I am now on my computer at home; after updating packages and rstudio, and installing blogdown and hugo, everything is running fine (although I still need to update my ~/.Rprofile).

Tags and categories

Getting links to tags and categories was as simple as editing the menu section of config.toml; the one trick is to add weight variables to get the order I want (the default is alphabetical). Here is the relevant bit of code:

[[menu.main]]
    name = "About"
    url = "/about/"
    weight = 1
[[menu.main]]
    name = "Categories"
    url = "/categories/"
    weight = 2
[[menu.main]]
    name = "Tags"
    url = "/tags/"
    weight = 3
[[menu.main]]
    name = "GitHub"
    url = "https://github.com/BruceKendall/InvasionHet"
    weight = 4

The one bit that is incomplete is that hugo is not building index.html files for the categories and tags directories.

One thing to try is to explictly set the taxonomies section of the config file, although it should be using these values by default (see https://gohugo.io/getting-started/configuration/).

Nope, that didn't do anything. Of note: the index.xml files are being updated; and the index.html files within each of the category and tag directories are being updated. I found a sample file at https://bwaycer.github.io/hugo_tutorial.hugo/templates/terms/; I had to take out the {{ .Site.LanguagePrefix }} from the alphabetical example to get it to work. Now I have category and tag lists, although the formatting is inconsistent with the rest of template.

The code in terms.html is:

{{ partial "header.html" . }}

<section id="main">
  <div>
    <h1 id="title">{{ .Title }}</h1>
    <ul>
    {{ $data := .Data }}
    {{ range $key, $value := .Data.Terms.Alphabetical }}
      <li><a href="/{{ $data.Plural }}/{{ $value.Name | urlize }}">{{ $value.Name }}</a> {{ $value.Count }}</li>
    {{ end }}
    </ul>
  </div>
</section>
{{ partial "footer.html" . }}

Setting up .Rprofile

There are a number of blogdown options that can be set in .Rprofile, including the default page author, the default file type, and whether to deamonize the server. I have set the following in my global ~/.Rprofile:

# Blogdown options
options(blogdown.author = "Bruce Kendall",
        blogdown.ext = ".Rmd")

I tried moving the knitr options and the ProjectTemplate loading into a local .Rprofile. The first thing I found is that the .Rprofile needs ot be in the same directory as the .Rmd files (content/posts/). The second thing I found was that, while the knitr options from, e.g., knitr::opts_knit$set() work that way, the call to ProjectTemplate::load.project() didn't make the datasets and functions available to the chunks in the .Rmd file.

So I can use the following local .Rprofile:

# Load global .Rprofile
if (file.exists("~/.Rprofile")) {
  base::sys.source("~/.Rprofile", envir = environment())
}

# Knitr options. Note that these mean:
#   - All output will be cached. This is desireable in case code/data changes in the 
#     future; but it means that all chunks should be labeled for reliable behavior. 
#     DEPENDENCIES ACROSS CODE CHUNKS MAY BE AN ISSUE.
#   - R code will run in the project root directory
project_root <- normalizePath("../../..")
knitr::opts_chunk$set(comment = '', cache = TRUE)
knitr::opts_knit$set(root.dir = project_root)

# Clean up
rm(project_root, local_dir)

However, I still need to start each Rmarkdown file with ProjectTemplate::load.project().

Setting up to use the blogdown notebook as a project webpage

We can serve up the notebook as a githob project webpage if the html is published to the /docs/ directory of the project. The easiest way to do this will be to move the blogdown directories to the top level of the project, and set Hugo to publish to /docs/ instead of /public/. We may also want the local (preview) version of the html to go somewhere that is not under version control, to avoid delays with Rstudio's version control (although at the moment I can't find the place where I read that tip).

One benefit is that I can then launch the webserver without changing directory first.

So the first step is to move all the contents of /notebook2/ to the root directory …. Done.

Then I need to reduce the upward movement in the local .Rprofile by one level … Done.

I confirm that this works for the local build.

I set publishDir = "docs/" in config.toml. This sends the local build there, which is perhaps not what I want.

When I pushed this, and activated the website feature on github, I did have a home page at https://brucekendall.github.io/InvasionHet/. But it didn't have any styling, and the links didn't work. I've now changed the baseurl in config.toml to point to this site. Let's see how that works… It didn't, but I left the trailing slash off. Let's add that and try…

Success! But the runway image got lost in the transition, I just moved that from public to docs. All is now good.

More tweaks

I adjusted the line width in main.css, and borrowed material from lists.html to make terms.html look more like the rest of the theme. I think that's good enough on the look and feel.

I also figured out that setting weight: 1 in the yaml header of a post will push it below unweighted posts with the same date. (This was to get the ordering right from yesterday).

Finally, I discovered that I needed to make some more tweaks in terms.html to make the links within the term lists work on github. But it appears to break things for the local server!

I do still need to write an “about” page (and for that matter a project readme), and make a pre-dated post that links to the bookdown version of the previous notebook (converting the individual posts would be more work than is warranted).