Merge branch 'main' into 2146_compute_tmf_bug

.github/workflows/templates.yml

@@ -1,17 +1,17 @@
----
 name: Check Templates
 
 on:
   workflow_dispatch:
   pull_request:
     branches:
       - main
-      - patch
+      - devel
 
 jobs:
   templates:
     name: Check Templates
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
-    if: github.event_name == 'pull_request'
+    secrets: inherit
     with:
       r-version: "4.1"
+      push-templates-data: true

inst/templates/ad_adae.R

@@ -133,5 +133,9 @@ adae <- adae %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adae, file = file.path(dir, "adae.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adae, file = file.path(dir, "adae.rda"), compress = "bzip2")

inst/templates/ad_adcm.R

@@ -138,5 +138,9 @@ adcm <- adcm %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adcm, file = file.path(dir, "adcm.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adcm, file = file.path(dir, "adcm.rda"), compress = "bzip2")

inst/templates/ad_adeg.R

@@ -330,5 +330,9 @@ adeg <- adeg %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adeg, file = file.path(dir, "adeg.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adeg, file = file.path(dir, "adeg.rda"), compress = "bzip2")

inst/templates/ad_adex.R

@@ -302,5 +302,9 @@ adex <- adex %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adex, file = file.path(dir, "adex.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adex, file = file.path(dir, "adex.rda"), compress = "bzip2")

inst/templates/ad_adlb.R

@@ -441,5 +441,9 @@ adlb <- adlb %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adlb, file = file.path(dir, "adlb.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adlb, file = file.path(dir, "adlb.rda"), compress = "bzip2")

inst/templates/ad_adlbhy.R

@@ -88,3 +88,10 @@ hylaw_params <- derive_param_exist_flag(
 # Row bind back to relevant adlb-like dataset
 adlbhy <- adlb_annotated %>%
   bind_rows(hylaw_params)
+
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adlbhy, file = file.path(dir, "adlbhy.rda"), compress = "bzip2")

inst/templates/ad_admh.R

@@ -169,5 +169,9 @@ admh <- admh %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(admh, file = file.path(dir, "admh.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(admh, file = file.path(dir, "admh.rda"), compress = "bzip2")

inst/templates/ad_adpc.R

@@ -502,5 +502,9 @@ adpc <- adpc_baselines %>%
 # ...
 # ---- Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adpc, file = file.path(dir, "adpc.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adpc, file = file.path(dir, "adcp.rda"), compress = "bzip2")

inst/templates/ad_adpp.R

@@ -153,5 +153,9 @@ adpp <- adpp_avisit %>%
 # ...
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adpp, file = file.path(dir, "adpp.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adpp, file = file.path(dir, "adpp.rda"), compress = "bzip2")

inst/templates/ad_adppk.R

@@ -461,5 +461,9 @@ adppk <- adppk_aseq %>%
 # ...
 # ---- Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adppk, file = file.path(dir, "adppk.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adppk, file = file.path(dir, "adppk.rda"), compress = "bzip2")

inst/templates/ad_adsl.R

@@ -239,5 +239,9 @@ adsl <- adsl %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(adsl, file = file.path(dir, "adsl.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(adsl, file = file.path(dir, "adsl.rda"), compress = "bzip2")

inst/templates/ad_advs.R

@@ -294,5 +294,9 @@ advs <- advs %>%
 
 # Save output ----
 
-dir <- tempdir() # Change to whichever directory you want to save the dataset in
-saveRDS(advs, file = file.path(dir, "advs.rds"), compress = "bzip2")
+dir <- file.path(getwd(), "tmp")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir)
+}
+save(advs, file = file.path(dir, "advs.rda"), compress = "bzip2")