Consistently use gfm rather than markdown_github

[peterdesmet]

Description

Some index.Rmd files used the deprecated variant: markdown_github, which results in a warning when knitting. This PR updates all index.Rmd files to consistently use the recommended gfm and 2-space indentation in yaml frontmatter:

output: 
  md_document:
    preserve_yaml: true
    variant: gfm

For some tutorials, this updates the index_files/figure-markdown_github to index_files/gfm. The PR has little to no effect on the website.

[florisvdh]

All seems fine, except in one Rmd file where some characters were escaped for an unknown reason. I suggest to revert that since it is not consistent with Pandoc's markdown.

[florisvdh]

Further, see #200 (comment). I advise to use gfm+footnotes instead of gfm.

Thanks for the efforts you have been doing here @peterdesmet 👍

[florisvdh]

I advise to use gfm+footnotes instead of gfm.

In order not to have to re-knit tutorials, you could just update the Rmd files here, so that this is taken care of next time they are knitted. But probably that is your approach already.

Caveat: some open pull requests contain new tutorials, so the changes may have to be applied there as well.

[florisvdh]

Caveat: some open pull requests contain new tutorials, so the changes may have to be applied there as well.

In order to limit this problem, can you have a further look at remaining tasks in this PR @peterdesmet, so that we get this in master? Thanks!

[peterdesmet]

@florisvdh the backslashes are removed. Do you want me to use gfm+footnotes everywhere or in specific places?

[florisvdh]

Do you want me to use gfm+footnotes everywhere or in specific places?

I suggest to do it everywhere, since often a new tutorial will be based on another one and we better do it consistently. If you wish, I could try to do this at once, with sed. Further, such update is best applied to existing PRs with new tutorials, not only master. Maybe the 'create tutorial' tutorial also needs checking.

If you'd find a way to let Hugo make the citation links that appear useful - i.e. the links which appear after adding link-citations: true - then that would be superb! I didn't find the solution in #200 (comment).

[peterdesmet]

@florisvdh I have

• Removed output frontmatter from index.md files that are not generated from index.Rmd
• Updated index.Rmd frontmatter to use gfm+footnotes and knitted where relevant. See e.g. footnotes at bottom, where they weren't there before at https://inbo.github.io/tutorials/tutorials/spatial_crs_coding/
• Updated create a tutorial to indicate the desired frontmatter

[peterdesmet]

And finally, I have updated the frontmatter in the open pull requests, so we don't reintroduce old frontmatter.

[florisvdh]

Perfect, well done 👍 . Thank you!