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citation & doi formatting #282

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merged 9 commits into from
Jul 5, 2024
Merged

citation & doi formatting #282

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e9e8ec1
process doi tags from Rd pages
zeileis Jul 4, 2024
0da065f
avoid non-standard evaluation in library()
zeileis Jul 4, 2024
058d69d
citation() formatting as HTML instead of verbatim
zeileis Jul 4, 2024
5cb905d
add @references with doi and @seealso for testing purposes
zeileis Jul 4, 2024
09719b8
add missing info in test pkg
etiennebacher Jul 4, 2024
eda9153
update snapshots
etiennebacher Jul 4, 2024
765cd99
Merge branch 'main' into zeileis/main
vincentarelbundock Jul 4, 2024
d7a1866
formatting
etiennebacher Jul 5, 2024
ab7c0bd
news
etiennebacher Jul 5, 2024
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18 changes: 15 additions & 3 deletions NEWS.md
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### Breaking changes

* Simplified rendering for Quarto websites. Previously, the website was rendered into `_quarto/_site` and manually copied over to `docs/`. The new version removes this logic and instead uses the `output-dir` project option. To transition, change `quarto_website.yml` to:
* Simplified rendering for Quarto websites. Previously, the website was rendered
into `_quarto/_site` and manually copied over to `docs/`. The new version removes
this logic and instead uses the `output-dir` project option. To transition, change
`quarto_website.yml` to:
``` yml
project:
output-dir: ../docs/
```

### New features

* `render_docs(freeze = TRUE)` now works correctly when output is `"quarto_website"`. Freezing a document needs to be set either at a project or per-file level. To do so, add to either `quarto_website.yml` or the frontmatter of a file:
* `render_docs(freeze = TRUE)` now works correctly when output is `"quarto_website"`.
Freezing a document needs to be set either at a project or per-file level. To do
so, add to either `quarto_website.yml` or the frontmatter of a file:

``` yml
execute:
freeze: auto
```
* For Quarto websites, `render_docs()` can use the `downlit` package to automatically link function calls to their documentation on the web. Turn off by modifying the `code-link` line in `altdoc/quarto_website.yml`
* For Quarto websites, `render_docs()` can use the `downlit` package to automatically
link function calls to their documentation on the web. Turn off by modifying
the `code-link` line in `altdoc/quarto_website.yml`
* Citation is now formatted with HTML instead of verbatim (#282, Achim Zeileis).
* The `\doi{}` tags in Rd files are now linked once rendered (#282, Achim Zeileis).



### Other changes

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15 changes: 13 additions & 2 deletions R/import_misc.R
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tryCatch(
{
name <- .pkg_name(src_dir)
cite <- utils::capture.output(print(utils::citation(name)))
c("# Citation", "", "```verbatim", cite, "```")
cite <- utils::citation(name)
head <- vapply(cite, function(x) {
if (is.null(x$header)) {
""
} else {
paste0(x$header, "\n\n")
}
}, character(1))
if (!is.null(attr(cite, "mheader"))) {
head[1] <- paste0(attr(cite, "mheader"), "\n\n", head[1])
}
cite <- paste0(head, format(cite, style = "html"))
c("# Citation", "", paste(cite, collapse = "\n\n"))
},
error = function(e) NULL)
)
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5 changes: 4 additions & 1 deletion R/rd2qmd.R
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# doesn't escape symbols between two $.
tmp <- gsub("\\$", "\\\\$", tmp)

# process \doi{...} tags that were expanded to \Sexpr[results=rd]{tools:::Rd_expr_doi("...")}
tmp <- gsub("(\\\\Sexpr\\[results=rd\\]\\{tools:::Rd_expr_doi\\(\\\")([^\\\"]+)(\\\"\\)\\})", "[doi:\\2](https://doi.org/\\2)", tmp)

# examples: evaluate code blocks (assume examples are always last)
pkg <- .pkg_name(path)
pkg_load <- paste0("library(", pkg, ")")
pkg_load <- paste0("library(\"", pkg, "\")")
idx <- which(tmp == "<h3>Examples</h3>")

if (length(idx) == 1) {
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45 changes: 28 additions & 17 deletions tests/testthat/_snaps/docsify/render_docs.md
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[35] ""
[36] "Some value"
[37] ""
[38] "## Examples"
[38] "## References"
[39] ""
[40] "``` r"
[41] "library(testpkg.altdoc)"
[42] ""
[43] "hello_base()"
[44] "```"
[45] ""
[46] " [1] \"Hello, world!\""
[47] ""
[48] "``` r"
[49] "mtcars$drat <- mtcars$drat + 1"
[50] "head(mtcars[[\"drat\"]], 2)"
[51] "```"
[52] ""
[53] " [1] 4.9 4.9"
[40] "Ihaka R, Gentleman R (1996). R: A Language for Data Analysis and"
[41] "Graphics. <em>Journal of Computational and Graphical Statistics</em>."
[42] "<b>5</b>(3), 299–314."
[43] "[doi:10.2307/139080](https://doi.org/10.2307/139080)"
[44] ""
[45] "## See Also"
[46] ""
[47] "<code>print</code>, <code>hello_r6</code>"
[48] ""
[49] "## Examples"
[50] ""
[51] "``` r"
[52] "library(\"testpkg.altdoc\")"
[53] ""
[54] "hello_base()"
[55] "```"
[56] ""
[57] " [1] \"Hello, world!\""
[58] ""
[59] "``` r"
[60] "mtcars$drat <- mtcars$drat + 1"
[61] "head(mtcars[[\"drat\"]], 2)"
[62] "```"
[63] ""
[64] " [1] 4.9 4.9"

