PEP8 and pylint cleanup

wwPDB · Sep 2, 2024 · 0426a68 · 0426a68
1 parent 04be615
commit 0426a68
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Showing 5 changed files with 27 additions and 27 deletions.
diff --git a/tox.ini b/tox.ini
@@ -47,9 +47,6 @@ minversion = 3.4.0
 skip_missing_interpreters = true
 skipsdist = false
 
-[pytest]
-python_files = "*PyTest.py"
-
 [testenv]
 passenv = CONFIG_SUPPORT_TOKEN_ENV,OE_LICENSE
 allowlist_externals = echo
@@ -80,7 +77,6 @@ commands =
     {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_2} --pattern "{[local_settings]test_pattern}"
     {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_3} --pattern "{[local_settings]test_pattern}"
     {envpython} -m unittest discover -v --start-directory {[local_settings]test_path_4} --pattern "{[local_settings]test_pattern}"
-    {envpython} -m pytest -v {[local_settings]test_path_1} --tb=short
     echo "Completed {envname}"
 
 #

diff --git a/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py b/wwpdb/apps/ann_tasks_v2/pcm/PcmCCDEditorForm.py
@@ -12,6 +12,7 @@
 from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
 from wwpdb.io.locator.PathInfo import PathInfo
 
+
 class PcmCCDEditorForm(object):
     """
     The CoordEditorForm class generates coordinate editor form.

diff --git a/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py b/wwpdb/apps/ann_tasks_v2/utils/GetCovalentBond.py
@@ -127,20 +127,20 @@ def __processCloseContactContent(self, jsonObj):
                 atom += "(" + tupL[5] + ")"
             #
             tablerow += "<td>" + tupL[16] + "</td><td>" + tupL[0] + "</td><td>" + tupL[1] + "</td><td>" + tupL[2] + tupL[3] + "</td><td>" \
-                      + atom + "</td><td>" + tupL[6] + "</td>"
+                + atom + "</td><td>" + tupL[6] + "</td>"
             atom = tupL[11]
             if tupL[12]:
                 atom += "(" + tupL[12] + ")"
             #
             tablerow += "<td>" + tupL[7] + "</td><td>" + tupL[8] + "</td><td>" + tupL[9] + tupL[10] + "</td><td>" + atom + "</td><td>" \
-                      + tupL[13] + "</td><td>" + tupL[14] + "</td>"
+                + tupL[13] + "</td><td>" + tupL[14] + "</td>"
             #
             tupL[6] = tupL[6].replace("_", "-")
             tupL[13] = tupL[13].replace("_", "-")
             bond_id = "covalent_bond_" + str(count)
             #
             tablerow += "<td>" + tupL[15] + '&nbsp; &nbsp; &nbsp; &nbsp; <input type="checkbox" id="' + bond_id + '" name="' + bond_id \
-                      + '" value="' + "_".join(tupL[:16]) + '"/></td>'
+                + '" value="' + "_".join(tupL[:16]) + '"/></td>'
             #
             tablerow += "</tr>\n"
             count += 1

diff --git a/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py b/wwpdb/apps/ann_tasks_v2/utils/PointSuite.py
@@ -14,16 +14,19 @@
 __license__ = "Creative Commons Attribution 3.0 Unported"
 __version__ = "V0.07"
 
-import json,os,sys,traceback
+import os
+import sys
+import traceback
 
 from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
 
 try:
     from mmcif.io.IoAdapterCore import IoAdapterCore as IoAdapter
-except:
+except ImportError:
     from mmcif.io.IoAdapterPy import IoAdapterPy as IoAdapter
 #
 
+
 class PointSuite(object):
     """ PointSuite class encapsulates running the programs defined in the suite.
     """
@@ -43,11 +46,11 @@ def __setup(self):
     def importMats(self, inputMatFilePath, logPath):
         """ Run PointSuite's "importmats" program
         """
-        exportList = [ os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), \
-                       os.path.join(self.__sessionPath, "import.matrix") ]
+        exportList = [os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"),
+                      os.path.join(self.__sessionPath, "import.matrix")]
         #
-        allFileList = [ os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"), \
-                        os.path.join(self.__sessionPath, "import.matrix"), logPath ]
+        allFileList = [os.path.join(self.__sessionPath, "import.biomt"), os.path.join(self.__sessionPath, "import.cif"),
+                       os.path.join(self.__sessionPath, "import.matrix"), logPath]
         #
         for filePath in allFileList:
             if os.access(filePath, os.F_OK):
@@ -75,7 +78,7 @@ def importMats(self, inputMatFilePath, logPath):
             tmpMatricesCifPath = os.path.join(self.__sessionPath, "tmp-import.cif")
             ofh = open(tmpMatricesCifPath, "w")
             ofh.write("data_matrices\n#\n%s\n" % data)
-            ofh.close() 
+            ofh.close()
             #
             try:
                 ioObj = IoAdapter()
@@ -96,7 +99,7 @@ def findFrame(self, modelCifPath, biomtFilePath, logPath):
         """
         frameCifPath = os.path.join(self.__sessionPath, "findframe.cif")
         #
-        for filePath in ( frameCifPath, logPath ):
+        for filePath in (frameCifPath, logPath):
             if os.access(filePath, os.F_OK):
                 os.remove(filePath)
             #
@@ -109,12 +112,12 @@ def findFrame(self, modelCifPath, biomtFilePath, logPath):
         dp.expLog(dstPath=logPath, appendMode=False)
         dp.cleanup()
 
