## ---New cell---
# for the blog this is principally to just remove
# rough notes; copy the 'mother' notebook to the blog folder
import sys
#sys.path.append('/media/sf_SharedFolder/Code/git_repos_of_mine/ipynb-workdocs') # (main ipynb-workdocs dir)
sys.path.append('/home/jgriffiths/Code/libraries_of_mine/github/ipynb-workdocs')
import ipynb_wd_utils as iwu
#iwu.run_nbconvert(nb_pfx = nb_pfx,
# pdf_title = nb_pfx,
# pdf_author = 'J. D. Griffiths',
# tex_changes=tex_changes)
res = iwu.run_nbconvert(nb_pfx = nb_pfx,
ipynb_wd_version = '0.2',
pdf_title=nb_pfx, #pdf_title,
pdf_author='J. D. Griffiths', #pdf_author,
tex_changes=tex_changes)
## ---New cell---
fname = nb_pfx + '__workdocs__' + today + '/' + nb_pfx\
+ '__pdf_nb__' + today + '_tidied.pdf'
## ---New cell---
!okular $fname
## ---New cell---
def run_nbconvert(nb_pfx,nb_list=None,pdf_title='',pdf_author = '',tex_changes=None, ipynb_wd_version='0.1', do_html_nb=True,do_html_file=True,do_slides_nb=True,do_slides_file=True,do_pdf_nb=True,do_pdf_file=True,remove_additional_files=False):
# ipynb-workdocs nbconvert:
# =========================
# Using ipynb-workdocs to
# a) filter out rough notes
# b) identify pdf cells
# c) identify slideshow cells
# e) identify html cells (maybe)
# Only need to do the 'second round' of ipynb-wordocs conversion for html and slides, not pdf
# (...running the pdf conversion anyway. But note that the main pdf for the chapter is compiled
# using the cam uni thesis template)
# Re: Use of ipynb-workdocs cell tags in this doc:
#
# - cells with notes / commented out text are marked as rough notes
# - cells with code in that is executed but no figure rendered are marked as 'omit_slides' + 'omit_pdf' + 'omit_html'
# (because don't want to include all the functional code in the html, pdf, or slides files)
#
# Usage
# ----
# > os.chdir('DoctoralThesis/notebooks/Chapter1')
# > import ipynb_wd_utils as iwu
# > iwu.run_nbconvert(nb_pfx='Chapter1',doc_title = 'Chapter 1', doc_author = 'J.D. Griffiths')
# Get the date
today = str(datetime.now()).split(' ')[0]
ipynb_wd_loc = '/'.join(iwu.__file__.split('/')[0:-1])
# If multiple notebooks, concatenate and run html convert separately for each
if type(nb_list) == list:
print '\n\nMultiple notebooks provided. Will run nbconvert on each separately and on concatenated notebook.\n'
# concatenate the notebooks
cat_cmd = 'python ' + ipynb_wd_loc + '/misc/nbcat.py ' # function borrowed from ipython tutorial code
for n in nb_list:
# Run this functionon the individual files
# (just for html)
iwu.run_nbconvert(n,do_pdf_nb=False,do_pdf_file=False,
do_slides_nb=False,do_slides_file=False,
remove_additional_files=False,ipynb_wd_version='0.2')
# Add to the concatenate list
cat_cmd += ' %s__master_nb.ipynb' %n
cat_cmd += ' > %s__master_nb.ipynb' %nb_pfx
res = mgc('system $cat_cmd')
print '\n%s\n\n%s' %(cat_cmd,'\n'.join(res))
# Make new folder and go there
cwd = os.getcwd()
outdir = cwd + '/%s__workdocs__%s' %(nb_pfx,today)
mgc('system rm -r $outdir')
mgc('system mkdir $outdir')
print '\ngoing to outdir and running stuff there'
os.chdir(outdir)
# Specify some filenames
master_nb = '%s__master_nb.ipynb' %nb_pfx # already exists
mother_nb = '%s__mother_nb__%s.ipynb' %(nb_pfx, today) # doesn't yet exist
