Merge pull request #344 from lorenzwalthert/r-v0.2.1

release v0.2.1

API

@@ -16,7 +16,7 @@ roxygenize_with_cache(key, dirs)
 snippet_generate(snippet, open = rstudioapi::isAvailable(), root = here::here())
 uninstall_precommit(scope = "repo", ask = "user", root = here::here())
 update_precommit()
-use_ci(ci = getOption("precommit.ci", "native"), force = FALSE, root = here::here())
+use_ci(ci = getOption("precommit.ci", "native"), force = FALSE, open = rstudioapi::isAvailable(), root = here::here())
 use_precommit(config_source = getOption("precommit.config_source"), force = FALSE, legacy_hooks = "forbid", open = rstudioapi::isAvailable(), install_hooks = TRUE, ci = getOption("precommit.ci", "native"), root = here::here())
 use_precommit_config(config_source = getOption("precommit.config_source"), force = FALSE, open = rstudioapi::isAvailable(), verbose = FALSE, root = here::here())
 version_precommit()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: precommit
 Title: Pre-Commit Hooks
-Version: 0.2.0.9002
+Version: 0.2.1
 Author: Lorenz Walthert
 Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
 Description: Useful git hooks for R building on top of the multi-language
@@ -48,4 +48,4 @@ Roxygen: list(markdown = TRUE, roclets = c( "rd", "namespace", "collate",
     if (rlang::is_installed("pkgapi")) "pkgapi::api_roclet" else {
     warning("Please install r-lib/pkgapi to make sure the file API is kept
     up to date"); NULL} ) )
-RoxygenNote: 7.1.1.9001
+RoxygenNote: 7.1.2

NEWS.md

@@ -1,6 +1,10 @@
-# precommit v0.2.0.9001 (Development version)
+# precommit v0.2.1
 
-# precommit v0.2.0.9000
+This is a maintenance release on the request of CRAN (#337) and to improve 
+experience with the `language: r` switch conducted in `v0.2.0`. In particular, 
+note that projects using {renv} and RStudio are not very compatible with hook 
+versions > 0.1.3.9014 and `autoupdate()` results in downgrading the hook 
+versions (#346).
 
 **API Changes**
 
@@ -17,6 +21,13 @@
 * `deps-in-desc` always excludes `README.md` (#336).
 * Document timeout and other problems with pre-commit.ci (#335).
 * simplify `roxygenize` problem handling (#338).
+* More executables on macOS are detected (#344).
+* Only hard dependencies are generated with 
+  `snippet_generate("additional-deps-roxygenize")` (#344)
+
+Thanks to all people who contributed to this release: 
+
+[@lorenzwalthert](https://github.com/lorenzwalthert), [@pat-s](https://github.com/pat-s), and [@smingerson](https://github.com/smingerson).
 
 # precommit v0.2.0
 
@@ -139,11 +150,11 @@ A big hand to all the contributors of this release:
 [@arbues6](https://github.com/arbues6), 
 [@b4D8](https://github.com/b4D8), 
 [@bart1](https://github.com/bart1), 
-[@dhersz](https://github.com/dhersz), [@github-actions[bot]](https://github.com/github-actions[bot]), [@joelnitta](https://github.com/joelnitta), 
+[@dhersz](https://github.com/dhersz), [@joelnitta](https://github.com/joelnitta), 
 [@jucor](https://github.com/jucor),
 [@lorenzwalthert](https://github.com/lorenzwalthert), [@lukasfeick-sw](https://github.com/lukasfeick-sw), [@MarkMc1089](https://github.com/MarkMc1089), 
 [@njtierney](https://github.com/njtierney), 
-[@pat-s](https://github.com/pat-s), [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]), [@pwildenhain](https://github.com/pwildenhain), and [@rossdrucker](https://github.com/rossdrucker)
+[@pat-s](https://github.com/pat-s), [@pwildenhain](https://github.com/pwildenhain), and [@rossdrucker](https://github.com/rossdrucker)
 
 For previous versions of `NEWS.md` with news bullet per patch release, see the 
 [latest `NEWS.md` before gathering](https://github.com/lorenzwalthert/precommit/blob/7a8740714ab868d20e981b8b80898d7be050e34e/NEWS.md).

