More work on release procedure

extras/Releasing/PackageCheckFunctions.R

@@ -39,7 +39,8 @@ checkPackage <- function(package, inCran) {
     sourcePackage <- remotes::download_version(package, type = "source")
     on.exit(unlink(sourcePackage))
   } else {
-    sourcePackage <- remotes::remote_download(remotes::github_remote(sprintf("%s/%s", gitHubOrganization, package)))
+    ref <- sprintf("v%s", packageVersion(package))
+    sourcePackage <- remotes::remote_download(remotes::github_remote(repo = sprintf("%s/%s", gitHubOrganization, package), ref = ref))
     on.exit(unlink(sourcePackage))
   } 
   sourceFolder <- tempfile(pattern = package)
@@ -51,6 +52,7 @@ checkPackage <- function(package, inCran) {
   if (dir.exists(docDir)) {
     unlink(docDir, recursive = TRUE)
   }
+  # devtools::check_built(path = sourcePath)
   rcmdcheck::rcmdcheck(path = sourcePath, args = c("--no-manual", "--no-multiarch"), error_on = "warning")
 }
 

extras/Releasing/RunCheckOnAllHadesPackages.R

@@ -2,17 +2,15 @@
 
 install.packages("rcmdcheck")
 
+reticulate::use_virtualenv("r-reticulate")
+
 source("PackageCheckFunctions.R")
 saveRDS(prepareForPackageCheck(), "Dependencies.rds")
 dependencies <- readRDS("Dependencies.rds")
 # Skipping Hydra, as renv seems to clash with skeleton renv environments:
 dependencies <- dependencies[dependencies$name != "Hydra", ]
-for (i in 25:nrow(dependencies)) {
-  if (dependencies$name[i] == "CohortGenerator") {
-    # Delete RedShift files from JDBC drivers folder, at least until this is released: https://github.com/OHDSI/DatabaseConnector/commit/c7e3e9b8dab2b04bebadfcf34f2049a23de66dac
-    toDelete <- list.files(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), "Redshift", full.names = TRUE)
-    unlink(toDelete, force = TRUE)
-  }
+for (i in 1:nrow(dependencies)) {
   checkPackage(package = dependencies$name[i], inCran = dependencies$inCran[i])
+
 }
 unlink("Dependencies.rds")

extras/Releasing/SetupPython.R

@@ -1,42 +1,17 @@
-# Code to work around renv bugs relating to Python
+# Code to install Python dependencies. Does not use conda as it was throwing inexplicable errors
 
-# Install all required dependencies --------------------------------------------
-packages <- c("scikit-survival","numpy","scipy","scikit-learn", "pandas","pydotplus","joblib", "sklearn-json")
-reticulate::conda_install(
-  envname='base', 
-  packages = packages, 
-  forge = TRUE, 
-  pip = FALSE, 
-  pip_ignore_installed = TRUE, 
-  conda = "auto"
-)
-reticulate::conda_install(
-  envname='r-reticulate', 
-  packages = packages, 
-  forge = TRUE, 
-  pip = FALSE, 
-  pip_ignore_installed = TRUE, 
-  conda = "auto"
-  )
-reticulate::use_condaenv("base")
-torch::install_torch()
-reticulate::use_condaenv("r-reticulate")
-torch::install_torch()
+# Install packages needed by PatientLevelPrediction ----------------------------
+PatientLevelPrediction::configurePython(envname = 'r-reticulate', envtype = "python")
+reticulate::use_virtualenv("r-reticulate")
+# Test:  np <- reticulate::import('numpy')
 
-# Copy Python from global to renv ----------------------------------------------
+# Packages needed by DeepPatientLevelPrediction --------------------------------
+reticulate::py_install(c("polars", "tqdm", "connectorx", "scikit-learn", "pyarrow"))
+reticulate::py_install("torch")
+# Test: torch <- reticulate::import('torch')
+pyarrow <- reticulate::import('pyarrow')
 
-# Under some (poorly understood) circumstances, reticulate creates a duplicate
-# r-reticulate environment. Use this code to copy all libraries from the main one
-# to the new one:
-envs <- reticulate::conda_list()
-envs <- envs[envs$name == 'r-reticulate', ]
-message(sprintf("Good r-reticulate: %s", envs$python[1]))
-message(sprintf("Evil r-reticulate: %s", envs$python[2]))
-# TODO: this somehow creates a r-reticulate folder in the r-reticulate folder. Need to fix
-unlink(dirname(envs$python[2]), recursive = TRUE)
-dir.create(dirname(envs$python[2]))
-file.copy(
-  from = dirname(envs$python[1]),
-  to = dirname(envs$python[2]),
-  recursive = TRUE
-)
+# reticulate::virtualenv_remove("r-reticulate")
+
+reticulate::virtualenv_list()
+reticulate::virtualenv_root()