From 70027f9a7e7e429a23540283f133769660e627bc Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Fri, 28 Apr 2023 11:24:28 +0100
Subject: [PATCH 01/47] Set dev version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e0513926c..75f214f32 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sandpaper
 Title: Create and Curate Carpentries Lessons
-Version: 0.11.15
+Version: 0.11.15.9000
 Authors@R: c(
     person(given = "Zhian N.",
            family = "Kamvar",

From 51c6995cb448e731dcb8f30e81a1d2e73dac416a Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Tue, 2 May 2023 17:15:50 +0100
Subject: [PATCH 02/47] Add `use_python()` helper

---
 NAMESPACE         |  1 +
 R/use_python.R    | 23 +++++++++++++++++++++++
 man/use_python.Rd | 35 +++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+)
 create mode 100644 R/use_python.R
 create mode 100644 man/use_python.Rd

diff --git a/NAMESPACE b/NAMESPACE
index fcf273ca2..8d936c8e6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -54,6 +54,7 @@ export(update_cache)
 export(update_github_workflows)
 export(update_varnish)
 export(use_package_cache)
+export(use_python)
 export(validate_lesson)
 export(work_with_cache)
 importFrom(assertthat,validate_that)
diff --git a/R/use_python.R b/R/use_python.R
new file mode 100644
index 000000000..d81de0804
--- /dev/null
+++ b/R/use_python.R
@@ -0,0 +1,23 @@
+#' Use Python
+#'
+#' Associate a version of Python with your lesson. This is essentially a wrapper
+#' around [renv::use_python()].
+#'
+#' @param path path to the current project
+#' @inheritParams renv::use_python
+#' @param ... Further arguments to be passed on to [renv::use_python()]
+#'
+#' @export
+#' @seealso [renv::use_python()]
+#' @return The path to the Python executable. Note that this function is mainly
+#'   called for its side effects.
+use_python <- function(path = ".", python = NULL,
+                       type = c("auto", "virtualenv", "conda", "system"), ...) {
+
+  renv::load(project = path)
+  on.exit({
+    invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
+  }, add = TRUE)
+  renv::use_python(python = python, type = type, ...)
+}
+
diff --git a/man/use_python.Rd b/man/use_python.Rd
new file mode 100644
index 000000000..f9c6aa881
--- /dev/null
+++ b/man/use_python.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/use_python.R
+\name{use_python}
+\alias{use_python}
+\title{Use Python}
+\usage{
+use_python(
+  path = ".",
+  python = NULL,
+  type = c("auto", "virtualenv", "conda", "system"),
+  ...
+)
+}
+\arguments{
+\item{path}{path to the current project}
+
+\item{python}{The path to the version of Python to be used with this project. See
+\strong{Finding Python} for more details.}
+
+\item{type}{The type of Python environment to use. When \code{"auto"} (the default),
+virtual environments will be used.}
+
+\item{...}{Further arguments to be passed on to \code{\link[renv:use_python]{renv::use_python()}}}
+}
+\value{
+The path to the Python executable. Note that this function is mainly
+called for its side effects.
+}
+\description{
+Associate a version of Python with your lesson. This is essentially a wrapper
+around \code{\link[renv:use_python]{renv::use_python()}}.
+}
+\seealso{
+\code{\link[renv:use_python]{renv::use_python()}}
+}

From 962339550de2af92376c87da07f111de2d98ca3d Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Tue, 2 May 2023 18:26:52 +0100
Subject: [PATCH 03/47] Add `py_install()` helpeer to add Python dependencies

---
 DESCRIPTION       |  3 ++-
 NAMESPACE         |  1 +
 R/use_python.R    | 43 +++++++++++++++++++++++++++++++++++++++++--
 man/py_install.Rd | 27 +++++++++++++++++++++++++++
 man/use_python.Rd |  2 +-
 5 files changed, 72 insertions(+), 4 deletions(-)
 create mode 100644 man/py_install.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 75f214f32..52a1bd295 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,7 +60,8 @@ Suggests:
     jsonlite,
     sessioninfo,
     mockr,
-    varnish (>= 0.2.1)
+    varnish (>= 0.2.1),
+    reticulate
 Additional_repositories: https://carpentries.r-universe.dev/
 Remotes:
   ropensci/tinkr,
diff --git a/NAMESPACE b/NAMESPACE
index 8d936c8e6..c87e44f8a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -24,6 +24,7 @@ export(move_episode)
 export(no_package_cache)
 export(package_cache_trigger)
 export(pin_version)
+export(py_install)
 export(renv_diagnostics)
 export(reset_episodes)
 export(reset_site)
diff --git a/R/use_python.R b/R/use_python.R
index d81de0804..d980c783a 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -1,7 +1,7 @@
 #' Use Python
 #'
 #' Associate a version of Python with your lesson. This is essentially a wrapper
-#' around [renv::use_python()].
+#' around [renv::use_python()]. To add Python packages, use [py_install()].
 #'
 #' @param path path to the current project
 #' @inheritParams renv::use_python
@@ -14,10 +14,49 @@
 use_python <- function(path = ".", python = NULL,
                        type = c("auto", "virtualenv", "conda", "system"), ...) {
 
-  renv::load(project = path)
+  ## Load the renv profile, unloading it upon exit
   on.exit({
     invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
   }, add = TRUE)
+  renv::load(project = path)
+
   renv::use_python(python = python, type = type, ...)
 }
 
+
+#' Install Python packages and add them to the cache
+#'
+#' Installs Python packages with [reticulate::py_install()] and then records
+#' them in the renv environment. This ensures [manage_deps()] keeps track of the
+#' Python packages as well.
+#'
+#' @param packages Python packages to be installed as a character vecto.
+#' @param path path to your lesson. Defaults to the current working directory.
+#' @param ... Further arguments to be passed to [reticulate::py_install()]
+#'
+#' @details
+#' Unlike with R packages, \pkg{renv} is not yet capable of automatically
+#' detecting Python dependencies. Therefore, this helper function is provided to
+#' correctly install Python packages and recording them in the renv environment.
+#' Subsequent calls of [manage_deps()] will then correctly restore the required
+#' Python packages if needed.
+#'
+#' @export
+py_install <- function(packages, path = ".",  ...) {
+
+  ## Load the renv profile, unloading it upon exit
+  renv::load(project = path)
+  on.exit({
+    invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
+  }, add = TRUE)
+
+  has_reticulate <- rlang::is_installed("reticulate")
+  if (!has_reticulate) {
+    cli::cli_alert("Adding `reticulate` as a dependency for Python package installation")
+    renv::install("reticulate")
+  }
+  reticulate::py_install(packages = packages, ...)
+
+  cli::cli_alert("Updating the package cache")
+  renv::snapshot(lockfile = renv::paths$lockfile(project = path), prompt = FALSE)
+}
diff --git a/man/py_install.Rd b/man/py_install.Rd
new file mode 100644
index 000000000..945645217
--- /dev/null
+++ b/man/py_install.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/use_python.R
+\name{py_install}
+\alias{py_install}
+\title{Install Python packages and add them to the cache}
+\usage{
+py_install(path = ".", packages, ...)
+}
+\arguments{
+\item{path}{path to your lesson. Defaults to the current working directory.}
+
+\item{packages}{Python packages to be installed as a character vecto.}
+
+\item{...}{Further arguments to be passed to \code{\link[reticulate:py_install]{reticulate::py_install()}}}
+}
+\description{
+Installs Python packages with \code{\link[reticulate:py_install]{reticulate::py_install()}} and then records
+them in the renv environment. This ensures \code{\link[=manage_deps]{manage_deps()}} keeps track of the
+Python packages as well.
+}
+\details{
+Unlike with R packages, \pkg{renv} is not yet capable of automatically
+detecting Python dependencies. Therefore, this helper function is provided to
+correctly install Python packages and recording them in the renv environment.
+Subsequent calls of \code{\link[=manage_deps]{manage_deps()}} will then correctly restore the required
+Python packages if needed.
+}
diff --git a/man/use_python.Rd b/man/use_python.Rd
index f9c6aa881..ff3a9a53e 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -28,7 +28,7 @@ called for its side effects.
 }
 \description{
 Associate a version of Python with your lesson. This is essentially a wrapper
-around \code{\link[renv:use_python]{renv::use_python()}}.
+around \code{\link[renv:use_python]{renv::use_python()}}. To add Python packages, use \code{\link[=py_install]{py_install()}}.
 }
 \seealso{
 \code{\link[renv:use_python]{renv::use_python()}}

From 1495f893acf083b5bc615bcb7084d03f0e8f14d8 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 11:47:40 +0100
Subject: [PATCH 04/47] Reactivate renv profile after adding Python

Workaround for https://github.com/rstudio/renv/issues/1217
---
 R/use_python.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/use_python.R b/R/use_python.R
index d980c783a..6258af922 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -18,9 +18,14 @@ use_python <- function(path = ".", python = NULL,
   on.exit({
     invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
   }, add = TRUE)
-  renv::load(project = path)
 
+  renv::load(project = path)
+  prof <- Sys.getenv("RENV_PROFILE")
   renv::use_python(python = python, type = type, ...)
+
+  ## NOTE: use_python() deactivates the default profile, see https://github.com/rstudio/renv/issues/1217
+  ## Workaround: re-activate the profile
+  renv::activate(project = path, profile = prof)
 }
 
 

From cea48bfc5eed7f5a8875a9ef620e79edecc3def3 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 11:57:08 +0100
Subject: [PATCH 05/47] Make sure Python dependencies also get restored by
 `manage_deps()`

---
 R/utils-renv.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/utils-renv.R b/R/utils-renv.R
index 7bd35a5e2..3d201b96e 100644
--- a/R/utils-renv.R
+++ b/R/utils-renv.R
@@ -288,8 +288,12 @@ callr_manage_deps <- function(path, repos, snapshot, lockfile_exists) {
   #    recorded.
   if (lockfile_exists) {
     cli::cli_alert("Restoring any dependency versions")
-    res <- renv::restore(project = path, library = renv_lib,
-      lockfile = renv_lock, prompt = FALSE)
+    # Load profile, this ensures Python dependencies also get restored
+    renv::load(project = path)
+    on.exit({
+      invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
+    }, add = TRUE)
+    res <- renv::restore(project = path, prompt = FALSE)
   }
   if (snapshot) {
     # 3. Load the current profile, unloading it when we exit

From 28425e8cae083933d1914d8da9949497a33f726b Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 13:27:54 +0100
Subject: [PATCH 06/47] Add option to set up Python in `create_lesson()`

---
 R/create_lesson.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/create_lesson.R b/R/create_lesson.R
index 5c91ba819..456296036 100644
--- a/R/create_lesson.R
+++ b/R/create_lesson.R
@@ -19,7 +19,8 @@
 #' on.exit(unlink(tmp))
 #' lsn <- create_lesson(tmp, name = "This Lesson", open = FALSE)
 #' lsn
-create_lesson <- function(path, name = fs::path_file(path), rmd = TRUE, rstudio = rstudioapi::isAvailable(), open = rlang::is_interactive()) {
+create_lesson <- function(path, name = fs::path_file(path), rmd = TRUE, rstudio = rstudioapi::isAvailable(), open = rlang::is_interactive(),
+                          add_python = FALSE, python = NULL, type = c("auto", "virtualenv", "conda", "system")) {
 
   path <- fs::path_abs(path)
   id <- cli::cli_status("{cli::symbol$arrow_right} Creating Lesson in {.file {path}}...")
@@ -92,6 +93,11 @@ create_lesson <- function(path, name = fs::path_file(path), rmd = TRUE, rstudio
   if (has_consent) {
     cli::cli_status_update("{cli::symbol$arrow_right} Managing Dependencies ...")
     manage_deps(path, snapshot = TRUE)
+
+    if (add_python) {
+      cli::cli_status_update("{cli::symbol$arrow_right} Setting up Python ...")
+      use_python(path = path, python = python, type = type)
+    }
   }
 
   cli::cli_status_update("{cli::symbol$arrow_right} Committing ...")