---

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[31] "## Examples"
[32] ""
[33] "``` r"
[34] "library(testpkg.altdoc)"
[34] "library(\"testpkg.altdoc\")"
[35] ""
[36] ""
[37] "examplesIf_true()"
Expand Down Expand Up @@ -420,7 +431,7 @@
[31] "## Examples"
[32] ""
[33] "``` r"
[34] "library(testpkg.altdoc)"
[34] "library(\"testpkg.altdoc\")"
[35] ""
[36] ""
[37] "examplesIf_false()"
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45 changes: 28 additions & 17 deletions tests/testthat/_snaps/docute/render_docs.md
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[35] ""
[36] "Some value"
[37] ""
[38] "## Examples"
[38] "## References"
[39] ""
[40] "``` r"
[41] "library(testpkg.altdoc)"
[42] ""
[43] "hello_base()"
[44] "```"
[45] ""
[46] " [1] \"Hello, world!\""
[47] ""
[48] "``` r"
[49] "mtcars$drat <- mtcars$drat + 1"
[50] "head(mtcars[[\"drat\"]], 2)"
[51] "```"
[52] ""
[53] " [1] 4.9 4.9"
[40] "Ihaka R, Gentleman R (1996). R: A Language for Data Analysis and"
[41] "Graphics. <em>Journal of Computational and Graphical Statistics</em>."
[42] "<b>5</b>(3), 299–314."
[43] "[doi:10.2307/139080](https://doi.org/10.2307/139080)"
[44] ""
[45] "## See Also"
[46] ""
[47] "<code>print</code>, <code>hello_r6</code>"
[48] ""
[49] "## Examples"
[50] ""
[51] "``` r"
[52] "library(\"testpkg.altdoc\")"
[53] ""
[54] "hello_base()"
[55] "```"
[56] ""
[57] " [1] \"Hello, world!\""
[58] ""
[59] "``` r"
[60] "mtcars$drat <- mtcars$drat + 1"
[61] "head(mtcars[[\"drat\"]], 2)"
[62] "```"
[63] ""
[64] " [1] 4.9 4.9"

---

Expand Down Expand Up @@ -365,7 +376,7 @@
[31] "## Examples"
[32] ""
[33] "``` r"
[34] "library(testpkg.altdoc)"
[34] "library(\"testpkg.altdoc\")"
[35] ""
[36] ""
[37] "examplesIf_true()"
Expand Down Expand Up @@ -411,7 +422,7 @@
[31] "## Examples"
[32] ""
[33] "``` r"
[34] "library(testpkg.altdoc)"
[34] "library(\"testpkg.altdoc\")"
[35] ""
[36] ""
[37] "examplesIf_false()"
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41 changes: 26 additions & 15 deletions tests/testthat/_snaps/mkdocs/render_docs.md
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Expand Up @@ -55,22 +55,33 @@
[35] ""
[36] "Some value"
[37] ""
[38] "## Examples"
[38] "## References"
[39] ""
[40] "``` r"
[41] "library(testpkg.altdoc)"
[42] ""
[43] "hello_base()"
[44] "```"
[45] ""
[46] " [1] \"Hello, world!\""
[47] ""
[48] "``` r"
[49] "mtcars$drat <- mtcars$drat + 1"
[50] "head(mtcars[[\"drat\"]], 2)"
[51] "```"
[52] ""
[53] " [1] 4.9 4.9"
[40] "Ihaka R, Gentleman R (1996). R: A Language for Data Analysis and"
[41] "Graphics. <em>Journal of Computational and Graphical Statistics</em>."
[42] "<b>5</b>(3), 299–314."
[43] "[doi:10.2307/139080](https://doi.org/10.2307/139080)"
[44] ""
[45] "## See Also"
[46] ""
[47] "<code>print</code>, <code>hello_r6</code>"
[48] ""
[49] "## Examples"
[50] ""
[51] "``` r"
[52] "library(\"testpkg.altdoc\")"
[53] ""
[54] "hello_base()"
[55] "```"
[56] ""
[57] " [1] \"Hello, world!\""
[58] ""
[59] "``` r"
[60] "mtcars$drat <- mtcars$drat + 1"
[61] "head(mtcars[[\"drat\"]], 2)"
[62] "```"
[63] ""
[64] " [1] 4.9 4.9"

---

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16 changes: 16 additions & 0 deletions tests/testthat/examples/testpkg.altdoc/R/hello_base.R
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#'
#' @param x A parameter
#'
#' @details
#' Some code with weird symbols: `pl$when(condition)` and `pl$then(output)`
#'
#' Some equations: \eqn{\partial Y / \partial X = a + \varepsilon/2}
#'
#'
#' @return Some value
#' @export
#'
#' @seealso \code{\link[base]{print}}, \code{\link{hello_r6}}
#'
#' @references Ihaka R, Gentleman R (1996).
#' R: A Language for Data Analysis and Graphics.
#' \emph{Journal of Computational and Graphical Statistics}. \bold{5}(3), 299--314.
#' \doi{10.2307/139080}
#'
#' @examples
#' hello_base()
#'
#' mtcars$drat <- mtcars$drat + 1
#' head(mtcars[["drat"]], 2)
hello_base <- function(x = 2) {
print("Hello, world!")
}
9 changes: 9 additions & 0 deletions tests/testthat/examples/testpkg.altdoc/man/hello_base.Rd
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