Closes #58 fixed appendix

.github/workflows/publish.yml

@@ -41,7 +41,8 @@ jobs:
             xportr
             pharmaverseadam
             link
-
+            sessioninfo
+
 
       - name: Install tinytex
         run: quarto install tool tinytex

R/appendix.R

@@ -1,9 +1,10 @@
+
 # markdown helpers --------------------------------------------------------
 
-markdown_appendix <- function(name, content) {
+markdown_appendix <- function (name, content) {
   paste(paste("##", name, "{.appendix}"), " ", content, sep = "\n")
 }
-markdown_link <- function(text, path) {
+markdown_link <- function (text, path) {
   paste0("[", text, "](", path, ")")
 }
 
@@ -57,7 +58,7 @@ 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") {
   appendices <- paste(
     markdown_appendix(
       name = "Last updated",
@@ -69,8 +70,7 @@ insert_appendix <- function(repo_spec, name, collection = "posts") {
       content = paste(
         insert_source(repo_spec, name, collection),
         insert_lockfile(repo_spec, name, collection),
-        sep = ", "
-      )
+        sep = ", ")
     ),
     sep = "\n"
   )

_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:

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))
   }

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 +49,11 @@ 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) {
+  # write session info to txt
+  session_info <- sessionInfo()
+  writeLines(capture.output(session_info), con = "session_info.txt")
+
   appendices <- paste(
     markdown_appendix(
       name = "Last updated",
@@ -67,7 +63,8 @@ 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 = ", "
       )

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()
 )
 ```

posts/2023-10-30_floating_point/session_info.txt

@@ -0,0 +1,25 @@
+R version 4.3.1 (2023-06-16)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Ubuntu 22.04.3 LTS
+
+Matrix products: default
+BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
+ [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+
+time zone: Etc/UTC
+tzcode source: system (glibc)
+
+attached base packages:
+[1] stats     graphics  grDevices datasets  utils     methods   base     
+
+other attached packages:
+[1] dplyr_1.1.3
+
+loaded via a namespace (and not attached):
+ [1] utf8_1.2.3        R6_2.5.1          lubridate_1.9.3   tidyselect_1.2.0  xfun_0.40         magrittr_2.0.3    glue_1.6.2        stringr_1.5.0     tibble_3.2.1      knitr_1.44        pkgconfig_2.0.3  
+[12] timechange_0.2.0  generics_0.1.3    lifecycle_1.0.3   cli_3.6.1         fansi_1.0.5       sessioninfo_1.2.2 vctrs_0.6.3       renv_1.0.3        compiler_4.3.1    rprojroot_2.0.3   here_1.0.1       
+[23] purrr_1.0.2       rstudioapi_0.15.0 tools_4.3.1       pillar_1.9.0      yaml_2.3.7        rlang_1.1.1       fs_1.6.3          stringi_1.7.12   

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()
+```