Merge commit '2fd494eb69f0dd6495bf6f8303075f451f8e8186'

Author: cderv

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,70 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) [Quarto ${{ matrix.config.quarto || 'release' }}]
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release', quarto: 'pre-release'}
+
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'release', quarto: 'pre-release'}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'release', quarto: 'pre-release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: ${{ matrix.config.quarto || 'release' }}
+
+      # replace with setting up QUARTO Pandoc for rmarkdown
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -1,24 +1,37 @@
 Package: quarto
 Title: R Interface to 'Quarto' Markdown Publishing System
-Version: 1.3
-Authors@R: 
-    person(given = "JJ",
-           family = "Allaire",
-           role = c("aut", "cre"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-0174-9868"))
-Description: Convert R Markdown documents and 'Jupyter' notebooks to a variety of
-  output formats using 'Quarto'.
-Imports: utils,rmarkdown,jsonlite,yaml,processx,rstudioapi,later,rsconnect (>= 0.8.26)
-Suggests: 
-    knitr,
-    testthat (>= 3.1.0)
-SystemRequirements: Quarto command line tools (https://github.com/quarto-dev/quarto-cli).
+Version: 1.3.3
+Authors@R: c(
+    person("JJ", "Allaire", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-0174-9868")),
+    person("Christophe", "Dervieux", , "[email protected]", role = c("aut"),
+           comment = c(ORCID = "0000-0003-4474-2498"))
+  )
+Description: Convert R Markdown documents and 'Jupyter' notebooks to a
+    variety of output formats using 'Quarto'.
 License: GPL (>= 2)
-URL: https://github.com/quarto-dev/quarto-r, https://quarto-dev.github.io/quarto-r/
+URL: https://github.com/quarto-dev/quarto-r,
+    https://quarto-dev.github.io/quarto-r/
 BugReports: https://github.com/quarto-dev/quarto-r/issues
+Imports: 
+    jsonlite,
+    later,
+    processx,
+    rmarkdown,
+    rsconnect (>= 0.8.26),
+    rstudioapi,
+    utils,
+    yaml
+Suggests: 
+    knitr,
+    testthat (>= 3.1.0),
+    withr,
+    xfun
+VignetteBuilder: 
+    knitr
+Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Config/testthat/edition: 3
-VignetteBuilder: knitr
+SystemRequirements: Quarto command line tools
+    (https://github.com/quarto-dev/quarto-cli).

NEWS.md

@@ -0,0 +1,9 @@
+# quarto (development version)
+
+* Add `profile` arguments to `quarto_render()` and `quarto_inspect()` (thanks, #95, @andrewheiss, #123, @salim-b).
+
+* Add `metadata` and `metadata_file` to `quarto_render()` to pass modify Quarto metadata from calling render. If both are set, `metadata` will be merged over `metadata_file` content. Internally, metadata will be passed as a `--metadata-file` to `quarto render` (thanks, @mcanouil, #52, @maelle, #49).
+
+* Added a `NEWS.md` file to track changes to the package.
+
+* `execute_params` in `quarto_render()` now converts boolean value to `true/false` correctly as expected by `quarto render` (thanks, @marianklose, #124).

R/backports.R

@@ -0,0 +1,4 @@
+
+if (getRversion() < "3.5.0") {
+  isFALSE <- function(x) identical(x, FALSE)
+}

R/inspect.R

@@ -4,12 +4,13 @@
 #' config and engines. Inspecting an input path return its formats, engine,
 #' and dependent resources.
 #'
+#' @inheritParams quarto_render
 #' @param input The input file or project directory to inspect.
 #'
-#' @return Named list. For input files, the list has members engine, format,
-#'  and resources. For projects the list has members engines and config
-#'
-#' @importFrom jsonlite fromJSON
+#' @return Named list. For input files, the list contains the elements
+#'   `quarto`, `engines`, `formats`, `resources`, plus `project` if the file is
+#'   part of a Quarto project. For projects, the list contains the elements
+#'   `quarto`, `dir`, `engines`, `config` and `files`.
 #'
 #' @examples
 #' \dontrun{
@@ -18,18 +19,26 @@
 #'
 #' # Inspect project
 #' quarto_inspect("myproject")
-#' }
 #'
+#' # Inspect project's advanced profile
+#' quarto_inspect(
+#'   input = "myproject",
+#'   profile = "advanced"
+#' )}
+#' @importFrom jsonlite fromJSON
 #' @export
-quarto_inspect <- function(input = ".") {
+quarto_inspect <- function(input = ".",
+                           profile = NULL) {
 
   quarto_bin <- find_quarto()
 
-  output <- system2(quarto_bin, stdout = TRUE, c(
-    "inspect",
-    path.expand(input)
-  ))
+  args <- c("inspect", path.expand(input))
 
-  fromJSON(output)
-}
+  if (!is.null(profile)) {
+    args <- c(args, c("--profile", paste0(profile, collapse = ",")))
+  }
+
+  res <- processx::run(quarto_bin, args, echo_cmd = getOption("quarto.echo_cmd", FALSE))
 
