This repository provides public-facing access to the content of the author instruction/policy pages for the Living Journal of Computational Molecular Molecular Science (LiveCoMS).
The journal itself is published via Scholastica at livecomsjournal.org, but full author instructions and policy information are maintained at livecomsjournal.github.io and this repository provides access to edit the content of the latter site.
If you have questions or concerns, please use our issue tracker here, or contact the managing editors at managing@livecomsjournal.org.
The subpages of livecomsjournal.github.io have a navigation column on the left (see livecomsjournal.github.io/authors/policies/ for an example). This navigation is read from _data/navigation.yml and is static, meaning that it needs to be re-generated whenever changes to the structure of a document are done. Specifically, the navigation consists of links to all first and second title levels (# Title and ## Title in Markdown), and if any of those are changed, the navigation needs to be updated.
There is a script named generate_navigation.py which generates the content of the navigation file. Calling
python3 generate_navigation.py > _data/navigation.yml
regenerates the navigation file with the current state of the Markdown-files. It does so by reading through all .md files (except index.md) in the _about_livecoms, _author_instructions and _editorial_policies and generating a menu item for every first-level or second-level title. It also read the frontmatter of each file and rewrites it in case no permalink or no sidebar tag is found.
The script is helpful, but probably not fool-proof - a visual inspection of the result via git diff, or even better a check of the result in a local jekyll installation is highly recommended before pushing the new navigation file to the master branch.
First you will need to install the gem for github-pages. Run the following command:
gem install github-pages
This will install the github-pages gem and all dependencies (including jekyll).
Later, to update the gem, type:
gem update github-pages
To build a local copy, go into the directory and type:
jekyll build
This will create (or modify) a _site/ directory, containing everything from assets/, and then the index.md and all pages/.md files, converted to html. (So there’ll be _site/index.html and the various _site/pages/.html.)
Do not commit this directory in a Pull Request!! Github will compile this directory on its own.
Type the following in order to “serve” the site. This will first run build, and so it does not need to be preceded by jekyll build.
jekyll serve
Now open your browser and go to http://localhost:4000