Added code to escape html characters in comments in input and also deleting so files after plumed has been run for testing

Author: Gareth Aneurin Tribello

PlumedToHTML/PlumedFormatter.py

@@ -1,6 +1,7 @@
 from pygments.formatter import Formatter
 from pygments.token import Text, Comment, Literal, Keyword, Name, Generic, String
 from requests.exceptions import InvalidJSONError
+import html
 import json
 
 class PlumedFormatter(Formatter):
@@ -156,7 +157,7 @@ def format(self, tokensource, outfile):
                outfile.write('<b name="' + self.egname + label + '" onclick=\'showPath("' + self.divname + '","' + self.egname + label + '","' + self.valcolors[valtype] + '")\'>' + value + '</b>')
             elif ttype==Comment :
                # Comments
-               outfile.write('<span style="color:blue" class="comment">' + value + '</span>' )
+               outfile.write('<span style="color:blue" class="comment">' + html.escape(value) + '</span>' )
             elif ttype==Name.Attribute :
                # KEYWORD in KEYWORD=whatever and FLAGS
                keywords.append( value.strip().upper() )

PlumedToHTML/PlumedToHTML.py

@@ -102,6 +102,9 @@ def test_plumed( executible, filename, header=[], shortcutfile=[], valuefile=[]
         with open(errtxtfile,"w") as stderr:
              with cd(run_folder):
                  plumed_out = subprocess.run(cmd, text=True, stdout=stdout, stderr=stderr )
+    # Remove *.so files from run folder to prevent clashes when we test with a different version of PLUMED
+    for item in os.listdir( run_folder ) :
+        if item.endswith(".so") : os.remove( os.path.join( run_folder, item ) ) 
     # write header and preamble to errfile
     with open(errfile,"w") as stderr:
         if len(header)>0 : print(header,file=stderr)
@@ -244,8 +247,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
     try :
        etree.parse(StringIO(html), etree.HTMLParser(recover=False))
     except etree.XMLSyntaxError as e:
-       pass
-       #raise Exception("Generated html is invalid as " + str(e.error_log) ) from e
+       raise Exception("Generated html is invalid as " + str(e.error_log) ) from e
 
     # Check everything that is marked as a clickable value has something that will appear
     # when you click it

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.58',
+     version='0.59',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",