Merge pull request #1188 from girder/code-cleanup

Minor code cleanup as recommended by pyupgrade.

docs/girder_config_options.rst

@@ -32,7 +32,7 @@ The yaml file has the following structure:
       # admin users get these settings
       admin:
         <key>: <value>
-    # The groups key specifes that specific user groups have distinct settings
+    # The groups key specifies that specific user groups have distinct settings
     groups:
       <group name>:
         <key>: <value>

girder/girder_large_image/__init__.py

@@ -293,8 +293,8 @@ def metadataSearchHandler(  # noqa
     if re.match(r'^(k|ke|key|key:)$', query.strip()):
         return {k: [] for k in types}
     phrases = re.findall(r'"[^"]*"|\'[^\']*\'|\S+', query)
-    fields = set(phrase.split('key:', 1)[1] for phrase in phrases
-                 if phrase.startswith('key:') and len(phrase.split('key:', 1)[1]))
+    fields = {phrase.split('key:', 1)[1] for phrase in phrases
+              if phrase.startswith('key:') and len(phrase.split('key:', 1)[1])}
     phrases = [phrase for phrase in phrases
                if not phrase.startswith('key:') or not len(phrase.split('key:', 1)[1])]
     if not len(fields):

girder/girder_large_image/models/image_item.py

@@ -220,7 +220,7 @@ def _tileFromHash(cls, item, x, y, z, mayRedirect=False, **kwargs):
                 tileData = tileCache[tileHash]
             else:
                 # It would be nice if we could test if tileHash was in
-                # tileCache, but memcached doesn't expose that functionaility
+                # tileCache, but memcached doesn't expose that functionality
                 with tileCacheLock:
                     tileData = tileCache[tileHash]
             tileMime = TileOutputMimeTypes.get(kwargs.get('encoding'), 'image/jpeg')
@@ -251,10 +251,10 @@ def _loadTileSource(cls, item, **kwargs):
                 file = File().load(item['largeImage']['fileId'], force=True)
                 localPath = File().getLocalFilePath(file)
                 open(localPath, 'rb').read(1)
-            except IOError:
+            except OSError:
                 logger.warning(
                     'Is the original data reachable and readable (it fails via %r)?', localPath)
-                raise IOError(localPath) from None
+                raise OSError(localPath) from None
             except Exception:
                 pass
             raise exc

girder/girder_large_image/rest/__init__.py

@@ -138,7 +138,7 @@ def getYAMLConfigFile(self, folder, name):
         'This replaces or creates an item in the specified folder with the '
         'specified name containing a single file also of the specified '
         'name.  The file is added to the default assetstore, and any existing '
-        'file may be permamently deleted.')
+        'file may be permanently deleted.')
     .modelParam('id', model=Folder, level=AccessType.WRITE)
     .param('name', 'The name of the file.', paramType='path')
     .param('config', 'The contents of yaml config file to validate.',

girder/girder_large_image/rest/tiles.py

@@ -636,7 +636,7 @@ def getDZITile(self, item, level, xandy, params):
         overlap = int(params.get('overlap', 0))
         if overlap < 0:
             raise RestException('Invalid overlap', code=400)
-        x, y = [int(xy) for xy in xandy.split('.')[0].split('_')]
+        x, y = (int(xy) for xy in xandy.split('.')[0].split('_'))
         _handleETag('getDZITile', item, level, xandy, params)
         metadata = self.imageItemModel.getMetadata(item, **params)
         level = int(level)

girder/girder_large_image/web_client/templates/itemView.pug

@@ -62,9 +62,9 @@ if metadataList.length
 if Array.isArray(extra.images)
   for ikey in extra.images
     if ikey === '*'
-      for likey in largeImageMetadata.images
-        if imageList.indexOf(likey) < 0
-          - imageList.push(likey);
+      for li_key in largeImageMetadata.images
+        if imageList.indexOf(li_key) < 0
+          - imageList.push(li_key);
     else if largeImageMetadata.images.indexOf(ikey) >= 0 && imageList.indexOf(ikey) < 0
       - imageList.push(ikey);
 if imageList.length

girder/girder_large_image/web_client/views/imageViewerWidget/geojs.js

@@ -157,7 +157,7 @@ var GeojsImageViewerWidget = ImageViewerWidget.extend({
             this._style = undefined;
             this._baseurl = this._layer.url();
             // use two layers to get smooth transitions until we load
-            // background quads.  Always cteate this, as styles will use
+            // background quads.  Always create this, as styles will use
             // this, even if pure frame do not.
             this._layer2 = this.viewer.createLayer('osm', this._layer._options);
             if (this._layer2.zIndex() > this._layer.zIndex()) {

