Closes 157 fix appendix for all (#162)

* Align tags

* Update templates

* update appendix to all scripts

* update call to appendix functions

* run on branch

* add call to library

* add library call to template

* update wordlist

* added call to dplyr library

* added call to dplyr library

* update all appendices

* added filename

* fixed path

* workflow to main

R/appendix.R

@@ -1,3 +1,4 @@
+library(dplyr)
 # markdown helpers --------------------------------------------------------
 
 markdown_appendix <- function(name, content) {
@@ -15,15 +16,16 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
+                          text = "Source",
+                          file_name) {
   path <- paste(
     host,
     repo_spec,
     "tree",
     branch,
     collection,
     name,
-    "index.qmd",
+    file_name,
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -39,25 +41,17 @@ insert_lockfile <- function(repo_spec, name,
                             collection = "posts",
                             branch = "main",
                             host = "https://github.com",
-                            text = "R environment") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "renv.lock",
-    sep = "/"
-  )
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
   return(markdown_link(text, path))
 }
 
 
 
 # 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 +61,8 @@ 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 = ", "
       )

inst/WORDLIST.txt

@@ -720,3 +720,5 @@ de
 RightTool
 Rlogo
 sessioninfo
+valuelevel
+writeup

inst/template/appendix.R

@@ -1,3 +1,4 @@
+library(dplyr)
 # markdown helpers --------------------------------------------------------
 
 markdown_appendix <- function(name, content) {
@@ -15,15 +16,16 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
+                          text = "Source",
+                          file_name) {
   path <- paste(
     host,
     repo_spec,
     "tree",
     branch,
     collection,
     name,
-    "code_sections.qmd",
+    file_name,
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -39,25 +41,17 @@ insert_lockfile <- function(repo_spec, name,
                             collection = "posts",
                             branch = "main",
                             host = "https://github.com",
-                            text = "R environment") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "renv.lock",
-    sep = "/"
-  )
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
   return(markdown_link(text, path))
 }
 
 
 
 # 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 +61,8 @@ 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 = ", "
       )

inst/template/template.txt

@@ -30,6 +30,8 @@ long_slug <- [SLUG]
 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/2023-06-27__hackathon_app/appendix.R

@@ -1,3 +1,4 @@
+library(dplyr)
 # markdown helpers --------------------------------------------------------
 
 markdown_appendix <- function(name, content) {
@@ -15,15 +16,16 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
+                          text = "Source",
+                          file_name) {
   path <- paste(
     host,
     repo_spec,
     "tree",
     branch,
     collection,
     name,
-    "index.qmd",
+    file_name,
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -39,25 +41,17 @@ insert_lockfile <- function(repo_spec, name,
                             collection = "posts",
                             branch = "main",
                             host = "https://github.com",
-                            text = "R environment") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "renv.lock",
-    sep = "/"
-  )
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
   return(markdown_link(text, path))
 }
 
 
 
 # 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 +61,8 @@ 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/2023-06-27__hackathon_app/index.qmd

@@ -15,7 +15,7 @@ editor:
 <!--------------- my typical setup ----------------->
 
 ```{r setup, include=FALSE}
-long_slug <- "2023-06-19_shiny_run_script"
+long_slug <- "2023-06-27__hackathon_app"
 # renv::use(lockfile = "renv.lock")
 ```
 
@@ -385,6 +385,8 @@ From our perspective, the application provided a great added value to the hackat
 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/2023-06-27_admiral/valuelevel/appendix.R

@@ -1,3 +1,4 @@
+library(dplyr)
 # markdown helpers --------------------------------------------------------
 
 markdown_appendix <- function(name, content) {
@@ -15,15 +16,16 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
+                          text = "Source",
+                          file_name) {
   path <- paste(
     host,
     repo_spec,
     "tree",
     branch,
     collection,
     name,
-    "index.qmd",
+    file_name,
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -39,25 +41,17 @@ insert_lockfile <- function(repo_spec, name,
                             collection = "posts",
                             branch = "main",
                             host = "https://github.com",
-                            text = "R environment") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "renv.lock",
-    sep = "/"
-  )
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
   return(markdown_link(text, path))
 }
 
 
 
 # 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 +61,8 @@ 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/2023-06-27_admiral/valuelevel/derive_param_computed.qmd

@@ -12,7 +12,7 @@ image: "derive_param_computed.jpg"
 <!--------------- my typical setup ----------------->
 
 ```{r setup1, include=FALSE}
-long_slug <- "admiral"
+long_slug <- "2023-06-27_admiral"
 # renv::use(lockfile = "renv.lock")
 ```
 
@@ -103,6 +103,8 @@ diffdf(adex_expected, adex_admiral, keys = c("USUBJID", "PARAMCD"))
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",
-  name = long_slug
+  name = paste0(long_slug, "/valuelevel"),
+  # file_name should be the name of your file
+  file_name = list.files() %>% stringr::str_subset(".qmd") %>% first()
 )
 ```

posts/2023-06-27_hackathon_writeup/appendix.R

@@ -1,3 +1,4 @@
+library(dplyr)
 # markdown helpers --------------------------------------------------------
 
 markdown_appendix <- function(name, content) {
@@ -15,15 +16,16 @@ insert_source <- function(repo_spec, name,
                           collection = "posts",
                           branch = "main",
                           host = "https://github.com",
-                          text = "source code") {
+                          text = "Source",
+                          file_name) {
   path <- paste(
     host,
     repo_spec,
     "tree",
     branch,
     collection,
     name,
-    "index.qmd",
+    file_name,
     sep = "/"
   )
   return(markdown_link(text, path))
@@ -39,25 +41,17 @@ insert_lockfile <- function(repo_spec, name,
                             collection = "posts",
                             branch = "main",
                             host = "https://github.com",
-                            text = "R environment") {
-  path <- paste(
-    host,
-    repo_spec,
-    "tree",
-    branch,
-    collection,
-    name,
-    "renv.lock",
-    sep = "/"
-  )
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
   return(markdown_link(text, path))
 }
 
 
 
 # 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 +61,8 @@ 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/2023-06-27_hackathon_writeup/index.qmd

@@ -12,7 +12,7 @@ image: "community.png"
 <!--------------- my typical setup ----------------->
 
 ```{r setup, include=FALSE}
-long_slug <- "2023-06-19_shiny_run_script"
+long_slug <- "2023-06-27_hackathon_writeup"
 # renv::use(lockfile = "renv.lock")
 ```
 
@@ -186,6 +186,8 @@ Please reach out to [Edoardo Mancini (product owner)](mailto:edoardo.mancini@roc
 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()
 )
 ```