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SciPy 2016: MDAnalysis Proceedings paper

Guidelines

• read the instructions for authors
• Only work on our paper in papers/oliver_beckstein

Contributing

Check out the repository:

git clone --depth=50  git@github.com:MDAnalysis/scipy_proceedings.git

will get you the 2016 branch (default) without too much garbage (shallow git copy is fine).

• work on this repository, or
• submit PRs against this repository
• generally, follow a pull request/merge workflow #11
  • submit PRs for small sections
  • assign reviewer (and hassle them to merge...)
  • be prepared to rebase your PR or merge and push the PR again

Use this issue tracker for the paper.

Formatting (style guide)

• use restructured text
• use the example paper to get an idea what's available
• use the bibtex file for bibliography
• line breaks
  • One line per independent clause #10 (Do not use hard line breaks inside sentences. In emacs, set your fill column to 9999 and use visual-line mode for soft breaks during display. Insert hard line breaks after each period.)
  • paragraphs are separated by at least a single empty line (two hard line breaks)
• use present tense #12

Generate draft PDF

There is a script make_paper.sh to generate a PDF from the RST. It requires Python and LaTeX to be installed

Makefile on branch with-PDF

To create MDAnalysis_SciPy_2016.pdf in the same directory as the input files (for quick checking that all looks good): Just run

git checkout with-PDF
git rebase 2016
make

and it will rebuild MDAnalysis_SciPy_2016.pdf if any input files changed.

Note: The local paper building Makefile only exists on the with-PDF branch. The 2016 branch need to be kept clean because it is pending as a submission (as scipy-conference/scipy_proceedings PR 212).

Manually

cd to the top level of the repo and run

./make_paper.sh papers/oliver_beckstein

and look at ./output/oliver_beckstein/paper.pdf