From b729c0ca33b3823104dd3f2dfd04c35a6647182b Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 13:28:20 +0100
Subject: [PATCH 07/47] Set working directory while setting up Python

Avoids some undesirable renv side effects.
---
 R/use_python.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/use_python.R b/R/use_python.R
index 6258af922..2d498d54c 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -14,13 +14,19 @@
 use_python <- function(path = ".", python = NULL,
                        type = c("auto", "virtualenv", "conda", "system"), ...) {
 
+  wd <- getwd()
+
   ## Load the renv profile, unloading it upon exit
   on.exit({
     invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
+    setwd(wd)
   }, add = TRUE)
 
+  ## Set up working directory, avoids some renv side effects
+  setwd(path)
   renv::load(project = path)
   prof <- Sys.getenv("RENV_PROFILE")
+
   renv::use_python(python = python, type = type, ...)
 
   ## NOTE: use_python() deactivates the default profile, see https://github.com/rstudio/renv/issues/1217

From 5ffacc6e7fbeb5d9a32d537e6770ca17bacc1c07 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 13:43:01 +0100
Subject: [PATCH 08/47] Update documentation for `create_lesson()`

---
 R/create_lesson.R | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/R/create_lesson.R b/R/create_lesson.R
index 456296036..963e537da 100644
--- a/R/create_lesson.R
+++ b/R/create_lesson.R
@@ -11,6 +11,16 @@
 #'   file extension in the lesson.
 #' @param rstudio create an RStudio project (defaults to if RStudio exits)
 #' @param open if interactive, the lesson will open in a new editor window.
+#' @param add_python if set to `TRUE`, will add Python as a dependency for the
+#'   lesson. See [use_python()] for details. Defaults to `FALSE`.
+#' @param python the path to the version of Python to be used. The default,
+#'   `NULL`, will prompt the user to select an appropriate version of Python in
+#'   interactive sessions. In non-interactive sessions, \pkg{renv} will attempt
+#'   to automatically select an appropriate version. See [renv::use_python()]
+#'   for more details.
+#' @param type the type of Python environment to use. When `"auto"`, the
+#'   default, virtual environments will be used. See [renv::use_python()] for
+#'   more details.
 #'
 #' @export
 #' @return the path to the new lesson

From 669141ce122621ed108d8af46439bd17eec2f9e8 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 13:53:51 +0100
Subject: [PATCH 09/47] Update documentation for `use_python()`

---
 R/use_python.R | 36 +++++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/R/use_python.R b/R/use_python.R
index 2d498d54c..67ad93e13 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -1,14 +1,29 @@
-#' Use Python
+#' Add Python as a lesson dependency
 #'
 #' Associate a version of Python with your lesson. This is essentially a wrapper
-#' around [renv::use_python()]. To add Python packages, use [py_install()].
+#' around [renv::use_python()].
 #'
 #' @param path path to the current project
 #' @inheritParams renv::use_python
 #' @param ... Further arguments to be passed on to [renv::use_python()]
 #'
+#' @details
+#' This helper function adds Python as a dependency to the \pkg{renv} lockfile
+#' and installs a Python environment of the specified `type`. This ensures any
+#' Python packages used for this lesson are installed separately from the user's
+#' main library, much like the R packages (see [manage_deps()]).
+#'
+#' Note that \pkg{renv} is not (yet) able to automatically detect Python package
+#' dependencies (e.g. from `import` statements). So any required Python packages
+#' still need to be installed manually. To facilitate this, the [py_install()]
+#' helper is provided. This will install Python packages in the correct
+#' environment and record them in a `requirements.txt` file, which will be
+#' tracked by \pkg{renv}. Subsequent calls of [manage_deps()] will then
+#' correctly restore the required Python packages if needed.
+#'
 #' @export
-#' @seealso [renv::use_python()]
+#' @rdname use_python
+#' @seealso [renv::use_python()], [py_install()]
 #' @return The path to the Python executable. Note that this function is mainly
 #'   called for its side effects.
 use_python <- function(path = ".", python = NULL,
@@ -37,22 +52,17 @@ use_python <- function(path = ".", python = NULL,
 
 #' Install Python packages and add them to the cache
 #'
-#' Installs Python packages with [reticulate::py_install()] and then records
-#' them in the renv environment. This ensures [manage_deps()] keeps track of the
-#' Python packages as well.
+#' To add Python packages, `py_install()` is provided, which installs Python
+#' packages with [reticulate::py_install()] and then records them in the renv
+#' environment. This ensures [manage_deps()] keeps track of the Python packages
+#' as well.
 #'
 #' @param packages Python packages to be installed as a character vecto.
 #' @param path path to your lesson. Defaults to the current working directory.
 #' @param ... Further arguments to be passed to [reticulate::py_install()]
 #'
-#' @details
-#' Unlike with R packages, \pkg{renv} is not yet capable of automatically
-#' detecting Python dependencies. Therefore, this helper function is provided to
-#' correctly install Python packages and recording them in the renv environment.
-#' Subsequent calls of [manage_deps()] will then correctly restore the required
-#' Python packages if needed.
-#'
 #' @export
+#' @rdname use_python
 py_install <- function(packages, path = ".",  ...) {
 
   ## Load the renv profile, unloading it upon exit

From 0b45377ebc8e6e215a00f1422150427e56015c92 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 14:01:56 +0100
Subject: [PATCH 10/47] Reoxygenize

---
 man/create_lesson.Rd | 18 +++++++++++++++++-
 man/py_install.Rd    | 27 ---------------------------
 man/use_python.Rd    | 34 +++++++++++++++++++++++++++++-----
 3 files changed, 46 insertions(+), 33 deletions(-)
 delete mode 100644 man/py_install.Rd

diff --git a/man/create_lesson.Rd b/man/create_lesson.Rd
index 2afaa0187..ca65dbd9d 100644
--- a/man/create_lesson.Rd
+++ b/man/create_lesson.Rd
@@ -9,7 +9,10 @@ create_lesson(
   name = fs::path_file(path),
   rmd = TRUE,
   rstudio = rstudioapi::isAvailable(),
-  open = rlang::is_interactive()
+  open = rlang::is_interactive(),
+  add_python = FALSE,
+  python = NULL,
+  type = c("auto", "virtualenv", "conda", "system")
 )
 }
 \arguments{
@@ -25,6 +28,19 @@ file extension in the lesson.}
 \item{rstudio}{create an RStudio project (defaults to if RStudio exits)}
 
 \item{open}{if interactive, the lesson will open in a new editor window.}
+
+\item{add_python}{if set to \code{TRUE}, will add Python as a dependency for the
+lesson. See \code{\link[=use_python]{use_python()}} for details. Defaults to \code{FALSE}.}
+
+\item{python}{the path to the version of Python to be used. The default,
+\code{NULL}, will prompt the user to select an appropriate version of Python in
+interactive sessions. In non-interactive sessions, \pkg{renv} will attempt
+to automatically select an appropriate version. See \code{\link[renv:use_python]{renv::use_python()}}
+for more details.}
+
+\item{type}{the type of Python environment to use. When \code{"auto"}, the
+default, virtual environments will be used. See \code{\link[renv:use_python]{renv::use_python()}} for
+more details.}
 }
 \value{
 the path to the new lesson
diff --git a/man/py_install.Rd b/man/py_install.Rd
deleted file mode 100644
index 945645217..000000000
--- a/man/py_install.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/use_python.R
-\name{py_install}
-\alias{py_install}
-\title{Install Python packages and add them to the cache}
-\usage{
-py_install(path = ".", packages, ...)
-}
-\arguments{
-\item{path}{path to your lesson. Defaults to the current working directory.}
-
-\item{packages}{Python packages to be installed as a character vecto.}
-
-\item{...}{Further arguments to be passed to \code{\link[reticulate:py_install]{reticulate::py_install()}}}
-}
-\description{
-Installs Python packages with \code{\link[reticulate:py_install]{reticulate::py_install()}} and then records
-them in the renv environment. This ensures \code{\link[=manage_deps]{manage_deps()}} keeps track of the
-Python packages as well.
-}
-\details{
-Unlike with R packages, \pkg{renv} is not yet capable of automatically
-detecting Python dependencies. Therefore, this helper function is provided to
-correctly install Python packages and recording them in the renv environment.
-Subsequent calls of \code{\link[=manage_deps]{manage_deps()}} will then correctly restore the required
-Python packages if needed.
-}
diff --git a/man/use_python.Rd b/man/use_python.Rd
index ff3a9a53e..7334d1a72 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -2,7 +2,8 @@
 % Please edit documentation in R/use_python.R
 \name{use_python}
 \alias{use_python}
-\title{Use Python}
+\alias{py_install}
+\title{Add Python as a lesson dependency}
 \usage{
 use_python(
   path = ".",
@@ -10,9 +11,11 @@ use_python(
   type = c("auto", "virtualenv", "conda", "system"),
   ...
 )
+
+py_install(packages, path = ".", ...)
 }
 \arguments{
-\item{path}{path to the current project}
+\item{path}{path to your lesson. Defaults to the current working directory.}
 
 \item{python}{The path to the version of Python to be used with this project. See
 \strong{Finding Python} for more details.}
@@ -20,7 +23,9 @@ use_python(
 \item{type}{The type of Python environment to use. When \code{"auto"} (the default),
 virtual environments will be used.}
 
