Use ruff for linting

.circleci/config.yml

@@ -202,7 +202,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: docs,flake8,lintclient
+          env: docs,lint,lintclient
       - store_artifacts:
           path: build/docs
       - persist_to_workspace:

.git-blame-ignore-revs

@@ -11,3 +11,5 @@
 497ddf38b1461da47d1d542003172603e2166b5f
 # PR 1148: Lint the client tests
 23ab7f011abaa71d0a4904a9da599174c38f64c3
+# PR 1257: Use ruff for linting
+dcda95e659a4eaa73cae85ab02f1b89059e63c32

CHANGELOG.md

@@ -10,6 +10,9 @@
 - Add an endpoint to make it easier to replace thumbnails ([#1253](../../pull/1253))
 - Presets from Large Image Configuration file ([#1248](../../pull/1248))
 
+### Changes
+- Minor code changes based on suggestions from ruff linting ([#1257](../../pull/1257))
+
 ### Bug Fixes
 - Guard against ICC profiles that won't parse ([#1245](../../pull/1245))
 - Fix filter button on item lists ([#1251](../../pull/1251))

docs/development.rst

@@ -19,7 +19,7 @@ By default, instead of storing test environments in a ``.tox`` directory, they a
 nodejs and npm for Girder Tests or Development
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-``nodejs`` version 12.x and a corresponding version of ``npm`` are required to build and test Girder client code.  See `nodejs <https://nodejs.org/en/download/>`_ for how to download and install it.  Remember to get version 12 or earlier.
+``nodejs`` version 14.x and a corresponding version of ``npm`` are required to build and test Girder client code.  See `nodejs <https://nodejs.org/en/download/>`_ for how to download and install it.  Remember to get version 12 or 14.
 
 Mongo for Girder Tests or Development
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -33,13 +33,13 @@ Tests are run via tox environments:
 
 .. code-block:: bash
 
-    tox -e test-py39,flake8,lintclient
+    tox -e test-py39,lint,lintclient
 
 Or, without Girder:
 
 .. code-block:: bash
 
-    tox -e core-py39,flake8
+    tox -e core-py39,lint
 
 You can build the docs.  They are created in the ``docs/build`` directory:
 

examples/algorithm_progression.py

@@ -64,8 +64,8 @@ def apply_algorithm(algorithm, input_filename, output_dir, params, param_space,
     filepath = Path(output_dir, filename)
 
     desc = dict(
-        **{'path': filename},
-        **{VARIABLE_LAYERS[i]: v for i, v in enumerate(iteration_id)}
+        path=filename,
+        **{VARIABLE_LAYERS[i]: v for i, v in enumerate(iteration_id)},
     )
 
     source = large_image.open(input_filename)
@@ -145,15 +145,16 @@ def sweep_algorithm(algorithm, input_filename, input_params, param_oder, output_
         input_params = {}
     input_params = {
         key: np.linspace(
-            float(value[0]), float(value[1]), int(value[2]), endpoint=len(value) > 3
+            float(value[0]), float(value[1]), int(value[2]), endpoint=len(value) > 3,
         )
         for key, value in input_params.items()
         if len(value) >= 3
     }
     param_order = list(input_params.keys())
 
     if not Path(input_filename).exists():
-        raise ValueError(f'Cannot locate file {input_filename}.')
+        msg = f'Cannot locate file {input_filename}.'
+        raise ValueError(msg)
 
     algorithm = algorithms.ALGORITHM_CODES[algorithm_code]
     sig = inspect.signature(algorithm)

examples/algorithms.py

@@ -16,17 +16,15 @@ def rgb_to_hsi(im):
     """
     im = np.moveaxis(im, -1, 0)
     if len(im) not in (3, 4):
-        raise ValueError(
-            'Expected 3-channel RGB or 4-channel RGBA image; '
-            'received a {}-channel image'.format(len(im))
-        )
+        msg = f'Expected 3-channel RGB or 4-channel RGBA image; received a {len(im)}-channel image'
+        raise ValueError(msg)
     im = im[:3]
     hues = (
         np.arctan2(3**0.5 * (im[1] - im[2]), 2 * im[0] - im[1] - im[2]) / (2 * np.pi)
     ) % 1
     intensities = im.mean(0)
     saturations = np.where(
-        intensities, 1 - im.min(0) / np.maximum(intensities, 1e-10), 0
+        intensities, 1 - im.min(0) / np.maximum(intensities, 1e-10), 0,
     )
     return np.stack([hues, saturations, intensities], -1)
 

