[Useful packages and matplotlib preamble]Here is a full #notebook preamble with some options to make the plots more publication ready.

bibpreprocessor.py

"""This preprocessor replaces bibliography code in markdowncell
"""

#-----------------------------------------------------------------------------
# Copyright (c) 2015, Julius Schulz
#
# Distributed under the terms of the Modified BSD License.
#
#-----------------------------------------------------------------------------

from nbconvert.preprocessors import *
import re
import os
import sys

class BibTexPreprocessor(Preprocessor):

    def create_bibentry(self, refkey, reference):
        entry  = "@article{" + refkey + ",\n"

        entry += "  author = {"
        entry += " and ".join(map(lambda a: a["family"] + ", " + a["given"], reference["author"]))
        entry += "}, \n"

        if ("title" in reference):
            entry += "  title = {" + reference["title"] + "}, \n"
        if ("issued" in reference):
            entry += "  year = {" + reference["issued"]["year"] + "}, \n"
        if ("container-title" in reference):
            entry += "  journal = {" + reference["container-title"] + "}, \n"
        if ("page" in reference):
            entry += "  pages = {" + re.sub("-", "--", reference["page"]) + "}, \n"
        if ("volume" in reference):
            entry += "  volume = {" + reference["volume"] + "}, \n"
        if ("issue" in reference):
            entry += "  issue = {" + reference["issue"] + "}, \n"
        if ("DOI" in reference):
            entry += "  doi = {" + reference["DOI"] + "}, \n"
        if ("URL" in reference):
            entry += "  url = {" + reference["URL"] + "}, \n"

        entry += "}\n"
        entry += "\n"
        return entry

    def create_bibfile(self, filename):
        if not os.path.exists(os.path.dirname(filename)):
            os.makedirs(os.path.dirname(filename))
        f = open(filename, "w")
        for r in self.references:
            if (sys.version_info > (3, 0)):
                f.write(self.create_bibentry(r, self.references[r]))
            else:
                f.write(self.create_bibentry(r, self.references[r]).encode('utf-8'))
        f.close()

    def preprocess(self, nb, resources):
        try:
          self.references = nb["metadata"]["cite2c"]["citations"]
          self.create_bibfile(resources["output_files_dir"]+"/"+resources["unique_key"]+".bib")
        except:
          print("Did not find cite2c")
        for index, cell in enumerate(nb.cells):
            nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
        return nb, resources

    def preprocess_cell(self, cell, resources, index):
        """
        Preprocess cell

        Parameters
        ----------
        cell : NotebookNode cell
            Notebook cell being processed
        resources : dictionary
            Additional resources used in the conversion process.  Allows
            preprocessors to pass variables into the Jinja engine.
        cell_index : int
            Index of the cell being processed (see base.py)
        """
        if cell.cell_type == "markdown":
            if "<div class=\"cite2c-biblio\"></div>" in cell.source:
                replaced = re.sub("<div class=\"cite2c-biblio\"></div>", r"\\bibliography{"+resources["output_files_dir"]+"/"+resources["unique_key"]+r"} \n ", cell.source)
                cell.source = replaced
        return cell, resources

jupyter_nbconvert_config.py

c = get_config()
c.Exporter.preprocessors = [ 'bibpreprocessor.BibTexPreprocessor', 'pre_pymarkdown.PyMarkdownPreprocessor' ]
c.Exporter.template_file = 'revtex_nocode.tplx'

metadata.json

{
  "latex_metadata": {
  "title": "Amazing Article",
  "author": "Julius C. F. Schulz",
  "affiliation": "Freie Universit\\\"at Berlin, Fachbereich Physik, 14195 Berlin, Germany"
  },
}

pre_pymarkdown.py

# -*- coding: utf-8 -*-
"""Nbconvert preprocessor for the python-markdown nbextension."""

import re

from nbconvert.preprocessors import Preprocessor


class PyMarkdownPreprocessor(Preprocessor):
    """
    :mod:`nbconvert` Preprocessor for the python-markdown nbextension.