-\item{...}{Further arguments to be passed on to \code{\link[renv:use_python]{renv::use_python()}}}
+\item{...}{Further arguments to be passed to \code{\link[reticulate:py_install]{reticulate::py_install()}}}
+
+\item{packages}{Python packages to be installed as a character vecto.}
 }
 \value{
 The path to the Python executable. Note that this function is mainly
@@ -28,8 +33,27 @@ called for its side effects.
 }
 \description{
 Associate a version of Python with your lesson. This is essentially a wrapper
-around \code{\link[renv:use_python]{renv::use_python()}}. To add Python packages, use \code{\link[=py_install]{py_install()}}.
+around \code{\link[renv:use_python]{renv::use_python()}}.
+
+To add Python packages, \code{py_install()} is provided, which installs Python
+packages with \code{\link[reticulate:py_install]{reticulate::py_install()}} and then records them in the renv
+environment. This ensures \code{\link[=manage_deps]{manage_deps()}} keeps track of the Python packages
+as well.
+}
+\details{
+This helper function adds Python as a dependency to the \pkg{renv} lockfile
+and installs a Python environment of the specified \code{type}. This ensures any
+Python packages used for this lesson are installed separately from the user's
+main library, much like the R packages (see \code{\link[=manage_deps]{manage_deps()}}).
+
+Note that \pkg{renv} is not (yet) able to automatically detect Python package
+dependencies (e.g. from \code{import} statements). So any required Python packages
+still need to be installed manually. To facilitate this, the \code{\link[=py_install]{py_install()}}
+helper is provided. This will install Python packages in the correct
+environment and record them in a \code{requirements.txt} file, which will be
+tracked by \pkg{renv}. Subsequent calls of \code{\link[=manage_deps]{manage_deps()}} will then
+correctly restore the required Python packages if needed.
 }
 \seealso{
-\code{\link[renv:use_python]{renv::use_python()}}
+\code{\link[renv:use_python]{renv::use_python()}}, \code{\link[=py_install]{py_install()}}
 }

From 4529311daa87f2cf6085e20c92699efe835ea243 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 14:13:46 +0100
Subject: [PATCH 11/47] Add examples for Python usage

---
 R/use_python.R    | 16 ++++++++++++++++
 man/use_python.Rd | 17 +++++++++++++++++
 2 files changed, 33 insertions(+)

diff --git a/R/use_python.R b/R/use_python.R
index 67ad93e13..a9b6e33b9 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -26,6 +26,22 @@
 #' @seealso [renv::use_python()], [py_install()]
 #' @return The path to the Python executable. Note that this function is mainly
 #'   called for its side effects.
+#' @examples
+#' \dontrun{
+#' tmp <- tempfile()
+#' on.exit(unlink(tmp))
+#'
+#' ## Create lesson with Python support
+#' lsn <- create_lesson(tmp, name = "This Lesson", open = FALSE, add_python = TRUE)
+#' lsn
+#'
+#' ## Add Python as a dependency to an existing lesson
+#' setwd(lsn)
+#' use_python()
+#'
+#' ## Install Python packages and record them as dependencies
+#' py_install("numpy")
+#' }
 use_python <- function(path = ".", python = NULL,
                        type = c("auto", "virtualenv", "conda", "system"), ...) {
 
diff --git a/man/use_python.Rd b/man/use_python.Rd
index 7334d1a72..f6ce78715 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -54,6 +54,23 @@ environment and record them in a \code{requirements.txt} file, which will be
 tracked by \pkg{renv}. Subsequent calls of \code{\link[=manage_deps]{manage_deps()}} will then
 correctly restore the required Python packages if needed.
 }
+\examples{
+\dontrun{
+tmp <- tempfile()
+on.exit(unlink(tmp))
+
+## Create lesson with Python support
+lsn <- create_lesson(tmp, name = "This Lesson", open = FALSE, add_python = TRUE)
+lsn
+
+## Add Python as a dependency to an existing lesson
+setwd(lsn)
+use_python()
+
+## Install Python packages and record them as dependencies
+py_install("numpy")
+}
+}
 \seealso{
 \code{\link[renv:use_python]{renv::use_python()}}, \code{\link[=py_install]{py_install()}}
 }

From ec2599f9967ca4dc9f880a6bba5436c480b9f7bf Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 16:18:36 +0100
Subject: [PATCH 12/47] Add unit tests for Python integration

---
 tests/testthat/test-use_python.R | 36 ++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 tests/testthat/test-use_python.R

diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
new file mode 100644
index 000000000..d49e599f4
--- /dev/null
+++ b/tests/testthat/test-use_python.R
@@ -0,0 +1,36 @@
+lsn <- restore_fixture()
+old_wd  <- setwd(lsn)
+withr::defer(setwd(old_wd))
+
+use_python(lsn, type = "virtualenv")
+
+
+test_that("use_python() adds Python environment", {
+  py_path <- fs::path(lsn, "renv/profiles/lesson-requirements/renv/python")
+
+  expect_true(fs::dir_exists(py_path))
+  expect_false(Sys.getenv("RETICULATE_PYTHON") == "")
+  py_config <- reticulate::py_config()
+  expect_true(py_config$available)
+  expect_true(py_config$forced == "RETICULATE_PYTHON")
+})
+
+## This relates to a bug in renv, see https://github.com/rstudio/renv/issues/1217
+test_that("use_python() does not remove renv/profile", {
+  expect_true(fs::file_exists(fs::path(lsn, "renv/profile")))
+})
+
+
+test_that("py_install() installs Python packages", {
+  py_install("numpy", path = lsn)
+
+  expect_no_error({numpy <- reticulate::import("numpy")})
+  expect_s3_class(numpy, "python.builtin.module")
+})
+
+
+test_that("py_install() updates requirements.txt", {
+  py_install("numpy", path = lsn)
+  req_file <- fs::path(lsn, "requirements.txt")
+  expect_true(grepl("^numpy", readLines(req_file)))
+})

From cc05834c0d4ad2fbaa3bd8fb8bea38e6df3e5ea5 Mon Sep 17 00:00:00 2001
From: Milan Malfait <milan.malfait94@gmail.com>
Date: Wed, 3 May 2023 17:19:27 +0100
Subject: [PATCH 13/47] Also test that `manage_deps()` plays nice with Python
 integration

---
 tests/testthat/test-manage_deps.R | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index eae7f41c5..2416b6d18 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -207,3 +207,31 @@ test_that("update_cache() will update old package versions", {
 
 })
 
+
+test_that("manage_deps() does not overwrite requirements.txt", {
+  old_wd <- setwd(lsn)
+  withr::defer(setwd(old_wd))
+
+  ## Set up Python and manually add requirements.txt without actually installing
+  ## the Python package, mimicking the scenario where a Python dependency is missing
+  use_python(lsn, type = "virtualenv")
+  req_file <- fs::path(lsn, "requirements.txt")
+  writeLines("numpy", req_file)
+
+  res <- manage_deps(lsn, quiet = TRUE)
+  expect_true(grepl("^numpy", readLines(req_file)))
+})
+
+
+test_that("manage_deps() restores Python dependencies", {
+  old_wd <- setwd(lsn)
+  withr::defer(setwd(old_wd))
+  use_python(lsn, type = "virtualenv")
+
+  req_file <- fs::path(lsn, "requirements.txt")
+  writeLines("numpy", req_file)
+  res <- manage_deps(lsn, quiet = TRUE)
+
+  expect_no_error({numpy <- reticulate::import("numpy")})
+  expect_s3_class(numpy, "python.builtin.module")
+})

From 1dd787a98e54e69f2aa9c5c732d61d4abe1b90cc Mon Sep 17 00:00:00 2001
From: zkamvar <zkamvar@users.noreply.github.com>
Date: Wed, 3 May 2023 17:31:47 +0000
Subject: [PATCH 14/47] Document

---
 man/build_episode_html.Rd | 6 +++---
 man/build_episode_md.Rd   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/man/build_episode_html.Rd b/man/build_episode_html.Rd
index 90a2df67f..978bb7c8e 100644
--- a/man/build_episode_html.Rd
+++ b/man/build_episode_html.Rd
@@ -57,7 +57,7 @@ they are doing.
 if (FALSE) {
 # 2022-04-15: this suddenly started throwing a check error
 # that says "connections left open: (file) and I can't figure out where the
-# hell its coming from, so I'm just going to not run this :( 
+# hell its coming from, so I'm just going to not run this :(
 if (.Platform$OS.type == "windows") {
   options("sandpaper.use_renv" = FALSE)
 }
@@ -78,7 +78,7 @@ if (rmarkdown::pandoc_available("2.11")) {
 fun_file <- file.path(tmp, "episodes", "files", "fun.Rmd")
 txt <- c(
  "---\ntitle: Fun times\n---\n\n",
- "# new page\n", 
+ "# new page\n",
  "This is coming from `r R.version.string`\n",
  "::: testimonial\n\n#### testimony!\n\nwhat\n:::\n"
 )
@@ -92,7 +92,7 @@ if (rmarkdown::pandoc_available("2.11")) {
   sandpaper:::set_globals(res)
   on.exit(clear_globals(), add = TRUE)
   # we can only build this if we have pandoc
-  build_episode_html(res, path_src = fun_file, 
+  build_episode_html(res, path_src = fun_file,
     pkg = pkgdown::as_pkgdown(file.path(tmp, "site"))
   )
 }
diff --git a/man/build_episode_md.Rd b/man/build_episode_md.Rd
index e34d3972f..f41af81a8 100644
--- a/man/build_episode_md.Rd
+++ b/man/build_episode_md.Rd
@@ -62,7 +62,7 @@ fun_file <- file.path(fun_dir, "episodes", "fun.Rmd")
 file.create(fun_file)
 txt <- c(
  "---\ntitle: Fun times\n---\n\n",
- "# new page\n", 
+ "# new page\n",
  "This is coming from `r R.version.string`"
 )
 writeLines(txt, fun_file)

From df07005341aa3e569984625373e4fe1119f4ec60 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 22 May 2023 11:35:53 +0100
Subject: [PATCH 15/47] Refactor: move reticulate installation to separate
 helper

---
 R/use_python.R | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/R/use_python.R b/R/use_python.R
index a9b6e33b9..238d46dc4 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -51,18 +51,20 @@ use_python <- function(path = ".", python = NULL,
   on.exit({
     invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
     setwd(wd)
-  }, add = TRUE)
+  }, add = TRUE, after = FALSE)
 
   ## Set up working directory, avoids some renv side effects
   setwd(path)
   renv::load(project = path)
   prof <- Sys.getenv("RENV_PROFILE")
 
+  install_reticulate(path = path)
   renv::use_python(python = python, type = type, ...)
 