girder/test_girder/test_tiles_rest.py

@@ -479,8 +479,9 @@ def testTilesDeleteJob(boundServer, admin, fsAssetstore, girderWorker):
                               data={'countdown': 10, 'fileId': fileId})
     assert result is None
     # If we end the test here, girder_worker may upload a file that gets
-    # discarded, but do so in a manner that interfers with cleaning up the test
-    # temp directory.  By running other tasks, this is less likely to occur.
+    # discarded, but do so in a manner that interferes with cleaning up the
+    # test temp directory.  By running other tasks, this is less likely to
+    # occur.
 
     # Creating it again should work
     tileMetadata = _postTileViaHttp(boundServer, admin, itemId, fileId)

large_image/tilesource/base.py

@@ -267,7 +267,7 @@ def _ignoreSourceNames(self, configKey, path, default=None):
         """
         Given a path, if it is an actual file and there is a setting
         "source_<configKey>_ignored_names", raise a TileSoruceError if the
-        path matches the ignore names setting regex in a case-insensitve
+        path matches the ignore names setting regex in a case-insensitive
         search.
 
         :param configKey: key to use to fetch value from settings.

large_image/tilesource/utilities.py

@@ -68,7 +68,7 @@ class JSONDict(dict):
     """Wrapper class to improve Jupyter repr of JSON-able dicts."""
 
     def __init__(self, *args, **kwargs):
-        super(JSONDict, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         # TODO: validate JSON serializable?
 
     def _repr_json_(self):

setup.py

@@ -66,10 +66,10 @@ def prerelease_local_scheme(version):
 }
 extraReqs.update(sources)
 extraReqs['sources'] = list(set(itertools.chain.from_iterable(sources.values())))
-extraReqs['all'] = list(set(itertools.chain.from_iterable(extraReqs.values())) | set([
+extraReqs['all'] = list(set(itertools.chain.from_iterable(extraReqs.values())) | {
     f'large-image-source-pil[all]{limit_version}',
     f'large-image-source-rasterio[all]{limit_version} ; python_version >= "3.8"',
-]))
+})
 
 setup(
     name='large-image',

sources/deepzoom/large_image_source_deepzoom/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import builtins
 import math
 import os

sources/deepzoom/large_image_source_deepzoom/girder_source.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 from girder_large_image.girder_tilesource import GirderTileSource
 
 from . import DeepzoomFileTileSource

sources/multi/large_image_source_multi/__init__.py

@@ -945,7 +945,7 @@ def _addSourceToTile(self, tile, sourceEntry, corners, scale):
             and the frame within the source to fetch.
         :param corners: the four corners of the tile in the main image space
             coordinates.
-        :param scale: power of 2 scale of the output; this is tne number of
+        :param scale: power of 2 scale of the output; this is the number of
             pixels that are conceptually aggregated from the source for one
             output pixel.
         :returns: a numpy array of the tile.

sources/rasterio/large_image_source_rasterio/__init__.py

@@ -990,7 +990,7 @@ def validateCOG(self, strict=True, warn=True):
         try:
             from rio_cogeo.cogeo import cog_validate
         except ImportError:
-            raise ImportError('Please insall `rio-cogeo` to check COG validity.')
+            raise ImportError('Please install `rio-cogeo` to check COG validity.')
 
         isValid, errors, warnings = cog_validate(self._largeImagePath, strict=strict)
 

sources/tiff/large_image_source_tiff/tiff_reader.py

@@ -375,7 +375,7 @@ def _toTileNum(self, x, y, transpose=False):
         :param y: The row index of the desired tile.
         :type y: int
         :param transpose: If true, transpose width and height
-        :type tranpose: boolean
+        :type transpose: boolean
         :return: The internal tile number of the desired tile.
         :rtype int
         :raises: InvalidOperationTiffError

sources/vips/large_image_source_vips/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import math
 import os
 import threading

sources/vips/large_image_source_vips/girder_source.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 from girder_large_image.girder_tilesource import GirderTileSource
 
 from . import VipsFileTileSource

utilities/converter/large_image_converter/__init__.py

@@ -746,7 +746,7 @@ def _is_multiframe(path):
             raise
         except Exception:
             logger.warning('Is the file reachable and readable? (%r)', path)
-            raise IOError(path) from None
+            raise OSError(path) from None
     pages = 1
     if 'n-pages' in image.get_fields():
         pages = image.get_value('n-pages')