script.\"\"\"\n\n\nimport os\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\nwith open(\"README.md\") as readme_file:\n    readme = readme_file.read()\n\n\ndef git_submodule_update():\n    ## submodule update\n    os.system(\"git submodule update --init --recursive\")\n\n\nclass CustomInstallCommand(install):\n    def run(self):\n        install.run(self)\n        git_submodule_update()\n\n\nclass CustomDevelopCommand(develop):\n    def run(self):\n        develop.run(self)\n        git_submodule_update()\n\n\nclass CustomEggInfoCommand(egg_info):\n    def run(self):\n        egg_info.run(self)\n        git_submodule_update()\n\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==1.22.0\",\n    \"scipy\",\n    \"SimpleITK!=2.0.*\",\n    \"torchvision\",\n    \"tqdm\",\n    \"torchio==0.18.57\",\n    \"pandas\",\n    \"pylint\",\n    \"scikit-learn>=0.23.2\",\n    \"scikit-image>=0.19.1\",\n    'pickle5>=0.0.11; python_version < \"3.8.0\"',\n    \"setuptools\",\n    \"seaborn\",\n    \"pyyaml\",\n    \"tiffslide\",\n    \"matplotlib\",\n    \"requests>=2.25.0\",\n    \"pyvips==2.2.1\",\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]\n\n# pytorch doesn't have LTS support on OSX - https://github.com/CBICA/GaNDLF/issues/389\nif sys.platform == \"darwin\":\n    requirements.append(\"torch==1.9.0\")\nelse:\n    requirements.append(\"torch==1.8.2\")\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, 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=\">=3.7\",\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        \"gandlf_collectStats\",\n        \"gandlf_patchMiner\",\n        \"gandlf_preprocess\",\n        \"gandlf_anonymizer\",\n        \"gandlf_verifyInstall\",\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 :: 3.7\",\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\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"}]}