   ## NOTE: use_python() deactivates the default profile, see https://github.com/rstudio/renv/issues/1217
   ## Workaround: re-activate the profile
   renv::activate(project = path, profile = prof)
+  invisible(path)
 }
 
 
@@ -83,17 +85,27 @@ py_install <- function(packages, path = ".",  ...) {
 
   ## Load the renv profile, unloading it upon exit
   renv::load(project = path)
+
   on.exit({
     invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
-  }, add = TRUE)
+  }, add = TRUE, after = FALSE)
 
-  has_reticulate <- rlang::is_installed("reticulate")
-  if (!has_reticulate) {
-    cli::cli_alert("Adding `reticulate` as a dependency for Python package installation")
-    renv::install("reticulate")
-  }
+  install_reticulate(path = path)
   reticulate::py_install(packages = packages, ...)
 
   cli::cli_alert("Updating the package cache")
   renv::snapshot(lockfile = renv::paths$lockfile(project = path), prompt = FALSE)
 }
+
+install_reticulate <- function(path) {
+  renv_lib <- renv::paths$library(project = path)
+  has_reticulate <- require("reticulate", lib.loc = renv_lib, quietly = TRUE, character.only = TRUE)
+  if (!has_reticulate) {
+    cli::cli_alert("Adding `reticulate` as a dependency")
+    ## Force reticulate to be recorded by renv
+    dep_file <- fs::path(path, "dependencies.R")
+    write("library(reticulate)", file = dep_file, append = TRUE)
+    renv::install("reticulate", library = renv_lib)
+  }
+  invisible(NULL)
+}

From 7deb07df3997e770ab6d39b7eeb875a0a7a706b5 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 22 May 2023 11:36:52 +0100
Subject: [PATCH 16/47] Improve tests, add helpers to manage renv during
 testing

---
 tests/testthat/helper-python.R   | 31 +++++++++++++++++++++++++++++++
 tests/testthat/test-use_python.R | 29 ++++++++++++++++-------------
 2 files changed, 47 insertions(+), 13 deletions(-)
 create mode 100644 tests/testthat/helper-python.R

diff --git a/tests/testthat/helper-python.R b/tests/testthat/helper-python.R
new file mode 100644
index 000000000..c75f50d59
--- /dev/null
+++ b/tests/testthat/helper-python.R
@@ -0,0 +1,31 @@
+## Helpers to temporarily load renv environment
+local_load_py_pkg <- function(lsn, package) {
+  local_renv_load(lsn)
+  reticulate::import(package)
+}
+
+## These helpers are used in `test-use_python.R`, they are implemented separately to ensure the
+## temporary loading of the renv environment doesn't interfere with the testing environment
+check_reticulate <- function(lsn) {
+  local_renv_load(lsn)
+  lib <- renv::paths$library(project = lsn)
+  withr::local_libpaths(lib)
+  rlang::is_installed("reticulate")
+}
+
+check_reticulate_config <- function(lsn) {
+  local_renv_load(lsn)
+  reticulate::py_config()
+}
+
+get_renv_env <- function(lsn, which = "RETICULATE_PYTHON") {
+  local_renv_load(lsn)
+  Sys.getenv(which)
+}
+
+## Temporarily load a renv profile, unloading it upon exit
+local_renv_load <- function(lsn, env = parent.frame()) {
+  ## NOTE: renv:::unload() is currently not exported: https://github.com/rstudio/renv/issues/1285
+  withr::defer(renv:::unload(project = lsn), envir = env)
+  renv::load(lsn)
+}
diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index d49e599f4..3f5cf79eb 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -1,36 +1,39 @@
+## Set up temporary lesson with Python installed, for use in all subsequent tests
 lsn <- restore_fixture()
-old_wd  <- setwd(lsn)
-withr::defer(setwd(old_wd))
-
-use_python(lsn, type = "virtualenv")
-
+lsn <- use_python(lsn)
 
 test_that("use_python() adds Python environment", {
   py_path <- fs::path(lsn, "renv/profiles/lesson-requirements/renv/python")
-
   expect_true(fs::dir_exists(py_path))
-  expect_false(Sys.getenv("RETICULATE_PYTHON") == "")
-  py_config <- reticulate::py_config()
+})
+
+test_that("reticulate is installed", {
+  has_reticulate <- check_reticulate(lsn)
+  expect_true(has_reticulate)
+})
+
+test_that("use_python() sets reticulate configuration", {
+  reticulate_python_env <- get_renv_env(lsn, "RETICULATE_PYTHON")
+  py_config <- check_reticulate_config(lsn)
+
+  expect_false(reticulate_python_env == "")
   expect_true(py_config$available)
   expect_true(py_config$forced == "RETICULATE_PYTHON")
 })
 
+
 ## This relates to a bug in renv, see https://github.com/rstudio/renv/issues/1217
 test_that("use_python() does not remove renv/profile", {
   expect_true(fs::file_exists(fs::path(lsn, "renv/profile")))
 })
 
-
 test_that("py_install() installs Python packages", {
   py_install("numpy", path = lsn)
+  numpy <- local_load_py_pkg(lsn, "numpy")
 
   expect_no_error({numpy <- reticulate::import("numpy")})
   expect_s3_class(numpy, "python.builtin.module")
-})
-
 
-test_that("py_install() updates requirements.txt", {
-  py_install("numpy", path = lsn)
   req_file <- fs::path(lsn, "requirements.txt")
   expect_true(grepl("^numpy", readLines(req_file)))
 })

From ac15e6c78a207dbc89d1ba0707c8db34f3daf917 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 22 May 2023 11:47:27 +0100
Subject: [PATCH 17/47] Use `requireNamespace()` instead of `require()`

---
 R/use_python.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/use_python.R b/R/use_python.R
index 238d46dc4..cadc51ea1 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -99,7 +99,7 @@ py_install <- function(packages, path = ".",  ...) {
 
 install_reticulate <- function(path) {
   renv_lib <- renv::paths$library(project = path)
-  has_reticulate <- require("reticulate", lib.loc = renv_lib, quietly = TRUE, character.only = TRUE)
+  has_reticulate <- requireNamespace("reticulate", lib.loc = renv_lib, quietly = TRUE)
   if (!has_reticulate) {
     cli::cli_alert("Adding `reticulate` as a dependency")
     ## Force reticulate to be recorded by renv

From 2df6d49fa971a47d45ba30081997e3ce07abbc35 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 22 May 2023 11:59:35 +0100
Subject: [PATCH 18/47] Set dev version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4cd8bec7b..729e415c1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sandpaper
 Title: Create and Curate Carpentries Lessons
-Version: 0.12.0
+Version: 0.12.0.9000
 Authors@R: c(
     person(given = "Zhian N.",
            family = "Kamvar",

From d096467966b4a8c1674b9e3d892eed405e18e2ca Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 22 May 2023 12:25:39 +0100
Subject: [PATCH 19/47] Skip `manage_deps()` tests on Windows

---
 tests/testthat/test-manage_deps.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 1f3cbe21c..0f6bf0b99 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -216,6 +216,9 @@ test_that("update_cache() will update old package versions", {
 
 
 test_that("manage_deps() does not overwrite requirements.txt", {
+  skip_on_cran()
+  skip_on_os("windows")
+
   old_wd <- setwd(lsn)
   withr::defer(setwd(old_wd))
 
@@ -231,6 +234,9 @@ test_that("manage_deps() does not overwrite requirements.txt", {
 
 
 test_that("manage_deps() restores Python dependencies", {
+  skip_on_cran()
+  skip_on_os("windows")
+
   old_wd <- setwd(lsn)
   withr::defer(setwd(old_wd))
   use_python(lsn, type = "virtualenv")

From fde134bbe2d1eaef0d368ebd3201ef38a49b531b Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Wed, 7 Jun 2023 11:30:16 +0100
Subject: [PATCH 20/47] Skip `use_python` tests on Windows

Not sure why they are not working. Assuming it has to do with renv.
---
 tests/testthat/test-use_python.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index 3f5cf79eb..81261bdcb 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -3,6 +3,7 @@ lsn <- restore_fixture()
 lsn <- use_python(lsn)
 
 test_that("use_python() adds Python environment", {
+  skip_on_os("windows")
   py_path <- fs::path(lsn, "renv/profiles/lesson-requirements/renv/python")
   expect_true(fs::dir_exists(py_path))
 })
@@ -13,6 +14,7 @@ test_that("reticulate is installed", {
 })
 
 test_that("use_python() sets reticulate configuration", {
+  skip_on_os("windows")
   reticulate_python_env <- get_renv_env(lsn, "RETICULATE_PYTHON")
   py_config <- check_reticulate_config(lsn)
 
@@ -24,10 +26,12 @@ test_that("use_python() sets reticulate configuration", {
 
 ## This relates to a bug in renv, see https://github.com/rstudio/renv/issues/1217
 test_that("use_python() does not remove renv/profile", {
+  skip_on_os("windows")
   expect_true(fs::file_exists(fs::path(lsn, "renv/profile")))
 })
 
 test_that("py_install() installs Python packages", {
+  skip_on_os("windows")
   py_install("numpy", path = lsn)
   numpy <- local_load_py_pkg(lsn, "numpy")
 

From 680c74e9ba1b5de309bd15e1ada3e9d38c10786c Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Thu, 8 Jun 2023 16:15:08 +0100
Subject: [PATCH 21/47] Check that reticulate can be installed and warn if it
 does not

---
 R/use_python.R                    | 15 ++++++++++++++-
 tests/testthat/test-manage_deps.R |  3 +++
 tests/testthat/test-use_python.R  | 14 ++++++++++++++
 3 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/R/use_python.R b/R/use_python.R
index cadc51ea1..3f5dcf648 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -100,7 +100,8 @@ py_install <- function(packages, path = ".",  ...) {
 install_reticulate <- function(path) {
   renv_lib <- renv::paths$library(project = path)
   has_reticulate <- requireNamespace("reticulate", lib.loc = renv_lib, quietly = TRUE)
-  if (!has_reticulate) {
+  reticulate_installable <- check_reticulate_installable()
+  if (!has_reticulate && reticulate_installable) {
     cli::cli_alert("Adding `reticulate` as a dependency")
     ## Force reticulate to be recorded by renv
     dep_file <- fs::path(path, "dependencies.R")
@@ -109,3 +110,15 @@ install_reticulate <- function(path) {
   }
   invisible(NULL)
 }
+
+check_reticulate_installable <- function() {
+  r_compatible <- is_r_version_greater_than(minimal_major = 4)
+  if (!r_compatible) {
+    cli::cli_warn("R version {minimal_major}.0 or higher is required for reticulate")
+  }
+  r_compatible
+}
+
+is_r_version_greater_than <- function(minimal_major = 4) {
+  R.version$major >= minimal_major
+}
diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 0f6bf0b99..d1f74f4a3 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -214,8 +214,10 @@ test_that("update_cache() will update old package versions", {
 
 })
 
+reticulate_installable <- check_reticulate_installable()
 
 test_that("manage_deps() does not overwrite requirements.txt", {
+  skip_if_not(reticulate_installable, "reticulate is not installable")
   skip_on_cran()
   skip_on_os("windows")
 
@@ -234,6 +236,7 @@ test_that("manage_deps() does not overwrite requirements.txt", {
 
 
 test_that("manage_deps() restores Python dependencies", {
+  skip_if_not(reticulate_installable, "reticulate is not installable")
   skip_on_cran()
   skip_on_os("windows")
 
diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index 81261bdcb..a5940b912 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -2,6 +2,10 @@
 lsn <- restore_fixture()
 lsn <- use_python(lsn)
 
+suppressWarnings({
+  reticulate_installable <- check_reticulate_installable()
+})
+
 test_that("use_python() adds Python environment", {
   skip_on_os("windows")
   py_path <- fs::path(lsn, "renv/profiles/lesson-requirements/renv/python")
@@ -9,10 +13,18 @@ test_that("use_python() adds Python environment", {
 })
 
 test_that("reticulate is installed", {
+  skip_if_not(reticulate_installable, "reticulate is not installable")
   has_reticulate <- check_reticulate(lsn)
   expect_true(has_reticulate)
 })
 
