Presentation on rewriting git history by ThierryO · Pull Request #372 · inbo/tutorials · GitHub

Description

The presentation of a BMK talk

Task list

My tutorial or article is placed in a subfolder of tutorials/content/
The novel tutorial has a meaningful name, in relation to the content of the tutorial.
The filename of my tutorial or article is index.md. In case of an Rmarkdown tutorial I have knitted my index.Rmd to index.md (both files are pushed to the repo).
yaml header:
- (recommended) I am included as author in the authors yaml tag, using [MY_AUTHOR_ID]. An author information file exists in <tutorials>/data/authors/<author>.toml.
- I have added categories to the YAML header and my category tags are from the list of categories.
- I have included meaningful and applicable tags (i.e. keywords) in the YAML header to improve the visibility of the new tutorial (see the tags listed in the tutorials website side bar).
- The date is in format YYYY-MM-DD and adjusted.
(recommended) I have previewed this PR locally (see steps below; ask previous contributors for help) and confirmed that the new content renders as expected.

Previewing the pull request

Thanks to GitHub Actions, an artifact (=zip file) of the rendered website is automatically created for each pull request.
This provides a way to preview how these updates will look on the website, useful to contributors and reviewers.

Instructions to preview the updated website

On the PR page, you can find a "details" link under "checks - On PR, build the site and ...". Go there, click on the top link in the left sidebar ("Summary"), and download the generated artifact at the bottom of the page.
Decompress it into a target directory, e.g. Downloads/tutorials_preview.
To preview the website, use a program which can serve http sites on your local machine. One such option is the servr package in R: & '\C:\Program Files\R\R-4.4.2\bin\Rscript.exe' -e "servr::httd('./tutorials_preview')" -p8887 (make sure to adjust the path to your Rscript.exe; on Linux, simply use Rscript -e [...]).
Point your browser to http://localhost:8887.
Review the updated website. As a contributor, you can push extra commits to update the PR. As a reviewer, you can accept/refuse/comment the PR.

Note: for step 3, you can use any other simple HTTP server to serve the current directory, e.g. Python http.server: python -m http.server 8887 --bind localhost --directory path/to/tutorials_preview

Alternative: Locally Building the Site

Alternatively, you can build the entire site locally (see the README for instructions); the Hugo preview server will update changes on the fly.
This requires Hugo to be installed on your computer.

Pull request overview

Adds a new tutorial section for “Rewriting git history”, implemented as a Quarto Reveal.js presentation (with a bundled flandersqmd revealjs extension) and an index.md page linking to the rendered presentation.html.

Changes:

Add Quarto Reveal.js presentation source (presentation.qmd) explaining git history rewriting workflows.
Add a Quarto project config and post-render script to produce/clean presentation artifacts.
Vendor a custom Quarto Reveal.js extension (_extensions/inbo/flandersqmd) with CSS/filters/fonts/images.

Reviewed changes

Copilot reviewed 11 out of 33 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
content/tutorials/git_rewrite_history/presentation.qmd	New slide deck content (dot graphs + git guidance).
content/tutorials/git_rewrite_history/index.md	Tutorial landing page linking to the generated HTML presentation.
content/tutorials/git_rewrite_history/_quarto.yml	Quarto project config for rendering the presentation.
content/tutorials/git_rewrite_history/post_render.R	Post-render clean-up/copy script for the generated presentation artifacts.
content/tutorials/git_rewrite_history/_extensions/inbo/flandersqmd/*	Bundled Reveal.js extension assets (SCSS/CSS, Lua filters, fonts/images, CSL).

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Spelling/grammar: “have checkout” should be “have checked out”.

Spelling/grammar: “as describe” should be “as described”.

The selector .reveal div.callout.callout-note.warning-style-default .callout-title looks like a typo (it targets a note callout, not a warning callout). As written, warning callouts may not get the intended title background color; this likely should target .callout-warning and the standard callout style class.

Suggested change

      
            .reveal div.callout.callout-note.warning-style-default .callout-title{
          
            .reveal div.callout.callout-warning.callout-style-default .callout-title{

Spelling: “carefull” should be “careful”.

basename() |> file.remove() will delete files in the current working directory matching those basenames. If Quarto's post-render runs from the project root, this can accidentally delete source assets if names collide. Safer: construct explicit paths to the files you intend to delete (e.g., within output/) and/or check file.exists() before removal.

Pandoc Lua attributes/classes are set using pandoc.Attr (or by mutating elem.attr.classes), but this filter assigns classes via vl_logo.attr = {class = ...} and passes { class = ... } directly to pandoc.Div(). This likely won't apply the classes (or may error on some Pandoc versions); use pandoc.Attr("", {"vl-tussen"}) / pandoc.Attr("", {"entity-tussen"}) consistently.

