Simplification for getting the files that are used for shortcuts and …

…valuedictionary

PlumedToHTML/PlumedToHTML.py

@@ -39,6 +39,7 @@ def test_and_get_html( inpt, name, actions=set({}) ) :
         Keyword arguments:
         inpt -- A string containing the PLUMED input
         name -- The name to use for this input in the html
+        actions -- Set that is filled with the actions that were used in this input
     """
     # Check if this is to be included by another input
     filename, keepfile = name + ".dat", False
@@ -53,15 +54,15 @@ def test_and_get_html( inpt, name, actions=set({}) ) :
     iff.write(test_inpt + "\n")
     iff.close()
     # Now do the test
-    broken = test_plumed( "plumed", filename, header="", shortcutfile=name + '.json', valuefile='values_' + name + '.json' )
+    broken = test_plumed( "plumed", filename, header="", printjson=True )
     # Retrieve the html that is output by plumed
-    html = get_html( inpt, name, name, ("master",), (broken,), ("plumed",), actions=actions )
+    html = get_html( inpt, filename, filename, ("master",), (broken,), ("plumed",), actions=actions )
     # Remove the tempory files that we created
     if not keepfile : os.remove(filename)
 
     return html
 
-def test_plumed( executible, filename, header=[], shortcutfile=[], valuefile=[] ) :
+def test_plumed( executible, filename, header=[], printjson=False, jsondir="./" ) :
     """
         Test if plumed can parse this input file
 
@@ -71,8 +72,8 @@ def test_plumed( executible, filename, header=[], shortcutfile=[], valuefile=[]
         executible   -- A string that contains the command for running plumed
         filename     -- A string that contains the name of the plumed input file to parse
         header       -- A string to put at the top of the error page that is output
-        shortcutfile -- The file on which to output the json file containing the expansed shortcuts.  If not present this is not output 
-        valuefile -- The file on which to output the dictionary explaining what each value represents.  If not present this is not output
+        printjson    -- Set true if you want to used plumed to print the files containing the expansions of shortcuts and the value dictionary 
+        jsondir      -- The directory in which to output the files containing the expansions of the shortcuts and the value dictionaries
     """
     # Get the information for running the code
     run_folder = str(pathlib.PurePosixPath(filename).parent)
@@ -88,10 +89,12 @@ def test_plumed( executible, filename, header=[], shortcutfile=[], valuefile=[]
     cmd = [executible, 'driver', '--plumed', plumed_file, '--natoms', str(natoms), '--parse-only', '--kt', '2.49']
     # Add everything to ensure we can run with replicas if needs be
     if int(nreplicas)>1 : cmd = ['mpirun', '-np', str(nreplicas)] + cmd + ['--multi', str(nreplicas)]
-    # Add the shortcutfile output if the user has asked for it
-    if len(shortcutfile)>0 : cmd = cmd + ['--shortcut-ofile', shortcutfile]
-    # Add the value dictionary if the user has asked for it
-    if len(valuefile)>0 : cmd = cmd + ['--valuedict-ofile', valuefile] 
+    if printjson :
+       plumed_file = os.path.basename(filename)
+       # Add the shortcutfile output if the user has asked for it 
+       cmd = cmd + ['--shortcut-ofile', jsondir + plumed_file + ".json"]
+       # Add the value dictionary if the user has asked for it
+       cmd = cmd + ['--valuedict-ofile', jsondir + plumed_file + "_values.json"] 
     # raw std output - to be zipped
     outfile=filename + "." + executible + ".stdout.txt"
     # raw std error - to be zipped
@@ -169,6 +172,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
        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
+       maxchecks -- Maximum number of checks to perform on plumed input.  Set this to reduce computational expense
        actions -- Set to store all the actions that have been used in the input
     """
 
@@ -203,15 +207,15 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
     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 searchjson :
-       with open('values_' + name + '.json') as f :
+    if os.path.exists( name + '_values.json') and searchjson :
+       with open( name + '_values.json') as f :
            try:
               valuedict = json.load(f)
            except json.JSONDecodeError as ve:
               raise Exception("invalid json for value dictionary", ve)
     else : valuedict = {}
     # Remove the tempory files that we created
-    if os.path.exists( 'values_' + name + '.json') : os.remove( 'values_' + name + ".json")
+    if os.path.exists( name + '_values.json') : os.remove( name + "_values.json")
 
     # Create the lexer that will generate the pretty plumed input
     lexerfile = os.path.join(os.path.dirname(__file__),"PlumedLexer.py")

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.70',
+     version='0.71',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",