if ipynb_wd_version == '0.2':
cherrypick_class_file = 'ipynb_wd_cherry_picking_preprocessor_3.py'
config_file = 'ipynb_wd_ipython_nbconvert_config_3.py'
elif ipynb_wd_version == '0.3':
cherrypick_class_file = 'ipynb_wd_cherry_picking_preprocessor_4.py'
config_file = 'ipynb_wd_ipython_nbconvert_config_4.py'
copy_writer_file = 'notebook_copy_writer.py'
ipynb_wd_loc = '/'.join(iwu.__file__.split('/')[0:-1])
cherry_picker_loc = ipynb_wd_loc + '/notebook_cherry_picker'
cherrypick_template = 'ipython nbconvert %s --CherryPickingPreprocessor.expression="%s" '\
'--config %s'
cp_cmd = 'cp %s/%s %s/' %(cwd,master_nb,outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
cp_cmd = 'cp %s/%s %s/' %(cherry_picker_loc,cherrypick_class_file,outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
cp_cmd = 'cp %s/%s %s/' %(cherry_picker_loc,copy_writer_file, outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
cp_cmd = 'cp %s/%s %s/' %(cherry_picker_loc,config_file, outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
# Make mother notebook (remove rough notes)
if ipynb_wd_version=='0.1':
thisexpr = "not rough_notes"
elif ipynb_wd_version=='0.2' or ipynb_wd_version=='0.3':
#thisexpr = '(not pdf) or (not html) or (not slides)'
#thisexpr = 'pdf or html or slides'
#thisexpr = 'not (not pdf) or not (not html) or not (not slides)'
thisexpr = 'pdf or html or slides'
in_nb = master_nb
out_nb = mother_nb
nbc_cmd = cherrypick_template %(in_nb, thisexpr, config_file)
mv_cmd = 'mv %s.output.ipynb %s' %(in_nb.split('.ipynb')[0], out_nb)
print '\nMaking mother notebook...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
# Make html notebook
if do_html_nb:
html_nb = '%s__html_nb__%s.ipynb' %(nb_pfx, today)
if ipynb_wd_version=='0.1':
thisexpr = "(not omit_html) or html_only"
elif ipynb_wd_version=='0.2' or ipynb_wd_version=='0.3':
thisexpr = 'html'
in_nb = mother_nb
out_nb = html_nb
nbc_cmd = cherrypick_template %(in_nb, thisexpr, config_file)
mv_cmd = 'mv %s.output.ipynb %s' %(in_nb.split('.ipynb')[0], out_nb)
print '\nMaking html notebook...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
# Make slides notebook
if do_slides_nb:
slides_nb = '%s__slides_nb__%s.ipynb' %(nb_pfx, today)
if ipynb_wd_version=='0.1':
thisexpr = "(not omit_slides) or slides_only"
elif (ipynb_wd_version=='0.2' or ipynb_wd_version=='0.3'):
thisexpr = "slides"
in_nb = mother_nb
out_nb = slides_nb
nbc_cmd = cherrypick_template %(in_nb, thisexpr, config_file)
mv_cmd = 'mv %s.output.ipynb %s' %(in_nb.split('.ipynb')[0], out_nb)
print '\nMaking slides notebook...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
# Make pdf notebook
if do_pdf_nb:
pdf_nb = '%s__pdf_nb__%s.ipynb' %(nb_pfx, today)
if ipynb_wd_version=='0.1':
thisexpr = "(not omit_pdf) or pdf_only"
elif (ipynb_wd_version=='0.2' or ipynb_wd_version=='0.3'):
thisexpr = "not (not pdf)"
in_nb = mother_nb
out_nb = pdf_nb
nbc_cmd = cherrypick_template %(in_nb, thisexpr, config_file)
mv_cmd = 'mv %s.output.ipynb %s' %(in_nb.split('.ipynb')[0], out_nb)
print '\nMaking pdf notebook...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
if do_html_file:
html_file = '%s__html__%s.html' %(nb_pfx, today)
print '\nMaking html file...'
