This repository contains the master specification document for the SBOL data model, formatted in LaTeX. The workflow for updating the specification is to clone, edit, and submit a pull request on the master.
Members of the SBOL Development Community may use the issue tracker to flag problems with the existing specification and review ongoing issues under consideration.
Before writing text for a non-trivial change, please have it approved by discussion as an Issue and/or SEP.
Proposed changes should be made in either a branch or a separate fork on GitHub. To do this, follow standard git branching or forking procedure.
Here is an example of git commands to achieve this:
git clone https://github.com/SynBioDex/SBOL-specification.git
git pull origin master — MAKE SURE NO ONE HAS MADE ANYMORE CHANGES
git checkout -b <newBranch> — CREATE NEW BRANCH
MAKE YOUR EDITS
git add <filesYouChanged>
git commit
git push origin <newBranch>
When you are ready for your changes to be reviewed for incorporation, create a pull request. If you need help on pull requests see: https://help.github.com/articles/about-pull-requests/
To build, run these commands and check the output for errors. If there are errors, resolve them and re-run the failed build step before proceeding.
pdflatex sbol2
bibtex sbol2
pdflatex sbol2
pdflatex sbol2
Note that pdflatex is run several times. Each successive pass mows down unresolved references from the previous passes. For example, the extra pdflatex commands set references correctly after bibtex completes. You don’t need to do this in every build unless the bibliography has changed. For development purposes, you may just need to run pdflatex once.
The git status command will show you which intermediate build products and logs you need to delete for a clean build.
Installing LaTeX on your system is beyond the scope of this README, however we will collect some tips here, in the interest of fostering collaboration.
Here is how one community member managed to install MacTex and BibTex on OS X 10.10.5 Yosemite in August 2016. This recipe was found on StackOverflow. Not all of these commands may be strictly necessary to build the SBOL2 pdf at this time. The bibdesk settings especially need curation. Please note that BasicTex alone did not suffice.
# First install homebrew from http://brew.sh then...
brew update
brew upgrade
brew tap caskroom/cask
brew install brew-cask
brew cask install mactex
brew cask install bibtex
brew cask install bibdesk
brew cask install texshop
brew cask install mendeley-desktop
sudo chown -R $USER /usr/local/texlive
tlmgr update --self
tlmgr update --all
defaults write TeXShop NSUserKeyEquivalents -dict-add "Typeset" "@t"
defaults write TeXShop "BibTeXengine" -string "biber"
defaults write TeXShop "Encoding" -string "IsoLatin"
defaults write edu.ucsd.cs.mmccrack.bibdesk "Cite Key Format" -string %y%u0"
defaults write edu.ucsd.cs.mmccrack.bibdesk BDSKLocalFileFormatKey -string Cite Key}%n0%e"
defaults write edu.ucsd.cs.mmccrack.bibdesk "Path to the papers folder" ing "Biblio"
defaults write edu.ucsd.cs.mmccrack.bibdesk "Cite String" -string "citep"
defaults write edu.ucsd.cs.mmccrack.bibdesk "Cite Key Autogenerate" -int 1
defaults write edu.ucsd.cs.mmccrack.bibdesk "Cite Key Format Preset" -int 0
defaults write edu.ucsd.cs.mmccrack.bibdesk "Cite Prepend Tilde" -int 1
defaults write edu.ucsd.cs.mmccrack.bibdesk "Startup Behavior" -int 4