Merge pull request #127 from b-rodrigues/patch-rix-and-nix-wrappers

- Patch `rix()` with `shell_hook = NULL` default, Nix-R wrappers `nix_build()` and `with_nix()`; update testfiles

.github/workflows/tests-r-via-system.yaml

@@ -28,13 +28,16 @@ jobs:
       - name: Install R packages
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::devtools, any::codetools
+          extra-packages: any::devtools, any::codetools any::covr
 
       - name: Install Nix
         uses: DeterminateSystems/nix-installer-action@main
 
       - name: devtools::test() via system R
         run: Rscript -e 'devtools::test()'
+
+        - name: covr::codecov() via system R
+        run: RScript -e 'covr::codecov(quiet = FALSE, clean = FALSE, install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"))
 
       - name: Show testthat output
         run: |

DESCRIPTION

@@ -31,4 +31,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

R/rix.R

@@ -18,15 +18,19 @@
 #'   interactively use "rstudio" or "code" for Visual Studio Code. For other editors,
 #'   use "other". This has been tested with RStudio, VS Code and Emacs. If other
 #'   editors don't work, please open an issue.
-#' @param project_path Character, defaults to the current working directory. Where to write
-#'   `default.nix`, for example "/home/path/to/project".
-#'   The file will thus be written to the file "/home/path/to/project/default.nix".
+#' @param project_path Character, defaults to the current working directory. 
+#'   Where to write `default.nix`, for example "/home/path/to/project".
+#'   The file will thus be written to the file 
+#'   "/home/path/to/project/default.nix".
 #' @param overwrite Logical, defaults to FALSE. If TRUE, overwrite the `default.nix`
 #'   file in the specified path.
 #' @param print Logical, defaults to FALSE. If TRUE, print `default.nix` to console.
-#' @param shell_hook Character, defaults to `"R --vanilla"`. Commands added to the shell_hook get
-#'   executed when the Nix shell starts (via `shellHook`). So by default, using `nix-shell default.nix` will
-#'   start R. Set to NULL if you want bash to be started instead.
+#' @param shell_hook Character of length 1, defaults to `NULL`. Commands added
+#'   to the `shellHook` variable executed when the Nix shell starts. So
+#'   by default, using `nix-shell default.nix` (or path with `shell.nix`) will 
+#'   start a specific program, possibly with flags (separated by space), and/or
+#'   do shell actions. You can for example use `shell_hook = R`, if you want to
+#'   directly enter the declared Nix R session.
 #' @details This function will write a `default.nix` in the chosen path. Using
 #'   the Nix package manager, it is then possible to build a reproducible
 #'   development environment using the `nix-build` command in the path. This
@@ -74,7 +78,8 @@
 #'     ide = "code",
 #'     project_path = path_default_nix,
 #'     overwrite = TRUE,
-#'     print = TRUE)
+#'     print = TRUE,
+#'     shell_hook = NULL)
 #' }
 rix <- function(r_ver = "latest",
                 r_pkgs = NULL,
@@ -85,7 +90,7 @@ rix <- function(r_ver = "latest",
                 project_path = ".",
                 overwrite = FALSE,
                 print = FALSE,
-                shell_hook = "R --vanilla"){
+                shell_hook = NULL){
 
   stopifnot("'ide' has to be one of 'other', 'rstudio' or 'code'" = (ide %in% c("other", "rstudio", "code")))
 

dev/flat_nix_build.Rmd

@@ -241,7 +241,8 @@ testthat::test_that("Testing that `nix_build()` builds derivation", {
   rix(
     r_ver = "latest",
     overwrite = TRUE,
-    project_path = path_subshell
+    project_path = path_subshell,
+    shell_hook = NULL
   )
 