    This :class:`~nbconvert.preprocessors.Preprocessor` replaces kernel code in
    markdown cells with the results stored in the cell metadata.
    """

    def replace_variables(self, source, variables):
        """
        Replace {{variablename}} with stored value
        """
        try:
            replaced = re.sub(
                "{{(.*?)}}", lambda m: variables.get(m.group(1), ''), source)
        except TypeError:
            replaced = source
        return replaced

    def preprocess_cell(self, cell, resources, index):
        """
        Preprocess cell

        Parameters
        ----------
        cell : NotebookNode cell
            Notebook cell being processed
        resources : dictionary
            Additional resources used in the conversion process.  Allows
            preprocessors to pass variables into the Jinja engine.
        cell_index : int
            Index of the cell being processed (see base.py)
        """
        if cell.cell_type == "markdown":
            if hasattr(cell['metadata'], 'variables'):
                variables = cell['metadata']['variables']
                if len(variables) > 0:
                    cell.source = self.replace_variables(
                        cell.source, variables)
        return cell, resources

PrettyTable.py

# class PrettyTable

class PrettyTable(list):
    """ Overridden list class which takes a 2-dimensional list of 
        the form [[1,2,3],[4,5,6]], and renders HTML and LaTeX Table in 
        IPython Notebook. For LaTeX export two styles can be chosen."""
    def __init__(self, initlist=[], extra_header=None, print_latex_longtable=True):
        self.print_latex_longtable = print_latex_longtable
        if extra_header is not None:
            if len(initlist[0]) != len(extra_header):
                raise ValueError("Header list must have same length as data has columns.")
            initlist = [extra_header]+list(initlist)
        super(PrettyTable, self).__init__(initlist)
    
    def latex_table_tabular(self):
        latex = ["\\begin{tabular}"]
        latex.append("{"+"|".join((["l"]*len(self[0])))+"}\n")
        for row in self:
            latex.append(" & ".join(map(format, row)))
            latex.append("\\\\ \n")
        latex.append("\\end{tabular}")
        return ''.join(latex)
    def latex_longtable(self):
        latex = ["\\begin{longtable}[c]{@{}"]
        latex.append("".join((["l"]*len(self[0]))))
        latex.append("@{}}\n")
        latex.append("\\toprule\\addlinespace\n")
        first = True
        for row in self:
            latex.append(" & ".join(map(format, row)))
            latex.append("\\\\\\addlinespace \n")
            if first:
                latex.append("\\midrule\\endhead\n")
                first = False
        latex.append("\\bottomrule \n \\end{longtable}")
        return ''.join(latex)
    def _repr_html_(self):
        html = ["<table>"]
        for row in self:
            html.append("<tr>")
            for col in row:
                html.append("<td>{0}</td>".format(col))
            html.append("</tr>")
        html.append("</table>")
        return ''.join(html)
    def _repr_latex_(self):
        if self.print_latex_longtable: 
            return self.latex_longtable()
        else: 
            return self.latex_table_tabular()

revtex_nocode.tplx

((*- extends 'article.tplx' -*))

((* block docclass *))
\documentclass[reprint, floatfix, groupaddress, prb]{revtex4-1}

\usepackage{placeins}

\AtBeginDocument{
\heavyrulewidth=.08em
\lightrulewidth=.05em
\cmidrulewidth=.03em
\belowrulesep=.65ex
\belowbottomsep=0pt
\aboverulesep=.4ex
\abovetopsep=0pt
\cmidrulesep=\doublerulesep
\cmidrulekern=.5em
\defaultaddspace=.5em
}

((* endblock docclass *))

% Author and Title from metadata
((* block maketitle *))

((*- if nb.metadata["latex_metadata"]: -*))
((*- if nb.metadata["latex_metadata"]["author"]: -*))
    \author{((( nb.metadata["latex_metadata"]["author"] )))}
((*- endif *))
((*- else -*))
    \author{Julius C. F. Schulz}
((*- endif *))

((*- if nb.metadata["latex_metadata"]: -*))
((*- if nb.metadata["latex_metadata"]["affiliation"]: -*))
    \affiliation{((( nb.metadata["latex_metadata"]["affiliation"] )))}
((*- endif *))
((*- endif *))

((*- if nb.metadata["latex_metadata"]: -*))
((*- if nb.metadata["latex_metadata"]["title"]: -*))
    \title{((( nb.metadata["latex_metadata"]["title"] )))}
((*- endif *))
((*- else -*))
    \title{((( resources.metadata.name )))}
((*- endif *))

\date{\today}
\maketitle
((* endblock maketitle *))