examples/average_color.py

@@ -3,7 +3,7 @@
 
 import argparse
 
-import numpy
+import numpy as np
 
 import large_image
 
@@ -36,13 +36,13 @@ def average_color(imagePath, magnification=None):
             resample=True):
         # The tile image data is in tile['tile'] and is a numpy
         # multi-dimensional array
-        mean = numpy.mean(tile['tile'], axis=(0, 1))
+        mean = np.mean(tile['tile'], axis=(0, 1))
         tileMeans.append(mean)
         tileWeights.append(tile['width'] * tile['height'])
         print('x: %d  y: %d  w: %d  h: %d  mag: %g  color: %g %g %g' % (
             tile['x'], tile['y'], tile['width'], tile['height'],
             tile['magnification'], mean[0], mean[1], mean[2]))
-    mean = numpy.average(tileMeans, axis=0, weights=tileWeights)
+    mean = np.average(tileMeans, axis=0, weights=tileWeights)
     print('Average color: %g %g %g' % (mean[0], mean[1], mean[2]))
     return mean
 

examples/sumsquare_color.py

@@ -3,7 +3,7 @@
 
 import argparse
 
-import numpy
+import numpy as np
 
 import large_image
 
@@ -33,12 +33,12 @@ def sum_squares(imagePath, magnification=None, **kwargs):
             tile['tile_overlap']['left']:
                 data.shape[1] - tile['tile_overlap']['right'],
             :]
-        sumsq = numpy.sum(data**2, axis=(0, 1))
+        sumsq = np.sum(data**2, axis=(0, 1))
         tileSumSquares.append(sumsq)
         print('x: %d  y: %d  w: %d  h: %d  mag: %g  sums: %d %d %d' % (
             tile['x'], tile['y'], tile['width'], tile['height'],
             tile['magnification'], sumsq[0], sumsq[1], sumsq[2]))
-    sumsq = numpy.sum(tileSumSquares, axis=0)
+    sumsq = np.sum(tileSumSquares, axis=0)
     print('Sum of squares: %d %d %d' % (sumsq[0], sumsq[1], sumsq[2]))
     return sumsq
 

girder/girder_large_image/__init__.py

@@ -153,7 +153,7 @@ def _updateJob(event):
                 'job_id': job['_id'],
                 'item_id': item['_id'],
                 'success': status == JobStatus.SUCCESS,
-                'status': status
+                'status': status,
             },
             user={'_id': job.get('userId')},
             expires=datetime.datetime.utcnow() + datetime.timedelta(seconds=30))
@@ -294,7 +294,8 @@ def metadataSearchHandler(  # noqa
     if any(typ not in models for typ in types):
         raise RestException('The metadata search is only able to search in %r.' % models)
     if not isinstance(query, str):
-        raise RestException('The search query must be a string.')
+        msg = 'The search query must be a string.'
+        raise RestException(msg)
     # If we have the beginning of the field specifier, don't do a search
     if re.match(r'^(k|ke|key|key:)$', query.strip()):
         return {k: [] for k in types}
@@ -307,7 +308,7 @@ def metadataSearchHandler(  # noqa
         pipeline = [
             {'$project': {'arrayofkeyvalue': {'$objectToArray': '$$ROOT.%s' % metakey}}},
             {'$unwind': '$arrayofkeyvalue'},
-            {'$group': {'_id': None, 'allkeys': {'$addToSet': '$arrayofkeyvalue.k'}}}
+            {'$group': {'_id': None, 'allkeys': {'$addToSet': '$arrayofkeyvalue.k'}}},
         ]
         for model in (searchModels or types):
             modelInst = ModelImporter.model(*model if isinstance(model, tuple) else [model])
@@ -588,7 +589,7 @@ def validateNonnegativeInteger(doc):
 
