Merge pull request #13 from wlandau/12

Use install.libs.R instead of configure

.github/workflows/install-internal.yaml

@@ -9,15 +9,19 @@ jobs:
   install-internal:
     runs-on: ubuntu-latest
 
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v3
 
     - name: Change the script so CmdStan always installs internally.
-      run: sed -i '2s/.*/if (TRUE) {/' inst/cmdstan.R
+      run: sed -i '1s/.*/choice <- "internal"/' src/install.libs.R
 
     - name: Remove GitHub Actions workflow files
-      run: rm -rf .github/workflws
+      run: rm -rf .github/workflows
 
     - name: Deploy to install-internal branch
       if: github.event_name != 'pull_request'

.gitignore

@@ -16,3 +16,5 @@ vignettes/*.html
 revdep
 cmdstan
 *.dll
+Makevars
+Makevars.win

DESCRIPTION

@@ -15,7 +15,7 @@ Description: Similar to 'rstantools' for 'rstan',
   and setting environment variables.
   Packages 'rstantools', 'cmdstanr', 'stannis', and
   'stanapi' are similar Stan clients with different objectives.
-Version: 0.0.4.9000
+Version: 0.0.4.9001
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/instantiate/,
   https://github.com/wlandau/instantiate
@@ -36,7 +36,6 @@ Depends:
   R (>= 4.0.0)
 Imports:
   fs,
-  pkglite,
   rlang,
   utils
 Suggests:
@@ -49,6 +48,7 @@ Suggests:
 Additional_repositories:
   https://mc-stan.org/r-packages/
 SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
+StagedInstall: no
 Encoding: UTF-8
 Language: en-US
 Config/testthat/edition: 3

NAMESPACE

@@ -10,7 +10,6 @@ export(stan_package_create)
 export(stan_package_model)
 export(stan_package_model_files)
 importFrom(fs,dir_copy)
-importFrom(pkglite,unpack)
 importFrom(rlang,abort)
 importFrom(rlang,check_installed)
 importFrom(rlang,inform)

NEWS.md

@@ -1,6 +1,8 @@
-# instantiate 0.0.4.9000 (development)
-
+# instantiate 0.0.4.9001 (development)
 
+* Use `install.libs.R` for both CmdStan in `instantiate` and Stan model compilation in packages (#1, #9, #12).
+* Stan models should now be in `src/stan/` instead of `inst/stan/` (#12). `inst/stan/` should still work for the next few versions, but it is now deprecated. When a modeling package is installed, its `install.libs.R` moves `src/stan/` to `bin/stan/` and then compiles models inside `bin/stan/`.
+* Disable staged installation for `instantiate` itself to help the hard-coded paths in CmdStan work as expected in "internal" installation.
 
 # instantiate 0.0.4
 

R/stan_cmdstan_exists.R

@@ -7,7 +7,7 @@
 #' @examples
 #' stan_cmdstan_exists()
 stan_cmdstan_exists <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL")
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = "")
 ) {
   path <- stan_cmdstan_path(cmdstan_install = cmdstan_install)
   cmdstan_valid(path)

