added converttonotebook.py

documentation/doxygen/converttonotebook.py

@@ -0,0 +1,391 @@
+import json
+import sys
+import textwrap
+import time
+import subprocess
+import os
+from nbformat import v3, v4
+from datetime import datetime, date
+
+starttime= time.time()
+
+#-------------------------------------
+#-------- Fuction definitions---------
+#-------------------------------------
+
+def unindenter(string):
+    """
+    Returns string with each line unindented by 3 spaces. If line isn't indented, it stays the same.
+    """
+    newstring=''
+    lines = string.splitlines()
+    for line in lines:
+        if line.startswith("   "):
+            print "yes"
+            newstring+= (line[3:] + "\n")
+        else:
+            print "no"
+            newstring+= (line + "\n")
+        print line
+    return newstring
+
+def pythonheader(text):
+    """
+    Extract author and descrition from header, eliminate header from text
+    """
+
+    lines = text.splitlines()
+
+    description=''
+    author=''
+    notebook=False
+    for i, line in enumerate(lines):
+        if line.startswith("## \\aut"):
+            author = line[11:]
+        if line.startswith("## \\note"):
+            notebook=True
+        if line.startswith("##"):
+            if not line.startswith("## \\") and not line == "##":
+                description+=(line[3:]+ '\n')
+        else:
+            break
+    newtext=''
+    for j in lines[i:]:
+        newtext += (j+"\n")
+
+    return newtext, description, author, notebook
+
+def pythoncomments (text):
+    """
+    Converts comments delimited by # or ## and on a new line into a markdown cell. For python files only
+    """
+    text=text.splitlines()
+    newtext=''
+    incomment=False
+    for i, line in enumerate(text):
+        if line.startswith("#") and not incomment: ## True if first line of comment
+            incomment=True
+            newtext+="# <markdowncell>\n"
+            newtext+=(line + "\n")
+        elif incomment and not line.startswith("#"): ## True if first line after comment
+            incomment=False
+            newtext+="# <codecell>\n"
+            newtext+=(line+"\n")
+        else:
+            newtext+=(line+"\n")
+    return newtext
+
+
+def cppheader(text):
+    """
+    Extract author and descrition from header, eliminate header from text
+    """
+    lines = text.splitlines()
+
+    description=''
+    author=''
+    notebook=False
+    for i, line in enumerate(lines):
+        if line.startswith("/// \\aut"):
+            author = line[12:]
+        if line.startswith("/// \\note"):
+            notebook=True
+        if line.startswith("///"):
+            if not line.startswith("/// \\") and not line == "///":
+                description+=(line[4:]+ '\n')
+        else:
+            break
+    newtext=''
+    for j in lines[i:]:
+        newtext += (j+"\n")
+
+    return newtext, description, author, notebook
+
+def cppfunction(text):
+    """
+    Extracts main function for the function enclosure. Creates a cell break above it.