Spelling: section title should be “Committing” (double ‘m’).

The display_person function builds raw HTML using unescaped values from person.name.*, person.email, and person.orcid, and returns it via pandoc.RawInline('html', ...). If any of these metadata fields contain characters like quotes or <script> tags (for example via flandersqmd.author in the document YAML), they will be injected directly into the generated HTML, enabling cross-site scripting in the rendered tutorial pages. To fix this, avoid concatenating unescaped metadata into HTML strings; instead, construct pandoc element nodes (e.g., Link, Str) so Pandoc escapes content correctly, or at minimum HTML-escape user-provided metadata before concatenation.

✨ Add presentation on rewriting git history

c65f4ab

ThierryO requested a review from Copilot March 4, 2026 11:29

Copilot started reviewing on behalf of ThierryO March 4, 2026 11:29 View session

Copilot AI reviewed Mar 4, 2026

View reviewed changes

add index file

bd68fe5

ThierryO force-pushed the rewrite branch from 894b7f7 to bd68fe5 Compare March 4, 2026 12:44

ThierryO requested a review from wlangera March 4, 2026 12:45

hansvancalster added the proposal tutorial label May 19, 2026

+              - apply the changes locally as describe in the previous chapter
+              - a simple `git push` will fail because of a diverging history
+              - you must use `git push --force` or `git push -f`
+              - be carefull because you can't undo that

+                  local url_div = pandoc.Div({pandoc.Para({pandoc.Str(this_url)})}, pandoc.Attr("", {"sidebar-url-tussen"}))
+                  ent_logo = pandoc.Div("", { class = "entity-tussen" })
+                  if (this_lang == "nl-BE") then
+                    if (entitycolours == "inbo") then
+                      vl_logo = pandoc.Image("Vlaanderen is wetenschap", "flanders-nl-transparent.png")
+                      ent_logo = pandoc.Image("Instituut voor Natuur- en Bosonderzoek", "inbo-nl-white.png")
+                      ent_logo.attr = {class = "entity-tussen"}
+                    else
+                      vl_logo = pandoc.Image("Vlaanderen, verbeelding werkt", "flanders-nl-intermediate.jpg")
+                    end
+                    vl_logo.attr = {class = "vl-tussen"}
+                  else

+              function display_person (person, i)
+                res = ""
+                if is_empty(person.name) then
+                  res = '<h1 class = "missing">!!! flandersqmd.authors element ' .. i .. ' has no name element!!!</h1>'
+                  return res
+                end
+                if is_empty(person.name.given) then
+                  res = '<h1 class = "missing">!!! flandersqmd.authors element ' .. i .. ' has no given element under name!!!</h1>'
+                  return res
+                end
+                if is_empty(person.name.family) then
+                  res = '<h1 class = "missing">!!! flandersqmd.authors element ' .. i .. ' has no given element under name!!!</h1>'
+                  return res
+                end
+                if is_empty(person.email) then
+                  res = pandoc.utils.stringify(person.name.given) .. ' ' .. pandoc.utils.stringify(person.name.family)
+                else
+                  res = res .. '<a href= "mailto:' .. pandoc.utils.stringify(person.email) .. '" class = "title email">' .. pandoc.utils.stringify(person.name.given) .. ' ' .. pandoc.utils.stringify(person.name.family) .. '</a>'
+                end
+                if (is_empty(person.orcid)) then
+                  return res
+                end
+                res = res .. '<a href="https://orcid.org/' .. pandoc.utils.stringify(person.orcid) .. '" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a>'
+                return res

Presentation on rewriting git history by ThierryO · Pull Request #372 · inbo/tutorials · GitHub

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Presentation on rewriting git history - #372

Presentation on rewriting git history#372
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		1. make sure you have checkout the correct branch
		- `git checkout my_feature`

		- apply the changes locally as describe in the previous chapter
		- a simple `git push` will fail because of a diverging history

	.reveal div.callout.callout-note.warning-style-default .callout-title{
	.reveal div.callout.callout-warning.callout-style-default .callout-title{

+              resources$contributes$format$revealjs[["format-resources"]] |>
+                basename() |>
+                file.remove() -> hide

		::::


		## Commiting to current branch

Presentation on rewriting git history by ThierryO · Pull Request #372 · inbo/tutorials · GitHub

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Presentation on rewriting git history - #372

Presentation on rewriting git history#372ThierryO wants to merge 2 commits intomasterinbo/tutorials:masterfrom rewriteinbo/tutorials:rewriteCopy head branch name to clipboard

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ThierryO commented Mar 4, 2026

Description

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Presentation on rewriting git history#372
ThierryO wants to merge 2 commits into
masterfrom
rewrite