R/stan_cmdstan_path.R

@@ -6,49 +6,50 @@
 #' @return Character of length 1, directory path to CmdStan. The path
 #'   may or may not exist. Returns the empty string `""` if the path
 #'   cannot be determined.
-#' @param cmdstan_install Character of length 1, how CmdStan was installed. The
-#'   installation method determines how `instantiate` looks up CmdStan.
-#'   Set the default value with the `CMDSTAN_INSTALL` environment variable.
+#' @param cmdstan_install Character of length 1, how to look for an installed
+#'   copy of CmdStan. See <https://wlandau.github.io/instantiate/> for details.
 #'   Choices:
-#'   1. `"internal"`: Use the copy of CmdStan installed internally inside the
-#'     `instantiate` package file system. Before using this option,
-#'     CmdStan must be installed in the package file system. To do this,
-#'     set the `CMDSTAN_INSTALL` environment variable to `"internal"` before
-#'     installing `instantiate`.
-#'   2. `"fixed"`: Use the copy of CmdStan that was located at the value
-#'     contained in `Sys.getenv("CMDSTAN")` at the time `instantiate`
-#'     was installed. In this case, the path to CmdStan is not inside
-#'     `instantiate` itself, but it is fixed at installation time
-#'     and does not depend on the current value of
-#'     `Sys.getenv("CMDSTAN")` at runtime.
-#'   3. `"cmdstanr"`: Let the `cmdstanr::cmdstan_path()` decide where
-#'     to look for CmdStan. The `cmdstanr` package must be installed. If it
-#'     is not installed, the function returns the empty string `""`.
-#'   4. `""` (default): Try all 3 options in the order above to find a valid
-#'     installed copy of CmdStan.
+#'   1. `""` (default): look at the original value that the `CMDSTAN_INSTALL`
+#'     environment variable contained when `instantiate` at the time
+#'     when it was installed.
+#'     If it was `"implicit"`, `"fixed"`, or `"internal"`, then choose
+#'     the corresponding option below. Otherwise, default to `"internal"`.
+#'   2. `"implicit"`: Let the `cmdstanr::cmdstan_path()` decide where
+#'     to look for CmdStan. As explained in the `cmdstanr` documentation,
+#'     the output of `cmdstanr::cmdstan_path()` depends
+#'     on the current value of the `CMDSTAN` environment variable.
+#'     The `cmdstanr` package must be installed. If it
+#'     is not installed, then `stan_cmdstan_path()`
+#'     returns the empty string `""`.
+#'   3. `"fixed"`: Use the path to CmdStan that was originally
+#'     contained in `Sys.getenv("CMDSTAN")` at the time when `instantiate`
+#'     was installed.
+#'   4. `"internal"`: Use the copy of CmdStan installed internally inside the
+#'     `instantiate` package file system. To use this option,
+#'     `instantiate` needs to have been originally installed with the
+#'     `CMDSTAN_INSTALL` environment variable set to `"internal"`.
 #' @examples
 #' stan_cmdstan_path()
 stan_cmdstan_path <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL")
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = "")
 ) {
   # It is not feasible to test all these cases in a single test coverage run.
   # Covered in several GitHub Actions workflows.
   # nocov start
-  install <- stan_cmdstan_install(cmdstan_install)
-  if (identical(install, "internal") || identical(install, "")) {
-    parent <- system.file("cmdstan", package = "instantiate", mustWork = FALSE)
-    out <- file.path(parent, list.files(parent)) %||% ""
-  }
-  if (identical(install, "fixed") || path_next(install, out)) {
-    out <- .Call(c_cmdstan_path)
+  install <- cmdstan_install
+  if (identical(install, "")) {
+    install <- .Call(c_cmdstan_path_install, PACKAGE = "instantiate")
   }
-  if (identical(install, "cmdstanr") || path_next(install, out)) {
+  stan_assert_install(install)
+  if (identical(install, "implicit") || identical(install, "")) {
     out <- cmdstanr_path()
+  } else if (identical(install, "fixed")) {
+    out <- .Call(c_cmdstan_path_fixed, PACKAGE = "instantiate")
+  } else if (identical(install, "internal")) {
+    bin <- system.file("bin", package = "instantiate", mustWork = FALSE)
+    parent <- file.path(bin, "cmdstan")
+    out <- file.path(parent, list.files(parent)) %||% ""
   }
   # nocov end
   out
 }
-
-path_next <- function(install, out) {
-  identical(install, "") && !any(dir.exists(out))
-}

R/stan_cmdstan_version.R

@@ -13,7 +13,7 @@
 #'   message(stan_cmdstan_version())
 #' }
 stan_cmdstan_version <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL"),
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = ""),
   error_on_NA = TRUE
 ) {
   stan_assert_cmdstanr()

R/stan_package.R

@@ -20,7 +20,6 @@
 #'   diagnosing compilation errors, and setting environment variables.
 #' @useDynLib instantiate, .registration = TRUE
 #' @importFrom fs dir_copy
-#' @importFrom pkglite unpack
 #' @importFrom rlang abort check_installed inform is_installed warn
 #' @importFrom utils capture.output globalVariables install.packages
 NULL

