Added code to generate mermaid graphs for plumed inputs

PlumedToHTML/PlumedToHTML.py

@@ -278,7 +278,34 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, actio
            if not soup.find("div",{"id": switchval + "_short"} ) : raise Exception("Generated html is invalid as could not find " + switchval + "_short")
         else : raise Exception("Could not find toggler command for " + val)
     return html
-
+
+def get_mermaid( inpt, force ) :
+    """
+     Generate the mermaid graph showing how data passes through PLUMED input file
+
+     Keyword arguments:
+     inpt -- A string containing the PLUMED input
+     force -- Bool that if true ensures we show the graph for the backwards pass through the action list
+    """
+    # Write the plumed input to a file
+    iff = open( "mermaid_plumed.dat", "w+")
+    iff.write(inpt+ "\n")
+    iff.close()
+    # Now check the input is OK
+    broken = test_plumed( "plumed", "mermaid_plumed.dat", header="" )
+    if broken!=0 : raise Exception("invalid plumed input file -- cannot create mermaid graph")
+    # Run mermaid
+    cmd = ['plumed', 'show_graph', '--plumed', 'mermaid_plumed.dat', '--out', 'mermaid.md']
+    if force : cmd.append("--force")
+    plumed_out = subprocess.run(cmd, capture_output=True, text=True )
+    mf = open("mermaid.md")
+    mermaid = mf.read()
+    mf.close()
+    # Remove stuff that was created
+    os.remove("mermaid_plumed.dat")
+    os.remove("mermaid.md")
+    return mermaid 
+
 def resolve_includes( srcdir, inpt, foundfiles ) :
     if not foundfiles or "INCLUDE" not in inpt : return foundfiles, inpt
 

PlumedToHTML/__init__.py

@@ -1 +1 @@
-from .PlumedToHTML import test_plumed, test_and_get_html, get_html, get_html_header, compare_to_reference
+from .PlumedToHTML import test_plumed, test_and_get_html, get_html, get_html_header, compare_to_reference, get_mermaid

PlumedToHTML/tests/test_mermaid.py

@@ -0,0 +1,41 @@
+from unittest import TestCase
+
+import os
+import subprocess
+from PlumedToHTML import get_mermaid
+
+class TestPlumedToHTMLMermaid(TestCase):
+   def testNormalGraph(self) :
+       inpt="d1: DISTANCE ATOMS=1,2\n PRINT ARG=d1 FILE=colvar"
+       mermaid_this = get_mermaid( inpt, False )
+       iff = open("test_mermaid.dat","w+")
+       iff.write(inpt)
+       iff.close()
+       cmd = ['plumed', 'show_graph', '--plumed', 'test_mermaid.dat', '--out', 'test_mermaid.md']
+       plumed_out = subprocess.run(cmd, capture_output=True, text=True )
+       mf = open("test_mermaid.md")
+       mermaid_pp = mf.read()
+       mf.close()
+       mermaid_this = get_mermaid( inpt, False )
+       os.remove("test_mermaid.dat")
+       os.remove("test_mermaid.md")
+       self.assertTrue( mermaid_pp == mermaid_this )
+
+   def testForceGraph(self) :
+       inpt="d1: DISTANCE ATOMS=1,2\n rr: RESTRAINT ARG=d1 KAPPA=10 AT=1"
+       mermaid_this = get_mermaid( inpt, True )
+       iff = open("test_mermaid.dat","w+")
+       iff.write(inpt)
+       iff.close()
+       cmd = ['plumed', 'show_graph', '--plumed', 'test_mermaid.dat', '--out', 'test_mermaid.md', '--force']
+       plumed_out = subprocess.run(cmd, capture_output=True, text=True )
+       mf = open("test_mermaid.md")
+       mermaid_pp = mf.read()
+       mf.close()
+       mermaid_this = get_mermaid( inpt, True )
+       os.remove("test_mermaid.dat")
+       os.remove("test_mermaid.md")
+       self.assertTrue( mermaid_pp == mermaid_this )
+
+
+

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.65',
+     version='0.66',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",