The current spec has been partially refactored into Markdown, and is now being built as a bookdown book. The chapters of the book are controlled by the file docs/_bookdown.yml, which lists the markdown chapters to be included and their order.
The book is built using R using either bookdown::render_book('index.Rmd') or rmarkdown::render_site(), both of which can be run from within RStudio using the Build tab of the provided emldocs.Rproj.
Still need to finish reorganizing the chapters and modularizing them, but at this point most content has been moved to Markdown. Also need to resolve the differences and redundancy of the README.md and the Chapter 1 of the prior spec, as both are now included in the book.
Reorganize book chapters with better flow and transitions
Eliminate redundancy between README and other chapters
Book output has been moved to the dist directory, and the structure is now complete. We also are now auto-generating the associated schema documentation files using oxygen via the script build_schema_documentation.sh, which creates html files for the schema docs in dist/schema. Still need to link in the docs to the book.
I also created a deploy_site.sh script to push the site to GitHub to the gh_pages branch for publication on GitHub pages.
link schema docs into bookdown
set up the eml.ecoinformatics.org CNAME for the GitHub pages site