Merge several Jupyter notebooks and then render them as pdf or docx

merged_notebook_doc.py

#https://stackoverflow.com/a/3207973/454773
from nbformat.v4 import new_notebook, new_markdown_cell
import nbformat
import io
import os
import subprocess
import random
import string

#from PyPDF2 import PdfFileMerger, PdfFileReader

def merged_notebooks_in_dir(dirpath,filenames):
    ''' Merge all notebooks in a directory into a single notebook '''

    fns = ['{}/{}'.format(dirpath, fn) for fn in filenames if '.ipynb_checkpoints' not in dirpath and fn.endswith('.ipynb')]
    if fns:
        merged = new_notebook()
        #Identify directory containing merged notebooks
        cell = '\n\n---\n\n# {}\n\n---\n\n'.format(dirpath)
        merged.cells.append(new_markdown_cell(cell))
    else: return
    
    for fn in fns:
        #print(fn)
        notebook_name = fn.split('/')[-1]
        with io.open(fn, 'r', encoding='utf-8') as f:
            nb = nbformat.read(f, as_version=4)
            #Identify filename of notebook
            cell = '\n\n---\n\n# {}\n\n---\n\n'.format(fn)
            merged.cells.append(new_markdown_cell(cell))
            merged.cells.extend(nb.cells)
            
    if not hasattr(merged.metadata, 'name'):
        merged.metadata.name = ''
        
    merged.metadata.name += "_merged"
    return nbformat.writes(merged)


def merged_notebooks_down_path(path, typ='docx', execute=False):
    ''' Walk a path, creating an output file in each directory that merges all notebooks in the directory  '''
    for (dirpath, dirnames, filenames) in os.walk(path):
        if '.ipynb_checkpoints' in dirpath: continue
        
        #Should we run the execute processor here on each notebook separately,
        # ensuring that images are embedded, and then merge the executed notebook files? 
        merged_nb = merged_notebooks_in_dir(dirpath,filenames)
        if not merged_nb: continue
        
        fn=''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10))
        with open('{}/{}.ipynbx'.format(dirpath,fn), 'w') as f:
            f.write(merged_nb)
        
        # Execute the merged notebook in its directory so that images are correctly handled
        # Using html_embed seems to cause pandoc to fall over?
        # The pdf conversion requires installation of texlive-xetex and inkscape
        # This adds significant weight to the VM: maybe we need an MT/prouction VM and a student build?
        # Inline code execution generated using python-markdown extension seems to break PDF generation
        #  at the first instance of inline code? Need to add a preprocessor?
        # We could maybe process the notebook inline rather than via the commandline
        # In such a case, the following may be a useful reference:
        #https://github.com/ipython-contrib/jupyter_contrib_nbextensions/blob/master/docs/source/exporting.rst
        execute = '  --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.allow_errors=True --execute' if execute else ''
        if typ=='pdf':
            cmd='jupyter nbconvert --to pdf {exe} "{fn}".ipynbx'.format(exe=execute, fn=fn)
            subprocess.check_call(cmd, shell=True, cwd=dirpath)
        elif typ in ['docx']:
            cmd='jupyter nbconvert --to html {exe} "{fn}".ipynbx'.format(exe=execute, fn=fn)
            subprocess.check_call(cmd, shell=True, cwd=dirpath)
            cmd='pandoc -s "{fn_out}".html -o _merged_notebooks.{typ}'.format(fn_out=fn, typ=typ)
            subprocess.check_call(cmd, shell=True, cwd=dirpath)
            os.remove("{}/{}.html".format(dirpath,fn))
        os.remove("{}/{}.ipynbx".format(dirpath,fn))