Merge branch 'staging'

lib/cli/actions.py

@@ -7,6 +7,7 @@
 
 import argparse
 import os
+from typing import Any, List, Optional, Tuple, Union
 
 
 # << FILE HANDLING >>
@@ -18,7 +19,7 @@ class _FullPaths(argparse.Action):  # pylint: disable=too-few-public-methods
     called directly. It is the base class for the various different file handling
     methods.
     """
-    def __call__(self, parser, namespace, values, option_string=None):
+    def __call__(self, parser, namespace, values, option_string=None) -> None:
         if isinstance(values, (list, tuple)):
             vals = [os.path.abspath(os.path.expanduser(val)) for val in values]
         else:
@@ -68,7 +69,7 @@ class FileFullPaths(_FullPaths):
     >>>        filetypes="video))"
     """
     # pylint: disable=too-few-public-methods
-    def __init__(self, *args, filetypes=None, **kwargs):
+    def __init__(self, *args, filetypes: Optional[str] = None, **kwargs) -> None:
         super().__init__(*args, **kwargs)
         self.filetypes = filetypes
 
@@ -110,7 +111,7 @@ class FilesFullPaths(FileFullPaths):  # pylint: disable=too-few-public-methods
     >>>        filetypes="image",
     >>>        nargs="+"))
     """
-    def __init__(self, *args, filetypes=None, **kwargs):
+    def __init__(self, *args, filetypes: Optional[str] = None, **kwargs) -> None:
         if kwargs.get("nargs", None) is None:
             opt = kwargs["option_strings"]
             raise ValueError(f"nargs must be provided for FilesFullPaths: {opt}")
@@ -144,7 +145,6 @@ class DirOrFileFullPaths(FileFullPaths):  # pylint: disable=too-few-public-metho
     >>>        action=DirOrFileFullPaths,
     >>>        filetypes="video))"
     """
-    pass  # pylint: disable=unnecessary-pass
 
 
 class DirOrFilesFullPaths(FileFullPaths):  # pylint: disable=too-few-public-methods
@@ -175,7 +175,20 @@ class DirOrFilesFullPaths(FileFullPaths):  # pylint: disable=too-few-public-meth
     >>>        action=DirOrFileFullPaths,
     >>>        filetypes="video))"
     """
-    pass  # pylint: disable=unnecessary-pass
+    def __call__(self, parser, namespace, values, option_string=None) -> None:
+        """ Override :class:`_FullPaths` __call__ function.
+
+        The input for this option can be a space separated list of files or a single folder.
+        Folders can have spaces in them, so we don't want to blindly expand the paths.
+
+        We check whether the input can be resolved to a folder first before expanding.
+        """
+        assert isinstance(values, (list, tuple))
+        folder = os.path.abspath(os.path.expanduser(" ".join(values)))
+        if os.path.isdir(folder):
+            setattr(namespace, self.dest, [folder])
+        else:  # file list so call parent method
+            super().__call__(parser, namespace, values, option_string)
 
 
 class SaveFileFullPaths(FileFullPaths):
@@ -235,7 +248,11 @@ class ContextFullPaths(FileFullPaths):
     >>>        action_option="-a"))
     """
     # pylint: disable=too-few-public-methods, too-many-arguments
-    def __init__(self, *args, filetypes=None, action_option=None, **kwargs):
+    def __init__(self,
+                 *args,
+                 filetypes: Optional[str] = None,
+                 action_option: Optional[str] = None,
+                 **kwargs) -> None:
         opt = kwargs["option_strings"]
         if kwargs.get("nargs", None) is not None:
             raise ValueError(f"nargs not allowed for ContextFullPaths: {opt}")
@@ -246,7 +263,7 @@ def __init__(self, *args, filetypes=None, action_option=None, **kwargs):
         super().__init__(*args, filetypes=filetypes, **kwargs)
         self.action_option = action_option
 
-    def _get_kwargs(self):
+    def _get_kwargs(self) -> List[Tuple[str, Any]]:
         names = ["option_strings",
                  "dest",
                  "nargs",
@@ -280,15 +297,15 @@ class Radio(argparse.Action):  # pylint: disable=too-few-public-methods
     >>>        action=Radio,
     >>>        choices=["foo", "bar"))
     """
-    def __init__(self, *args, **kwargs):
+    def __init__(self, *args, **kwargs) -> None:
         opt = kwargs["option_strings"]
         if kwargs.get("nargs", None) is not None:
             raise ValueError(f"nargs not allowed for Radio buttons: {opt}")
         if not kwargs.get("choices", []):
             raise ValueError(f"Choices must be provided for Radio buttons: {opt}")
         super().__init__(*args, **kwargs)
 
