STYLE: Update python code with statement fixes

This fixes many of the pycodestyle E7 statement error codes.

Bulk of updates performed using autopep8 CLI
with the following command:

  autopep8 --in-place --select E701,E703,E712,E713,E714,E741 $(git ls-files '*.py')

See https://github.com/hhatto/autopep8#readme

References:

* Multiple statements on one line (colon)
  See https://www.flake8rules.com/rules/E701.html

* Statement ends with a semicolon
  See https://www.flake8rules.com/rules/E703.html

* Comparison to true should be 'if cond is true:' or 'if cond:'
  See https://www.flake8rules.com/rules/E712.html

* Test for membership should be 'not in'
  See https://www.flake8rules.com/rules/E713.html

* Test for object identity should be 'is not'
  See https://www.flake8rules.com/rules/E714.html

* Do not use variables named 'I', 'O', or 'l'
  See https://www.flake8rules.com/rules/E741.html

.flake8

@@ -46,22 +46,10 @@ ignore = \
   E402, \
   # the backslash is redundant between bracket
   E502, \
-  # multiple statements on one line (colon)
-  E701, \
-  # statement ends with a semicolon
-  E703, \
-  # comparison to True should be 'if cond is True:' or 'if cond:'
-  E712, \
-  # test for membership should be 'not in'
-  E713, \
-  # test for object identity should be 'is not'
-  E714, \
   # do not use bare 'except'
   E722, \
   # do not assign a lambda expression, use a def
   E731, \
-  # ambiguous variable name 'l'
-  E741, \
   # 'from module import *' used; unable to detect undefined names
   F403, \
   # Name may be undefined, or defined from star import

Applications/SlicerApp/Testing/Python/MeasureStartupTimes.py

@@ -49,8 +49,10 @@ def collect_startup_times_normal(output_file, drop_cache=False, display_output=F
     (duration, result) = runSlicerAndExitWithTime(slicer_executable, test, drop_cache=drop_cache)
     (returnCode, stdout, stderr) = result
     if display_output:
-        if stdout: print("STDOUT [%s]\n" % stdout)
-        if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+        if stdout:
+            print("STDOUT [%s]\n" % stdout)
+        if stderr and returnCode == EXIT_SUCCESS:
+            print("STDERR [%s]\n" % stderr)
     results[" ".join(test)] = duration
     with open(output_file, 'w') as file:
         file.write(json.dumps(results, indent=4))
@@ -84,8 +86,10 @@ def collect_startup_times_overall(output_file, drop_cache=False, display_output=
 
         (returnCode, stdout, stderr) = result
         if display_output:
-            if stdout: print("STDOUT [%s]\n" % stdout)
-            if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+            if stdout:
+                print("STDOUT [%s]\n" % stdout)
+            if stderr and returnCode == EXIT_SUCCESS:
+                print("STDERR [%s]\n" % stderr)
 
     with open(output_file, 'w') as file:
         file.write(json.dumps(results, indent=4))
@@ -155,8 +159,10 @@ def collect_startup_times_including_one_module(output_file, module_list, drop_ca
         (duration, result) = runSlicerAndExitWithTime(slicer_executable, test, drop_cache=drop_cache)
         (returnCode, stdout, stderr) = result
         if display_output:
-            if stdout: print("STDOUT [%s]\n" % stdout)
-            if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+            if stdout:
+                print("STDOUT [%s]\n" % stdout)
+            if stderr and returnCode == EXIT_SUCCESS:
+                print("STDERR [%s]\n" % stderr)
         if returnCode != EXIT_SUCCESS:
             # XXX Ignore module with dependencies
             duration = None
@@ -180,8 +186,10 @@ def collect_startup_times_excluding_one_module(output_file, module_list, drop_ca
         (duration, result) = runSlicerAndExitWithTime(slicer_executable, ['--testing', '--modules-to-ignore', moduleName], drop_cache=drop_cache)
         (returnCode, stdout, stderr) = result
         if display_output:
-            if stdout: print("STDOUT [%s]\n" % stdout)
-            if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+            if stdout:
+                print("STDOUT [%s]\n" % stdout)
+            if stderr and returnCode == EXIT_SUCCESS:
+                print("STDERR [%s]\n" % stderr)
         if returnCode != EXIT_SUCCESS:
             # XXX Ignore module with dependencies
             duration = None
@@ -204,8 +212,10 @@ def collect_startup_times_modules_to_load(output_file, modules_to_load, module_l
     (duration, result) = runSlicerAndExitWithTime(slicer_executable, test, drop_cache=drop_cache)
     (returnCode, stdout, stderr) = result
     if display_output:
-        if stdout: print("STDOUT [%s]\n" % stdout)
-        if stderr and returnCode == EXIT_SUCCESS: print("STDERR [%s]\n" % stderr)
+        if stdout:
+            print("STDOUT [%s]\n" % stdout)
+        if stderr and returnCode == EXIT_SUCCESS:
+            print("STDERR [%s]\n" % stderr)
 
