Makefile to convert Markdown to PDF. Depends on Pandoc 1.19.1, pandoc-citeproc 0.10.4.1, pandoc-crossref 0.2.5.0, Python 3, click 6.6, bibtexparser 0.6.2

get_bib.py

from bibtexparser import load as load_bib
from bibtexparser.bwriter import BibTexWriter
from bibtexparser.bibdatabase import BibDatabase
import click

@click.command()
@click.argument('keys_filename', type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True))
@click.argument('bibtex_filename', type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True))
@click.argument('output_filename', type=click.Path(file_okay=True, dir_okay=False, writable=True))
@click.option('-v/-V', '--verbose/--no-verbose', default=False)
def main(keys_filename, bibtex_filename, output_filename, verbose):
	with open(keys_filename) as f:
		citation_keys = (line.strip() for line in f.readlines())
	if verbose:
		print("Read {} keys from {}".format(len(citation_keys), citation_keys))

	with open(bibtex_filename) as f:
		main_bib = load_bib(f)
	if verbose:
		print("Read {} entries from {}".format(len(main_bib.entries), bibtex_filename))

	out_bib = BibDatabase()
	for key in citation_keys:
		e = main_bib.entries_dict[key]
		out_bib.entries.append(e)

	if verbose:
		print("Writing {} entries to {}".format(len(out_bib.entries), output_filename))
	writer = BibTexWriter()
	with open(output_filename, 'w') as f:
	    f.write(writer.write(out_bib))


if __name__ == '__main__':
	main()%

get_citations.py

import re

import click

@click.command()
@click.argument('markdown_filename', type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True))
@click.argument('keys_filename', type=click.Path(file_okay=True, dir_okay=False, writable=True))
def main(markdown_filename, keys_filename):
	pattern = re.compile('@(\w+\d{4})')
	with open(markdown_filename) as f:
		groups = (pattern.findall(line) for line in f)
		groups = sum((g for g in groups if g), [])
	groups = set(groups)
	with open(keys_filename, 'wt') as f:
		for g in groups:
			print(g, file=f)

if __name__ == '__main__':
	main()

Makefile

main_bib=~/library.bib
ms_bib=bibtex.bib
citation_keys=citation_keys
pdf=ms.pdf
md=ms.md
csl=evolution.csl

diagram_dot = diagram.dot
diagram_pdf = diagram.pdf

list:
	@sh -c "$(MAKE) -p no_targets__ | awk -F':' '/^[a-zA-Z0-9][^\$$#\/\\t=]*:([^=]|$$)/ {split(\$$1,A,/ /);for(i in A)print A[i]}' | grep -v '__\$$' | grep -v 'make\[1\]' | grep -v 'Makefile' | sort"
no_targets__:

$(citation_keys): $(md)
	python get_citations.py $(md) $(citation_keys)

$(ms_bib): $(citation_keys) $(main_bib)
	python get_bibtex.py $(citation_keys) $(main_bib) $@

$(pdf): $(md) $(ms_bib) $(diagram_pdf)
	pandoc -r markdown+simple_tables+table_captions+yaml_metadata_block -s -S $< -o $@ --filter pandoc-crossref --filter pandoc-citeproc --bibliography=$(ms_bib) --csl $(csl) --latex-engine=xelatex --number-sections
	@open $(pdf)

$(diagram_pdf): $(diagram_dot)
	dot $< -Tpdf -Kdot -o$@

model_diagram: $(diagram_pdf)

build: $(pdf)

edit: $(md)
	@subl $<

read: $(pdf)
	@open $(pdf)