Format comments

Author: willdunklin

slicer_cli_web/singularity/slicer_cli_web_singularity/commands.py

@@ -16,13 +16,14 @@ def singularity_version():
     @staticmethod
     def singularity_pull(name: str, uri: str = 'docker'):
         """
-        This method is used to generate the command for the singualrity pull function for pulling images from online.
+        This method is used to generate the command for the singualrity pull function for pulling
+        images from online.
         Args:
-        name(str.required) - Takes in a string that should specify the image name and tag as a single string '<image_name>:<tag>'
-        uri(str, optional) - If you want to pull the images from other that Dockerhub, you need to pass in that uri as a string
+        name(str.required) - image name and tag as a single string '<image_name>:<tag>'
+        uri(str, optional) - image uri (necessary for Dockerhub)
 
         Returns:
-        A list of strings formatted to be supplied to the subprocess module of python that handles  pull.
+        List of strings for singularity subprocess command.
         """
         sif_name = generate_image_name_for_singularity(name)
         return ['apptainer', 'pull', '--force', sif_name, f'{uri}://{name}']
@@ -54,8 +55,9 @@ def singularity_get_env(image: str, run_parameters=None):
     @staticmethod
     def singularity_inspect(imageName, option='-l', json_format=True):
         """
-        This function is used to get the apptainer command for inspecting the sif file. By default, it inspects the labels in a json format,
-        but you can you any option allowed by apptainer by setting the option flag appropriately and also the json flag is set to True by default.
+        This function is used to get the apptainer command for inspecting the sif file. By default,
+        it inspects the labels in a json format, but you can you any option allowed by apptainer
+        by setting the option flag appropriately and also the json flag is set to True by default.
         """
         sif_name = generate_image_name_for_singularity(imageName)
         cmd = ['apptainer', 'inspect']

slicer_cli_web/singularity/slicer_cli_web_singularity/girder_worker_plugin/direct_singularity_run.py

@@ -28,7 +28,8 @@ def __call__(self, *args, **kwargs):
 
 def check_local_sif_image(image):
     """
-    Pulls the specified Plugin image (Ususally a docker image) onto the singularity container if the image is not present
+    Pulls the specified Plugin image (Ususally a docker image) onto the singularity container
+    if the image is not present
     """
     # Image path - Image path has to be present in tmp/images folder
     if not image:

slicer_cli_web/singularity/slicer_cli_web_singularity/job.py

@@ -26,11 +26,14 @@ def is_valid_path(path):
 
 
 def is_singularity_installed(path=None):
-    """This function is used to check whether singularity is availble on the target system.
-    This function is useful to make sure that singularity is accessible from a SLURM job submitted to HiperGator
+    """
+    This function is used to check whether singularity is availble on the target system.
+    This function is useful to make sure that singularity is accessible from a SLURM job submitted
+    to HiperGator
 
     Args:
-        path (str, optional): If the user wants to provide a specific path where singularity is installed, you can provide that path. Defaults to None.
+        path (str, optional): If the user wants to provide a specific path where singularity is
+                              installed, you can provide that path. Defaults to None.
 
     Returns:
     bool: True if singualrity is successfully accessible on the target system. False otherwise
@@ -54,14 +57,16 @@ def is_singularity_installed(path=None):
 
 def find_local_singularity_image(name: str, path=''):
     """
-    Check if the image is present locally on the system in a specified path. For our usecase, we insall the images to a specific path on /blue directory, which can be modified
-    via the argument to the function
+    Check if the image is present locally on the system in a specified path. For our usecase, we
+    insall the images to a specific path on /blue directory, which can be modified via the argument
+    to the function
 
     Args:
         name(str, required) - The name of the docker image with the tag <image>:<tag>.
-        path(str, optional) - This path refers to the path on the local file system designated for placing singularity images after they are pulled from the interweb.
+        path(str, optional) - This path refers to the path on the local file system designated for
+                              placing singularity images after they are pulled from the interweb.
     Returns:
-    bool: True if the singularity image is avaialble on the given path on the local host system. False otherwise.
+    bool: True if singularity image is avaialble on the given path on host system. False otherwise.
 
     """
     try:
@@ -73,20 +78,24 @@ def find_local_singularity_image(name: str, path=''):
         path = os.getenv('SIF_IMAGE_PATH', '')
         if not is_valid_path(path):
             logger.exception(
-                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and ensure the path has appropriate access')
+                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and'
+                'ensure the path has appropriate access')
             raise Exception(
-                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and ensure the path has appropriate access')
+                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and'
+                'ensure the path has appropriate access')
     return os.path.exists(path + sif_name)
 
 
 def pull_image_and_convert_to_sif(names):
     """
-    This is the function similar to the pullDockerImage function that pulls the image from Dockerhub or other instances if it's supported in the future
+    This is the function similar to the pullDockerImage function that pulls the image from
+    Dockerhub or other instances if it's supported in the future
     Args:
-    names(List(str), required) -> The list of image names of the format <img>:<tag> provided as a string
+    names(List(str), required) -> The list of image names of the format <img>:<tag>
 
