cltool formatting can now deal with command line inputs that use plumed-runtime and mpirun

Author: Gareth Aneurin Tribello

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PlumedToHTML"
-version = "0.109"
+version = "0.110"
 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/PlumedCLtoolLexer.py

@@ -1,5 +1,5 @@
 from pygments.lexer import RegexLexer, bygroups, include
-from pygments.token import Text, Keyword, Name, String, Comment
+from pygments.token import Text, Keyword, Name, String, Comment, Literal
 
 class PlumedCLtoolLexer(RegexLexer):
     name = 'plumedcltool'
@@ -14,8 +14,16 @@ class PlumedCLtoolLexer(RegexLexer):
             (r'#DEFAULT plumed\n',Comment.Special),
             # Find the end of a default section
             (r'#ENDDEFAULT plumed\n',Comment.Special),
+            # Find commands that use MPI and that take an input file
+            (r'(^\s*mpirun\s+-np)(\s+[0-9]+\s+)(plumed)(\s+)(\S+\b)(\s*<\s*)(\S+\b)', bygroups(Literal, Text, String, Text, Keyword, Text, Name.Decorator)), 
+            # With plumed-runtime and MPI
+            (r'(^\s*mpirun\s+-np)(\s+[0-9]+\s+)(plumed-runtime)(\s+)(\S+\b)', bygroups(Literal, Text, String, Text, Keyword)),
+            # Find commands that use MPI
+            (r'(^\s*mpirun\s+-np)(\s+[0-9]+\s+)(plumed)(\s+)(\S+\b)', bygroups(Literal, Text, String, Text, Keyword)),
             # Find commands that take an input file
             (r'(^\s*plumed)(\s+)(\S+\b)(\s*<\s*)(\S+\b)', bygroups(String, Text, Keyword, Text, Name.Decorator)),
+            # Find the name of the command if we are using plumed-runtime
+            (r'(^\s*plumed-runtime)(\s+)(\S+\b)', bygroups(String, Text, Keyword)),
             # Find the name of the command
             (r'(^\s*plumed)(\s+)(\S+\b)', bygroups(String, Text, Keyword)),
             # Deals with keywords with equals sign

src/PlumedToHTML/PlumedFormatter.py

@@ -4,6 +4,7 @@
 from pygments.lexers.c_cpp import CppLexer
 from pygments.formatters import HtmlFormatter
 from requests.exceptions import InvalidJSONError
+import re
 import html
 import json
 
@@ -61,8 +62,11 @@ def format(self, tokensource, outfile):
                # Non PLUMED stuff
                outfile.write( value )
             elif ttype==Literal :
+               # mpirun -np for command line tools
+               if re.search("mpirun\s+-np", value ) :
+                   outfile.write('<span class="plumedtooltip">' + value + '<span class="right">Run instances of PLUMED on this number of MPI processes<i></i></span></span>') 
                # __FILL__ for incomplete values
-               if( value=="__FILL__" ) : 
+               elif( value=="__FILL__" ) : 
                    outfile.write('<span style="background-color:yellow">__FILL__</span>')
                # This is for vim syntax expression
                elif "vim:" in value :
@@ -188,6 +192,7 @@ def format(self, tokensource, outfile):
             elif ttype==String or ttype==String.Double :
                # Labels of actions
                if not self.broken and action!="" and label!="" and label!=value.strip() : raise Exception("label for " + action + " is not what is expected.  Is " + label + " should be " + value.strip() )
+               elif value.strip()=="plumed-runtime" : label = "plumed"
                elif label=="" : label = html.escape( value.strip() ) 
                valtype = "mix"
                if label in self.valuedict.keys() :
@@ -263,7 +268,7 @@ def format(self, tokensource, outfile):
                   # Store name of action in set that contains all action names
                   self.actions.add(action)
                if default_state!=0 or shortcut_state==1 : 
-                  if label!="" and label!=act_label : raise Exception("mismatched label and act_label for shortcut/default") 
+                  if label!="" and label!=act_label : raise Exception("mismatched label and act_label for shortcut/default label=" + label + " act_label=" + act_label ) 
                if notooltips :
                     outfile.write('<span class="plumedtooltip" style="color:green">' + value.strip() + '<span class="right">This action is not part of PLUMED and was included by using a LOAD command <a href="' + self.keyword_dict["LOAD"]["hyperlink"] + '" style="color:green">More details</a><i></i></span></span>') 
                elif shortcut_state==1 and default_state==1 :