     results = {}
     results[" ".join(modulesToIgnore)] = duration

Applications/SlicerApp/Testing/Python/SlicerBoundsTest.py

@@ -55,8 +55,8 @@ def setUp(self):
         slicer.mrmlScene.Clear(0)
 
     def assertListAlmostEquals(self, list, expected):
-        for l, e in zip(list, expected):
-            self.assertAlmostEqual(l, e)
+        for list_item, expected_item in zip(list, expected):
+            self.assertAlmostEqual(list_item, expected_item)
 
     def runTest(self):
         """Run as few or as many tests as needed here.

Base/Python/slicer/slicerqt.py

@@ -12,7 +12,8 @@
 #      that way the following try/except could be avoided.
 try:
     import slicer.cli
-except: pass
+except:
+    pass
 
 
 # -----------------------------------------------------------------------------

Base/Python/slicer/util.py

@@ -209,7 +209,8 @@ def lookupTopLevelWidget(objectName):
     from slicer import app
     for w in app.topLevelWidgets():
         if hasattr(w, 'objectName'):
-            if w.objectName == objectName: return w
+            if w.objectName == objectName:
+                return w
     # not found
     raise RuntimeError("Failed to obtain reference to '%s'" % objectName)
 
@@ -1259,7 +1260,7 @@ def reloadScriptedModule(moduleName):
     filePath = modulePath(moduleName)
     p = os.path.dirname(filePath)
 
-    if not p in sys.path:
+    if p not in sys.path:
         sys.path.insert(0, p)
 
     with open(filePath, encoding='utf8') as fp:

Modules/Loadable/Markups/Testing/Python/MarkupsInViewsSelfTest.py

@@ -341,7 +341,7 @@ def test_MarkupsInViewsSelfTest1(self):
         logic = MarkupsInViewsSelfTestLogic()
         retval = logic.run()
 
-        if retval == True:
+        if retval is True:
             self.delayDisplay('Test passed!')
         else:
             self.delayDisplay('Test failed!')

Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorDrawEffect.py

@@ -235,7 +235,8 @@ def addPoint(self, ras):
 
         # Don't allow adding points on except on the active slice
         # (where first point was laid down)
-        if self.activeSliceOffset != currentSliceOffset: return
+        if self.activeSliceOffset != currentSliceOffset:
+            return
 
         # Keep track of node state (in case of pan/zoom)
         sliceNode = sliceLogic.GetSliceNode()

Modules/Loadable/SubjectHierarchy/Testing/Python/SubjectHierarchyCorePluginsSelfTest.py

@@ -108,7 +108,7 @@ def section_SetupPathsAndNames(self):
         self.cloneNodeNamePostfix = slicer.qSlicerSubjectHierarchyCloneNodePlugin().getCloneNodeNamePostfix()
 
         # Test printing of all context menu actions and their section numbers
-        pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler().instance();
+        pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler().instance()
         print(pluginHandler.dumpContextMenuActions())
 
     # ------------------------------------------------------------------------------

Modules/Scripted/DICOM/DICOM.py

@@ -125,10 +125,10 @@ def onURLReceived(self, urlString):
         for key, value in query.queryItems(qt.QUrl.FullyDecoded):
             queryMap[key] = qt.QUrl.fromPercentEncoding(value)
 
-        if not "dicomweb_endpoint" in queryMap:
+        if "dicomweb_endpoint" not in queryMap:
             logging.debug("DICOM module ignores URL without dicomweb_endpoint query parameter: " + urlString)
             return
-        if not "studyUID" in queryMap:
+        if "studyUID" not in queryMap:
             logging.debug("DICOM module ignores URL without studyUID query parameter: " + urlString)
             return
 