-    def __call__(self, parser, namespace, values, option_string=None):
+    def __call__(self, parser, namespace, values, option_string=None) -> None:
         setattr(namespace, self.dest, values)
 
 
@@ -308,15 +325,15 @@ class MultiOption(argparse.Action):  # pylint: disable=too-few-public-methods
     >>>        action=MultiOption,
     >>>        choices=["foo", "bar"))
     """
-    def __init__(self, *args, **kwargs):
+    def __init__(self, *args, **kwargs) -> None:
         opt = kwargs["option_strings"]
         if not kwargs.get("nargs", []):
             raise ValueError(f"nargs must be provided for MultiOption: {opt}")
         if not kwargs.get("choices", []):
             raise ValueError(f"Choices must be provided for MultiOption: {opt}")
         super().__init__(*args, **kwargs)
 
-    def __call__(self, parser, namespace, values, option_string=None):
+    def __call__(self, parser, namespace, values, option_string=None) -> None:
         setattr(namespace, self.dest, values)
 
 
@@ -363,7 +380,11 @@ class Slider(argparse.Action):  # pylint: disable=too-few-public-methods
     >>>        type=float,
     >>>        default=5.00))
     """
-    def __init__(self, *args, min_max=None, rounding=None, **kwargs):
+    def __init__(self,
+                 *args,
+                 min_max: Optional[Union[Tuple[int, int], Tuple[float, float]]] = None,
+                 rounding: Optional[int] = None,
+                 **kwargs) -> None:
         opt = kwargs["option_strings"]
         if kwargs.get("nargs", None) is not None:
             raise ValueError(f"nargs not allowed for Slider: {opt}")
@@ -380,7 +401,7 @@ def __init__(self, *args, min_max=None, rounding=None, **kwargs):
         self.min_max = min_max
         self.rounding = rounding
 
-    def _get_kwargs(self):
+    def _get_kwargs(self) -> List[Tuple[str, Any]]:
         names = ["option_strings",
                  "dest",
                  "nargs",
@@ -394,5 +415,5 @@ def _get_kwargs(self):
                  "rounding"]  # Decimal places to round floats to or step interval for ints
         return [(name, getattr(self, name)) for name in names]
 
-    def __call__(self, parser, namespace, values, option_string=None):
+    def __call__(self, parser, namespace, values, option_string=None) -> None:
         setattr(namespace, self.dest, values)

scripts/extract.py

@@ -229,7 +229,37 @@ def n_embeddings(self) -> np.ndarray:
         return retval
 
     @classmethod
-    def _validate_inputs(cls,
+    def _files_from_folder(cls, input_location: List[str]) -> List[str]:
+        """ Test whether the input location is a folder and if so, return the list of contained
+        image files, otherwise return the original input location
+
+        Parameters
+        ---------
+        input_files: list
+            A list of full paths to individual files or to a folder location
+
+        Returns
+        -------
+        bool
+            Either the original list of files provided, or the image files that exist in the
+            provided folder location
+        """
+        if not input_location or len(input_location) > 1:
+            return input_location
+
+        test_folder = input_location[0]
+        if not os.path.isdir(test_folder):
+            logger.debug("'%s' is not a folder. Returning original list", test_folder)
+            return input_location
+
+        retval = [os.path.join(test_folder, fname)
+                  for fname in os.listdir(test_folder)
+                  if os.path.splitext(fname)[-1].lower() in _image_extensions]
+        logger.info("Collected files from folder '%s': %s", test_folder,
+                    [os.path.basename(f) for f in retval])
+        return retval
+
+    def _validate_inputs(self,
                          filter_files: Optional[List[str]],
                          nfilter_files: Optional[List[str]]) -> Tuple[List[str], List[str]]:
         """ Validates that the given filter/nfilter files exist, are image files and are unique
@@ -252,17 +282,7 @@ def _validate_inputs(cls,
         retval: List[List[str]] = []
 
         for files in (filter_files, nfilter_files):
-
-            if isinstance(files, list) and len(files) == 1 and os.path.isdir(files[0]):
-                # Get images from folder, if folder passed in
-                dirname = files[0]
-                files = [os.path.join(dirname, fname)
-                         for fname in os.listdir(dirname)
-                         if os.path.splitext(fname)[-1].lower() in _image_extensions]
-                logger.debug("Collected files from folder '%s': %s", dirname,
-                             [os.path.basename(f) for f in files])
-
-            filt_files = [] if files is None else files
+            filt_files = [] if files is None else self._files_from_folder(files)
             for file in filt_files:
                 if (not os.path.isfile(file) or
                         os.path.splitext(file)[-1].lower() not in _image_extensions):