R/exec.R

@@ -147,12 +147,24 @@ path_derive_precommit_exec_win_python3plus_candidates <- function() {
 
 
 path_derive_precommit_exec_macOS <- function() {
+  path_derive_precommit_exec_macOS_candidates() %>%
+    path_derive_precommit_exec_impl()
+}
+
+path_derive_precommit_exec_macOS_candidates <- function() {
+  candidate_system <- fs::dir_ls(
+    path_if_exist("/Library/Frameworks/Python.framework/Versions/"),
+    # avoid alias to /Library/Frameworks/Python.framework/Versions/Current/
+    regexp = "[0-9]$"
+  )
+
+  candidate_user <- fs::dir_ls(path_if_exist("~/Library/Python/"))
   c(
-    fs::path(sort(fs::dir_ls(path_if_exist("~/Library/Python/")), decreasing = TRUE), "bin"), # pip
+    fs::path(sort(candidate_user, decreasing = TRUE), "bin"), # pip
+    fs::path(sort(candidate_system, decreasing = TRUE), "bin"),
     "/usr/local/bin", # homebrew
     "/opt/homebrew/bin" # homebrew Apple Silicon (M1 chip)
-  ) %>%
-    path_derive_precommit_exec_impl()
+  )
 }
 
 #' Derive the pre-commit executable from the path

R/release.R

@@ -172,7 +172,7 @@ sys_call <- function(...) {
 
 git_branch_set <- function(is_cran) {
   if (is_cran) {
-    branch_name <- paste0("r-v", desc::desc_get_version())
+    branch_name <- paste0("rc-v", desc::desc_get_version())
 
     sys_call(
       "git",

R/roxygen2.R

@@ -107,12 +107,14 @@ roxygen_assert_additional_dependencies <- function() {
     # case used in package but not installed
     rlang::abort(paste0(
       "The roxygenize hook requires all dependencies of your package to be listed in ",
-      "the file `.pre-commit-config.yaml`.",
+      "the file `.pre-commit-config.yaml`. ",
       "Call `precommit::snippet_generate('additional-deps-roxygenize')` ",
-      "to generate that list or ",
-      "comment out the hook under \n\n",
-      "`    -   id: roxygenize` \n\n to deactivate the hook.",
-      "\n\nThe initial error (from `pkgload::load_all()`) was: ",
+      "to generate that list or, to completely deactivate the hook, ",
+      "comment out all lines corresponding to that hook under \n\n",
+      "    -   id: roxygenize\n",
+      "        some_key_under_id_roxygenize: comment-out-as-well\n",
+      "    -   id: some-other-hook-do-not-comment-out\n\n",
+      "The initial error (from `pkgload::load_all()`) was: ",
       conditionMessage(out), ".\n\n"
     ))
   }

R/setup.R

@@ -8,6 +8,10 @@
 #'   managed by pre-commit. "forbid", the default, will cause  `use_precommit()`
 #'   to fail if there are such hooks. "allow" will run these along with
 #'   pre-commit. "remove" will delete them.
+#' @param open Whether or not to open `.pre-commit-config.yaml` after
+#'   it's been placed in your repo as well as
+#'   [pre-commit.ci](https://pre-commit.ci) (if `ci = "native"`). The default is
+#'   `TRUE` when working in RStudio.
 #' @inheritParams fallback_doc
 #' @inheritParams use_precommit_config
 #' @inheritSection use_precommit_config Copying an existing config file
@@ -54,13 +58,8 @@ use_precommit <- function(config_source = getOption("precommit.config_source"),
   install_repo(root, install_hooks, legacy_hooks)
   if (open) {
     open_config(root)
-    use_ci(ci)
-  } else {
-    if (ci == "gha") {
-      use_ci(ci, force = force, root = root)
-    }
   }
-
+  use_ci(ci, force = force, open = open, root = root)
   invisible(NULL)
 }
 