R/stan_package_compile.R

@@ -3,13 +3,13 @@
 #' @family packages
 #' @description Compile all Stan models in a directory, usually in a package.
 #' @details If building a package using `instantiate`, all Stan model files
-#'   must live in a folder called `inst/stan/` in the package source
+#'   must live in a folder called `src/stan/` in the package source
 #'   directory.
 #' @return `NULL` (invisibly). Called for its side effects.
 #' @inheritParams stan_cmdstan_path
 #' @param models Character vector of file paths to Stan model source code
-#'   files. Defaults to the Stan files in `./inst/stan/`
-#'   because all the Stan model files must live in the `inst/stan/` folder
+#'   files. Defaults to the Stan files in `./src/stan/`
+#'   because all the Stan model files must live in the `src/stan/` folder
 #'   for an R package built with `instantiate`.
 #' @param verbose Logical of length 1, whether to set the
 #'   `cmdstanr_verbose` global option to print more compiler messages
@@ -43,7 +43,7 @@
 #' }
 stan_package_compile <- function(
   models = instantiate::stan_package_model_files(),
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL"),
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = ""),
   verbose = TRUE,
   quiet = FALSE,
   pedantic = FALSE,

R/stan_package_configure.R

@@ -2,12 +2,12 @@
 #' @export
 #' @family packages
 #' @description Write configuration files in an R package which
-#'   compile all the Stan models in `inst/stan/` when the package installs.
+#'   compile all the Stan models in `src/stan/` when the package installs.
 #' @details Writes configuration scripts `configure` and `configure.win`
 #'   in the directory specified by the `path` argument.
 #' @return `NULL` (invisibly). Called for its side effects.
 #' @param path Character of length 1, file path to the package which will
-#'   contain Stan models in `inst/stan/` at installation time.
+#'   contain Stan models in `src/stan/` at installation time.
 #' @param overwrite Logical of length 1, whether to overwrite any existing
 #'   configuration files.
 #' @examples
@@ -38,20 +38,17 @@ stan_package_configure <- function(path = getwd(), overwrite = FALSE) {
     package = "instantiate",
     mustWork = TRUE
   )
-  in_configure <- system.file(
-    file.path("configuration", "configure"),
-    package = "instantiate",
-    mustWork = TRUE
-  )
-  in_configure_win <- system.file(
-    file.path("configuration", "configure.win"),
+  in_install <- system.file(
+    file.path("configuration", "install.libs.R"),
     package = "instantiate",
     mustWork = TRUE
   )
+  src <- file.path(path, "src")
   out_cleanup <- file.path(path, "cleanup")
   out_cleanup_win <- file.path(path, "cleanup.win")
-  out_configure <- file.path(path, "configure")
-  out_configure_win <- file.path(path, "configure.win")
+  out_install <- file.path(src, "install.libs.R")
+  out_makevars <- file.path(src, "Makevars")
+  out_makevars_win <- file.path(src, "Makevars.win")
   file.copy(
     from = in_cleanup,
     to = out_cleanup,
@@ -63,16 +60,20 @@ stan_package_configure <- function(path = getwd(), overwrite = FALSE) {
     to = out_cleanup_win,
     overwrite = overwrite
   )
+  if (!file.exists(src)) {
+    dir.create(src)
+  }
   file.copy(
-    from = in_configure,
-    to = out_configure,
+    from = in_install,
+    to = out_install,
     overwrite = overwrite,
     copy.mode = TRUE
   )
-  file.copy(
-    from = in_configure_win,
-    to = out_configure_win,
-    overwrite = overwrite
-  )
+  if (!file.exists(out_makevars)) {
+    file.create(out_makevars)
+  }
+  if (!file.exists(out_makevars_win)) {
+    file.create(out_makevars_win)
+  }
   invisible()
 }