Modules/Scripted/DICOMLib/DICOMBrowser.py

@@ -217,15 +217,15 @@ def promptForExtensions(self):
             displayedTypeDescriptions = []
             for extension in extensionsToOffer:
                 typeDescription = extension['typeDescription']
-                if not typeDescription in displayedTypeDescriptions:
+                if typeDescription not in displayedTypeDescriptions:
                     # only display each data type only once
                     message += '  ' + typeDescription + '\n'
                     displayedTypeDescriptions.append(typeDescription)
             message += "\nThe following extension%s not installed, but may help you work with this data:\n\n" % pluralOrNot
             displayedExtensionNames = []
             for extension in extensionsToOffer:
                 extensionName = extension['name']
-                if not extensionName in displayedExtensionNames:
+                if extensionName not in displayedExtensionNames:
                     # only display each extension name only once
                     message += '  ' + extensionName + '\n'
                     displayedExtensionNames.append(extensionName)
@@ -488,7 +488,7 @@ def loadCheckedLoadables(self):
     def showReferenceDialogAndProceed(self):
         referencesDialog = DICOMReferencesDialog(self, loadables=self.referencedLoadables)
         answer = referencesDialog.exec_()
-        if referencesDialog.rememberChoiceAndStopAskingCheckbox.checked == True:
+        if referencesDialog.rememberChoiceAndStopAskingCheckbox.checked is True:
             if answer == qt.QMessageBox.Yes:
                 qt.QSettings().setValue('DICOM/automaticallyLoadReferences', qt.QMessageBox.Yes)
             if answer == qt.QMessageBox.No:
@@ -497,7 +497,7 @@ def showReferenceDialogAndProceed(self):
             # each check box corresponds to a referenced loadable that was selected by examine;
             # if the user confirmed that reference should be loaded, add it to the self.loadablesByPlugin dictionary
             for plugin in self.referencedLoadables:
-                for loadable in [l for l in self.referencedLoadables[plugin] if l.selected]:
+                for loadable in [loadable_item for loadable_item in self.referencedLoadables[plugin] if loadable_item.selected]:
                     if referencesDialog.checkboxes[loadable].checked:
                         self.loadablesByPlugin[plugin].append(loadable)
                 self.loadablesByPlugin[plugin] = list(set(self.loadablesByPlugin[plugin]))
@@ -507,7 +507,7 @@ def showReferenceDialogAndProceed(self):
 
     def addReferencesAndProceed(self):
         for plugin in self.referencedLoadables:
-            for loadable in [l for l in self.referencedLoadables[plugin] if l.selected]:
+            for loadable in [loadable_item for loadable_item in self.referencedLoadables[plugin] if loadable_item.selected]:
                 self.loadablesByPlugin[plugin].append(loadable)
             self.loadablesByPlugin[plugin] = list(set(self.loadablesByPlugin[plugin]))
         self.proceedWithReferencedLoadablesSelection()
@@ -615,7 +615,7 @@ def _addLoadableCheckboxes(self):
         self.checkBoxGroupBox = qt.QGroupBox("References")
         self.checkBoxGroupBox.setLayout(qt.QFormLayout())
         for plugin in self.loadables:
-            for loadable in [l for l in self.loadables[plugin] if l.selected]:
+            for loadable in [loadable_item for loadable_item in self.loadables[plugin] if loadable_item.selected]:
                 checkBoxText = loadable.name + ' (' + plugin.loadType + ') '
                 cb = qt.QCheckBox(checkBoxText, self)
                 cb.checked = True

Modules/Scripted/DICOMLib/DICOMUtils.py

@@ -63,7 +63,7 @@ def loadPatientByUID(patientUID):
         raise OSError('DICOM module or database cannot be accessed')
 
     patientUIDstr = str(patientUID)
-    if not patientUIDstr in slicer.dicomDatabase.patients():
+    if patientUIDstr not in slicer.dicomDatabase.patients():
         raise OSError('No patient found with DICOM database UID %s' % patientUIDstr)
 
     # Select all series in selected patient
@@ -864,7 +864,7 @@ def importFromDICOMWeb(dicomWebEndpoint, studyInstanceUID, seriesInstanceUID=Non
 
         seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
         seriesInstanceUIDs = []
-        if not seriesInstanceUID is None:
+        if seriesInstanceUID is not None:
             seriesInstanceUIDs = [seriesInstanceUID]
         else:
             for series in seriesList:

Modules/Scripted/DICOMPlugins/DICOMGeAbusPlugin.py

@@ -156,7 +156,7 @@ def getMetadata(self, filePath):
             fieldInfo = fieldsInfo[fieldName]
             if not fieldInfo['required']:
                 continue
-            if not fieldName in fieldValues:
+            if fieldName not in fieldValues:
                 raise ValueError(f"Mandatory field {fieldName} was not found")
 
         return fieldValues

Modules/Scripted/ExtensionWizard/ExtensionWizard.py

@@ -357,7 +357,7 @@ def loadModules(self, path, depth=1):
                     for module in modulesToLoad:
                         rawPath = os.path.dirname(module.path)
                         path = qt.QDir(rawPath)
-                        if not path in searchPaths:
+                        if path not in searchPaths:
                             searchPaths.append(path)
                             rawSearchPaths.append(rawPath)
                             modified = True

Modules/Scripted/ExtensionWizard/ExtensionWizardLib/EditableTreeWidget.py

@@ -113,8 +113,8 @@ def updateActions(self):
 
         last = self.topLevelItemCount - 2
 
-        self._shiftUpAction.enabled = len(rows) and not 0 in rows
-        self._shiftDownAction.enabled = len(rows) and not last in rows
+        self._shiftUpAction.enabled = len(rows) and 0 not in rows
+        self._shiftDownAction.enabled = len(rows) and last not in rows
         self._deleteAction.enabled = True if len(rows) else False
 
     # ---------------------------------------------------------------------------

Modules/Scripted/SampleData/SampleData.py

@@ -672,7 +672,7 @@ def downloadFromSource(self, source, maximumAttemptsCount=3):
                 resultFilePaths.append(filePath)
 
                 if loadFileType == 'ZipFile':
-                    if loadFile == False:
+                    if loadFile is False:
                         resultNodes.append(filePath)
                         break
                     outputDir = slicer.mrmlScene.GetCacheManager().GetRemoteCacheDirectory() + "/" + os.path.splitext(os.path.basename(filePath))[0]
@@ -690,7 +690,7 @@ def downloadFromSource(self, source, maximumAttemptsCount=3):
                         resultNodes.append(filePath)
                         break
                 elif nodeName:
-                    if loadFile == False:
+                    if loadFile is False:
                         resultNodes.append(filePath)
                         break
                     loadedNode = self.loadNode(filePath, nodeName, loadFileType, source.loadFileProperties.copy())

