Tiny backward compatible Python 3 tweaks for planemo_ext/tool_factory_2/

planemo_ext/tool_factory_2/getlocalrpackages.py

@@ -12,7 +12,7 @@ def find_packages(prefix="package_r_"):
     #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh
     #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh
     eprefix = prefix
-    if prefix.find('/') <> -1:
+    if prefix.find('/') != -1:
         eprefix = prefix.replace('/','\/') # for grep
     path = '.'
     # fails on nitesh's recent mac - locate not working 
@@ -48,5 +48,5 @@ def testapi():
 
 
 if __name__ == "__main__":
-    print find_packages()
-   
+    print(find_packages())
+

planemo_ext/tool_factory_2/rgToolFactory2.py

@@ -358,7 +358,7 @@ def __init__(self,opts=None):
         if opts.input_tab:
             tests = []
             for i,intab in enumerate(opts.input_tab): # if multiple, make tests
-                if intab.find(',') <> -1:
+                if intab.find(',') != -1:
                     (gpath,uname) = intab.split(',')
                 else:
                     gpath = uname = intab
@@ -436,7 +436,7 @@ def __init__(self,opts=None):
         self.interpreter_name = 'SYSTEM'
         self.interpreter_version = 'SYSTEM'
         self.interpreter_revision = 'SYSTEM'
-        if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
+        if opts.envshpath != 'system': # need to parse out details for our tool_dependency
             try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
                 # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local env.sh
                 packdetails = opts.envshpath.split(os.path.sep)[-4:-1]  # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
@@ -518,7 +518,7 @@ def makeXML(self):
         xdict['interpreter_name'] = self.interpreter_name
         xdict['requirements'] = ''
         if self.opts.include_dependencies == "yes":
-            if self.opts.envshpath <> 'system':
+            if self.opts.envshpath != 'system':
                 xdict['requirements'] = self.protorequirements_interpreter % xdict       
             else:    
                 xdict['requirements'] = self.protorequirements
@@ -643,11 +643,11 @@ def makeTooltar(self):
         os.mkdir(testdir) # make tests directory
         for i,intab in enumerate(self.opts.input_tab):
             si = self.opts.input_tab[i]
-            if si.find(',') <> -1:
+            if si.find(',') != -1:
                 s = si.split(',')[0]
                 si = s
             dest = os.path.join(testdir,os.path.basename(si))
-            if si <> dest:
+            if si != dest:
                 shutil.copyfile(si,dest)
         if self.opts.output_tab:
             shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
@@ -765,7 +765,7 @@ def makeHtml(self):
         galhtmlpostfix = """</div></body></html>\n"""
 
         flist = os.listdir(self.opts.output_dir)
-        flist = [x for x in flist if x <> 'Rplots.pdf']
+        flist = [x for x in flist if x != 'Rplots.pdf']
         flist.sort()
         html = []
         html.append(galhtmlprefix % progname)
@@ -774,7 +774,7 @@ def makeHtml(self):
         if len(flist) > 0:
             logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
             logfiles.sort()
-            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
+            logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)]
             logfiles.append(os.path.abspath(self.tlog)) # make it the last one
             pdflist = []
             npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
@@ -803,7 +803,7 @@ def makeHtml(self):
                     realname = os.path.basename(logfname)
                     sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
                     ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
-                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
+                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove
                 nacross = 1
                 npdf = len(ourpdfs)
 
@@ -866,7 +866,7 @@ def run(self):
         Some devteam tools have this defensive stderr read so I'm keeping with the faith
         Feel free to update. 
         """
-        if self.opts.envshpath <> 'system':
+        if self.opts.envshpath != 'system':
             shell_source(self.opts.envshpath)
             # this only happens at tool generation - the generated tool relies on the dependencies all being set up
             # at toolshed installation by sourcing local env.sh 
@@ -895,7 +895,7 @@ def run(self):
             p = subprocess.Popen(self.cl,shell=False)
             retval = p.wait()
         if self.opts.output_dir:
-            if retval <> 0 and err: # problem
+            if retval != 0 and err: # problem
                 print >> sys.stderr,err
         if self.opts.make_HTML:
             self.makeHtml()