remove memory leaks w/open().write(); while at it clean up warnings shown by spyder

Author: briantoby

GSASII/GSASIIdataGUI.py

@@ -457,6 +457,7 @@ def ShowVersions():
     if GSASIIpath.HowIsG2Installed().startswith('git'):
         try:
             import git
+            git
         except ImportError as msg:
             if 'Failed to initialize' in msg.msg:
                 print('The gitpython package is unable to locate a git installation.')
@@ -473,6 +474,7 @@ def ShowVersions():
     # warn if problems with requests package
     try:
         import requests
+        requests
     except:
         print('Warning: Python requests package not installed (required for\n'+
               ' GSAS-II to access web pages or self-install binary modules)')
@@ -639,6 +641,7 @@ def _Add_FileMenuItems(self, parent):
         if GSASIIpath.GetConfigValue('debug'):
             try:
                 import IPython
+                IPython
                 item = parent.Append(wx.ID_ANY,"IPython Console",'')
                 self.Bind(wx.EVT_MENU,
                               lambda event:GSASIIpath.IPyBreak(),
@@ -5743,6 +5746,7 @@ def OnClusterAnalysis(self,event):
         try:
             SKLearn = False
             import sklearn.cluster
+            sklearn.cluster
             SKLearn = True
         except:
             res = GSASIIpath.condaInstall('scikit-learn')
@@ -7410,7 +7414,8 @@ def OnAddNotebook(event):
     def OnSaveNotebook(event):
         filename = os.path.splitext(G2frame.GSASprojectfile)[0]+'_notebook.txt'
         filename = os.path.join(G2frame.dirname,filename)
-        open(filename,'w').write(textBox.GetText())
+        with open(filename,'w') as fp:
+            fp.write(textBox.GetText())
         print(f'Notebook contents written into {filename}')
     def onPlotNotebook():
         'Locate R values from the Notebook and plot them'

GSASII/GSASIIpath.py

@@ -9,7 +9,7 @@
 import sys
 import platform
 import glob
-import pathlib
+#import pathlib
 import subprocess
 import datetime as dt
 try:
@@ -507,7 +507,7 @@ def gitCheckForUpdates(fetch=True,g2repo=None):
             g2repo.remote().fetch()
             fetched = True
         except git.GitCommandError as msg:
-            print(f'Failed to get updates from {g2repo.remote().url}')
+            print(f'Failed to get updates from {g2repo.remote().url}\nerror: {msg}')
     try:
         head = g2repo.head.ref
         tracking = head.tracking_branch()
@@ -798,7 +798,8 @@ def InstallGitBinary(tarURL, instDir, nameByVersion=False, verbose=True):
         tar.close()
         if verbose: print(f'Downloading {tarURL}')
         r = requests.get(tarURL, allow_redirects=True)
-        open(tar.name, 'wb').write(r.content)
+        with open(tar.name, 'wb') as fp:
+            fp.write(r.content)
         # open in tar
         tarobj = tarfile.open(name=tar.name)
         if nameByVersion:
@@ -928,7 +929,8 @@ def downloadDirContents(dirlist,targetDir,orgName=gitTutorialOwn, repoName=gitTu
         r = requests.get(URL, allow_redirects=True)
         outfil = os.path.join(targetDir,fil)
         if r.status_code == 200:
-            open(outfil, 'wb').write(r.content)
+            with open(outfil, 'wb') as fp:
+                fp.write(r.content)
             print(f'wrote {outfil}')
         elif r.status_code == 404:
             print(f'Warning: {fil} is likely a subdirectory of directory {"/".join(dirlist)!r}')
@@ -1030,7 +1032,8 @@ def exceptHook(*args):
     This routine is only used when debug=True is set in the configuration settings
     '''
     try:
-        from IPython.core import ultratb
+        #from IPython.core import ultratb
+        import IPython.core.ultratb
     except:
         pass
 
