Demo pkgdown website for bio3d v3.0

Quick and dirty test of possible pkgdown based bio3d website. See: < https://bioboot.github.io/web_demo/ >

Requirements

Install the pkgdown and tidytemplate packages from CRAN.

Then we also need the following files in the bio3d package route directory (copies of these live in this repo under SETUP_SITE/ dir - just copy these to the package root dir):

• _pkgdown.yml
• index.md
• logo.png
• FAQ.md
• NEWS.md

The main one here is the _pkgdown.yml setting file (see example in SETUP_SITE/ dir).

The rest are basically just regular old markdown text files that will be rendered to HTML by pkgdown build_site() function and used to comprise the website.

Logo

The logo was made with the hexSticker package in the cwd:

library("hexSticker")

# Logo with text
sticker("tmp_logo1.png", package="bio3d",
			h_fill="white", h_color="#5484F5",
			p_color="#5484F5",
			p_y = 1.50, p_x = 1.01,
			p_family="Aller_Rg",
			p_size=10, s_x=1.01, s_y=.80, s_width=1,
			filename="logo_txt.png")

# Logo without text - i like this one best
sticker("tmp_logo1.png", package="",
			h_fill="white", h_color="#5484F5",
			p_color="#5484F5",
			p_y = 1.50, p_x = 1.01,
			p_family="Aller_Rg",
			p_size=10, s_x=0.99, s_y=0.99, s_width=1.15,
			filename="logo_notxt.png")

Workflow

Use build_site() and build_home() from the pkgdown package to render and view site changes. The lazy=TRUE option is usefull whilst editing.

The vignettes require some special handeling, see below.

Vignettes

The vignettes are annoying for a number of reasons - one is we don't include them in the package because they are too big (really this should be solved with a .build_ignore type mechanism). Another is they are in a separate "online" dir and we need to pass the path to each one relative to the vignettes dir to build_article/

Here is one way

build_article(name="online/pdb_vignette/Bio3D_pdb")

This places the output in the articles dir of the main website docs/ dir:

docs/articles/

N.B. Note that the vignettes themselves were pulled from git@bitbucket.org:Grantlab/bio3d-vignettes.git and placed into the main vignettes/online dir of the bio3d package root dir. They need to be in a sub-dir of vignettes/ here so as to not be included in the built package for CRAN etc.

To Do: setup a git sub-module for these vignettes...