+test_that("A warning is generated when reticulate is not installable", {
+  skip_if(reticulate_installable, "reticulate is installable")
+  expect_warning(install_reticulate(lsn))
+  has_reticulate <- check_reticulate(lsn)
+  expect_false(has_reticulate)
+})
+
 test_that("use_python() sets reticulate configuration", {
   skip_on_os("windows")
   reticulate_python_env <- get_renv_env(lsn, "RETICULATE_PYTHON")
@@ -31,7 +43,9 @@ test_that("use_python() does not remove renv/profile", {
 })
 
 test_that("py_install() installs Python packages", {
+  skip_if_not(reticulate_installable, "reticulate is not installable")
   skip_on_os("windows")
+
   py_install("numpy", path = lsn)
   numpy <- local_load_py_pkg(lsn, "numpy")
 

From da24671e40431f31eda1ec816046125ae5d8c17f Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Thu, 8 Jun 2023 17:31:18 +0100
Subject: [PATCH 22/47] Small bug fix

---
 R/use_python.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/use_python.R b/R/use_python.R
index 3f5dcf648..889108639 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -112,7 +112,8 @@ install_reticulate <- function(path) {
 }
 
 check_reticulate_installable <- function() {
-  r_compatible <- is_r_version_greater_than(minimal_major = 4)
+  minimal_major <- 4
+  r_compatible <- is_r_version_greater_than(minimal_major = minimal_major)
   if (!r_compatible) {
     cli::cli_warn("R version {minimal_major}.0 or higher is required for reticulate")
   }

From a589e1c522918af907670b7a9e21b90386424624 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Wed, 14 Jun 2023 09:16:11 +0100
Subject: [PATCH 23/47] Add `use_python` to pkgdown config

---
 _pkgdown.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 104d19518..6088974c3 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -18,7 +18,7 @@ code:
 reference:
  - title: "Lesson Creation"
    desc: >
-     Provision new lessons and/or episodes. These functions will likely only 
+     Provision new lessons and/or episodes. These functions will likely only
      be used once.
  - contents:
    - create_lesson
@@ -35,7 +35,7 @@ reference:
  - title: "Lesson Development Helpers"
    desc: >
      Functions to programmatically assess and modify configuration and source
-     elements of a lesson. These are often used when developing a lesson. 
+     elements of a lesson. These are often used when developing a lesson.
  - contents:
    - get_drafts
    - get_config
@@ -50,7 +50,7 @@ reference:
    - strip_prefix
  - title: "The Pacakge Cache"
    desc: >
-     Lessons with generated content (R Markdown lessons) have an extra file 
+     Lessons with generated content (R Markdown lessons) have an extra file
      called `renv/profiles/lesson-requirments/renv.lock` that records the
      package versions used to build the lesson. These functions provide ways for
      you to manage these packages and turn it on or off while previewing the
@@ -58,6 +58,7 @@ reference:
  - contents:
    - use_package_cache
    - manage_deps
+   - use_python
  - title: "Updating Lesson Tools"
    desc: >
      Lesson updates will happen automatically on a regular schedule on GitHub.
@@ -78,7 +79,7 @@ reference:
    - ci_session_info
    - git_worktree_setup
  - title: "[Internal] Build Components"
-   desc: > 
+   desc: >
      Individual components to provision files and build a lesson locally
  - contents:
    - this_lesson
@@ -131,4 +132,3 @@ articles:
  - title: "In Progress"
    contents:
    - articles/internationalisation
-

From 69c62b7d3eb91551161cd0b4354fcc83929db4c4 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 19 Jun 2023 11:42:58 +0200
Subject: [PATCH 24/47] Get R CMD check to succeed on `oldrel-4`

---
 tests/testthat/test-use_python.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index a5940b912..88612ea9e 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -27,6 +27,7 @@ test_that("A warning is generated when reticulate is not installable", {
 
 test_that("use_python() sets reticulate configuration", {
   skip_on_os("windows")
+  skip_if_not(reticulate_installable, "reticulate is not installable")
   reticulate_python_env <- get_renv_env(lsn, "RETICULATE_PYTHON")
   py_config <- check_reticulate_config(lsn)
 

From 9f99900f820a80b20d2ac5cc81a047333f256b92 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 23 Oct 2023 11:44:18 +0100
Subject: [PATCH 25/47] Make sure the correct project is loaded in renv

---
 R/use_python.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/use_python.R b/R/use_python.R
index 889108639..3a48c1b1b 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -55,7 +55,7 @@ use_python <- function(path = ".", python = NULL,
 
   ## Set up working directory, avoids some renv side effects
   setwd(path)
-  renv::load(project = path)
+  renv::load(project = ".") # load the default renv profile from the working directory
   prof <- Sys.getenv("RENV_PROFILE")
 
   install_reticulate(path = path)

From 5869aaf491dcd4cfaeeb3f9b8e86289c76a5bc27 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 14:20:52 +0000
Subject: [PATCH 26/47] Tests: add `with_renv_profile()` helper

Allows running relevant checks with the test lesson's renv profile.
---
 tests/testthat/helper-python.R | 47 +++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 21 deletions(-)

diff --git a/tests/testthat/helper-python.R b/tests/testthat/helper-python.R
index c75f50d59..ef5ad7df8 100644
--- a/tests/testthat/helper-python.R
+++ b/tests/testthat/helper-python.R
@@ -1,31 +1,36 @@
-## Helpers to temporarily load renv environment
-local_load_py_pkg <- function(lsn, package) {
-  local_renv_load(lsn)
-  reticulate::import(package)
-}
-
 ## These helpers are used in `test-use_python.R`, they are implemented separately to ensure the
 ## temporary loading of the renv environment doesn't interfere with the testing environment
+
+## Allows running relevant checks with the test lesson's renv profile
+with_renv_profile <- function(path, code, profile = "lesson-requirements", ...) {
+  path <- normalizePath(path)
+  code <- rlang::enexpr(code)
+  callr::r(
+    func = function(path, code) {
+      setwd(path)
+      renv::load(path)
+      eval(code)
+    },
+    args = list(path = path, code = code),
+    env = c(callr::rcmd_safe_env(), "RENV_PROFILE" = profile),
+    ...
+  )
+}
+
+get_renv_env <- function(lsn, which = "RETICULATE_PYTHON") {
+  which <- rlang::enexpr(which)
+  with_renv_profile(lsn, Sys.getenv(!!which))
+}
+
 check_reticulate <- function(lsn) {
-  local_renv_load(lsn)
-  lib <- renv::paths$library(project = lsn)
-  withr::local_libpaths(lib)
-  rlang::is_installed("reticulate")
+  with_renv_profile(lsn, rlang::is_installed("reticulate"))
 }
 
 check_reticulate_config <- function(lsn) {
-  local_renv_load(lsn)
-  reticulate::py_config()
+  with_renv_profile(lsn, reticulate::py_config())
 }
 
-get_renv_env <- function(lsn, which = "RETICULATE_PYTHON") {
-  local_renv_load(lsn)
-  Sys.getenv(which)
+local_load_py_pkg <- function(lsn, package) {
+  with_renv_profile(lsn, reticulate::import(package))
 }
 
-## Temporarily load a renv profile, unloading it upon exit
-local_renv_load <- function(lsn, env = parent.frame()) {
-  ## NOTE: renv:::unload() is currently not exported: https://github.com/rstudio/renv/issues/1285
-  withr::defer(renv:::unload(project = lsn), envir = env)
-  renv::load(lsn)
-}

From 0ebc409c6aadb0692c4c47785fe7e460a192fdc1 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 15:41:30 +0000
Subject: [PATCH 27/47] Add option to open lesson project in `use_python()`

---
 R/create_lesson.R | 2 +-
 R/use_python.R    | 9 ++++++++-
 man/use_python.Rd | 3 +++
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/R/create_lesson.R b/R/create_lesson.R
index 963e537da..b134bb501 100644
--- a/R/create_lesson.R
+++ b/R/create_lesson.R
@@ -106,7 +106,7 @@ create_lesson <- function(path, name = fs::path_file(path), rmd = TRUE, rstudio
 
     if (add_python) {
       cli::cli_status_update("{cli::symbol$arrow_right} Setting up Python ...")
-      use_python(path = path, python = python, type = type)
+      use_python(path = path, python = python, type = type, open = FALSE)
     }
   }
 
diff --git a/R/use_python.R b/R/use_python.R
index 3a48c1b1b..6e76dce13 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -5,6 +5,7 @@
 #'
 #' @param path path to the current project
 #' @inheritParams renv::use_python
+#' @param open if interactive, the lesson will open in a new editor window.
 #' @param ... Further arguments to be passed on to [renv::use_python()]
 #'
 #' @details
@@ -43,7 +44,8 @@
 #' py_install("numpy")
 #' }
 use_python <- function(path = ".", python = NULL,
-                       type = c("auto", "virtualenv", "conda", "system"), ...) {
+                       type = c("auto", "virtualenv", "conda", "system"),
+                       open = rlang::is_interactive(), ...) {
 
   wd <- getwd()
 
@@ -64,6 +66,11 @@ use_python <- function(path = ".", python = NULL,
   ## NOTE: use_python() deactivates the default profile, see https://github.com/rstudio/renv/issues/1217
   ## Workaround: re-activate the profile
   renv::activate(project = path, profile = prof)
+  if (open) {
+    if (usethis::proj_activate(path)) {
+      on.exit()
+    }
+  }
   invisible(path)
 }
 
diff --git a/man/use_python.Rd b/man/use_python.Rd
index f6ce78715..898da81bd 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -9,6 +9,7 @@ use_python(
   path = ".",
   python = NULL,
   type = c("auto", "virtualenv", "conda", "system"),
+  open = rlang::is_interactive(),
   ...
 )
 
@@ -23,6 +24,8 @@ py_install(packages, path = ".", ...)
 \item{type}{The type of Python environment to use. When \code{"auto"} (the default),
 virtual environments will be used.}
 
+\item{open}{if interactive, the lesson will open in a new editor window.}
+
 \item{...}{Further arguments to be passed to \code{\link[reticulate:py_install]{reticulate::py_install()}}}
 
 \item{packages}{Python packages to be installed as a character vecto.}

From bd6249231c61dd866c94d0b804357f3133808e85 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 15:44:54 +0000
Subject: [PATCH 28/47] Add `with_renv_factory()` helper

