From eb10dcf837ee83d5d1b262c514ca531ba64167b7 Mon Sep 17 00:00:00 2001
From: StefanThoma <40463122+StefanThoma@users.noreply.github.com>
Date: Thu, 2 May 2024 15:37:59 +0200
Subject: [PATCH] Closes #58 fixed appendix (#152)

* added session info and fixed link to source

* fix category extraction, not sure what for

* added session info site

* CICD checks fixed

* remove session info at post level

* update to include roxygen

* added spell_check

* added spell_check

* fix

* update workflow

* new spell check workflow

* UPDATE WORKFLOW

* fix styling

* delete other spell check
---
 .github/workflows/publish.yml                 |  4 +++-
 .github/workflows/spellcheck.yml              |  4 ++++
 _quarto.yml                                   |  2 ++
 index.qmd                                     |  4 ++--
 inst/WORDLIST.txt                             |  4 ++++
 posts/2023-10-30_floating_point/appendix.R    | 21 +++++++------------
 .../floating_point.qmd                        |  4 +++-
 session_info.qmd                              |  9 ++++++++
 8 files changed, 34 insertions(+), 18 deletions(-)
 create mode 100644 session_info.qmd

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 2e393cbf..0a1ee4bf 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -41,7 +41,9 @@ jobs:
             xportr
             pharmaverseadam
             link
-            
+            sessioninfo
+            roxygen2
+
 
       - name: Install tinytex
         run: quarto install tool tinytex
diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml
index 43cb4c01..2c382002 100644
--- a/.github/workflows/spellcheck.yml
+++ b/.github/workflows/spellcheck.yml
@@ -13,6 +13,10 @@ jobs:
         run: if (!require("spelling")) install.packages("spelling")
         shell: Rscript {0}
 
+      - name: Install roxygen2
+        run: if (!require("roxygen2")) install.packages("roxygen2")
+        shell: Rscript {0}
+
       - name: Run Spelling Check test
         run: spelling::spell_check_files(list.files(pattern = ".*.qmd$", recursive = TRUE), ignore = readr::read_lines("inst/WORDLIST.txt"))
         shell: Rscript {0}
diff --git a/_quarto.yml b/_quarto.yml
index 7a4f1b2f..98beb36b 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -17,6 +17,8 @@ website:
       - icon: github
         aria-label: github
         href: https://github.com/pharmaverse/blog
+      - text: "Session Info"
+        href: session_info.html
 format:
   html:
     theme:
diff --git a/index.qmd b/index.qmd
index f9b104e0..c88c619a 100644
--- a/index.qmd
+++ b/index.qmd
@@ -27,14 +27,14 @@ posts <- list.dirs(
 )
 
 # extract the slugs
-slugs <- gsub("^.*_", "", posts)
+slugs <- sub(".*?_", "", posts)
 
 # lines to insert to a netlify _redirect file
 post_redirects <- paste0("/", slugs, " ", "/posts/", posts)
 
 # function to extract post categories from index.qmd files
 get_post_categories <- function(post) {
-  file <- here::here("posts", post) |> fs::path("index.qmd")
+  file <- here::here("posts", post) |> list.files(pattern = ".qmd", full.names = TRUE)
   if (!fs::file_exists(file)) {
     return(character(0))
   }
diff --git a/inst/WORDLIST.txt b/inst/WORDLIST.txt
index ca25d01e..a81d5ab5 100644
--- a/inst/WORDLIST.txt
+++ b/inst/WORDLIST.txt
@@ -716,3 +716,7 @@ img
 src
 svg
 wikimedia
+de
+RightTool
+Rlogo
+sessioninfo
diff --git a/posts/2023-10-30_floating_point/appendix.R b/posts/2023-10-30_floating_point/appendix.R
index ece5203f..fe465c37 100644
--- a/posts/2023-10-30_floating_point/appendix.R
+++ b/posts/2023-10-30_floating_point/appendix.R
@@ -15,17 +15,9 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "code_sections.qmd",
-    sep = "/"
-  )
+                          text = "Session info",
+                          file_name) {
+  path <- "https://pharmaverse.github.io/blog/_site/session_info.html"
   return(markdown_link(text, path))
 }
 
@@ -47,7 +39,7 @@ insert_lockfile <- function(repo_spec, name,
     branch,
     collection,
     name,
-    "renv.lock",
+    "session_info.txt",
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -57,7 +49,7 @@ insert_lockfile <- function(repo_spec, name,
 
 # top level function ------------------------------------------------------
 
-insert_appendix <- function(repo_spec, name, collection = "posts") {
+insert_appendix <- function(repo_spec, name, collection = "posts", file_name) {
   appendices <- paste(
     markdown_appendix(
       name = "Last updated",
@@ -67,7 +59,8 @@ insert_appendix <- function(repo_spec, name, collection = "posts") {
     markdown_appendix(
       name = "Details",
       content = paste(
-        insert_source(repo_spec, name, collection),
+        insert_source(repo_spec, name, collection, file_name = file_name),
+        # get renv information,
         insert_lockfile(repo_spec, name, collection),
         sep = ", "
       )
diff --git a/posts/2023-10-30_floating_point/floating_point.qmd b/posts/2023-10-30_floating_point/floating_point.qmd
index 52e43e73..e511e50d 100644
--- a/posts/2023-10-30_floating_point/floating_point.qmd
+++ b/posts/2023-10-30_floating_point/floating_point.qmd
@@ -353,6 +353,8 @@ I.e. `.Machine$double.eps / 1.8` is still detectable, while `.Machine$double.eps
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",
-  name = long_slug
+  name = long_slug,
+  # file_name should be the name of your file
+  file_name = list.files() %>% stringr::str_subset(".qmd") %>% first()
 )
 ```
diff --git a/session_info.qmd b/session_info.qmd
new file mode 100644
index 00000000..301a711e
--- /dev/null
+++ b/session_info.qmd
@@ -0,0 +1,9 @@
+---
+title: "Session Info"
+description: "This page displays the session information for the site."
+---
+
+```{r}
+library(sessioninfo)
+session_info()
+```