   out <- nix_build(

dev/flat_rix.Rmd

@@ -34,15 +34,19 @@ you use another IDE, you can leave the "ide" argument blank:
 #'   interactively use "rstudio" or "code" for Visual Studio Code. For other editors,
 #'   use "other". This has been tested with RStudio, VS Code and Emacs. If other
 #'   editors don't work, please open an issue.
-#' @param project_path Character, defaults to the current working directory. Where to write
-#'   `default.nix`, for example "/home/path/to/project".
-#'   The file will thus be written to the file "/home/path/to/project/default.nix".
+#' @param project_path Character, defaults to the current working directory. 
+#'   Where to write `default.nix`, for example "/home/path/to/project".
+#'   The file will thus be written to the file 
+#'   "/home/path/to/project/default.nix".
 #' @param overwrite Logical, defaults to FALSE. If TRUE, overwrite the `default.nix`
 #'   file in the specified path.
 #' @param print Logical, defaults to FALSE. If TRUE, print `default.nix` to console.
-#' @param shell_hook Character, defaults to `"R --vanilla"`. Commands added to the shell_hook get
-#'   executed when the Nix shell starts (via `shellHook`). So by default, using `nix-shell default.nix` will
-#'   start R. Set to NULL if you want bash to be started instead.
+#' @param shell_hook Character of length 1, defaults to `NULL`. Commands added
+#'   to the `shellHook` variable executed when the Nix shell starts. So
+#'   by default, using `nix-shell default.nix` (or path with `shell.nix`) will 
+#'   start a specific program, possibly with flags (separated by space), and/or
+#'   do shell actions. You can for example use `shell_hook = R`, if you want to
+#'   directly enter the declared Nix R session.
 #' @details This function will write a `default.nix` in the chosen path. Using
 #'   the Nix package manager, it is then possible to build a reproducible
 #'   development environment using the `nix-build` command in the path. This
@@ -90,7 +94,8 @@ you use another IDE, you can leave the "ide" argument blank:
 #'     ide = "code",
 #'     project_path = path_default_nix,
 #'     overwrite = TRUE,
-#'     print = TRUE)
+#'     print = TRUE,
+#'     shell_hook = NULL)
 #' }
 rix <- function(r_ver = "latest",
                 r_pkgs = NULL,
@@ -101,7 +106,7 @@ rix <- function(r_ver = "latest",
                 project_path = ".",
                 overwrite = FALSE,
                 print = FALSE,
-                shell_hook = "R --vanilla"){
+                shell_hook = NULL){
 
   stopifnot("'ide' has to be one of 'other', 'rstudio' or 'code'" = (ide %in% c("other", "rstudio", "code")))
 
@@ -409,7 +414,8 @@ testthat::test_that("Snapshot test of rix()", {
         ),
         ide = ide,
         project_path = path_default_nix,
-        overwrite = TRUE)
+        overwrite = TRUE,
+        shell_hook = NULL)
 
     paste0(path_default_nix, "/default.nix")
 
@@ -454,7 +460,9 @@ testthat::test_that("Quarto gets added to sys packages", {
         r_pkgs = pkgs,
         ide = "other",
         project_path = path_default_nix,
-        overwrite = TRUE)
+        overwrite = TRUE,
+        shell_hook = NULL
+      )
 
     paste0(path_default_nix, "/default.nix")
 

dev/flat_with_nix.Rmd

@@ -890,8 +890,6 @@ testthat::test_that("Testing `with_nix()` if Nix is installed", {
   # R version 3.5.3 on Nixpkgs does not build for aarch64-darwin (ARM macOS)
   skip_if(Sys.info()["sysname"] == "Darwin")
 
-  skip_on_covr()
-
   path_subshell <- tempdir()
 
   rix_init(
@@ -903,7 +901,8 @@ testthat::test_that("Testing `with_nix()` if Nix is installed", {
   rix(
     r_ver = "3.5.3",
     overwrite = TRUE,
-    project_path = path_subshell
+    project_path = path_subshell,
+    shell_hook = NULL
   )
 
   out_subshell <- with_nix(
@@ -919,12 +918,12 @@ testthat::test_that("Testing `with_nix()` if Nix is installed", {
     message_type = "simple"
   )
 
