From d10698ce08667b98de0233d8bd907db3ee81bbd2 Mon Sep 17 00:00:00 2001
From: tylermorganwall <tylermorganwall@users.noreply.github.com>
Date: Sun, 18 Feb 2024 22:06:04 -0500
Subject: [PATCH] raymolecule v0.5.3: Add pkgdown helper function to only run
 some code in pkgdown during CRAN check

---
 DESCRIPTION              |  2 +-
 NAMESPACE                |  1 +
 R/get_molecule.R         | 17 +++++++++++------
 R/run_documentation.R    | 13 +++++++++++++
 _pkgdown.yml             |  4 ++++
 man/get_molecule.Rd      | 17 +++++++++++------
 man/run_documentation.Rd | 18 ++++++++++++++++++
 7 files changed, 59 insertions(+), 13 deletions(-)
 create mode 100644 R/run_documentation.R
 create mode 100644 man/run_documentation.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 9afb472..44ccec9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: raymolecule
 Type: Package
 Title: Parse and Render Molecular Structures in 3D
-Version: 0.5.2
+Version: 0.5.3
 Date: 2024-2-18
 Authors@R: c(person("Tyler", "Morgan-Wall", email = "tylermw@gmail.com",
     role = c("aut", "cph", "cre"), comment = c(ORCID = "0000-0002-3131-3814")))
diff --git a/NAMESPACE b/NAMESPACE
index d5c8572..82e3e96 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export(get_molecule)
 export(read_pdb)
 export(read_sdf)
 export(render_model)
+export(run_documentation)
 importFrom(magrittr,"%>%")
 importFrom(rayrender,add_object)
 importFrom(rayrender,glossy)
diff --git a/R/get_molecule.R b/R/get_molecule.R
index 0e9559d..c2905d9 100644
--- a/R/get_molecule.R
+++ b/R/get_molecule.R
@@ -8,28 +8,33 @@
 #' @export
 #'
 #' @examples
-#' \donttest{
+#' if(run_documentation()) {
 #' get_molecule("caffeine") %>%
 #'   generate_full_scene() %>%
 #'   render_model()
-#'
+#' }
+#' if(run_documentation()) {
 #' #estradiol (aka estrogen)
 #' get_molecule(5757) %>%
 #'   generate_full_scene() %>%
 #'   render_model()
-#'
+#' }
+#' if(run_documentation()) {
 #' get_molecule("testosterone") %>%
 #'   generate_full_scene() %>%
 #'   render_model()
-#'
+#' }
+#' if(run_documentation()) {
 #' get_molecule("aspirin") %>%
 #'   generate_full_scene() %>%
 #'   render_model()
-#'
+#' }
+#' if(run_documentation()) {
 #' get_molecule("rutoside") %>%
 #'   generate_full_scene() %>%
 #'   render_model()
-#'
+#' }
+#' if(run_documentation()) {
 #' #If the 3D SDF doesn't exist, this function will pull the 2D SDF and inform the user
 #' get_molecule("cyanocobalamin") %>%
 #'   generate_full_scene() %>%
diff --git a/R/run_documentation.R b/R/run_documentation.R
new file mode 100644
index 0000000..e89f20b
--- /dev/null
+++ b/R/run_documentation.R
@@ -0,0 +1,13 @@
+#' @title Run Documentation
+#'
+#' @description This function determines if the examples are being run in pkgdown. It is not meant to be called by the user.
+#'
+#' @export
+#'
+#' @return Boolean value.
+#' @examples
+#' # See if the documentation should be run.
+#' run_documentation()
+run_documentation = function() {
+  return(identical(Sys.getenv("IN_PKGDOWN"), "true"))
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index a498e98..25d2e31 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -21,6 +21,10 @@ reference:
     desc: "Function to get included example data."
     contents:
       - starts_with("get")
+  - title: "pkgdown utils"
+    desc: "Internal but must be exported to meet CRAN guidelines"
+    contents:
+      - starts_with("run")
 
 navbar:
   title: "raymolecule"
diff --git a/man/get_molecule.Rd b/man/get_molecule.Rd
index 8bd3104..0b4e61b 100644
--- a/man/get_molecule.Rd
+++ b/man/get_molecule.Rd
@@ -16,28 +16,33 @@ List giving the atom locations and the connections between atoms.
 Loads the structure of a molecule by fetching an SDF file from Pubchem, which can be piped to generate_full_scene
 }
 \examples{
-\donttest{
+if(run_documentation()) {
 get_molecule("caffeine") \%>\%
   generate_full_scene() \%>\%
   render_model()
-
+}
+if(run_documentation()) {
 #estradiol (aka estrogen)
 get_molecule(5757) \%>\%
   generate_full_scene() \%>\%
   render_model()
-
+}
+if(run_documentation()) {
 get_molecule("testosterone") \%>\%
   generate_full_scene() \%>\%
   render_model()
-
+}
+if(run_documentation()) {
 get_molecule("aspirin") \%>\%
   generate_full_scene() \%>\%
   render_model()
-
+}
+if(run_documentation()) {
 get_molecule("rutoside") \%>\%
   generate_full_scene() \%>\%
   render_model()
-
+}
+if(run_documentation()) {
 #If the 3D SDF doesn't exist, this function will pull the 2D SDF and inform the user
 get_molecule("cyanocobalamin") \%>\%
   generate_full_scene() \%>\%
diff --git a/man/run_documentation.Rd b/man/run_documentation.Rd
new file mode 100644
index 0000000..c22b8e7
--- /dev/null
+++ b/man/run_documentation.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_documentation.R
+\name{run_documentation}
+\alias{run_documentation}
+\title{Run Documentation}
+\usage{
+run_documentation()
+}
+\value{
+Boolean value.
+}
+\description{
+This function determines if the examples are being run in pkgdown. It is not meant to be called by the user.
+}
+\examples{
+# See if the documentation should be run.
+run_documentation()
+}