@@ -78,10 +77,20 @@ use_precommit <- function(config_source = getOption("precommit.config_source"),
 #'   to `NULL` if you don't want to use a continuous integration.
 #' @param force Whether or not to overwrite an existing ci config file (only
 #'   relevant for `ci = "gha"`).
+#' @param open Whether or not to open [pre-commit.ci](https://pre-commit.ci)
+#'   (if `ci = "native"`). The default is `TRUE` when working in RStudio.
 #' @inheritParams fallback_doc
 #' @export
 use_ci <- function(ci = getOption("precommit.ci", "native"),
-                   force = FALSE, root = here::here()) {
+                   force = FALSE,
+                   open = rstudioapi::isAvailable(),
+                   root = here::here()) {
+  if (!fs::file_exists(fs::path(root, ".pre-commit-config.yaml"))) {
+    rlang::abort(paste0(
+      "Your repo has no `.pre-commit-config.yaml` file, please initialize ",
+      "{precommit} with `precommit::use_precommit()`."
+    ))
+  }
   if (is.na(ci)) {
     return()
   } else if (ci == "gha") {
@@ -99,16 +108,28 @@ use_ci <- function(ci = getOption("precommit.ci", "native"),
       "{.code https://github.com/lorenzwalthert/precommit}."
     ))
   } else if (ci == "native") {
-    cli::cli_ul('You may need to skip the roxygenize hook in the CI run as explained in {.code vignette("ci", package = "precommit")}')
-    Sys.sleep(2)
-    cli::cli_ul("Sign in with GitHub to authenticate {.url https://pre-commit.ci}.")
+    cli::cli_ul(paste0(
+      "Sign in with GitHub to authenticate {.url https://pre-commit.ci} and ",
+      "then come back to complete the set-up process."
+    ))
     Sys.sleep(2)
-    utils::browseURL("https://pre-commit.ci")
+    if (open) {
+      utils::browseURL("https://pre-commit.ci")
+    }
   } else {
     rlang::abort(
       'Argument `ci` must be one of `"native"` (default), `"gha"` or `NULL`.'
     )
   }
+  config <- readLines(fs::path(root, ".pre-commit-config.yaml"))
+  if (length(grep("^ *- *id *: *roxygenize", config)) > 0) {
+    cli::cli_ul(paste0(
+      "It seems like you are using the roxygenize hook. This requires further ",
+      "edits in your {.code .pre-commit-config.yaml}, please run ",
+      "{.code precommit::snippet_generate('additional-deps-roxygenize')} to ",
+      "proceed."
+    ))
+  }
 }
 
 #' Auto-update your hooks
@@ -136,13 +157,50 @@ autoupdate <- function(root = here::here()) {
         preamble = "Running precommit autoupdate failed."
       )
     }
+    ensure_renv_precommit_compat(root = root)
     invisible(out$exit_status)
   })
 }
 
+ensure_renv_precommit_compat <- function(root = here::here()) {
+  withr::local_dir(root)
+  path_config <- ".pre-commit-config.yaml"
+  config_lines <- readLines(path_config, encoding = "UTF-8")
+  has_renv <- fs::file_exists("renv.lock")
+  if (!has_renv) {
+    return()
+  }
+
+  rev <- rev_read(path_config)
+  rlang::with_handlers(
+    {
+      rev <- rev_as_pkg_version(rev)
+      maximal_rev <- package_version("0.1.3.9014")
+      if (rev > maximal_rev) {
+        rlang::warn(paste0(
+          "It seems like you want to use {renv} and {precommit} in the same ",
+          "repo. This is not well supported for users of RStudio and ",
+          "`precommit > 0.1.3.9014` at the moment (details: ",
+          "https://github.com/lorenzwalthert/precommit/issues/342). ",
+          "Autoupdate aborted and `rev:` in `.pre-commit-config.yaml` set to ",
+          "a version compatible with {renv}."
+        ))
+        config_lines <- gsub(
+          paste0("^ *rev *: *", "v", as.character(rev)),
+          "    rev: v0.1.3.9014",
+          config_lines
+        )
+        withr::local_options(encoding = "native.enc")
+        writeLines(enc2utf8(config_lines), path_config, useBytes = TRUE)
+      }
+    },
+    error = function(e) NULL
+  )
+}
+
 
