conf.py

extensions = ['sphinxcontrib.bibtex']

# Add any paths that contain templates here, relative to this directory.

author_first = u'Matthias'
author_last= u'Bussonnier'
author_full = u' '.join([author_first,author_last])

source_suffix = '.rst'
master_doc = 'index'
project = u'Actin gel dynamics'
copyright = u'2014, '+author_full 
version = '1.0'
release = '1.0'
today_fmt =  '%B %d, %Y at %X %Z'

exclude_patterns = ['_build','index-latex.rst']
if tags.has('latex') or tags.has('latex-web') or tags.has('latex-print'):
    exclude_patterns.remove('index-latex.rst')
    exclude_patterns.append('index.rst')
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# The paper size ('letter' or 'a4').
latex_paper_size = 'letter'

# The font size ('10pt', '11pt' or '12pt').
latex_font_size = '10pt'

latex_documents = [
  ('index-latex', 'actingeldynamics.tex', u'Actin Gels dynamics',
   author_full, 'manual', False),
]

index-latex.rst

Contents

.. toctree::
   :maxdepth: 2

   parts/part1
   parts/bar

References

.. bibliography:: library.bib
   :encoding: latex+utf8
   :style: alpha

index.rst

Contents

.. toctree::
   :maxdepth: 2

   parts/part1
   parts/bar

References

.. bibliography:: library.bib
   :encoding: latex+utf8
   :style: alpha

library.bib

@article{Iwabuchi2010,
abstract = {The plant organelles, chloroplast and nucleus, change their position in response to light. In Arabidopsis thaliana leaf cells, chloroplasts and nuclei are distributed along the inner periclinal wall in darkness. In strong blue light, they become positioned along the anticlinal wall, while in weak blue light, only chloroplasts are accumulated along the inner and outer periclinal walls. Blue-light dependent positioning of both organelles is mediated by the blue-light receptor phototropin and controlled by the actin cytoskeleton. Interestingly, however, it seems that chloroplast movement requires short, fine actin filaments organized at the chloroplast edge, whereas nuclear movement does cytoplasmic, thick actin bundles intimately associated with the nucleus. Although there are many similarities between photo-relocation movements of chloroplasts and nuclei, plant cells appear to have evolved distinct mechanisms to regulate actin organization required for driving the movements of these organelles.},
author = {Iwabuchi, Kosei and Takagi, Shingo},
doi = {10.1104/pp.109.149526},
file = {:Users/matthiasbussonnier/Library/Application Support/Mendeley Desktop/Downloaded/Iwabuchi, Takagi - 2010 - Actin-based mechanisms for light-dependent intracellular positioning of nuclei and chloroplasts in Arabidopsis.pdf:pdf},
issn = {1559-2324},
journal = {Plant signaling \& behavior},
keywords = {Actins,Actins: physiology,Arabidopsis,Arabidopsis: cytology,Arabidopsis: radiation effects,Cell Nucleus,Cell Nucleus: physiology,Cell Nucleus: radiation effects,Chloroplasts,Chloroplasts: physiology,Chloroplasts: radiation effects,Cytoskeleton,Cytoskeleton: physiology,Light,Plant Leaves,Plant Leaves: cytology},
month = aug,
number = {8},
pages = {1010--3},
pmid = {20724834},
title = {{Actin-based mechanisms for light-dependent intracellular positioning of nuclei and chloroplasts in Arabidopsis.}},
url = {http://www.plantphysiol.org/content/152/3/1309},
volume = {5},
year = {2010}
}

Makefile

# Makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS    =
SPHINXBUILD   = sphinx-build
PAPER         =
BUILDDIR      = _build

# Internal variables.
PAPEROPT_a4     = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .

.PHONY: clean latex latexpdf


clean:
	-rm -rf $(BUILDDIR)/*

latex:
	$(SPHINXBUILD) -b latex -t latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
	@echo "Run \`make' in that directory to run these through (pdf)latex" \
	      "(use \`make latexpdf' here to do that automatically)."

latexpdf:
	$(SPHINXBUILD) -b latex -t latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
	@echo "Running LaTeX files through pdflatex..."
	make -C $(BUILDDIR)/latex all-pdf
	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."