nbc_cmd = 'ipython nbconvert --to html %s' %html_nb
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
if do_pdf_file:
# Make pdf file
# If no changes to texfile are required, just use
# 'nbconvert --to latex --post PDF'...
# If changes to texfile are required, use
# 'nbconvert --to latex'...
# 'tidy_texfile()'...
# 'pdflatex'...
print '\nMaking pdf file...'
pdf_file = '%s__pdf__%s.pdf' %(nb_pfx, today)
nbc2pdf_template = 'nbc_tpl__latex_report_nocode.tplx'
# Get the pdf template
cp_cmd = 'cp %s/templates/%s %s/' %(ipynb_wd_loc,nbc2pdf_template, outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
# Fill in doc title and doc author in the pdf template
temp_tpl = '/tmp/tmp_tplx.tplx'
res = mgc('system cp $nbc2pdf_template $temp_tpl')
open(nbc2pdf_template, 'w+').write(open(temp_tpl, 'r')\
.read().replace('DOC_TITLE', pdf_title)\
.replace('DOC_AUTHOR', pdf_author))
if tex_changes is None:
nbc_cmd = 'ipython nbconvert --to latex --post PDF --template %s %s' %(nbc2pdf_template, pdf_nb)
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
# Rename output
mv_cmd = 'mv %s %s' %(pdf_nb.replace('.ipynb', '.pdf'), pdf_file)
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
else:
# Nbconvert to latex
nbc_cmd = 'ipython nbconvert --to latex --template %s %s' %(nbc2pdf_template,pdf_nb)
print '\nMaking tex file...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
# Tidy texfile
orig_texfile = pdf_nb.split('.ipynb')[0]+'.tex'
new_texfile = pdf_nb.split('.ipynb')[0]+'_tidied.tex'
tidy_texfile(orig_texfile,
tex_changes=tex_changes,
new_texfile = new_texfile)
# Run pdflatex
print 'running pdflatex'
_cmd = 'pdflatex -interaction=nonstopmode %s' %new_texfile
res1 = mgc('system $_cmd')
print '\nrunning pdflatex:\n\n%s\n\nresult:\n\n%s' %(_cmd,'\n'.join(res1))
res2 = mgc('system $_cmd')
print '\nrunning pdflatex:\n\n%s\n\nresult:\n\n%s' %(_cmd,'\n'.join(res1))
res3 = mgc('system $_cmd')
print '\nrunning pdflatex:\n\n%s\n\nresult:\n\n%s' %(_cmd,'\n'.join(res3))
# Rename to the name of pdf_nb
mv_cmd = 'mv ' + new_texfile.split('.tex')[0]+'.ipynb' + ' ' + pdf_file
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\nresult:\n\n%s' %(_cmd,'\n'.join(res3))
# Make slides file
if do_slides_file:
slides_file = '%s__slides__%s.slides.html' %(nb_pfx, today)
nbc2slides_template = 'nbc_tpl__slides_reveal_output_toggle.tpl'
# get the slides template
cp_cmd = 'cp %s/templates/%s %s/' %(ipynb_wd_loc,nbc2slides_template, outdir)
res = mgc('system $cp_cmd')
print '\n%s\n\n%s' %(cp_cmd,'\n'.join(res))
nbc_cmd = 'ipython nbconvert --to slides --template %s %s' %(nbc2slides_template, slides_nb)
mv_cmd = 'mv %s %s' %(slides_nb.replace('.ipynb', '.slides.html'), slides_file)
print '\nMaking slides file...'
res = mgc('system $nbc_cmd')
print '\nrunning nbconvert:\n\n%s\n\nresult:\n\n%s' %(nbc_cmd,'\n'.join(res))
res = mgc('system $mv_cmd')
print '\nrenaming output:\n\n%s\n\n\n%s' %(mv_cmd,'\n'.join(res))
if remove_additional_files:
mgc('system rm *.py*')
mgc('system rm *.tex')
mgc('system rm *.toc')
mgc('system rm *.tpl*')
# return to start dir
os.chdir(cwd)
print '\n\n\n\nDone! :) \n\n'
