How to convert Jupyter notebook to PDF via Latex? - pdf

Question

I am trying to convert a Jupyter notebook to pdf via Latex using nbconvert, in order to automatically include citations to articles contained in a separate .bib file. I worked according to the tutorial/example here. Such a tutorial was suggested in the nbconvert documentation, here.
I have the following files in the same directory in which I am running the Jupyter notebook:
citations.tplx (the template to be used to include the bibliography)
references.bib (a .bib file containing the citations, taken from Google Scholar)
Inside the markdown cells, I use the following syntax to cite a work:
<cite data-cite="cortez2009modeling">(Cortez, 2009)</cite>
where such a work in the .bib file is reported as follows:
#article{cortez2009modeling,
title={Modeling wine preferences by data mining from physicochemical properties},
author={Cortez, Paulo and Cerdeira, Ant{\'o}nio and Almeida, Fernando and Matos, Telmo and Reis, Jos{\'e}},
journal={Decision support systems},
volume={47},
number={4},
pages={547--553},
year={2009},
publisher={Elsevier}
}
In a new notebook, also saved in the same location, I run the following command, also taken by the tutorial mentioned above:
%%bash
jupyter nbconvert --to latex --template citations.tplx --post pdf my_notebook.ipynb
I get a very long output, full of warnings, but basically, the error is:
ModuleNotFoundError: No module named 'pdf'
I also tried to do this according to other tutorials on the web, but even when the PDF file was indeed generated (using a slightly different nbconvert command), my citations were not captured in the text (a question mark would appear instead), and there was no bibliography at the end of the document. A warning would say there were 'problems' with Bibtex, but nothing more.
In the following, I report the complete output of the command I wrote above:
Traceback (most recent call last):
File "/opt/anaconda3/bin/jupyter-nbconvert", line 11, in <module>
sys.exit(main())
File "/opt/anaconda3/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 844, in launch_instance
app.initialize(argv)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in inner
return method(app, *args, **kwargs)
File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 290, in initialize
super().initialize(argv)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in inner
return method(app, *args, **kwargs)
File "/opt/anaconda3/lib/python3.8/site-packages/jupyter_core/application.py", line 225, in initialize
self.parse_command_line(argv)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in inner
return method(app, *args, **kwargs)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 713, in parse_command_line
self.update_config(self.cli_config)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/configurable.py", line 220, in update_config
self._load_config(config)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/configurable.py", line 190, in _load_config
warn(msg)
File "/opt/anaconda3/lib/python3.8/contextlib.py", line 120, in __exit__
next(self.gen)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/traitlets.py", line 1214, in hold_trait_notifications
self.notify_change(change)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/traitlets.py", line 1227, in notify_change
return self._notify_observers(change)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/traitlets.py", line 1264, in _notify_observers
c(event)
File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 265, in _postprocessor_class_changed
self.postprocessor_factory = import_item(new)
File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/utils/importstring.py", line 38, in import_item
return __import__(parts[0])
ModuleNotFoundError: No module named 'pdf'
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
<ipython-input-22-c5829f9d50d0> in <module>
----> 1 get_ipython().run_cell_magic('bash', '', 'jupyter nbconvert --to latex --template citations.tplx --post pdf Orlando_Taddeo_CW.ipynb\n')
/opt/anaconda3/envs/tf/lib/python3.7/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
2397 with self.builtin_trap:
2398 args = (magic_arg_s, cell)
-> 2399 result = fn(*args, **kwargs)
2400 return result
2401
/opt/anaconda3/envs/tf/lib/python3.7/site-packages/IPython/core/magics/script.py in named_script_magic(line, cell)
140 else:
141 line = script
--> 142 return self.shebang(line, cell)
143
144 # write a basic docstring:
/opt/anaconda3/envs/tf/lib/python3.7/site-packages/decorator.py in fun(*args, **kw)
230 if not kwsyntax:
231 args, kw = fix(args, kw, sig)
--> 232 return caller(func, *(extras + args), **kw)
233 fun.__name__ = func.__name__
234 fun.__doc__ = func.__doc__
/opt/anaconda3/envs/tf/lib/python3.7/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
/opt/anaconda3/envs/tf/lib/python3.7/site-packages/IPython/core/magics/script.py in shebang(self, line, cell)
243 sys.stderr.flush()
244 if args.raise_error and p.returncode!=0:
--> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
246
247 def _run_script(self, p, cell, to_close):
CalledProcessError: Command 'b'jupyter nbconvert --to latex --template citations.tplx --post pdf Orlando_Taddeo_CW.ipynb\n'' returned non-zero exit status 1.
Could anyone please shed some light on this? I really can't figure out why it does not work.
Thank you very much in advance.