+    Creates new cells for all help functions, and adds the %%cpp -d magic on top of all of them
+    """
+    lines=text.splitlines()
+    functionline=0
+    mainbrace=0
+
+    for i,line in enumerate(lines):
+        if "void" in line and name in line:
+            functionline=i
+        if functionline and line == "}" and not mainbrace:
+            mainbrace=i
+
+    newtext=''
+
+    if functionline:
+        for line in lines[:functionline]:
+            newtext += (line+"\n")
+        newtext+="# <codecell>\n"
+
+        unindent=''
+        for line in lines[functionline+2:mainbrace]:
+            unindent += (line+"\n")
+        newtext+=unindenter(unindent)
+        for line in lines[mainbrace+1:]:
+            newtext += (line+"\n")
+    else:
+        for line in lines:
+            newtext += (line+"\n")
+
+    ## print text
+    ## print newtext
+    ## print functionline
+
+    ## for i, line in enumerate(lines):
+    ##      print str(i) + "       " +  line
+
+    ## print "Functionline, mainbrace: ", functionline, mainbrace
+
+    ## for i, line in enumerate(newtext.splitlines()):
+    ##      print str(i) + "       " +  line
+
+
+    return newtext, functionline, mainbrace-2
+
+def cpphelpers(text, functionline, mainbrace):
+
+    lines=text.splitlines()
+    helperlines=[]
+    helperbraces=[]
+    inhelper=False
+    for i,line in enumerate(lines):
+        if "void" in line and lines[i+1] == "{":
+            helperlines.append(i)
+            inhelper=True
+        if inhelper and line == "}":
+            helperbraces.append(i)
+            inhelper=False
+
+    helpers = []
+    for i , helper in enumerate(helperlines):
+        for j, brace in enumerate(helperbraces):
+            try:
+                if helperlines[i+1] < brace:
+                    break
+                else:
+                    helpers.append([helper,brace])
+            except:
+                 if helperlines[-1] < helperbraces [-1]:
+                     helpers.append([helperlines[-1] , helperbraces [-1]])
+                     break
+
+    print helperlines, helperbraces
+    print helpers
+    for i, line in enumerate(lines):
+        print str(i) + "       " +  line
+    print helpers
+
+
+    newtext=''
+    counter=0
+    for i , line in enumerate(lines):
+        inhelper=False
+        for pair in helpers:
+            if pair[0] <= i <= pair[1]:
+                inhelper = True
+        if not inhelper and (i < functionline or i > mainbrace):
+            print line
+            newtext += (line+"\n")
+            counter+=1  
+
+    print "*************"
+    print "^^Not helper, not main ^^"
+    print "*************"
+
+    for pair in helpers:
+        newtext+= "# <markdowncell>\n A helper function is created: \n# <codecell>\n%%cpp -d\n"
+        counter+=4
+        for line in lines[pair[0]:pair[1]+1]:
+            print line
+            newtext += (line+"\n")
+            counter+=1
+        print "*************"
+        print "^^helper ^^"
+
+    print "*************"
+    print " Main below"
+    print "*************"
+    for i , line in enumerate(lines):
+        inhelper=False
+        if functionline <= i <= mainbrace:
+            print line
+            newtext += (line+"\n")
+
+    return newtext, counter
+
+def cppcomments (text, counter):
+    """
+    Converts comments delimited by // and on a new line into a markdown cell. For C++ files only.
+    """
+    text=text.splitlines()
+    newtext=''
+    incomment=False
+
+    for i, line in enumerate(text):
+        if i <= counter:
+            newtext+=(line+"\n")
+        elif line.startswith("//") and not incomment: ## True if first line of comment
+            incomment=True
+            newtext+="# <markdowncell>\n"
+            newtext+=("# " + line[2:]+"\n")
+        elif incomment and not line.startswith("//"):## True if first line after comment
+            incomment=False
+            newtext+="# <codecell>\n"
+            newtext+=(line+"\n")
+        elif incomment and line.startswith("//"): ## True if in the middle of a comment block
+            newtext+=("# " + line[2:]+"\n")
+        else:
+            newtext+=(line+"\n")
+
+        print str(i)  + "    "+ str(i <= counter) + "    " + line
+
+    return newtext
+
+#-------------------------------------
+#----- Preliminary definitions--------
+#-------------------------------------
+
+
+## Extract and define the name of the file as well as its derived names
+pathname = str(sys.argv[1])
+pathnoext = os.path.dirname(pathname)
+filename = os.path.basename(pathname)
+name,extension = filename.split(".")
