Consistently use gfm rather than markdown_github by peterdesmet · Pull Request #285 · inbo/tutorials · GitHub

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.

Could not run knit for r_database_access and r_gbif_name_matching

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.

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

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

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.

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!

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

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).

The following lines caused an error in read.bib(): Error in charToDate(x) : character string is not in a standard unambiguous format @florisvdh removing the lines causes a warning (already better than an error), which also happens for 4 other entries (6 in total now): ignoring entry 'heijmans_spatial_2019' (line 106) because : A bibentry of bibtype ‘Book’ has to specify the field: publisher Can you fix this?

Also use 2 space indent

Mostly only index.Rmd containing footnotes were knitted

This reverts commit 580e6d5.

@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

See #285

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

Perfect, well done 👍 . Thank you!

See #285

peterdesmet added 5 commits November 17, 2021 16:40

Change yaml indentation to 2 spaces

742dd25

Add gfm where missing + remove html_document

b1da604

Remove unused figure

25d21f8

Cleanup whitespace

cfcf21b

Change markdown_github to gfm

a63e887

Could not run knit for r_database_access and r_gbif_name_matching

peterdesmet requested a review from damianooldoni November 17, 2021 15:59

peterdesmet mentioned this pull request Nov 17, 2021

Limitations of Hugo + gfm for authoring tutorials #200

Closed

florisvdh requested changes Dec 7, 2021

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Comment thread content/tutorials/r_citations_markdown/index.Rmd Outdated

Comment thread content/tutorials/r_citations_markdown/index.Rmd Outdated

Comment thread content/tutorials/r_citations_markdown/index.Rmd Outdated

Comment thread content/tutorials/r_citations_markdown/index.Rmd

florisvdh reviewed Dec 7, 2021

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florisvdh mentioned this pull request Jan 27, 2022

Add Zenodo vignette from checklist package #297

Merged

4 tasks

Remove erroneously included backslashes

2ad0621

peterdesmet added 6 commits January 28, 2022 13:51

Merge branch 'master' into gfm

eaae0d3

Remove output settings for all index.md NOT generated by index.Rmd

ade5366

Also use 2 space indent

Use gfm+footnotes in index.Rmd + knit

1e893b0

Mostly only index.Rmd containing footnotes were knitted

Update create tutorial to include the desired properties

dc161a8

Revert "Remove lines that cause error"

c9b14c1

This reverts commit 580e6d5.

peterdesmet added a commit that referenced this pull request Jan 28, 2022

Use frontmatter used elsewhere

c748ab6

See #285

peterdesmet added a commit that referenced this pull request Jan 28, 2022

Use frontmatter used elsewhere

36316c4

See #285

peterdesmet added a commit that referenced this pull request Jan 28, 2022

Use frontmatter used elsewhere

afae2c8

See #285

peterdesmet added a commit that referenced this pull request Jan 28, 2022

Use frontmatter used elsewhere

e835fa1

See #285

peterdesmet requested a review from florisvdh January 28, 2022 15:43

florisvdh approved these changes Jan 31, 2022

View reviewed changes

florisvdh merged commit b21a805 into master Jan 31, 2022

florisvdh deleted the gfm branch January 31, 2022 08:10

falkmielke pushed a commit that referenced this pull request Mar 12, 2025

Use frontmatter used elsewhere

b714e11

See #285

Consistently use gfm rather than markdown_github by peterdesmet · Pull Request #285 · inbo/tutorials · GitHub

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Consistently use gfm rather than markdown_github - #285

Consistently use gfm rather than markdown_github#285
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Consistently use gfm rather than markdown_github by peterdesmet · Pull Request #285 · inbo/tutorials · GitHub

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Consistently use gfm rather than markdown_github - #285

Consistently use gfm rather than markdown_github#285florisvdh merged 12 commits intomasterinbo/tutorials:masterfrom gfminbo/tutorials:gfmCopy head branch name to clipboard

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Consistently use gfm rather than markdown_github#285
florisvdh merged 12 commits into
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florisvdh commented Jan 27, 2022 •
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