---
 R/utils-renv.R           | 29 +++++++++++++++++++++++++++++
 man/with_renv_factory.Rd | 28 ++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 man/with_renv_factory.Rd

diff --git a/R/utils-renv.R b/R/utils-renv.R
index b9470511e..c9839eb0e 100644
--- a/R/utils-renv.R
+++ b/R/utils-renv.R
@@ -313,3 +313,32 @@ callr_manage_deps <- function(path, repos, snapshot, lockfile_exists) {
   }
   return(NULL)
 }
+
+#' Generate a function to run in a renv profile
+#'
+#' This is a [Function operator](https://adv-r.hadley.nz/function-operators.html) which will
+#' generate a function that will run in a renv profile. This is useful for running code in a
+#' separate R subprocess with [`callr::r()`], to avoid *renv* side effects related to interactive
+#' sessions.
+#'
+#' @param func The function to be evaluated after loading the renv environment.
+#' @param renv_path The path to the renv environment to load. Usually a directory created by
+#'   [`create_lesson()`]
+#' @param renv_profile Optional profile to load. Defaults to "lesson-requirements".
+#' @param ... Additional arguments to be passed to `func`.
+#'
+#' @return The result of evaluating `func(...)` after loading the renv environment.
+#'
+#' @keywords internal
+with_renv_factory <- function(func, renv_path, renv_profile = "lesson-requirements") {
+  force(func); force(renv_path); force(renv_profile)
+
+  function(...) {
+    renv_path <- normalizePath(renv_path)
+    withr::local_dir(renv_path)
+    withr::local_envvar(c("RENV_PROFILE" = renv_profile))
+    renv::load(renv_path)
+
+    func(...)
+  }
+}
diff --git a/man/with_renv_factory.Rd b/man/with_renv_factory.Rd
new file mode 100644
index 000000000..2faa358ec
--- /dev/null
+++ b/man/with_renv_factory.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils-renv.R
+\name{with_renv_factory}
+\alias{with_renv_factory}
+\title{Generate a function to run in a renv profile}
+\usage{
+with_renv_factory(func, renv_path, renv_profile = "lesson-requirements")
+}
+\arguments{
+\item{func}{The function to be evaluated after loading the renv environment.}
+
+\item{renv_path}{The path to the renv environment to load. Usually a directory created by
+\code{\link[=create_lesson]{create_lesson()}}}
+
+\item{renv_profile}{Optional profile to load. Defaults to "lesson-requirements".}
+
+\item{...}{Additional arguments to be passed to \code{func}.}
+}
+\value{
+The result of evaluating \code{func(...)} after loading the renv environment.
+}
+\description{
+This is a \href{https://adv-r.hadley.nz/function-operators.html}{Function operator} which will
+generate a function that will run in a renv profile. This is useful for running code in a
+separate R subprocess with \code{\link[callr:r]{callr::r()}}, to avoid \emph{renv} side effects related to interactive
+sessions.
+}
+\keyword{internal}

From 3a629cd6723c8bc4abb31e07f0b1881d8ab53487 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 15:45:36 +0000
Subject: [PATCH 29/47] Refactor `use_python` functions to use
 `with_renv_factory()`

Avoids renv side effects when running in interactive sessions
---
 R/use_python.R | 88 ++++++++++++++++++++++++++++++--------------------
 1 file changed, 53 insertions(+), 35 deletions(-)

diff --git a/R/use_python.R b/R/use_python.R
index 6e76dce13..17c8fd287 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -47,25 +47,30 @@ use_python <- function(path = ".", python = NULL,
                        type = c("auto", "virtualenv", "conda", "system"),
                        open = rlang::is_interactive(), ...) {
 
-  wd <- getwd()
+  ## Make sure reticulate is installed
+  install_reticulate(path = path)
 
-  ## Load the renv profile, unloading it upon exit
-  on.exit({
-    invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
-    setwd(wd)
-  }, add = TRUE, after = FALSE)
+  ## Generate function to run in separate R process
+  use_python_with_renv <- function(path, python, type, ...) {
+    prof <- Sys.getenv("RENV_PROFILE")
+    renv::use_python(project = path, python = python, type = type, ...)
 
-  ## Set up working directory, avoids some renv side effects
-  setwd(path)
-  renv::load(project = ".") # load the default renv profile from the working directory
-  prof <- Sys.getenv("RENV_PROFILE")
+    ## NOTE: use_python() deactivates the default profile,
+    ## see https://github.com/rstudio/renv/issues/1217
+    ## Workaround: re-activate the profile
+    renv::activate(project = path, profile = prof)
+  }
+  callr_use_python <- with_renv_factory(use_python_with_renv,
+    renv_path = path, renv_profile = "lesson-requirements"
+  )
 
-  install_reticulate(path = path)
-  renv::use_python(python = python, type = type, ...)
+  ## Run in separate R process
+  callr::r(
+    func = function(f, path, python, type,  ...) f(path = path, python = python , type = type, ...),
+    args = list(f = callr_use_python, path = path, python = python, type = type, ...),
+    show = TRUE
+  )
 
-  ## NOTE: use_python() deactivates the default profile, see https://github.com/rstudio/renv/issues/1217
-  ## Workaround: re-activate the profile
-  renv::activate(project = path, profile = prof)
   if (open) {
     if (usethis::proj_activate(path)) {
       on.exit()
@@ -90,32 +95,45 @@ use_python <- function(path = ".", python = NULL,
 #' @rdname use_python
 py_install <- function(packages, path = ".",  ...) {
 
-  ## Load the renv profile, unloading it upon exit
-  renv::load(project = path)
+  ## Ensure reticulate is installed
+  install_reticulate(path = path)
 
-  on.exit({
-    invisible(utils::capture.output(renv::deactivate(project = path), type = "message"))
-  }, add = TRUE, after = FALSE)
+  py_install_with_renv <- function(packages, ...) {
+    reticulate::py_install(packages = packages, ...)
+    cli::cli_alert("Updating the package cache")
+    renv::snapshot(prompt = FALSE)
+  }
+  callr_py_install <- with_renv_factory(py_install_with_renv,
+    renv_path = path, renv_profile = "lesson-requirements"
+  )
 
-  install_reticulate(path = path)
-  reticulate::py_install(packages = packages, ...)
+  ## Run in separate R process
+  callr::r(
+    func = function(f, packages) f(packages = packages),
+    args = list(f = callr_py_install, packages = packages),
+    show = TRUE
+  )
 
-  cli::cli_alert("Updating the package cache")
-  renv::snapshot(lockfile = renv::paths$lockfile(project = path), prompt = FALSE)
+  invisible(TRUE)
 }
 
-install_reticulate <- function(path) {
-  renv_lib <- renv::paths$library(project = path)
-  has_reticulate <- requireNamespace("reticulate", lib.loc = renv_lib, quietly = TRUE)
-  reticulate_installable <- check_reticulate_installable()
-  if (!has_reticulate && reticulate_installable) {
-    cli::cli_alert("Adding `reticulate` as a dependency")
-    ## Force reticulate to be recorded by renv
-    dep_file <- fs::path(path, "dependencies.R")
-    write("library(reticulate)", file = dep_file, append = TRUE)
-    renv::install("reticulate", library = renv_lib)
+
+## Helper to install reticulate in the lesson's renv environment and record it as a dependency
+install_reticulate <- function(path, quiet = FALSE) {
+
+  if (!check_reticulate_installable()) {
+    cli::cli_alert("`reticulate` can not be installed on this system. Skipping installation.")
+    return(invisible(FALSE))
   }
-  invisible(NULL)
+
+  ## Record reticulate as a dependency for renv
+  dep_file <- fs::path(path, "dependencies.R")
+  write("library(reticulate)", file = dep_file, append = TRUE)
+
+  ## Install reticulate through manage_deps()
+  manage_deps(path = path, quiet = quiet)
+
+  invisible(TRUE)
 }
 
 check_reticulate_installable <- function() {

From 4833219130cd611115a09832f2955a7cf0ee9e29 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 15:46:31 +0000
Subject: [PATCH 30/47] Bug fix for `local_load_py_pkg()`; need to unquote
 argument

---
 tests/testthat/helper-python.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/helper-python.R b/tests/testthat/helper-python.R
index ef5ad7df8..c3d782f42 100644
--- a/tests/testthat/helper-python.R
+++ b/tests/testthat/helper-python.R
@@ -31,6 +31,7 @@ check_reticulate_config <- function(lsn) {
 }
 
 local_load_py_pkg <- function(lsn, package) {
-  with_renv_profile(lsn, reticulate::import(package))
+  package <- rlang::enexpr(package)
+  with_renv_profile(lsn, reticulate::import(!!package))
 }
 

From fab1a3a88453f90cee8642b4354936e70c0cf28d Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 30 Oct 2023 16:13:38 +0000
Subject: [PATCH 31/47] Load Python packages from renv environment in tests

---
 tests/testthat/test-manage_deps.R | 4 +---
 tests/testthat/test-use_python.R  | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 4d64e35b0..5ce75c138 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -240,14 +240,12 @@ test_that("manage_deps() restores Python dependencies", {
   skip_on_cran()
   skip_on_os("windows")
 
-  old_wd <- setwd(lsn)
-  withr::defer(setwd(old_wd))
   use_python(lsn, type = "virtualenv")
 
   req_file <- fs::path(lsn, "requirements.txt")
   writeLines("numpy", req_file)
   res <- manage_deps(lsn, quiet = TRUE)
 
-  expect_no_error({numpy <- reticulate::import("numpy")})
+  expect_no_error({numpy <- local_load_py_pkg(lsn, "numpy")})
   expect_s3_class(numpy, "python.builtin.module")
 })
diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index 88612ea9e..d97ac8a34 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -50,7 +50,7 @@ test_that("py_install() installs Python packages", {
   py_install("numpy", path = lsn)
   numpy <- local_load_py_pkg(lsn, "numpy")
 
-  expect_no_error({numpy <- reticulate::import("numpy")})
+  expect_no_error({numpy <- local_load_py_pkg(lsn, "numpy")})
   expect_s3_class(numpy, "python.builtin.module")
 
   req_file <- fs::path(lsn, "requirements.txt")

From e7fe19668670f2c53541931853fbaab7382d693d Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Tue, 7 Nov 2023 15:18:34 +0000
Subject: [PATCH 32/47] Create pull.yml

---
 .github/pull.yml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .github/pull.yml

diff --git a/.github/pull.yml b/.github/pull.yml
new file mode 100644
index 000000000..ca7d27801
--- /dev/null
+++ b/.github/pull.yml
@@ -0,0 +1,8 @@
+version: "1"
+rules:
+  - base: main
+    upstream: carpentries:main
+    mergeMethod: hardreset
+    mergeUnstable: false
+label: ":arrow_heading_down: pull"  # Optional
+conflictLabel: "merge-conflict"     # Optional, on merge conflict assign a custom label, Default: merge-conflict

From 694f66d8c094794d6e73589b7b41cb1eb6b53d0d Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Thu, 16 Nov 2023 12:18:32 +0100
Subject: [PATCH 33/47] Use default pull config

---
 .github/pull.yml | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 .github/pull.yml

diff --git a/.github/pull.yml b/.github/pull.yml
deleted file mode 100644
index ca7d27801..000000000
--- a/.github/pull.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-version: "1"
-rules:
-  - base: main
-    upstream: carpentries:main
-    mergeMethod: hardreset
-    mergeUnstable: false
-label: ":arrow_heading_down: pull"  # Optional
-conflictLabel: "merge-conflict"     # Optional, on merge conflict assign a custom label, Default: merge-conflict