+outname= filename + ".ipynb"
+
+## print pathname, filename, name, extension, outname
+## Extract output directory
+try:
+    outdir = str(sys.argv[2])
+except:
+    outdir = pathnoext + "/"
+
+## Find and define the time and date this script is run
+date = datetime.now().strftime("%A, %B %d, %Y at %I:%M %p")
+
+
+#-------------------------------------
+#------------ Main Program------------
+#-------------------------------------
+
+with open(pathname) as fpin:
+    text = fpin.read()
+
+if extension == "py":
+    ## print "Python"
+    text, description, author, notebook = pythonheader(text)
+
+elif extension ==  "c" or extension == "C":
+    ## print "C++"
+    ## print text
+
+    text, description, author, notebook = cppheader(text)
+
+
+def main(text):
+
+    ## Convert the comments to markdown cells
+    ## For C++ extract main function
+
+    if extension ==  ("C" or "c" or "cpp" or "c++") :
+        #print "C++"
+        ## print text
+        text, functionline, mainbrace = cppfunction(text)
+        ## print text
+
+        text, counter = cpphelpers(text, functionline, mainbrace)
+        text = cppcomments(text, counter)
+        ## print text
+
+    if extension == "py":
+        #print "Python"
+        text = pythoncomments(text)
+
+## Add the title and header of the notebook    
+    text= "# <markdowncell> \n# # %s\n# %s# \n# This notebook tutorial was automatically generated from the macro found in the ROOT repository on %s.\n# **Author:** %s \n# <codecell>\n%s" % (name.title(), description, date, author, text)
+
+    if extension == ("C" or "c" or "cpp" or "c++"):
+        text +="\n# <markdowncell> \n# Draw all canvases \n# <codecell>\ngROOT->GetListOfCanvases()->Draw()"
+    if extension == "py":
+        text +="\n# <markdowncell> \n# Draw all canvases \n# <codecell>\nimport ROOT \ngROOT.GetListOfCanvases().Draw()"
+
+    print text
+
+    nbook = v3.reads_py(text)  
+    nbook = v4.upgrade(nbook)  # Upgrade v3 to v4
+
+    jsonnometa = v4.writes(nbook) + "\n"
+
+    json_data = json.loads(jsonnometa)
+
+    # add the corresponding metadata
+    if extension == "py": 
+        json_data[u'metadata']={
+       "kernelspec": {
+       "display_name": "Python 2",
+       "language": "python",
+       "name": "python2"
+      },
+      "language_info": {
+       "codemirror_mode": {
+       "name": "ipython",
+       "version": 2
+       },
+       "file_extension": ".py",
+       "mimetype": "text/x-python",
+       "name": "python",
+       "nbconvert_exporter": "python",
+       "pygments_lexer": "ipython2",
+       "version": "2.7.10"
+      }
+      }
+    else:
+        json_data[u'metadata']={
+      "kernelspec": {
+       "display_name": "ROOT C++",
+       "language": "c++",
+       "name": "root"
+      },
+      "language_info": {
+       "codemirror_mode": "text/x-c++src",
+       "file_extension": ".C",
+       "mimetype": " text/x-c++src",
+       "name": "c++"
+      }
+     }
+
+        ## print json.dumps(json_data)
+        ## print type(json.dumps(json_data))
+
+    ## write the json file with the metadata
+    with open(outdir+outname, 'w') as f:
+        json.dump(json_data, f, indent=1, sort_keys=True)
+
+    ## The two commands to create an html version of the notebook and a notebook with the output
+    ## command1 = "jupyter nbconvert --to html --execute /Users/Pau/Desktop/" + outname
+    ## command2 = "jupyter nbconvert --to notebook --execute /Users/Pau/Desktop/" + outname
+    #print command1
+    #print command2
+    #subprocess.call(command1)
+    #subprocess.call(command2)
+    print time.time() - starttime
+    subprocess.call(["jupyter", "nbconvert","--ExecutePreprocessor.timeout=60", "--to=html", "--execute",  outdir+outname])
+    subprocess.call(["jupyter", "nbconvert","--ExecutePreprocessor.timeout=60", "--to=notebook", "--execute",  outdir+outname])
+    os.remove(outdir+outname)
+
+os.environ["DYLD_LIBRARY_PATH"] = os.environ["ROOTSYS"] + "/lib"
+
+
+if notebook and extension == ("C" or "c" or "cpp" or "c++" or "py"):
+    main(text)
+    print time.time() - starttime
+else:
+    print "Nope"
+
+