Bug fix for testing for keywords.

This fixes a problem when numbered keyword detection was done wrongly if you are checking the keywords for the last action in the input file.

Author: Gareth Aneurin Tribello

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PlumedToHTML"
-version = "0.121"
+version = "0.122"
 description = "A package for creating prettified HTML for PLUMED files"
 authors = [{ name = "Gareth Tribello", email = "[email protected]" }]
 maintainers = [{ name = "Daniele Rapetti", email = "[email protected]" }]

src/PlumedToHTML/PlumedFormatter.py

@@ -38,15 +38,8 @@ def format(self, tokensource, outfile):
         for ttype, value in tokensource :
             # This checks if we are at the start of a new action.  If we are we should be reading a value or an action and the label and action for the previous one should be set
             if len(action)>0 and (ttype==String or ttype==Keyword or ttype==Comment.Preproc) :
-               if action==self.checkaction :
-                  for key in keywords :
-                      if key in self.keyword_dict[action]["syntax"] : 
-                         self.checkaction_keywords.add( key )
-                      else :
-                         # This makes sure we find numbered keywords
-                         for kkkk in self.keyword_dict[action]["syntax"] :
-                             if kkkk=="output" or self.keyword_dict[action]["syntax"][kkkk]["multiple"]==0 : continue
-                             if kkkk in key : self.checkaction_keywords.add( kkkk )
+               if action==self.checkaction : 
+                  self.storeKeywordsForCheckAction( keywords )
                if notooltips : 
                   # Reset everything for the new action
                   action, label, keywords, notooltips = "", "", [], False
@@ -302,9 +295,8 @@ def format(self, tokensource, outfile):
                else :
                      outfile.write('<span class="plumedtooltip" style="color:green">' + value.strip() + '<span class="right">'+ self.keyword_dict[action]["description"] + ' <a href="' + self.keyword_dict[action]["hyperlink"] + '" style="color:green">More details</a><i></i></span></span>')
         # Check if there is stuff to output for the last action in the file
-        if action==self.checkaction :
-           for key in keywords :
-               self.checkaction_keywords.add( key )
+        if action==self.checkaction : 
+           self.storeKeywordsForCheckAction( keywords )
         if len(label)>0 and label not in all_labels and label not in self.valuedict.keys() :
            all_labels.add( label )
            if action in self.keyword_dict and "output" in self.keyword_dict[action]["syntax"] : self.writeValuesData( outfile, action, label, keywords, self.keyword_dict[action]["syntax"]["output"] )
@@ -354,4 +346,14 @@ def writeValueInfo( self, outfile, label, span_label, valinfo ) :
 
     def getCheckActionKeywords( self ) :
         return self.checkaction_keywords 
+
+    def storeKeywordsForCheckAction( self, keywords ) :
+        for key in keywords :
+            if key in self.keyword_dict[self.checkaction]["syntax"] : 
+               self.checkaction_keywords.add( key )
+            else : 
+               # This makes sure we find numbered keywords
+               for kkkk in self.keyword_dict[self.checkaction]["syntax"] :
+                   if kkkk=="output" or self.keyword_dict[self.checkaction]["syntax"][kkkk]["multiple"]==0 : continue
+                   if kkkk in key : self.checkaction_keywords.add( kkkk )
 

tests/test_keyword_list.py

@@ -34,3 +34,38 @@ def testReadKeywords(self) :
        with open("check_keywords_file", "w") as ofile :
            PlumedToHTML.processMarkdownString( inpt, "check_keyword", ("plumed",), ("master",), actions, ofile, checkaction="DISTANCE", checkactionkeywords=keyset )
        self.assertTrue( keyset==set({"COMPONENTS"}) )
+
+       inpt = """
+```plumed
+# Define two groups of atoms
+g: GROUP ATOMS=1-5
+h: GROUP ATOMS=6-20
+  
+# Calculate the CONTACT_MATRIX for the atoms in group g
+cg: CONTACT_MATRIX GROUP=g SWITCH={RATIONAL R_0=0.1}
+
+# Calculate the CONTACT_MATRIX for the atoms in group h
+ch: CONTACT_MATRIX GROUP=h SWITCH={RATIONAL R_0=0.2}
+
+# Calculate the CONTACT_MATRIX between the atoms in group g and group h
+cgh: CONTACT_MATRIX GROUPA=g GROUPB=h SWITCH={RATIONAL R_0=0.15}
+
+# Now calculate the contact matrix between the atoms in group h and group h
+# Notice this is just the transpose of cgh
+cghT: TRANSPOSE ARG=cgh
+
+# And concatenate the matrices together to construct the adjacency matrix between the
+# adjacency matrices
+m: CONCATENATE ...
+ MATRIX11=cg MATRIX12=cgh
+ MATRIX21=cghT MATRIX22=ch
+...
+```
+"""
+
+       actions = set({})
+       keyset = set({"MATRIX"})
+       with open("check_keywords_file", "w") as ofile :
+           PlumedToHTML.processMarkdownString( inpt, "check_keyword", ("plumed",), ("master",), actions, ofile, checkaction="CONCATENATE", checkactionkeywords=keyset )
+       print( "final keyset", keyset )
+       self.assertTrue( keyset==set({}) )