+  fromJSON(res$stdout)
+}

R/quarto-args.R

@@ -0,0 +1,9 @@
+cli_arg_profile <- function(profile, ...) {
+  arg <- c("--profile", paste0(profile, collapse = ","))
+  append_cli_args(arg, ...)
+}
+
+append_cli_args <- function(new, append_to = NULL, after = length(append_to)) {
+  if (!is.null(append_to)) return(append(append_to, new, after))
+  new
+}

R/render.R

@@ -25,18 +25,27 @@
 #' @param use_freezer Force use of frozen computations for an incremental
 #'  file render.
 #' @param cache Cache execution output (uses knitr cache and jupyter-cache
-#'   respectively for Rmd and Jupyter input files).
+#'  respectively for Rmd and Jupyter input files).
 #' @param cache_refresh Force refresh of execution cache.
+#' @param metadata An optional named list used to override YAML
+#'   metadata. It will be passed as a YAML file to `--metadata-file` CLI flag.
+#'   This will be merged over `metadata-file` options if both are
+#'   specified.
+#' @param metadata_file A yaml file passed to `--metadata-file` CLI flags to
+#'   overrite metadata. This will be merged with `metadata` if both are
+#'   specified, with low precedence on `metadata` options.
 #' @param debug Leave intermediate files in place after render.
 #' @param quiet Suppress warning and other messages.
+#' @param profile [Quarto project
+#'   profile(s)](https://quarto.org/docs/projects/profiles.html) to use. Either
+#'   a character vector of profile names or `NULL` to use the default profile.
 #' @param pandoc_args Additional command line options to pass to pandoc.
 #' @param as_job Render as an RStudio background job. Default is "auto",
 #'   which will render individual documents normally and projects as
 #'   background jobs. Use the `quarto.render_as_job` R option to control
 #'   the default globally.
 #'
 #' @importFrom rmarkdown relative_to
-#' @importFrom yaml write_yaml
 #'
 #' @examples
 #' \dontrun{
@@ -49,6 +58,9 @@
 #'
 #' # Render Jupyter Markdown
 #' quarto_render("notebook.md")
+#'
+#' # Override metadata
+#' quarto_render("notebook.Rmd", override = list(lang = "fr", echo = "false"))
 #' }
 #' @export
 quarto_render <- function(input = NULL,
@@ -63,8 +75,11 @@ quarto_render <- function(input = NULL,
                           use_freezer = FALSE,
                           cache = NULL,
                           cache_refresh = FALSE,
+                          metadata = NULL,
+                          metadata_file = NULL,
                           debug = FALSE,
                           quiet = FALSE,
+                          profile = NULL,
                           pandoc_args = NULL,
                           as_job = getOption("quarto.render_as_job", "auto")) {
 
@@ -146,12 +161,28 @@ quarto_render <- function(input = NULL,
   if (isTRUE(cache_refresh)) {
     args <- c(args, "--cache-refresh")
   }
+  # metadata to pass to quarto render
+  if (!missing(metadata)) {
+    # We merge meta if there is metadata_file passed
+    if (!missing(metadata_file)) {
+      metadata <- merge_list(yaml::read_yaml(metadata_file, eval.expr = FALSE), metadata)
+    }
+    meta_file <- tempfile(pattern = "quarto-meta", fileext = ".yml")
+    on.exit(unlink(meta_file), add = TRUE)
+    write_yaml(metadata, meta_file)
+    args <- c(args, "--metadata-file", meta_file)
+  } else if (!missing(metadata_file)) {
+    args <- c(args, "--metadata-file", metadata_file)
+  }
   if (isTRUE(debug)) {
     args <- c(args, "--debug")
   }
   if (isTRUE(quiet)) {
     args <- c(args, "--quiet")
   }
+  if (!is.null(profile)) {
+    args <- cli_arg_profile(profile, args)
+  }
   if (!is.null(pandoc_args)) {
     args <- c(args, pandoc_args)
   }
@@ -162,9 +193,3 @@ quarto_render <- function(input = NULL,
   # no return value
   invisible(NULL)
 }
-
-
-
-
-
-

R/utils.R

@@ -3,3 +3,22 @@
 relative_to_wd <- function(path) {
   relative_to(getwd(), path)
 }
+
+#' @importFrom yaml write_yaml
+write_yaml <- function(x, file) {
+  handlers <- list(
+    # Handle yes/no from 1.1 to 1.2
+    # https://github.com/vubiostat/r-yaml/issues/131
+    logical = function(x) {
+    value <- ifelse(x, "true", "false")
+    structure(value, class = "verbatim")
+  })
+  yaml::write_yaml(x, file, handlers = handlers)
+}
+
+
+# inline knitr:::merge_list()
+merge_list <- function(x, y) {
+  x[names(y)] <- y
+  x
+}

README.md

@@ -2,6 +2,7 @@
 
 <!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/quarto)](https://CRAN.R-project.org/package=quarto)
+[![R-CMD-check](https://github.com/quarto-dev/quarto-r/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/quarto-dev/quarto-r/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 [Quarto](https://quarto.org) is an open-source scientific and technical publishing system built on [Pandoc](https://pandoc.org).