PEP8 and black formatting

wwpdb/apps/ann_tasks_v2/check/Check.py

@@ -31,7 +31,6 @@
 
 
 class Check(PublicPdbxFile):
-
     """
     Encapsulates dictioanry-level PDBx/mmCIF checking.
 

wwpdb/apps/ann_tasks_v2/check/XmlCheck.py

@@ -25,7 +25,6 @@
 
 
 class XmlCheck(PublicPdbxFile):
-
     """
     Encapsulates PDBML/XML checking.
     """

wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py

@@ -27,7 +27,6 @@
 
 
 class EmEditUtils(SessionWebDownloadUtils):
-
     """
     Edit volume data file header records and related data stored in model files.
 

wwpdb/apps/ann_tasks_v2/em3d/EmModelUtils.py

@@ -28,7 +28,6 @@
 
 
 class EmModelUtils(PdbxStyleIoUtil):
-
     """
     Manage map header updates in model file -
 

wwpdb/apps/ann_tasks_v2/em3d/EmUtils.py

@@ -45,7 +45,6 @@
 
 
 class EmUtils(SessionWebDownloadUtils):
-
     """
     Manages mapfix (view and edit) and em2m operations.
 

wwpdb/apps/ann_tasks_v2/io/PdbxIoUtils.py

@@ -29,7 +29,6 @@
 
 
 class PdbxFileIo(object):
-
     """Read PDBx data files and package content as PDBx container object or container object list
     Write PDBx data using source PDBx container object list source content.
 
@@ -80,7 +79,6 @@ def writeContainerList(self, fPath, containerList=None):
 
 
 class ModelFileIo(object):
-
     """
     Assemble sample and coordinate sequence details from model coordinate data file.
 

wwpdb/apps/ann_tasks_v2/report/PdbxReport.py

@@ -110,7 +110,7 @@ def makeTabularReport(self, filePath=None, contentType=None, idCode=None, layout
                 dd = self.doReport(contentType)
                 rdd = PdbxReportDepictBootstrap(styleObject=PdbxGeometryReportCategoryStyle(), includePath=includePath, verbose=self.__verbose, log=self.__lfh)
                 oL = rdd.render(dd, style=layout, leadingHtmlL=leadingHtmlL, trailingHtmlL=trailingHtmlL)
-            
+
             if contentType in ["links-report"]:
                 self.setFilePath(filePath, fileFormat=fileFormat, idCode=idCode)
                 dd = self.doReport(contentType)

wwpdb/apps/ann_tasks_v2/report/PdbxReportDepictBootstrap.py

@@ -28,6 +28,7 @@ class PdbxReportDepictBootstrap(PdbxDepictBootstrapBase):
     This version uses Bootstrap CSS framework constructs.
 
     """
+
     MAX_LINES = 12
 
     def __init__(self, styleObject=None, includePath=None, verbose=False, log=sys.stderr):
@@ -538,7 +539,7 @@ def __markupRow(self, catName, rD):
                         itemValue,
                         itemValue,
                     )
-        
+
         if catName == "struct_conn":
             itemName = "_struct_conn.id"
             if itemName in rD:

wwpdb/apps/ann_tasks_v2/report/styles/LinksReport.py

@@ -3,7 +3,6 @@
 
 """
 
-
 from mmcif_utils.style.PdbxCategoryStyleBase import PdbxCategoryStyleBase
 
 
@@ -14,7 +13,7 @@ class PdbxLinksReportCategoryStyle(PdbxCategoryStyleBase):
     ]
     _cDict = {
         "struct_conn": [
-            ('_struct_conn.id', '%s', 'str', ''),
+            ("_struct_conn.id", "%s", "str", ""),
             ("_struct_conn.pdbx_leaving_atom_flag", "%s", "str", ""),
             ("_struct_conn.ptnr1_auth_asym_id", "%s", "str", ""),
             ("_struct_conn.ptnr1_auth_comp_id", "%s", "str", ""),
@@ -36,8 +35,10 @@ class PdbxLinksReportCategoryStyle(PdbxCategoryStyleBase):
     #
 
     def __init__(self):
-        super(PdbxLinksReportCategoryStyle, self).__init__(styleId=PdbxLinksReportCategoryStyle._styleId,
-                                                              catFormatL=PdbxLinksReportCategoryStyle._categoryInfo,
-                                                              catItemD=PdbxLinksReportCategoryStyle._cDict,
-                                                              excludeList=PdbxLinksReportCategoryStyle._excludeList,
-                                                              suppressList=PdbxLinksReportCategoryStyle._suppressList)
+        super(PdbxLinksReportCategoryStyle, self).__init__(
+            styleId=PdbxLinksReportCategoryStyle._styleId,
+            catFormatL=PdbxLinksReportCategoryStyle._categoryInfo,
+            catItemD=PdbxLinksReportCategoryStyle._cDict,
+            excludeList=PdbxLinksReportCategoryStyle._excludeList,
+            suppressList=PdbxLinksReportCategoryStyle._suppressList,
+        )

wwpdb/apps/ann_tasks_v2/status/StatusUpdate.py

@@ -36,7 +36,6 @@
 
 
 class StatusUpdate(object):
-
     """Update release status items."""
 
     def __init__(self, reqObj, IoAdapter=IoAdapterCore(), verbose=False, log=sys.stderr):
@@ -260,7 +259,7 @@ def __setEmStatusDetails(self, cObj, statusD, processSite=None, annotatorInitial
             "map_hold_date",
             "header_release_date",
             "replace_existing_entry_flag",
-            "title"
+            "title",
             # Do not add process_site here.  Handled internally below
         ]
 

wwpdb/apps/ann_tasks_v2/utils/SessionDownloadUtils.py

@@ -26,7 +26,6 @@
 
 
 class SessionDownloadUtils(object):
-
     """Common methods for managing download operations for project files within the session context."""
 
     #

wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py

@@ -3727,8 +3727,7 @@ def _launchFromIdcodeOp(self):
         return rC
 
     def _autoProcessNmrCombinedDataFile(self, identifier):
-        """
-        """
+        """ """
         if self._verbose:
             self._lfh.write("+CommonTasksWebAppWorker._autoProcessNmrCombinedDataFile() starting with identifier %s\n" % identifier)
         #
@@ -3742,8 +3741,7 @@ def _autoProcessNmrCombinedDataFile(self, identifier):
         #
 
     def _autoProcessNmrChemShifts(self, identifier):
-        """
-        """
+        """ """
         try:
             csUtil = NmrChemShiftProcessUtils(siteId=self._siteId, verbose=self._verbose, log=self._lfh)
             csUtil.setWorkingDirPath(dirPath=self._sessionPath)