     Raises:
-    If pulling of any of the images fails, the function raises an error with the list of images that failed.
+    If pulling of any of the images fails, the function raises an error with the list of images
+    that failed.
     """
     failedImageList = []
     for name in names:
@@ -209,7 +218,9 @@ def _get_last_workdir(imageName):
 
 def get_local_singularity_output(imgName, cmdArg: str):
     """
-    This function is used to run the singularity command locally for non-resource intensive tasks such as getting schema, environment variables and so on and return that output to the calling function
+    This function is used to run the singularity command locally for non-resource intensive tasks
+    such as getting schema, environment variables and so on and return that output to the calling
+    function
     """
     try:
         pwd = _get_last_workdir(imgName)
@@ -235,9 +246,11 @@ def find_and_remove_local_sif_files(name: str, path=None):
         path = os.getenv('SIF_IMAGE_PATH', '')
         if not is_valid_path(path):
             logger.exception(
-                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and ensure the path has appropriate access')
+                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and'
+                'ensure the path has appropriate access')
             raise Exception(
-                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and ensure the path has appropriate access')
+                'Please provide a valid path or set the environment variable "SIF_IMAGE_PATH" and'
+                'ensure the path has appropriate access')
         filename = os.path.join(path, sif_name)
         if os.path.exists(filename):
             os.remove(filename)

slicer_cli_web/singularity/slicer_cli_web_singularity/singularity_image.py

@@ -38,8 +38,10 @@ def _split(name):
 
 class SingularityImage:
     """
-    This class is used to produce the Singularity equivalent of the Docker Image object as part of the Python SDK. This helps us to
-    reuse all the functions where Docker is not not directly involved rather the snapshort of the Docker Image object should suffice to perform the necessaray operations
+    This class is used to produce the Singularity equivalent of the Docker Image object as part
+    of the Python SDK. This helps us to reuse all the functions where Docker is not not directly
+    involved rather the snapshort of the Docker Image object should suffice to perform the
+    necessaray operations
     """
 
     def __init__(self, local_sif_file: str):
@@ -182,7 +184,10 @@ def _create(name, singularity_image_object, user, baseFolder):
                                        creator=user, reuseExisting=True)
 
         # add docker image labels as meta data
-        labels = {} if not singularity_image_object.labels else singularity_image_object.labels.copy()
+        labels = {}
+        if singularity_image_object.labels:
+            labels = singularity_image_object.labels.copy()
+
         if 'description' in labels:
             tag['description'] = labels['description']
             del labels['description']

slicer_cli_web/singularity/slicer_cli_web_singularity/utils.py

@@ -4,7 +4,8 @@
 
 def sanitize_and_return_json(res: str):
     """
-    This function tries to parse the given str as json in couple different ways. If the output is still not json or a python dictionary, it raises an error.
+    This function tries to parse the given str as json in couple different ways. If the output is
+    still not json or a python dictionary, it raises an error.
     """
     try:
         res = json.loads(res)
@@ -26,7 +27,8 @@ def sanitize_and_return_json(res: str):
 
 def is_valid_image_name_format(image_str: str):
     """
-    This function is used to validate whether the user supplied a valid string <img>:<tag> as an argument for functions like singularity pull
+    This function is used to validate whether the user supplied a valid string <img>:<tag> as an
+    argument for functions like singularity pull
 
     Args:
     image_str(str, required) - The string that needs to be validated.
@@ -41,7 +43,8 @@ def is_valid_image_name_format(image_str: str):
 
 def generate_image_name_for_singularity(image_str: str):
     """
-    We need to generate the image name for storing the .sif files on the filesystem so that it is standardized, so it can be referenced in future calls.
+    We need to generate the image name for storing the .sif files on the filesystem so that it is
+    standardized, so it can be referenced in future calls.
 
     Args:
     image_str (str,required) - the image_name in the format <img>:<tag>
@@ -58,11 +61,14 @@ def generate_image_name_for_singularity(image_str: str):
 
 def switch_to_sif_image_folder(image_path: str = ''):
     """
-    This function is used to handle Issues that is occuring when Singularity switches directory when running a plugin and not having the context of where the SIF IMAGES are located for subsequent image pulls.
+    This function is used to handle Issues that is occuring when Singularity switches directory
+    when running a plugin and not having the context of where the SIF IMAGES are located for
+    subsequent image pulls.
     This function ensures that Singularity always looks for the plugins in the proper location
 
     Args:
-    image_path (str, optional) - This parameter is highly optional and is not recommended unless a specific use-case arises in the future
+    image_path (str, optional) - This parameter is highly optional and is not recommended unless a
+    specific use-case arises in the future
 
     Returns:
     None