Added functionality to track keywords used in a particular action on a markdown page

Author: Gareth Aneurin Tribello

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PlumedToHTML"
-version = "0.116"
+version = "0.117"
 description = "A package for creating prettified HTML for PLUMED files"
 authors = [{ name = "Gareth Tribello", email = "gareth.tribello@gmail.com" }]
 maintainers = [{ name = "Daniele Rapetti", email = "iximiel@gmail.com" }]

src/PlumedToHTML/PlumedFormatter.py

@@ -21,6 +21,8 @@ def __init__(self, **options) :
         self.auxinputlines=options["auxinputlines"]
         self.valuedict=options["valuedict"]
         self.actions=options["actions"]
+        self.checkaction=options["checkaction"]
+        self.checkaction_keywords = set({})
         self.valcolors = { 
            "scalar": "black", 
            "atoms": "violet", 
@@ -301,6 +303,9 @@ def format(self, tokensource, outfile):
         outfile.write('</pre>')
 
     def writeValuesData( self, outfile, action, label, keywords, outdict ) :
+        if action==self.checkaction :
+           for key in keywords :
+               self.checkaction_keywords.add( key )
         # Some header stuff 
         outfile.write('<span style="display:none;" id="' + self.egname + label + r'">')
         outfile.write('The ' + action + ' action with label <b>' + label + '</b>')
@@ -337,4 +342,7 @@ def writeValueInfo( self, outfile, label, span_label, valinfo ) :
             outfile.write('<tr><td width="5%">' + key + '</td><td width="5%"><font color="' + self.valcolors[value["type"]] +'">' + value["type"] + '</font></td><td>' + value["description"] + '</td></tr>')
         outfile.write('</table>') 
         outfile.write('</span>')
+
+    def getCheckActionKeywords( self ) :
+        return self.checkaction_keywords 
 

src/PlumedToHTML/PlumedToHTML.py

@@ -214,7 +214,7 @@ def get_cltoolfile_html( inpt, name, plumedexe ) :
     # Setup the formatter 
     formatfile = os.path.join(os.path.dirname(__file__),"PlumedFormatter.py")
     valuedict, actions = {}, set()
-    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict["cltools"], input_name=name, hasload=False, broken=False, auxinputs=[], auxinputlines=[], valuedict=valuedict, actions=actions )  
+    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict["cltools"], input_name=name, hasload=False, broken=False, auxinputs=[], auxinputlines=[], valuedict=valuedict, actions=actions, checkaction="" )  
     return highlight( inpt, plumed_lexer, plumed_formatter )
 
 def get_cltoolarg_html( inpt, name, plumedexe ) :
@@ -258,10 +258,10 @@ def get_cltoolarg_html( inpt, name, plumedexe ) :
     # Setup the formatter
     formatfile = os.path.join(os.path.dirname(__file__),"PlumedFormatter.py")
     valuedict, actions = {}, set()
-    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict["cltools"], input_name=name, hasload=False, broken=False, auxinputs=[], auxinputlines=[], valuedict=valuedict, actions=actions )  
+    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict["cltools"], input_name=name, hasload=False, broken=False, auxinputs=[], auxinputlines=[], valuedict=valuedict, actions=actions, checkaction="" )  
     return highlight( inpt, plumed_lexer, plumed_formatter )
 
-def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxchecks=None, actions=set({}), ghmarkdown=True ) :
+def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxchecks=None, actions=set({}), ghmarkdown=True, checkaction="", checkactionkeywords=set({}) ) :
     """
        Generate the html representation of a PLUMED input file
 
@@ -355,7 +355,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
     keyword_dict = getPlumedSyntax( plumedexe )
     # Setup the formatter
     formatfile = os.path.join(os.path.dirname(__file__),"PlumedFormatter.py")
-    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict, input_name=name, hasload=found_load, broken=any(broken), auxinputs=inputfiles, auxinputlines=inputfilelines, valuedict=valuedict, actions=actions )
+    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_dict=keyword_dict, input_name=name, hasload=found_load, broken=any(broken), auxinputs=inputfiles, auxinputlines=inputfilelines, valuedict=valuedict, actions=actions, checkaction=checkaction )
 
     # Now generate html of input
     html = '<div class="plumedpreheader">\n'
@@ -404,6 +404,13 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
     else : 
        # html += highlight( final_inpt, plumed_lexer, HtmlFormatter() )
        html += highlight( final_inpt, plumed_lexer, plumed_formatter )
+
+    # Now remove keywords that appear in examples
+    mykeywords = plumed_formatter.getCheckActionKeywords()
+    for key in mykeywords : 
+        if key in checkactionkeywords :
+           checkactionkeywords.remove(key)
+
     # Test output is valid parsable html
     try :
        etree.parse(StringIO(html), etree.HTMLParser(recover=False))
@@ -669,7 +676,7 @@ def processMarkdown( filename, plumedexe, plumed_names, actions, jsondir="./", g
        ninputs, nfail = processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile, jsondir, ghmarkdown )
     return ninputs, nfail
 
-def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile, jsondir="./", ghmarkdown=True ) :
+def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile, jsondir="./", ghmarkdown=True, checkaction="ignore", checkactionkeywords=set({}) ) :
     """
        Process a string of markdown that contains LUMED input files using PlumedtoHTML
 
@@ -789,7 +796,9 @@ def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofil
                                plumedexe, 
                                usejson=(not success[-1]),
                                actions=actions,
-                               ghmarkdown=ghmarkdown )
+                               ghmarkdown=ghmarkdown,
+                               checkaction=checkaction,
+                               checkactionkeywords=checkactionkeywords )
              # Print the html for the solution
              if ghmarkdown : ofile.write( "{% raw %}\n" + html + "\n {% endraw %} \n" )
              else : ofile.write( html )

tests/test_formatter.py

@@ -21,7 +21,7 @@ def testSimple(self) :
        keydict = getPlumedSyntax( ("plumed",) )
 
        # Setup a plumed formatter
-       f = PlumedFormatter( keyword_dict=keydict, input_name="testout", hasload=False, broken=False, actions=set({}), valuedict=dict({}), auxinputs=[], auxinputlines=[] )
+       f = PlumedFormatter( keyword_dict=keydict, input_name="testout", hasload=False, broken=False, actions=set({}), valuedict=dict({}), auxinputs=[], auxinputlines=[], , actions=actions, checkaction="" )
 
        # Now run over all the inputs in the json
        for item in tests["regtests"] :