src/PlumedToHTML/PlumedToHTML.py

@@ -231,15 +231,20 @@ def get_cltoolarg_html( inpt, name, plumedexe ) :
     """
     # Get the cltool that we are using
     pl, tool = inpt.split()[0], inpt.split()[1]
-    if pl!="plumed" :
-       raise Exception("first word in the command should be plumed")
+    if re.search("^mpirun\s+-np\s+[0-9]+\s+plumed",inpt) : 
+       tool = inpt.split()[4]
+    elif pl!="plumed" and pl!="plumed-runtime" :
+       raise Exception("first word in the command should be plumed or plumed-runtime")
     # Create the lexer that will generate the pretty plumed input
     lexerfile = os.path.join(os.path.dirname(__file__),"PlumedCLtoolLexer.py")
     plumed_lexer = load_lexer_from_file(lexerfile, "PlumedCLtoolLexer" )
      # Get the plumed syntax file
     defstr, keyword_dict = inpt, getPlumedSyntax( plumedexe )
     # Find the default values in the dictionary
-    if inpt.split()[2]!="-h" and inpt.split()[2]!="--help" and keyword_dict["cltools"][tool]["inputtype"]!="file" : 
+    ishelp = False
+    if len(inpt.split())>2 and (inpt.split()[2]=="-h" or inpt.split()[2]=="--help") :
+       ishelp = True 
+    if not ishelp and keyword_dict["cltools"][tool]["inputtype"]!="file" : 
        for key, dicti in keyword_dict["cltools"][tool]["syntax"].items() :
            if "default" not in dicti.keys() or dicti["default"]=="off" or key in inpt : continue
            defstr += " " + key + " " + dicti["default"]
@@ -669,6 +674,7 @@ def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofil
     cltoolregexps, clfileregexps = [], []
     for key, data in plumed_syntax["cltools"].items() :
         cltoolregexps.append("plumed\s+" + key )
+        cltoolregexps.append("plumed-runtime\s+" + key )
         if data["inputtype"]=="file" :
            clfileregexps.append( "#TOOL\s*=\s*" + key )
 

tdata/cltooltests.json

@@ -35,6 +35,24 @@
           "index": 5,
           "output": "<div class=\"highlight\"><pre><span></span><span class=\"s\">plumed</span> <span class=\"k\">simplemd</span> &lt; <span class=\"nd\">in</span>\n</pre></div>\n",
           "tooltips": ["simplemd", "in"]
-       }
+       },
+       {
+          "input": "plumed-runtime benchmark --kernel /path/to/lib/libplumedKernel.so",
+          "index": 6,
+          "output": "<div class=\"highlight\"><pre><span></span><span class=\"s\">plumed-runtime</span> <span class=\"k\">benchmark</span> <span class=\"na\">--kernel</span> /path/to/lib/libplumedKernel.so\n</pre></div>\n",
+          "tooltips": ["benchmark", "--kernel", "benchmark", "--kernel", "--plumed", "--natoms", "--nsteps", "--maxtime", "--sleep", "--atom-distribution"]
+       },
+       {
+          "input": "plumed benchmark",
+          "index": 7,
+          "output": "<div class=\"highlight\"><pre><span></span><span class=\"s\">plumed</span> <span class=\"k\">benchmark</span>\n</pre></div>\n",
+          "tooltips": ["benchmark", "benchmark", "--plumed", "--kernel", "--natoms", "--nsteps", "--maxtime", "--sleep", "--atom-distribution"]
+       },
+       {
+          "input": "mpirun -np 4 plumed-runtime benchmark",
+          "index": 8,
+          "output": "<div class=\"highlight\"><pre><span></span><span class=\"l\">mpirun -np</span> 4 <span class=\"s\">plumed-runtime</span> <span class=\"k\">benchmark</span>\n</pre></div>\n",
+          "tooltips": ["mpirun -np", "benchmark", "mpirun -np", "benchmark", "--plumed", "--kernel", "--natoms", "--nsteps", "--maxtime", "--sleep", "--atom-distribution"]
+       } 
    ]
 }