% New mechanism for rendering figures with captions
((*- block data_png -*))
((*- if cell.metadata.widefigure: -*))
    ((( draw_widefigure_with_caption(output.metadata.filenames['image/png'], cell.metadata.caption, cell.metadata.label) )))
((*- else -*))
    ((*- if cell.metadata.caption: -*))
        ((*- if cell.metadata.label: -*))
            ((( draw_figure_with_caption(output.metadata.filenames['image/png'], cell.metadata.caption, cell.metadata.label) )))
        ((*- else -*))
            ((( draw_figure_with_caption(output.metadata.filenames['image/png'], cell.metadata.caption, "") )))
        ((*- endif *))
    ((*- else -*))
        ((( draw_figure_with_caption(output.metadata.filenames['image/png'], "") )))
    ((*- endif *))
((*- endif *))
((*- endblock -*))
((*- block data_jpg -*))
((*- if cell.metadata.caption: -*))
    ((*- if cell.metadata.label: -*))
        ((( draw_figure_with_caption(output.metadata.filenames['image/jpeg'], cell.metadata.caption, cell.metadata.label) )))
    ((*- else -*))
        ((( draw_figure_with_caption(output.metadata.filenames['image/jpeg'], cell.metadata.caption, "") )))
    ((*- endif *))
((*- else -*))
    ((( draw_figure_with_caption(output.metadata.filenames['image/jpeg'], "") )))
((*- endif *))
((*- endblock -*))
((*- block data_svg -*))
((*- if cell.metadata.caption: -*))
    ((*- if cell.metadata.label: -*))
        ((( draw_figure_with_caption(output.metadata.filenames['image/svg+xml'], cell.metadata.caption, cell.metadata.label) )))
    ((*- else -*))
        ((( draw_figure_with_caption(output.metadata.filenames['image/svg+xml'], cell.metadata.caption, "") )))
    ((*- endif *))
((*- else -*))
    ((( draw_figure_with_caption(output.metadata.filenames['image/svg+xml'], "") )))
((*- endif *))
((*- endblock -*))
((*- block data_pdf -*))
((*- if cell.metadata.widefigure: -*))
    ((( draw_widefigure_with_caption(output.metadata.filenames['application/pdf'], cell.metadata.caption, cell.metadata.label) )))
((*- else -*))
    ((*- if cell.metadata.caption: -*))
        ((*- if cell.metadata.label: -*))
            ((( draw_figure_with_caption(output.metadata.filenames['application/pdf'], cell.metadata.caption, cell.metadata.label) )))
        ((*- else -*))
            ((( draw_figure_with_caption(output.metadata.filenames['application/pdf'], cell.metadata.caption, "") )))
        ((*- endif *))
    ((*- else -*))
        ((( draw_figure_with_caption(output.metadata.filenames['application/pdf'], "") )))
    ((*- endif *))
((*- endif *))
((*- endblock -*))

% Draw a figure using the graphicx package.
((* macro draw_figure_with_caption(filename, caption, label) -*))
((* set filename = filename | posix_path *))
((*- block figure scoped -*))
    \begin{figure}
        \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{((( filename )))}\end{center}
        \caption{((( caption )))}
        \label{((( label )))}
    \end{figure}
((*- endblock figure -*))
((*- endmacro *))

% Draw a figure using the graphicx package.
((* macro draw_widefigure_with_caption(filename, caption, label) -*))
((* set filename = filename | posix_path *))
((*- block figure_wide scoped -*))
    \begin{figure*}
        \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{((( filename )))}\end{center}
        \caption{((( caption )))}
        \label{((( label )))}
    \end{figure*}
((*- endblock figure_wide -*))
((*- endmacro *))



% Disable input cells
((* block input_group *))
((* endblock input_group *))

snippet.py

# load libraries and set plot parameters
import numpy as np
import prettytable as pt

import matplotlib.pyplot as plt
%matplotlib inline

from IPython.display import set_matplotlib_formats
set_matplotlib_formats('pdf', 'png')
plt.rcParams['savefig.dpi'] = 75

plt.rcParams['figure.autolayout'] = False
plt.rcParams['figure.figsize'] = 10, 6
plt.rcParams['axes.labelsize'] = 18
plt.rcParams['axes.titlesize'] = 20
plt.rcParams['font.size'] = 16
plt.rcParams['lines.linewidth'] = 2.0
plt.rcParams['lines.markersize'] = 8
plt.rcParams['legend.fontsize'] = 14

plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = "serif"
plt.rcParams['font.serif'] = "cm"
plt.rcParams['text.latex.preamble'] = r"\usepackage{subdepth}, \usepackage{type1cm}"