-    def makeAssembly(self, modelCifPath, transmtFilePath, logPath): 
+    def makeAssembly(self, modelCifPath, transmtFilePath, logPath):
         """ Run PointSuite's "makeassembly" program
         """
         assemblyCifPath = os.path.join(self.__sessionPath, "assembly.cif")
         #
-        for filePath in ( assemblyCifPath, logPath ):
+        for filePath in (assemblyCifPath, logPath):
             if os.access(filePath, os.F_OK):
                 os.remove(filePath)
             #
@@ -132,7 +135,7 @@ def mergeAssemblyInfo(self, inModelCifPath, assemblyCifPath, outModelCifPath, lo
         """
         modifiedAssemblyCifPath = os.path.join(self.__sessionPath, "assembly-with-data-block.cif")
         #
-        for filePath in ( outModelCifPath, modifiedAssemblyCifPath, logPath ):
+        for filePath in (outModelCifPath, modifiedAssemblyCifPath, logPath):
             if os.access(filePath, os.F_OK):
                 os.remove(filePath)
             #
@@ -146,7 +149,7 @@ def mergeAssemblyInfo(self, inModelCifPath, assemblyCifPath, outModelCifPath, lo
         #
         ofh = open(modifiedAssemblyCifPath, "w")
         ofh.write("data_assembly\n#\n%s\n" % data)
-        ofh.close() 
+        ofh.close()
         #
         dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
         dp.imp(inModelCifPath)

diff --git a/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py b/wwpdb/apps/ann_tasks_v2/webapp/CommonTasksWebAppWorker.py
@@ -3743,7 +3743,7 @@ def _uploadBiomtFileOp(self):
             rC.setError(errMsg="No file uploaded")
             return rC
         #
-        originalUploadFileName = wuu.getUploadFileName(fileTag="file")
+        # originalUploadFileName = wuu.getUploadFileName(fileTag="file")
         #
         entryId = self._reqObj.getValue("entryid")
         entryFileName = self._reqObj.getValue("entryfilename")
@@ -3760,8 +3760,8 @@ def _uploadBiomtFileOp(self):
         findframeLogPath = os.path.join(self._sessionPath, "findframe.log")
         makeassemblyLogPath = os.path.join(self._sessionPath, "makeassembly.log")
         mergeLogPath = os.path.join(self._sessionPath, "merge.log")
-        for filePath in ( sessionInputFilePath, importBiomtPath, importCifPath, importMatrixPath, frameCifPath, transmtCifPath, \
-                          assemblyCifPath, updatedModelCifPath, importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath ):
+        for filePath in (sessionInputFilePath, importBiomtPath, importCifPath, importMatrixPath, frameCifPath, transmtCifPath,
+                         assemblyCifPath, updatedModelCifPath, importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath):
             if os.access(filePath, os.F_OK):
                 os.remove(filePath)
             #
@@ -3781,16 +3781,16 @@ def _uploadBiomtFileOp(self):
                     if os.access(transmtCifPath, os.R_OK):
                         pts.makeAssembly(os.path.join(self._sessionPath, entryFileName), transmtCifPath, makeassemblyLogPath)
                     #
-                # 
+                #
 #               ifh = open(sessionInputFilePath, "r")
 #               data = ifh.read()
 #               ifh.close()
 #               #
 #               text = 'Uploaded "' + originalUploadFileName + '" file:\n' + data
                 text = ""
                 #
-                for fileTup in ( ( "import.biomt", importBiomtPath ), ( "import.cif", importCifPath ), \
-                                 ( "import.matrix", importMatrixPath ), ( "assembly.cif", assemblyCifPath ) ):
+                for fileTup in (("import.biomt", importBiomtPath), ("import.cif", importCifPath),
+                                ("import.matrix", importMatrixPath), ("assembly.cif", assemblyCifPath)):
                     if not os.access(fileTup[1], os.R_OK):
                         continue
                     #
@@ -3801,7 +3801,7 @@ def _uploadBiomtFileOp(self):
                     if text:
                         text += "\n\n"
                     #
-                    text += '"' + fileTup[0] + '" file:\n' + data 
+                    text += '"' + fileTup[0] + '" file:\n' + data
                 #
                 successfulFlag = False
                 if os.access(assemblyCifPath, os.R_OK):
@@ -3826,7 +3826,7 @@ def _uploadBiomtFileOp(self):
                 rC.set("summary", summary_text)
                 #
                 log_text = ""
-                for filePath in ( importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath ):
+                for filePath in (importmatsLogPath, findframeLogPath, makeassemblyLogPath, mergeLogPath):
                     if not os.access(filePath, os.F_OK):
                         continue
                     #