Quick and dirty test of possible pkgdown based bio3d website. See: < https://bioboot.github.io/web_demo/ >
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.
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")
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.
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 mainvignettes/online
dir of the bio3d package root dir. They need to be in a sub-dir ofvignettes/
here so as to not be included in the built package for CRAN etc.
To Do: setup a git sub-module for these vignettes...