diff --git a/src/PlumedToHTML/PlumedToHTML.py b/src/PlumedToHTML/PlumedToHTML.py
index f6fcfdc..7a09dc6 100644
--- a/src/PlumedToHTML/PlumedToHTML.py
+++ b/src/PlumedToHTML/PlumedToHTML.py
@@ -51,7 +51,7 @@ def getPlumedSyntax( plumedexe ) :
raise InvalidJSONError(ve)
return keyword_dict
-def test_and_get_html( inpt, name, actions=set({}) ) :
+def test_and_get_html( inpt, name, actions=set({}), test_plumed_kwargs={}) :
"""
Test if the plumed input is broken and generate the html syntax
@@ -75,7 +75,7 @@ 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="", printjson=True )
+ broken = test_plumed( "plumed", filename, header="", printjson=True, **test_plumed_kwargs)
# Retrieve the html that is output by plumed
html = get_html( inpt, filename, filename, ("master",), (broken,), ("plumed",), actions=actions )
# Remove the tempory files that we created
@@ -83,7 +83,7 @@ def test_and_get_html( inpt, name, actions=set({}) ) :
return html
-def test_plumed( executible, filename, header=[], printjson=False, jsondir="./", cmdTimeout:"None|float"=None, ghmarkdown=True ) :
+def test_plumed( executible, filename, header="", printjson=False, jsondir="./", cmdTimeout:"None|float"=None, ghmarkdown=True ) :
"""
Test if plumed can parse this input file
@@ -136,7 +136,8 @@ def test_plumed( executible, filename, header=[], printjson=False, jsondir="./",
# write header and preamble to errfile
with open(errfile,"w") as stderr:
- if len(header)>0 : print(header,file=stderr)
+ if len(header)>0 :
+ print(header,file=stderr)
print("Stderr for source: ",re.sub("^data/","",filename)," ",file=stderr)
print("Download: [zipped raw stdout](" + plumed_file + "." + executible + ".stdout.txt.zip) - [zipped raw stderr](" + plumed_file + "." + executible + ".stderr.txt.zip) ",file=stderr)
if ghmarkdown : print("{% raw %}\n",file=stderr)
@@ -449,7 +450,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
else : raise Exception("Could not find toggler command for " + val)
return html
-def get_mermaid( executible, inpt, force ) :
+def get_mermaid( executible, inpt, force, test_plumed_kwargs={} ) :
"""
Generate the mermaid graph showing how data passes through PLUMED input file
@@ -462,7 +463,7 @@ def get_mermaid( executible, inpt, force ) :
iff.write(inpt+ "\n")
iff.close()
# Now check the input is OK
- broken = test_plumed( executible, "mermaid_plumed.dat", header="" )
+ broken = test_plumed( executible, "mermaid_plumed.dat",**test_plumed_kwargs)
if broken!=0 : raise Exception("invalid plumed input file -- cannot create mermaid graph")
# Run mermaid
cmd = [executible, 'show_graph', '--plumed', 'mermaid_plumed.dat', '--out', 'mermaid.md']
@@ -657,7 +658,8 @@ def compare_to_reference( output, reference ) :
return True
-def processMarkdown( filename, plumedexe, plumed_names, actions, jsondir="./", ghmarkdown=True ) :
+def processMarkdown( filename, plumedexe, plumed_names, actions, jsondir="./", ghmarkdown=True,
+ *,test_plumed_kwargs={} ) :
"""
Process a markdown file that contains PLUMED input files using PlumedtoHTML
@@ -667,6 +669,7 @@ def processMarkdown( filename, plumedexe, plumed_names, actions, jsondir="./", g
plumed_names -- the names of the plumed executibles to use in the badges
actions -- names of actions used in the plumed inputs in this markdown file
jsondir -- The directory in which to output the files containing the expansions of the shortcuts and the value dictionaries
+ test_plumed_kwargs -- a dictionary of extra keywords to pass to the test_plumed utility, only "header" and "cmdTimeout" works
"""
if not os.path.exists(filename) :
raise RuntimeError("Found no file called " + filename + " in lesson")
@@ -675,10 +678,13 @@ def processMarkdown( filename, plumedexe, plumed_names, actions, jsondir="./", g
inp = f.read()
with open( filename, "w+" ) as ofile:
- ninputs, nfail = processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile, jsondir, ghmarkdown )
+ ninputs, nfail = processMarkdownString( inp, filename, plumedexe, plumed_names,
+ actions, ofile, jsondir, ghmarkdown, test_plumed_kwargs=test_plumed_kwargs )
return ninputs, nfail
-def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile, jsondir="./", ghmarkdown=True, checkaction="ignore", checkactionkeywords=set({}) ) :
+def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofile,
+ jsondir="./", ghmarkdown=True, checkaction="ignore", checkactionkeywords=set({}),
+ *,test_plumed_kwargs={}) :
"""
Process a string of markdown that contains LUMED input files using PlumedtoHTML
@@ -691,6 +697,7 @@ def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofil
dirname -- the directory in which to find solution files
ofile -- the file on which to output the processed markdown
jsondir -- The directory in which to output the files containing the expansions of the shortcuts and the value dictionaries
+ test_plumed_kwargs -- a dictionary of extra keywords to pass to the test_plumed utility, only "header" and "cmdTimeout" works
"""
dirname = os.path.dirname(filename)
if dirname=="" : dirname = "."
@@ -782,12 +789,17 @@ def processMarkdownString( inp, filename, plumedexe, plumed_names, actions, ofil
# PlumedToHTML finds them when we do get_html (i.e. these will be in
# the data directory where the calculation is run)
if incomplete :
- success[i]=test_plumed(plumedexe[i], solutionfile, ghmarkdown=ghmarkdown )
+ success[i]=test_plumed(plumedexe[i], solutionfile, ghmarkdown=ghmarkdown,
+ **test_plumed_kwargs)
else :
success[i]=test_plumed(plumedexe[i], solutionfile,
- printjson=True, jsondir=jsondir, ghmarkdown=ghmarkdown )
+ printjson=True, jsondir=jsondir, ghmarkdown=ghmarkdown,
+ **test_plumed_kwargs)
else :
- success[i]=test_plumed( plumedexe[i], solutionfile, ghmarkdown=ghmarkdown )
+ success[i]=test_plumed( plumedexe[i],
+ solutionfile,
+ ghmarkdown=ghmarkdown,
+ **test_plumed_kwargs,)
if(success[i]!=0 and success[i]!="custom") : nfail[i] = nfail[i] + 1
# Use PlumedToHTML to create the input with all the bells and whistles
html = get_html(plumed_inp,