 
 @setting_utilities.validator({
-    constants.PluginSettings.LARGE_IMAGE_DEFAULT_VIEWER
+    constants.PluginSettings.LARGE_IMAGE_DEFAULT_VIEWER,
 })
 def validateDefaultViewer(doc):
     doc['value'] = str(doc['value']).strip()

girder/girder_large_image/loadmodelcache.py

@@ -79,6 +79,6 @@ def loadModel(resource, model, plugin='_core', id=None, allowCookie=False,
             'tokenId': tokenStr,
             'expiry': time.time() + LoadModelCacheExpiryDuration,
             'result': entry,
-            'hits': 0
+            'hits': 0,
         }
     return entry

girder/girder_large_image/models/image_item.py

@@ -62,14 +62,15 @@ def createImageItem(self, item, fileObj, user=None, token=None,
         logger.info('createImageItem called on item %s (%s)', item['_id'], item['name'])
         # Using setdefault ensures that 'largeImage' is in the item
         if 'fileId' in item.setdefault('largeImage', {}):
-            raise TileGeneralError('Item already has largeImage set.')
+            msg = 'Item already has largeImage set.'
+            raise TileGeneralError(msg)
         if fileObj['itemId'] != item['_id']:
-            raise TileGeneralError(
-                'The provided file must be in the provided item.')
+            msg = 'The provided file must be in the provided item.'
+            raise TileGeneralError(msg)
         if (item['largeImage'].get('expected') is True and
                 'jobId' in item['largeImage']):
-            raise TileGeneralError(
-                'Item is scheduled to generate a largeImage.')
+            msg = 'Item is scheduled to generate a largeImage.'
+            raise TileGeneralError(msg)
 
         item['largeImage'].pop('expected', None)
         item['largeImage'].pop('sourceName', None)
@@ -90,8 +91,8 @@ def createImageItem(self, item, fileObj, user=None, token=None,
                 logger.info(
                     'createImageItem will not use item %s (%s) as a largeImage',
                     item['_id'], item['name'])
-                raise TileGeneralError(
-                    'A job must be used to generate a largeImage.')
+                msg = 'A job must be used to generate a largeImage.'
+                raise TileGeneralError(msg)
             logger.debug(
                 'createImageItem creating a job to generate a largeImage for item %s (%s)',
                 item['_id'], item['name'])
@@ -175,8 +176,8 @@ def _createLargeImageLocalJob(
 
     def convertImage(self, item, fileObj, user=None, token=None, localJob=True, **kwargs):
         if fileObj['itemId'] != item['_id']:
-            raise TileGeneralError(
-                'The provided file must be in the provided item.')
+            msg = 'The provided file must be in the provided item.'
+            raise TileGeneralError(msg)
         if not localJob:
             return self._createLargeImageJob(item, fileObj, user, token, toFolder=True, **kwargs)
         return self._createLargeImageLocalJob(item, fileObj, user, toFolder=True, **kwargs)
@@ -220,10 +221,11 @@ def _tileFromHash(cls, item, x, y, z, mayRedirect=False, **kwargs):
     @classmethod
     def _loadTileSource(cls, item, **kwargs):
         if 'largeImage' not in item:
-            raise TileSourceError('No large image file in this item.')
+            msg = 'No large image file in this item.'
+            raise TileSourceError(msg)
         if item['largeImage'].get('expected'):
-            raise TileSourceError('The large image file for this item is '
-                                  'still pending creation.')
+            msg = 'The large image file for this item is still pending creation.'
+            raise TileSourceError(msg)
 
         sourceName = item['largeImage']['sourceName']
         try:
@@ -374,7 +376,7 @@ def _getAndCacheImageOrData(
         if not hasattr(self, '_getAndCacheImageOrDataLock'):
             self._getAndCacheImageOrDataLock = {
                 'keys': {},
-                'lock': threading.Lock()
+                'lock': threading.Lock(),
             }
         keylock = None
         with self._getAndCacheImageOrDataLock['lock']:

girder/girder_large_image/rest/__init__.py

@@ -81,16 +81,16 @@ def _itemFindRecursive(self, origItemFind, folderId, text, name, limit, offset,
                 'connectToField': 'parentId',
                 'depthField': '_depth',
                 'as': '_folder',
-                'startWith': '$_id'
+                'startWith': '$_id',
             }},
-            {'$group': {'_id': '$_folder._id'}}
+            {'$group': {'_id': '$_folder._id'}},
         ]
         children = [ObjectId(folderId)] + next(Folder().collection.aggregate(pipeline))['_id']
         if len(children) > 1:
             filters = (filters.copy() if filters else {})
             if text:
                 filters['$text'] = {
-                    '$search': text
+                    '$search': text,
                 }
             if name:
                 filters['name'] = name
@@ -121,7 +121,7 @@ def _itemFindRecursive(self, origItemFind, folderId, text, name, limit, offset,
         'for admins).')
     .modelParam('id', model=Folder, level=AccessType.READ)
     .param('name', 'The name of the file.', paramType='path')
-    .errorResponse()
+    .errorResponse(),
 )
 @boundHandler()
 def getYAMLConfigFile(self, folder, name):
@@ -142,7 +142,7 @@ def getYAMLConfigFile(self, folder, name):
     .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.',
-           paramType='body')
+           paramType='body'),
 )
 @boundHandler()
 def putYAMLConfigFile(self, folder, name, config):

girder/girder_large_image/rest/item_meta.py

@@ -25,13 +25,13 @@ class InternalMetadataItemResource(Item):
     def __init__(self, apiRoot):
         super().__init__()
         apiRoot.item.route(
-            'GET', (':itemId', 'internal_metadata', ':key'), self.getMetadataKey
+            'GET', (':itemId', 'internal_metadata', ':key'), self.getMetadataKey,
         )
         apiRoot.item.route(
-            'PUT', (':itemId', 'internal_metadata', ':key'), self.updateMetadataKey
+            'PUT', (':itemId', 'internal_metadata', ':key'), self.updateMetadataKey,
         )
         apiRoot.item.route(
-            'DELETE', (':itemId', 'internal_metadata', ':key'), self.deleteMetadataKey
+            'DELETE', (':itemId', 'internal_metadata', ':key'), self.deleteMetadataKey,
         )
 
     @describeRoute(
@@ -44,7 +44,7 @@ def __init__(self, apiRoot):
             default='meta',
         )
         .errorResponse('ID was invalid.')
-        .errorResponse('Read access was denied for the item.', 403)
+        .errorResponse('Read access was denied for the item.', 403),
     )
     @access.user(scope=TokenScope.DATA_READ)
     @loadmodel(model='item', map={'itemId': 'item'}, level=AccessType.READ)
@@ -55,7 +55,7 @@ def getMetadataKey(self, item, key, params):
 
     @describeRoute(
         Description(
-            'Overwrite the value for a single internal metadata key on this item.'
+            'Overwrite the value for a single internal metadata key on this item.',
         )
         .param('itemId', 'The ID of the item.', paramType='path')
         .param(
@@ -72,7 +72,7 @@ def getMetadataKey(self, item, key, params):
             paramType='body',
         )
         .errorResponse('ID was invalid.')
-        .errorResponse('Write access was denied for the item.', 403)
+        .errorResponse('Write access was denied for the item.', 403),
     )
     @access.user(scope=TokenScope.DATA_WRITE)
     @loadmodel(model='item', map={'itemId': 'item'}, level=AccessType.WRITE)
@@ -90,7 +90,7 @@ def updateMetadataKey(self, item, key, params):
             default='meta',
         )
         .errorResponse('ID was invalid.')
-        .errorResponse('Write access was denied for the item.', 403)
+        .errorResponse('Write access was denied for the item.', 403),
     )
     @access.user(scope=TokenScope.DATA_WRITE)
     @loadmodel(model='item', map={'itemId': 'item'}, level=AccessType.READ)