From 6360ece023dfccca619a8b02531fbfee15df726a Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 4 Dec 2023 22:08:25 +0000
Subject: [PATCH 34/47] Fix `manage_deps()` Python-related tests

Activate Python outside of `test_that()` blocks
---
 tests/testthat/test-manage_deps.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 5ce75c138..d3e5e60f7 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -215,6 +215,7 @@ test_that("update_cache() will update old package versions", {
 })
 
 reticulate_installable <- check_reticulate_installable()
+use_python(lsn, type = "virtualenv", open = FALSE)
 
 test_that("manage_deps() does not overwrite requirements.txt", {
   skip_if_not(reticulate_installable, "reticulate is not installable")
@@ -226,7 +227,6 @@ test_that("manage_deps() does not overwrite requirements.txt", {
 
   ## Set up Python and manually add requirements.txt without actually installing
   ## the Python package, mimicking the scenario where a Python dependency is missing
-  use_python(lsn, type = "virtualenv")
   req_file <- fs::path(lsn, "requirements.txt")
   writeLines("numpy", req_file)
 
@@ -240,8 +240,6 @@ test_that("manage_deps() restores Python dependencies", {
   skip_on_cran()
   skip_on_os("windows")
 
-  use_python(lsn, type = "virtualenv")
-
   req_file <- fs::path(lsn, "requirements.txt")
   writeLines("numpy", req_file)
   res <- manage_deps(lsn, quiet = TRUE)

From 32593ed969e02f879cd73819e2e4c81698fb9412 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Tue, 5 Dec 2023 15:59:51 +0000
Subject: [PATCH 35/47] Allow for multiple lines in `requirements.txt` during
 tests

---
 tests/testthat/test-manage_deps.R | 4 +++-
 tests/testthat/test-use_python.R  | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index d3e5e60f7..da2769d40 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -228,10 +228,11 @@ test_that("manage_deps() does not overwrite requirements.txt", {
   ## Set up Python and manually add requirements.txt without actually installing
   ## the Python package, mimicking the scenario where a Python dependency is missing
   req_file <- fs::path(lsn, "requirements.txt")
+  if (file.exists(req_file)) fs::file_delete(req_file)
   writeLines("numpy", req_file)
 
   res <- manage_deps(lsn, quiet = TRUE)
-  expect_true(grepl("^numpy", readLines(req_file)))
+  expect_true(grepl("^numpy", readLines(req_file))[1])
 })
 
 
@@ -241,6 +242,7 @@ test_that("manage_deps() restores Python dependencies", {
   skip_on_os("windows")
 
   req_file <- fs::path(lsn, "requirements.txt")
+  if (file.exists(req_file)) fs::file_delete(req_file)
   writeLines("numpy", req_file)
   res <- manage_deps(lsn, quiet = TRUE)
 
diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index d97ac8a34..5258b353e 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -54,5 +54,5 @@ test_that("py_install() installs Python packages", {
   expect_s3_class(numpy, "python.builtin.module")
 
   req_file <- fs::path(lsn, "requirements.txt")
-  expect_true(grepl("^numpy", readLines(req_file)))
+  expect_true(any(grepl("^numpy", readLines(req_file))))
 })

From 57923a854620f6079322bde9fa5fc171c5ff5a9f Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Thu, 7 Mar 2024 18:24:16 +0000
Subject: [PATCH 36/47] Minor test fixes

Correctly check for lines in `requirements.txt`
---
 tests/testthat/test-manage_deps.R | 5 +++--
 tests/testthat/test-use_python.R  | 9 ++++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index da2769d40..7cb82b03f 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -229,10 +229,11 @@ test_that("manage_deps() does not overwrite requirements.txt", {
   ## the Python package, mimicking the scenario where a Python dependency is missing
   req_file <- fs::path(lsn, "requirements.txt")
   if (file.exists(req_file)) fs::file_delete(req_file)
-  writeLines("numpy", req_file)
+  numpy_version <- "numpy==1.26.4"
+  writeLines(numpy_version, req_file)
 
   res <- manage_deps(lsn, quiet = TRUE)
-  expect_true(grepl("^numpy", readLines(req_file))[1])
+  expect_true(numpy_version %in% readLines(req_file))
 })
 
 
diff --git a/tests/testthat/test-use_python.R b/tests/testthat/test-use_python.R
index 5258b353e..5afbd5021 100644
--- a/tests/testthat/test-use_python.R
+++ b/tests/testthat/test-use_python.R
@@ -47,12 +47,15 @@ test_that("py_install() installs Python packages", {
   skip_if_not(reticulate_installable, "reticulate is not installable")
   skip_on_os("windows")
 
-  py_install("numpy", path = lsn)
+  numpy_version <- "numpy==1.26.4"
+  py_install(numpy_version, path = lsn)
   numpy <- local_load_py_pkg(lsn, "numpy")
 
-  expect_no_error({numpy <- local_load_py_pkg(lsn, "numpy")})
+  expect_no_error({
+    numpy <- local_load_py_pkg(lsn, "numpy")
+  })
   expect_s3_class(numpy, "python.builtin.module")
 
   req_file <- fs::path(lsn, "requirements.txt")
-  expect_true(any(grepl("^numpy", readLines(req_file))))
+  expect_true(numpy_version %in% readLines(req_file))
 })

From 857421b01849355f0d8aa94f79c27d6ec948f725 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 3 Jun 2024 18:03:50 +0100
Subject: [PATCH 37/47] Add `quiet` option for `use_python`

---
 R/use_python.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/use_python.R b/R/use_python.R
index 17c8fd287..ec7601fdc 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -45,10 +45,10 @@
 #' }
 use_python <- function(path = ".", python = NULL,
                        type = c("auto", "virtualenv", "conda", "system"),
-                       open = rlang::is_interactive(), ...) {
+                       open = rlang::is_interactive(), ..., quiet = FALSE) {
 
   ## Make sure reticulate is installed
-  install_reticulate(path = path)
+  install_reticulate(path = path, quiet = quiet)
 
   ## Generate function to run in separate R process
   use_python_with_renv <- function(path, python, type, ...) {
@@ -68,7 +68,7 @@ use_python <- function(path = ".", python = NULL,
   callr::r(
     func = function(f, path, python, type,  ...) f(path = path, python = python , type = type, ...),
     args = list(f = callr_use_python, path = path, python = python, type = type, ...),
-    show = TRUE
+    show = !quiet
   )
 
   if (open) {

From fe9311dba2e505a3d175ba21be1e50a02b504a33 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Mon, 3 Jun 2024 18:04:10 +0100
Subject: [PATCH 38/47] Test that `update_cache()` doesn't remove Python
 dependencies

---
 tests/testthat/test-manage_deps.R | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 7cb82b03f..07e9ec21f 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -215,7 +215,7 @@ test_that("update_cache() will update old package versions", {
 })
 
 reticulate_installable <- check_reticulate_installable()
-use_python(lsn, type = "virtualenv", open = FALSE)
+use_python(lsn, type = "virtualenv", open = FALSE, quiet = TRUE)
 
 test_that("manage_deps() does not overwrite requirements.txt", {
   skip_if_not(reticulate_installable, "reticulate is not installable")
@@ -250,3 +250,16 @@ test_that("manage_deps() restores Python dependencies", {
   expect_no_error({numpy <- local_load_py_pkg(lsn, "numpy")})
   expect_s3_class(numpy, "python.builtin.module")
 })
+
+
+test_that("update_cache does not remove uninstalled Python dependencies from requirements.txt", {
+  skip_if_not(reticulate_installable, "reticulate is not installable")
+  skip_on_cran()
+  skip_on_os("windows")
+
+  req_file <- fs::path(lsn, "requirements.txt")
+  writeLines("imnotinstalled", req_file)
+
+  res <- update_cache(lsn, prompt = FALSE, quiet = TRUE)
+  expect_true("imnotinstalled" %in% readLines(req_file))
+})

From 5893b4d409e6d0f00a56c8226cf92a309f5dfbdc Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Tue, 4 Jun 2024 12:45:21 +0100
Subject: [PATCH 39/47] Use a real Python package to test `update_cache()`

---
 tests/testthat/test-manage_deps.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 07e9ec21f..f80467f01 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -258,8 +258,8 @@ test_that("update_cache does not remove uninstalled Python dependencies from req
   skip_on_os("windows")
 
   req_file <- fs::path(lsn, "requirements.txt")
-  writeLines("imnotinstalled", req_file)
+  writeLines("pandas", req_file)
 
   res <- update_cache(lsn, prompt = FALSE, quiet = TRUE)
-  expect_true("imnotinstalled" %in% readLines(req_file))
+  expect_true("pandas" %in% readLines(req_file))
 })

From 61192277548c81eaa7112962d77dcd5670724877 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Tue, 4 Jun 2024 12:46:00 +0100
Subject: [PATCH 40/47] Make sure current requirements are installed before
 updating cache

Fixes https://github.com/LearnToDiscover/sandpaper/issues/68
---
 R/manage_deps.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/manage_deps.R b/R/manage_deps.R
index 8a65efcbf..91b6c90e3 100644
--- a/R/manage_deps.R
+++ b/R/manage_deps.R
@@ -112,6 +112,11 @@ update_cache <- function(path = ".", profile = "lesson-requirements", prompt = i
     Sys.setenv("RENV_PROFILE" = prof)
   }, add = TRUE)
   Sys.setenv("RENV_PROFILE" = profile)
+
+  # Make sure the current requirements are installed, this also avoids removing any uninstalled
+  # Python dependencies in requirements.txt
+  manage_deps(path = path, profile = profile, snapshot = snapshot, quiet = quiet)
+
   renv::load(project = path)
   lib <- renv::paths$library(project = path)
   if (prompt) {

From 2131f99f88ba03d090142a65cffaab270153036d Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Thu, 6 Jun 2024 15:38:13 +0100
Subject: [PATCH 41/47] Don't overwrite existing `requirements.txt` file in
 tests

---
 tests/testthat/test-manage_deps.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index f80467f01..7303e058b 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -258,8 +258,9 @@ test_that("update_cache does not remove uninstalled Python dependencies from req
   skip_on_os("windows")
 
   req_file <- fs::path(lsn, "requirements.txt")
-  writeLines("pandas", req_file)
+  write("pandas", req_file, append = TRUE, sep = "\n")
 
   res <- update_cache(lsn, prompt = FALSE, quiet = TRUE)
-  expect_true("pandas" %in% readLines(req_file))
+  print(readLines(req_file))
+  expect_true(any(grepl("pandas", readLines(req_file))))
 })

From d28e74a72dca8279fcb487b71f983e2acc4f4cde Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 16:04:22 +0100
Subject: [PATCH 42/47] Make sure `with_renv_factory` deactivates renv upon
 completion

---
 R/utils-renv.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/utils-renv.R b/R/utils-renv.R
index c9839eb0e..81cbbd880 100644
--- a/R/utils-renv.R
+++ b/R/utils-renv.R
@@ -314,6 +314,7 @@ callr_manage_deps <- function(path, repos, snapshot, lockfile_exists) {
   return(NULL)
 }
 