R/stan_package_create.R

@@ -23,31 +23,25 @@ stan_package_create <- function(path = tempfile()) {
     !file.exists(path),
     message = "path must be a valid file path that does not already exist."
   )
-  packed <- system.file(
-    "example.txt",
-    package = "instantiate",
-    mustWork = TRUE
+  source <- system.file("example", package = "instantiate", mustWork = TRUE)
+  fs::dir_copy(path = source, new_path = path, overwrite = TRUE)
+  file.rename(
+    from = file.path(path, "gitignore"),
+    to = file.path(path, ".gitignore")
   )
-  temp <- tempfile()
-  on.exit(unlink(x = temp, recursive = TRUE))
-  pkglite::unpack(
-    input = packed,
-    output = temp,
-    install = FALSE,
-    quiet = TRUE
+  file.rename(
+    from = file.path(path, "rbuildignore"),
+    to = file.path(path, ".Rbuildignore")
   )
-  temp <- file.path(temp, "example")
-  fs::dir_copy(
-    path = temp,
-    new_path = path,
-    overwrite = TRUE
+  file.rename(
+    from = file.path(path, "github"),
+    to = file.path(path, ".github")
   )
-  unlink(x = temp, recursive = TRUE)
   message(
     paste0(
-      "Package with an internal Stan model created at ",
+      "Package with an internal Stan model created at directory path \"",
       path,
-      ". Configure with stan_package_configure() before installing."
+      "\". Configure with stan_package_configure() before installing."
     )
   )
   invisible()

R/stan_package_model.R

@@ -27,16 +27,38 @@ stan_package_model <- function(
   name,
   package,
   library = NULL,
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL")
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = "")
 ) {
   stan_assert_cmdstanr()
   stan_assert(name, is.character(.), !anyNA(.), nzchar(.))
   stan_assert(package, is.character(.), !anyNA(.), nzchar(.))
   stan_file <- get(x = "system.file", envir = globalenv()) (
+    file.path("bin", "stan", paste0(name, ".stan")),
+    package = package,
+    lib.loc = library,
+    mustWork = FALSE
+  )
+  stan_file_inst <- get(x = "system.file", envir = globalenv()) (
     file.path("stan", paste0(name, ".stan")),
     package = package,
     lib.loc = library,
-    mustWork = TRUE
+    mustWork = FALSE
+  )
+  if (file.exists(stan_file_inst)) {
+    stan_deprecate(
+      name = "Stan files installed to inst/stan/",
+      date = "2024-01-03",
+      version = "0.0.4.9001",
+      alternative = paste(
+        "Reinstall your Stan modeling package so your",
+        "compiled models are in bin/stan/ instead."
+      )
+    )
+    stan_file <- if_any(file.exists(stan_file), stan_file, stan_file_inst)
+  }
+  stan_assert(
+    file.exists(stan_file),
+    message = sprintf("Stan model file \"%s\" not found.", stan_file)
   )
   exe_file <- file.path(dirname(stan_file), name)
   exe_file <- if_any(stan_on_windows(), paste0(exe_file, ".exe"), exe_file)

R/stan_package_model_files.R

@@ -2,11 +2,11 @@
 #' @export
 #' @family packages
 #' @description List all the paths to the Stan model files in a package.
-#' @details All Stan models must live in the `inst/stan/` directory in the
+#' @details All Stan models must live in the `src/stan/` directory in the
 #'   package file system.
 #' @return Character vector of paths to Stan model files in the package.
-#' @param path Character of length 1, path to the root directory of the
-#'   R package with the Stan models.
+#' @param path Character of length 1, root path to start from when searching
+#'   for Stan model files.
 #' @examples
 #' path <- tempfile()
 #' stan_package_create(path = path)
@@ -20,8 +20,12 @@ stan_package_model_files <- function(path = getwd()) {
     length(.) == 1L,
     message = "invalid package directory path in stan_package_model_files()"
   )
-  path <- file.path(path, "inst", "stan")
-  out <- list.files(path, full.names = TRUE, pattern = "\\.stan$")
+  out <- list.files(
+    path,
+    full.names = TRUE,
+    recursive = TRUE,
+    pattern = "\\.stan$"
+  )
   stan_assert(
     length(out) > 0L,
     message = paste0(