Added option to allow you to set whether to look for json or not

Author: Gareth Aneurin Tribello

PlumedToHTML/PlumedToHTML.py

@@ -55,7 +55,7 @@ def test_and_get_html( inpt, name, actions=set({}) ) :
     # Now do the test
     broken = test_plumed( "plumed", filename, header="", shortcutfile=name + '.json', valuefile='values_' + name + '.json' )
     # Retrieve the html that is output by plumed
-    html = get_html( inpt, name, name, ("master",), (broken,), ("plumed",), actions )
+    html = get_html( inpt, name, name, ("master",), (broken,), ("plumed",), actions=actions )
     # Remove the tempory files that we created
     if not keepfile : os.remove(filename)
 
@@ -155,7 +155,7 @@ def manage_incomplete_inputs( inpt ) :
        return complete, incomplete
    return inpt, ""
 
-def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
+def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, actions=set({}) ) :
     """
        Generate the html representation of a PLUMED input file
 
@@ -171,9 +171,16 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
        tested -- The versions of plumed that were testd
        broken -- The outcome of running test plumed on the input
        plumedexe -- The plumed executibles that were used.  The first one is the one that should be used to create the input file annotations
+       usejson -- Bool that tells you whether or not to look for json files that are generated by plumed driver
        actions -- Set to store all the actions that have been used in the input
     """
 
+    # Check if we are looking for json files
+    if usejson is None :
+       searchjson = False
+       if not any(broken) : searchjson = True
+    else : searchjson = usejson
+
     # If we find the fill command then split up the input file to find the solution
     inpt, incomplete = manage_incomplete_inputs( inpt )
 
@@ -185,7 +192,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
     found_load = "LOAD " in inpt
 
     # Check for shortcut file and build the modified input to read the shortcuts
-    if os.path.exists( name + '.json' ) and not any(broken) :
+    if os.path.exists( name + '.json' ) and searchjson :
        # Read json file containing shortcuts
        with open(name + '.json') as f :
            try:
@@ -199,7 +206,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
     if os.path.exists( name + '.json' ) : os.remove( name + ".json")  
 
     # Check for value dictionary to use to create labels
-    if os.path.exists( 'values_' + name + '.json') and not any(broken) :
+    if os.path.exists( 'values_' + name + '.json') and searchjson :
        with open('values_' + name + '.json') as f :
            try:
               valuedict = json.load(f)
@@ -251,7 +258,7 @@ 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:
-       raise Exception("Generated html is invalid as " + str(e.error_log) ) from e
+       raise Exception("Generated html is invalid as " + str(e.error_log) + " plumed input is \n\n" + final_inpt ) 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='0.61',
+     version='0.62',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",