+
 #' Generate a function to run in a renv profile
 #'
 #' This is a [Function operator](https://adv-r.hadley.nz/function-operators.html) which will
@@ -334,6 +335,9 @@ with_renv_factory <- function(func, renv_path, renv_profile = "lesson-requiremen
   force(func); force(renv_path); force(renv_profile)
 
   function(...) {
+    on.exit({
+      invisible(utils::capture.output(renv::deactivate(project = renv_path), type = "message"))
+    }, add = TRUE)
     renv_path <- normalizePath(renv_path)
     withr::local_dir(renv_path)
     withr::local_envvar(c("RENV_PROFILE" = renv_profile))
@@ -342,3 +346,5 @@ with_renv_factory <- function(func, renv_path, renv_profile = "lesson-requiremen
     func(...)
   }
 }
+
+

From 94c5c9cd36f5af5b1d1d35c228a0d2a5c87d1d10 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 16:06:00 +0100
Subject: [PATCH 43/47] Refactor `update_cache()` to use `with_renv_factory()`

---
 R/manage_deps.R | 45 ++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 40 insertions(+), 5 deletions(-)

diff --git a/R/manage_deps.R b/R/manage_deps.R
index 91b6c90e3..e046f6ace 100644
--- a/R/manage_deps.R
+++ b/R/manage_deps.R
@@ -104,23 +104,31 @@ manage_deps <- function(path = ".", profile = "lesson-requirements", snapshot =
 #'   if it's running in an interactive session.
 #' @rdname dependency_management
 #' @export
-update_cache <- function(path = ".", profile = "lesson-requirements", prompt = interactive(), quiet = !prompt, snapshot = TRUE) {
-  path <- root_path(path)
+update_cache <- function(path = ".", profile = "lesson-requirements", prompt = interactive(),
+                         quiet = !prompt, snapshot = TRUE) {
+
   prof <- Sys.getenv("RENV_PROFILE")
   on.exit({
-    invisible(utils::capture.output(renv::deactivate(path), type = "message"))
     Sys.setenv("RENV_PROFILE" = prof)
   }, add = TRUE)
   Sys.setenv("RENV_PROFILE" = profile)
+  path <- root_path(path)
 
   # Make sure the current requirements are installed, this also avoids removing any uninstalled
   # Python dependencies in requirements.txt
   manage_deps(path = path, profile = profile, snapshot = snapshot, quiet = quiet)
 
-  renv::load(project = path)
   lib <- renv::paths$library(project = path)
+  updates <- callr::r(
+    func = function(f, lib) f(lib),
+    args = list(
+      f = with_renv_factory(check_for_updates, renv_path = path, renv_profile = profile),
+      lib = lib
+    ),
+    show = !quiet
+  )
+
   if (prompt) {
-    updates <- renv::update(library = lib, check = TRUE, prompt = TRUE)
     if (isTRUE(updates)) {
       return(invisible())
     }
@@ -140,6 +148,33 @@ update_cache <- function(path = ".", profile = "lesson-requirements", prompt = i
       return(invisible())
     }
   }
+
+  sho <- !(quiet || identical(Sys.getenv("TESTTHAT"), "true"))
+  out <- callr::r(
+    func = function(f, path, lib, snapshot) f(path, lib, snapshot),
+    args = list(
+      f = with_renv_factory(callr_update_cache, renv_path = path, renv_profile = profile),
+      path = path,
+      lib = lib,
+      snapshot = snapshot
+    ),
+    show = !quiet,
+    spinner = sho,
+    user_profile = FALSE,
+    env = c(callr::rcmd_safe_env(),
+      "R_PROFILE_USER" = fs::path(tempfile(), "nada"),
+      "RENV_CONFIG_CACHE_SYMLINKS" = renv_cache_available()
+    )
+  )
+  invisible(out)
+}
+
+check_for_updates <- function(lib) {
+  cli::cli_alert("Checking for updates")
+  renv::update(library = lib, check = TRUE, prompt = TRUE)
+}
+
+callr_update_cache <- function(path, lib, snapshot) {
   updates <- renv::update(library = lib, prompt = FALSE)
   if (snapshot) {
     renv::snapshot(lockfile = renv::paths$lockfile(project = path), prompt = FALSE)

From 46318692d6706ea6f92576d6fb8ae5c5cd5d37ef Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 16:06:39 +0100
Subject: [PATCH 44/47] Clean up tests

---
 tests/testthat/test-manage_deps.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 7303e058b..08b565592 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -206,10 +206,13 @@ test_that("update_cache() will update old package versions", {
   skip_if_offline()
   skip_if(covr::in_covr())
 
+  pkg <- "sessioninfo"
+  old_pkg_version <- "1.1.0"
+  pin_version(glue::glue("{pkg}@{old_pkg_version}"), path = fs::path(lsn, "episodes"))
 
   res <- update_cache(path = fs::path(lsn, "episodes"), prompt = FALSE, quiet = FALSE)
   expect_true(
-    package_version(res$sessioninfo$Version) > package_version("1.1.0")
+    package_version(res[[pkg]]$Version) > package_version(old_pkg_version)
   )
 
 })
@@ -260,7 +263,6 @@ test_that("update_cache does not remove uninstalled Python dependencies from req
   req_file <- fs::path(lsn, "requirements.txt")
   write("pandas", req_file, append = TRUE, sep = "\n")
 
-  res <- update_cache(lsn, prompt = FALSE, quiet = TRUE)
-  print(readLines(req_file))
+  res <- update_cache(lsn, prompt = FALSE, quiet = FALSE)
   expect_true(any(grepl("pandas", readLines(req_file))))
 })

From 3540c9929036ba3eb6ed81c5b66d490925afce51 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 16:21:22 +0100
Subject: [PATCH 45/47] roxygenise

---
 DESCRIPTION            | 2 +-
 NAMESPACE              | 1 +
 man/known_languages.Rd | 1 +
 man/template.Rd        | 3 +++
 man/use_python.Rd      | 3 ++-
 man/yaml_list.Rd       | 4 +++-
 6 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ff9c775bb..cbb361b71 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -108,7 +108,7 @@ Config/testthat/parallel: false
 Config/Needs/check: rstudio/renv
 Config/potools/style: explicit
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://carpentries.github.io/sandpaper/, https://github.com/carpentries/sandpaper/, https://carpentries.github.io/workbench/
 BugReports: https://github.com/carpentries/sandpaper/issues/
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 6d9062aa8..e0ade642d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -38,6 +38,7 @@ export(set_instructors)
 export(set_learners)
 export(set_profiles)
 export(strip_prefix)
+export(template_citation)
 export(template_conduct)
 export(template_config)
 export(template_contributing)
diff --git a/man/known_languages.Rd b/man/known_languages.Rd
index 4ee2b95b7..0fcef5554 100644
--- a/man/known_languages.Rd
+++ b/man/known_languages.Rd
@@ -22,6 +22,7 @@ details of how to do so in the source code for {sandpaper}.
 
 \if{html}{\out{<div class="sourceCode">}}\preformatted{#> - en
 #> - es
+#> - fr
 #> - ja
 #> - uk
 }\if{html}{\out{</div>}}
diff --git a/man/template.Rd b/man/template.Rd
index 72f4105d7..1f1f23a2b 100644
--- a/man/template.Rd
+++ b/man/template.Rd
@@ -4,6 +4,7 @@
 \alias{template_gitignore}
 \alias{template_episode}
 \alias{template_links}
+\alias{template_citation}
 \alias{template_config}
 \alias{template_conduct}
 \alias{template_index}
@@ -23,6 +24,8 @@ template_episode()
 
 template_links()
 
+template_citation()
+
 template_config()
 
 template_conduct()
diff --git a/man/use_python.Rd b/man/use_python.Rd
index 898da81bd..71fd912e0 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -10,7 +10,8 @@ use_python(
   python = NULL,
   type = c("auto", "virtualenv", "conda", "system"),
   open = rlang::is_interactive(),
-  ...
+  ...,
+  quiet = FALSE
 )
 
 py_install(packages, path = ".", ...)
diff --git a/man/yaml_list.Rd b/man/yaml_list.Rd
index aea4ad033..c6edd157c 100644
--- a/man/yaml_list.Rd
+++ b/man/yaml_list.Rd
@@ -25,7 +25,9 @@ cat(yaml::as.yaml(hx)) # representation in yaml
 #> - a
 #> - b
 #> - c
-cat(whisker::whisker.render("hello: \{\{hello\}\}", hx)) # messed up whisker
+}\if{html}{\out{</div>}}
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{cat(whisker::whisker.render("hello: \{\{hello\}\}", hx)) # messed up whisker
 #> hello: a,b,c
 }\if{html}{\out{</div>}}
 

From 2330acd9f472f15a62fb26235cd403f5964da077 Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 16:33:28 +0100
Subject: [PATCH 46/47] Add mising param doc

---
 R/use_python.R    | 1 +
 man/use_python.Rd | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/R/use_python.R b/R/use_python.R
index ec7601fdc..6f6db95bf 100644
--- a/R/use_python.R
+++ b/R/use_python.R
@@ -6,6 +6,7 @@
 #' @param path path to the current project
 #' @inheritParams renv::use_python
 #' @param open if interactive, the lesson will open in a new editor window.
+#' @param quiet if `TRUE`, suppresses output.
 #' @param ... Further arguments to be passed on to [renv::use_python()]
 #'
 #' @details
diff --git a/man/use_python.Rd b/man/use_python.Rd
index 71fd912e0..177995e78 100644
--- a/man/use_python.Rd
+++ b/man/use_python.Rd
@@ -29,6 +29,8 @@ virtual environments will be used.}
 
 \item{...}{Further arguments to be passed to \code{\link[reticulate:py_install]{reticulate::py_install()}}}
 
+\item{quiet}{if \code{TRUE}, suppresses output.}
+
 \item{packages}{Python packages to be installed as a character vecto.}
 }
 \value{

From 71432420dac388037d3353d50ffb5c5bb5eff73d Mon Sep 17 00:00:00 2001
From: Milan Malfait <m.malfait@ucl.ac.uk>
Date: Fri, 7 Jun 2024 17:43:53 +0100
Subject: [PATCH 47/47] Use smaller Python package to speed up test

---
 tests/testthat/test-manage_deps.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-manage_deps.R b/tests/testthat/test-manage_deps.R
index 08b565592..576f6b7b7 100644
--- a/tests/testthat/test-manage_deps.R
+++ b/tests/testthat/test-manage_deps.R
@@ -261,8 +261,8 @@ test_that("update_cache does not remove uninstalled Python dependencies from req
   skip_on_os("windows")
 
   req_file <- fs::path(lsn, "requirements.txt")
-  write("pandas", req_file, append = TRUE, sep = "\n")
+  write("art", req_file, append = TRUE, sep = "\n")
 
   res <- update_cache(lsn, prompt = FALSE, quiet = FALSE)
-  expect_true(any(grepl("pandas", readLines(req_file))))
+  expect_true(any(grepl("art", readLines(req_file))))
 })