Modules/Scripted/SegmentStatistics/SegmentStatistics.py

@@ -369,7 +369,7 @@ def registerPlugin(plugin):
             if key.count(".") > 0:
                 logging.warning("Plugin keys should not contain extra '.' as it might mix pluginname.measurementkey in "
                                 "the parameter node")
-        if not plugin.__class__ in SegmentStatisticsLogic.registeredPlugins:
+        if plugin.__class__ not in SegmentStatisticsLogic.registeredPlugins:
             SegmentStatisticsLogic.registeredPlugins.append(plugin.__class__)
         else:
             logging.warning("SegmentStatisticsLogic.registerPlugin will not register plugin because \
@@ -454,7 +454,7 @@ def computeStatistics(self):
                 segmentID = visibleSegmentIds.GetValue(segmentIndex)
                 self.updateStatisticsForSegment(segmentID)
         finally:
-            if not transformedSegmentationNode is None:
+            if transformedSegmentationNode is not None:
                 # We made a copy and hardened the segmentation transform
                 self.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
                 slicer.mrmlScene.RemoveNode(transformedSegmentationNode)
@@ -549,8 +549,10 @@ def getHeaderNames(self, nonEmptyKeysOnly=True):
                 if dicomBasedName and 'DICOM.UnitsCode' in info and info['DICOM.UnitsCode']:
                     entry.SetFromString(info['DICOM.UnitsCode'])
                     units = entry.GetCodeValue()
-                    if len(units) > 0 and units[0] == '[' and units[-1] == ']': units = units[1:-1]
-                    if len(units) > 0: name += ' [' + units + ']'
+                    if len(units) > 0 and units[0] == '[' and units[-1] == ']':
+                        units = units[1:-1]
+                    if len(units) > 0:
+                        name += ' [' + units + ']'
                 elif 'units' in info and info['units'] and len(info['units']) > 0:
                     units = info['units']
                     name += ' [' + units + ']'
@@ -805,14 +807,16 @@ def test_SegmentStatisticsPlugins(self):
         segStatLogic.exportToTable(resultsTableNode)
         segStatLogic.showTable(resultsTableNode)
         self.assertEqual(segStatLogic.getStatistics()["Test_2", "LabelmapSegmentStatisticsPlugin.voxel_count"], 9807)
-        with self.assertRaises(KeyError): segStatLogic.getStatistics()["Test_4", "ScalarVolumeSegmentStatisticsPlugin.voxel count"]
+        with self.assertRaises(KeyError):
+            segStatLogic.getStatistics()["Test_4", "ScalarVolumeSegmentStatisticsPlugin.voxel count"]
         # assert there are no result for this segment
         segStatLogic.updateStatisticsForSegment('Test_4')
         segStatLogic.exportToTable(resultsTableNode)
         segStatLogic.showTable(resultsTableNode)
         self.assertEqual(segStatLogic.getStatistics()["Test_2", "LabelmapSegmentStatisticsPlugin.voxel_count"], 9807)
         self.assertEqual(segStatLogic.getStatistics()["Test_4", "LabelmapSegmentStatisticsPlugin.voxel_count"], 380)
-        with self.assertRaises(KeyError): segStatLogic.getStatistics()["Test_5", "ScalarVolumeSegmentStatisticsPlugin.voxel count"]
+        with self.assertRaises(KeyError):
+            segStatLogic.getStatistics()["Test_5", "ScalarVolumeSegmentStatisticsPlugin.voxel count"]
         # assert there are no result for this segment
 
         # calculate measurements for all segments

Modules/Scripted/SegmentStatistics/SegmentStatisticsPlugins/LabelmapSegmentStatisticsPlugin.py

@@ -122,14 +122,14 @@ def computeStatistics(self, segmentID):
                 temp = statFilterOptions
                 statFilterOptions = []
                 for option in temp:
-                    if not option in self.obbKeys:
+                    if option not in self.obbKeys:
                         statFilterOptions.append(option)
                 statFilterOptions.append("oriented_bounding_box")
 
                 temp = requestedOptions
                 requestedOptions = []
                 for option in temp:
-                    if not option in self.obbKeys:
+                    if option not in self.obbKeys:
                         requestedOptions.append(option)
                 requestedOptions.append("oriented_bounding_box")
 
@@ -142,14 +142,14 @@ def computeStatistics(self, segmentID):
                 temp = statFilterOptions
                 statFilterOptions = []
                 for option in temp:
-                    if not option in self.principalAxisKeys:
+                    if option not in self.principalAxisKeys:
                         statFilterOptions.append(option)
                 statFilterOptions.append("principal_axes")
 
                 temp = requestedOptions
                 requestedOptions = []
                 for option in temp:
-                    if not option in self.principalAxisKeys:
+                    if option not in self.principalAxisKeys:
                         requestedOptions.append(option)
                 requestedOptions.append("principal_axes")
                 requestedOptions.append("centroid_ras")

Modules/Scripted/SegmentStatistics/SegmentStatisticsPlugins/SegmentStatisticsPluginBase.py

@@ -149,9 +149,12 @@ def createDefaultOptionsWidget(self):
             info = self.getMeasurementInfo(key)
             if info and ("name" in info or "description" in info):
                 label = info["name"] if "name" in info else info["description"]
-                if "name" in info: tooltip += "\nname: " + str(info["name"])
-                if "description" in info: tooltip += "\ndescription: " + str(info["description"])
-                if "units" in info: tooltip += "\nunits: " + (str(info["units"]) if info["units"] else "n/a")
+                if "name" in info:
+                    tooltip += "\nname: " + str(info["name"])
+                if "description" in info:
+                    tooltip += "\ndescription: " + str(info["description"])
+                if "units" in info:
+                    tooltip += "\nunits: " + (str(info["units"]) if info["units"] else "n/a")
             checkbox = qt.QCheckBox(label, self.optionsWidget)
             checkbox.checked = key in requestedKeys
             checkbox.setToolTip(tooltip)