@@ -1082,6 +1085,7 @@ def InvokeDebugOpts():
             global pdbBreak
             pdbBreak = pdb.set_trace
             import IPython
+            IPython
             global IPyBreak
             IPyBreak = IPyBreak_base
             sys.excepthook = exceptHook
@@ -1093,11 +1097,23 @@ def InvokeDebugOpts():
         os.environ['PYTHONBREAKPOINT'] = '0'
 
 def TestSPG(fpth):
+    '''Test if pyspg.[so,.pyd] can be run from a location in the path
+    Do not modify the path if not.
+    '''
     try:
         from . import pyspg
+        pyspg
         return True
     except ImportError:
-        return _old_TestSPG(fpth)
+        return False
+    try:
+        pyspg.sgforpy('P -1')
+    except Exception as err:
+        print(70*'=')
+        print(f'Module pyspg in {fpth!r} could not be run\nerror msg: {err}')
+        print(70*'=')
+        return False
+    return True
 
 def _old_TestSPG(fpth):
     '''Test if pyspg.[so,.pyd] can be run from a location in the path
@@ -1158,11 +1174,12 @@ def SetBinaryPath(showConfigMsg=False):
     global BinaryPathLoaded,binaryPath,BinaryPathFailed
     if BinaryPathLoaded or BinaryPathFailed: return
     try:
-        inpver = intver(np.__version__)
+        intver(np.__version__)
     except (AttributeError,TypeError): # happens on building docs
         return
     try:
         from GSASII import pypowder
+        pypowder
         binaryPath = None   # special value to indicate that binaries have been installed into package
         if showConfigMsg:
             print(f'GSAS-II binaries co-located with GSAS-II: {os.path.dirname(__file__)}')
@@ -1358,6 +1375,7 @@ def condaTest(requireAPI=False):
         # is the conda package available?
         try:
             import conda.cli.python_api
+            conda.cli.python_api
         except:
             print('You do not have the conda package installed in this environment',
                   '\nConsider using the "conda install conda" command')
@@ -1567,12 +1585,12 @@ def addCondaPkg():
         script += 'conda install conda -n '+currenv+' -y'
         p = subprocess.Popen(script,shell=True,env={},
                          #stdout=subprocess.PIPE,
-                         stderr=subprocess.PIPE)
-    out,err = MakeByte2str(p.communicate())
-    #print('Output from adding conda:\n',out)
-    if err:
-        print('Note error/warning:')
-        print(err)
+                         stderr=subprocess.PIPE,
+                         encoding='UTF-8')
+    out,err = p.communicate()
+    if out is not None and GetConfigValue('debug'): print('Output from adding conda:\n',out)
+    if err and err is not None:
+        print('Note error/warning from running conda:\n',err)
     if currenv == "base":
         print('\nUnexpected action: adding conda to base environment???')
 #==============================================================================