-                                        # On a recent version of R, set.seed(1234);sample(seq(1,10), 5)
-                                        # returns c(10, 6, 5, 4, 1)
-                                        # but not on versions prior to 3.6
+  # On a recent version of R, set.seed(1234);sample(seq(1,10), 5)
+  # returns c(10, 6, 5, 4, 1)
+  # but not on versions prior to 3.6
   testthat::expect_true(
-              all(c(2, 6, 5, 8, 9) == out_subshell)
-            )
+    all(c(2, 6, 5, 8, 9) == out_subshell)
+  )
 })
 
 testthat::test_that("Test `with_nix()` if Nix is installed on R 4.2.0", {
@@ -936,8 +935,6 @@ testthat::test_that("Test `with_nix()` if Nix is installed on R 4.2.0", {
   
   skip_if_not(nix_shell_available())
 
-  skip_on_covr()
-
   path_subshell <- tempdir()
 
   rix_init(
@@ -949,7 +946,8 @@ testthat::test_that("Test `with_nix()` if Nix is installed on R 4.2.0", {
   rix(
     r_ver = "4.2.0",
     overwrite = TRUE,
-    project_path = path_subshell
+    project_path = path_subshell,
+    shell_hook = NULL
   )
 
   df <- data.frame(a = 1:3, b = 4:6)

inst/extdata/default.nix

@@ -1,34 +1,49 @@
-# This file was generated by the {rix} R package v0.5.1.9000 on 2024-01-29
+# This file was generated by the {rix} R package v0.5.1.9000 on 2024-02-02
 # with following call:
-# >rix(r_ver = "902d74314fae5eb824bc7b597bd4d39640345557",
-#  > r_pkgs = NULL,
-#  > system_pkgs = NULL,
+# >rix(r_ver = "94b122adfc90316feaea838f29aa3f2e3de2b203",
+#  > r_pkgs = c("dplyr",
+#  > "AER@1.2-8"),
+#  > system_pkgs = c("quarto"),
 #  > git_pkgs = list(package_name = "rix",
 #  > repo_url = "https://github.com/b-rodrigues/rix/",
 #  > branch_name = "master",
-#  > commit = "11f6898fde38a4793a7f53900c88d2fd930e882f"),
+#  > commit = "da581f90273cb1ccfedbe18808097bf33b84d63c"),
 #  > ide = "other",
 #  > project_path = "inst/extdata",
-#  > overwrite = TRUE)
-# It uses nixpkgs' revision 902d74314fae5eb824bc7b597bd4d39640345557 for reproducibility purposes
-# which will install R version latest
+#  > overwrite = TRUE,
+#  > print = TRUE,
+#  > shell_hook = NULL)
+# It uses nixpkgs' revision 94b122adfc90316feaea838f29aa3f2e3de2b203 for reproducibility purposes
+# which will install R as it was as of nixpkgs revision: 94b122adfc90316feaea838f29aa3f2e3de2b203
 # Report any issues to https://github.com/b-rodrigues/rix
 let
- pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/902d74314fae5eb824bc7b597bd4d39640345557.tar.gz") {};
-  git_archive_pkgs = [(pkgs.rPackages.buildRPackage {
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/94b122adfc90316feaea838f29aa3f2e3de2b203.tar.gz") {};
+ rpkgs = builtins.attrValues {
+  inherit (pkgs.rPackages) dplyr;
+};
+ git_archive_pkgs = [(pkgs.rPackages.buildRPackage {
     name = "rix";
     src = pkgs.fetchgit {
       url = "https://github.com/b-rodrigues/rix/";
       branchName = "master";
-      rev = "11f6898fde38a4793a7f53900c88d2fd930e882f";
-      sha256 = "sha256-8Svbdu2qySZRfcXmf6PcqdtSJoHI2t9nC2XUUS9KuRo=";
+      rev = "da581f90273cb1ccfedbe18808097bf33b84d63c";
+      sha256 = "sha256-eDAxkXSrX+Q5TWwzkwMDG5rB8VXFKaLJLLKEJEvxjeo=";
+    };
+    propagatedBuildInputs = builtins.attrValues {
+      inherit (pkgs.rPackages) httr jsonlite sys;
+    };
+  }) (pkgs.rPackages.buildRPackage {
+    name = "AER";
+    src = pkgs.fetchzip {
+      url = "https://cran.r-project.org/src/contrib/Archive/AER/AER_1.2-8.tar.gz";
+      sha256 = "sha256-OqxXcnUX/2C6wfD5fuNayc8OU+mstI3tt4eBVGQZ2S0=";
     };
     propagatedBuildInputs = builtins.attrValues {
-      inherit (pkgs.rPackages) codetools httr jsonlite sys;
+      inherit (pkgs.rPackages) car lmtest sandwich survival zoo Formula;
     };
-  }) ];
+  })];
   system_packages = builtins.attrValues {
-  inherit (pkgs) R glibcLocales nix ;
+  inherit (pkgs) R glibcLocales nix quarto;
 };
   in
   pkgs.mkShell {
@@ -40,6 +55,6 @@ let
     LC_PAPER = "en_US.UTF-8";
     LC_MEASUREMENT = "en_US.UTF-8";
 