GSASII/GSASIIphsGUI.py

@@ -3043,7 +3043,8 @@ def _showWebPage(event):
             txt = event.GetEventObject().page
             tmp = tempfile.NamedTemporaryFile(suffix='.html',
                         delete=False)
-            open(tmp.name,'w').write(txt.replace(
+            with open(tmp.name,'w') as fp:
+                fp.write(txt.replace(
                 '<HEAD>',
                 '<head><base href="https://stokes.byu.edu/iso/">',
                 ))
@@ -3100,7 +3101,8 @@ def _showWebPage(event):
                 flags=re.IGNORECASE)[0]
         except IndexError:
             tmp1 = tempfile.NamedTemporaryFile(suffix='.html')
-            open(tmp1.name,'w').write(r1.text.replace(
+            with open(tmp1.name,'w') as fp:
+                fp.write(r1.text.replace(
                 '<HEAD>',
                 '<head><base href="https://stokes.byu.edu/iso/">',
                 ))
@@ -3273,7 +3275,8 @@ def _showWebPage(event):
             num = event.GetEventObject().IndexNum
             tmp = tempfile.NamedTemporaryFile(suffix='.html',
                         delete=False)
-            open(tmp.name,'w').write(pagelist[num].replace(
+            with open(tmp.name,'w') as fp:
+                fp.write(pagelist[num].replace(
                 '<head>',
                 '<head><base href="https://www.cryst.ehu.es/">',
                 ))
@@ -3454,13 +3457,13 @@ def showSuperResults(G2frame,msgs,pagelist,fileList,ReSearch,parentpage,msg=None
             '''Show a summary with info from a search of supergroups in
             :func:`OnSuperSearch` (in :func:`UpdatePhaseData`)
             '''
-            import SUBGROUPS
             def _showWebPage(event):
                 import tempfile
                 f = event.GetEventObject().webFile
                 tmp = tempfile.NamedTemporaryFile(suffix='.html',
                                 delete=False)
-                open(tmp.name,'w').write(f.replace(
+                with open(tmp.name,'w') as fp:
+                    fp.write(f.replace(
                         '<head>',
                         '<head><base href="https://www.cryst.ehu.es/">',
                         ))
@@ -7952,7 +7955,7 @@ def Runfullrmc(event):
                 shutil.rmtree(rmcname)
             else:
                 return
-        G2G.G2MessageBox(G2frame,f'For use of fullrmc, please cite:\n\n'+
+        G2G.G2MessageBox(G2frame,'For use of fullrmc, please cite:\n\n'+
                              G2G.GetCite('fullrmc')+
                              '\n\nNote: A more advanced version of fullrmc can be found at www.fullrmc.com',
                              'Please cite fullrmc')
@@ -8014,7 +8017,7 @@ def RunRMCProfile(event):
             rmcexe = os.path.split(rmcfile)[0]
         #print(rmcexe)
         wx.MessageBox(
-            f' For use of RMCProfile, please cite:\n\n'+
+            ' For use of RMCProfile, please cite:\n\n'+
             G2G.GetCite("RMCProfile"),
             caption='RMCProfile',style=wx.ICON_INFORMATION)
         if os.path.isfile(pName+'.his6f'):
@@ -17004,6 +17007,7 @@ def checkPDFfit(G2frame):
     # see if diffpy has been installed directly
     try:
         from diffpy.pdffit2 import PdfFit
+        PdfFit
         return True
     except:
         pass
@@ -17012,6 +17016,7 @@ def checkPDFfit(G2frame):
     # Python in a separate environment
     try:     # have conda. Can we access it programmatically?
         import conda.cli.python_api
+        conda.cli.python_api
     except:
         G2G.G2MessageBox(G2frame,'You are running a directly installed Python. You will need to install PDFfit2 directly as well, preferably in a separate virtual environment.')
         return

GSASII/GSASIIpwd.py

@@ -3457,7 +3457,8 @@ def fullrmcDownload():
               'https://github.com/bachiraoun/fullrmc/tree/master/standalones',
               '\nCreating '+fil,
               '\nThis may take a while...')
-    open(fil, "wb").write(requests.get(URL).content)
+    with open(fil, "wb") as fp:
+        fp.write(requests.get(URL).content)
     print('...Download completed')
     if setXbit:
         import stat
@@ -3474,6 +3475,8 @@ def findPDFfit():
     try:
         from diffpy.pdffit2 import PdfFit
         import diffpy
+        PdfFit
+        diffpy
         return sys.executable
     except Exception as msg:
         print('Error importing PDFfit2:\n',msg)

GSASII/GSASIIpwdGUI.py

@@ -5153,15 +5153,15 @@ def _showWebPage(event):
             import tempfile
             txt = event.GetEventObject().page
             tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
-            open(tmp.name,'w').write(txt.replace('<HEAD>',
-                '<head><base href="https://stokes.byu.edu/iso/">',))
+            with open(tmp.name,'w') as fp:
+                fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/iso/">',))
             fileList.append(tmp.name)
             G2G.ShowWebPage('file://'+tmp.name,G2frame)
         def showWebtext(txt):
             import tempfile
             tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
-            open(tmp.name,'w').write(txt.replace('<HEAD>',
-                '<head><base href="https://stokes.byu.edu/iso/">',))
+            with open(tmp.name,'w') as fp:
+                fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/iso/">',))
             fileList.append(tmp.name)
             G2G.ShowWebPage('file://'+tmp.name,G2frame)
 