-    buildInputs = [ git_archive_pkgs   system_packages  ];
-      shellHook = "R --vanilla";
+    buildInputs = [ git_archive_pkgs rpkgs  system_packages  ];
+
   }

tests/testthat/_snaps/rix/code_default.nix

@@ -54,5 +54,5 @@ let
     LC_MEASUREMENT = "en_US.UTF-8";
 
     buildInputs = [ git_archive_pkgs rpkgs tex system_packages  ];
-      shellHook = "R --vanilla";
+
   }

tests/testthat/_snaps/rix/no_quarto_default.nix

@@ -18,5 +18,5 @@ let
     LC_MEASUREMENT = "en_US.UTF-8";
 
     buildInputs = [  rpkgs  system_packages  ];
-      shellHook = "R --vanilla";
+
   }

tests/testthat/_snaps/rix/other_default.nix

@@ -54,5 +54,5 @@ let
     LC_MEASUREMENT = "en_US.UTF-8";
 
     buildInputs = [ git_archive_pkgs rpkgs tex system_packages  ];
-      shellHook = "R --vanilla";
+
   }

tests/testthat/_snaps/rix/rstudio_default.nix

@@ -57,5 +57,5 @@ let
     LC_MEASUREMENT = "en_US.UTF-8";
 
     buildInputs = [ git_archive_pkgs rpkgs tex system_packages rstudio_pkgs ];
-      shellHook = "R --vanilla";
+
   }

tests/testthat/_snaps/rix/yes_quarto_default.nix

@@ -18,5 +18,5 @@ let
     LC_MEASUREMENT = "en_US.UTF-8";
 
     buildInputs = [  rpkgs  system_packages  ];
-      shellHook = "R --vanilla";
+
   }

tests/testthat/test-nix_build.R

@@ -23,7 +23,8 @@ testthat::test_that("Testing that `nix_build()` builds derivation", {
   rix(
     r_ver = "latest",
     overwrite = TRUE,
-    project_path = path_subshell
+    project_path = path_subshell,
+    shell_hook = NULL
   )
 
   out <- nix_build(

tests/testthat/test-rix.R

@@ -21,7 +21,8 @@ testthat::test_that("Snapshot test of rix()", {
         ),
         ide = ide,
         project_path = path_default_nix,
-        overwrite = TRUE)
+        overwrite = TRUE,
+        shell_hook = NULL)
 
     paste0(path_default_nix, "/default.nix")
 
@@ -64,7 +65,9 @@ testthat::test_that("Quarto gets added to sys packages", {
         r_pkgs = pkgs,
         ide = "other",
         project_path = path_default_nix,
-        overwrite = TRUE)
+        overwrite = TRUE,
+        shell_hook = NULL
+      )
 
     paste0(path_default_nix, "/default.nix")