@@ -5273,7 +5273,7 @@ def _get_opt_val(opt_name, out):
                 data["origintype"] = "method2"
                 data["orderparam"] = radio_val + '" CHECKED'
                 data["isofilename"] = ""
-                out5 = requests.post(isoformsite, data=data).text
+                requests.post(isoformsite, data=data).text
 
                 continue
 

GSASII/ISODISTORT.py

@@ -15,7 +15,8 @@
 isoformsite = 'https://iso.byu.edu/iso/isodistortform.php'
 
 def HandleError(out):
-    open('out.html','wb').write(out.encode("utf-8"))
+    with open('out.html','wb') as fp:
+        fp.write(out.encode("utf-8"))
     url = os.path.realpath('out.html')
     try:
         os.startfile(url)
@@ -263,7 +264,8 @@ def GetISODISTORTcif(Phase):
     #     print(item,data2[item])
     out4 = requests.post(isoformsite,data=data2).text
     #print(out4)
-    #open('pyout4.html','wb').write(out4.encode("utf-8"))
+    #with open('pyout4.html','wb') as fp:
+        #fp.write(out4.encode("utf-8"))
 
     #retrieve data needed for next(last) step
 

GSASII/SUBGROUPS.py

@@ -378,8 +378,10 @@ def GetSupergroup(SGnum,dlg=None):
         out1 = GSASIIpath.postURL(Site,{'gnum':SGnum,'show':'show','click':click}
                                 ,timeout=timeout)
         if not out1: return None
-        #open(f'/tmp/{click}.html','w').write(out1)
-        #open(f'/tmp/last.html','w').write(out1)
+        #with open(f'/tmp/{click}.html','w') as fp:
+        #    fp.write(out1)
+        #with open(f'/tmp/last.html','w') as fp:
+        #    fp.write(out1)
         if dlg: dlg.Update(2+i,newmsg=f'processing {line[1]}, #{i+1} of {len(xforms)}')
         mvlist = []
         for s in [i.split('</pre>')[0] for i in out1.split('<pre>')[1::2]]:
@@ -556,7 +558,8 @@ def BilbaoSymSearch1(sgnum, phase, maxdelta=2, angtol=None,
     return scanBilbaoSymSearch1(page0,postdict)+[savedcookies]
 
 def scanBilbaoSymSearch1(page0,postdict):
-    #open(f'/tmp/pseudosym0.html','w').write(page0)
+    #open(f'/tmp/pseudosym0.html','w') as fp:
+    #    fp.write(page0)
     valsdict = {} # base for all supergroups 
     csdict = {}   # supergroups w/default selection value
     rowdict = {}  # information in table row for each supergroup

GSASII/install/makeLinux.py

@@ -24,7 +24,7 @@
 The path to Python is determined from the version of Python used to
 run this script.
 '''
-import sys, os, os.path, stat, shutil, subprocess, plistlib
+import sys, os, os.path, stat, shutil
 import datetime
 desktop_template = """
 [Desktop Entry]
@@ -104,7 +104,6 @@ def Usage():
              stat.S_IXUSR | stat.S_IRUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IXOTH)
 
     script = ''
-    import shutil
     for term in ("lxterminal", "gnome-terminal", 'konsole', "xterm",
                          "terminator", "terminology", "tilix"):
         try:
@@ -151,9 +150,8 @@ def Usage():
     for f,t in zip((dfile,mfile),('Desktop','Menu')):
         if f is None: continue
         try:
-            open(f,'w').write(desktop_template.format(
-                terminal,
-                G2start+add2script,G2icon))
+            with open(f,'w') as fp:
+                fp.write(desktop_template.format(terminal,G2start+add2script,G2icon))
             os.chmod(
                 dfile,
                 stat.S_IWUSR | stat.S_IXUSR | stat.S_IRUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IXOTH)

GSASII/install/makeMacApp.py

@@ -76,8 +76,7 @@
 '''
 
 from __future__ import division, print_function
-import sys, os, os.path, stat, shutil, subprocess, plistlib
-import platform
+import sys, os, os.path, subprocess
 def Usage():
     print(f"\nUsage:\n\tpython {os.path.abspath(sys.argv[0])} [install_path] [<GSAS-II_script>] [Python_loc]\n")
     sys.exit()
@@ -147,7 +146,8 @@ def Usage():
         print(f"\nRemoving {g2Name!r}")
         os.remove(g2Name)
     #os.symlink(G2script,g2Name)
-    open(g2Name,'w').write('''# this script starts GSAS-II when not installed into Python
+    with open(g2Name,'w') as fp:
+        fp.write('''# this script starts GSAS-II when not installed into Python
 # it will be called from the GSAS-II.app AppleScript
 # it should be not be renamed or moved
 import sys,os