 upstream_repo_url_is_outdated <- function() {
-  purrr::map_chr(yaml::read_yaml(".pre-commit-config.yaml")$repos, ~ .x$repo) %>%
+  rev_read(".pre-commit-config.yaml") %>%
     grepl("https://github.com/lorenzwalthert/pre-commit-hooks", ., fixed = TRUE) %>%
     any()
 }
@@ -156,7 +214,7 @@ upstream_repo_url_is_outdated <- function() {
 #'
 #' * additional-deps-roxygenize: Code to paste into
 #'   `.pre-commit-config.yaml` for the additional dependencies required by
-#'   roxygen2.
+#'   the roxygenize hook.
 #' @param snippet Name of the snippet.
 #' @param open Whether or not to open the .pre-commit-config.yaml. The default
 #' is `TRUE` when working in  RStudio. Otherwise, we recommend manually opening
@@ -175,20 +233,29 @@ snippet_generate <- function(snippet = "",
       "\n"
     ))
     deps <- desc::desc_get_deps()
-    non_r_deps <- deps[!(deps$type == "Depends" & deps$package == "R"), ]
-    non_r_deps <- non_r_deps[order(non_r_deps$package), ]
-    snippet_generate_impl_additional_deps_roxygenize(non_r_deps$package) %>%
+    hard_dependencies <- deps[(deps$type %in% c("Depends", "Imports")), "package"]
+    hard_dependencies_vec <- hard_dependencies %>%
+      setdiff("R")
+    if (length(hard_dependencies_vec) < 1) {
+      cli::cli_alert_success(paste0(
+        "According to {.code DESCRIPTION}`, there are no hard dependencies of ",
+        "your package. You are set."
+      ))
+      return()
+    }
+    hard_dependencies %>%
+      snippet_generate_impl_additional_deps_roxygenize() %>%
       cat(sep = "")
     cat("\n")
-    cli::cli_ul(
+    cli::cli_ul(paste0(
       "Replace the `id: roxygenize` key in `.pre-commit-config.yaml` with the ",
       "above code."
-    )
+    ))
     cli::cli_alert_info(paste0(
       "Note that CI services like {.url pre-commit.ci} have build-time ",
-      "restrictions and installing the above dependencies may exceed those. ",
-      "To skip the hook on {.url pre-commit.ci}, see ",
-      '{.code vignette("ci", package = "precommit")}.'
+      "restrictions and installing the above dependencies may exceed those, ",
+      "resulting in a timeout. See ",
+      '{.code vignette("ci", package = "precommit")} for details and solutions.'
     ))
     remote_deps <- rlang::with_handlers(
       desc::desc_get_field("Remotes"),
@@ -198,7 +265,7 @@ snippet_generate <- function(snippet = "",
       rlang::warn(paste0(
         "It seems you have remote dependencies in your `DESCRIPTION`. You ",
         "need to edit the above list manually to match the syntax `renv::install()` ",
-        "understands, i.e. if you have in your `DESCRIPTION`", "
+        "understands, i.e. if you have in your `DESCRIPTION`
 
 Imports:
     tidyr
@@ -221,8 +288,7 @@ You need in your `.pre-commit-config.yaml`
 
 snippet_generate_impl_additional_deps_roxygenize <- function(packages, with_version = FALSE) {
   out <- paste0(
-    "        -    ", packages, if (with_version) "@",
-    if (with_version) purrr::map_chr(packages, ~ as.character(packageVersion(.x))), "\n",
+    "        -    ", packages, "\n",
     collapse = ""
   ) %>%
     sort()

R/testing.R

@@ -139,7 +139,7 @@ hook_state_create <- function(tempdir,
                               env) {
   withr::local_dir(tempdir)
   files <- fs::path_rel(path_candidate_temp, tempdir)
-  # https://r.789695.n4.nabble.com/Error-message-Rscript-should-not-be-used-without-a-path-td4748071.html
+  # https://stat.ethz.ch/pipermail/r-devel/2018-February/075507.html
   system2(paste0(Sys.getenv("R_HOME"), "/bin/Rscript"),
     args = c(path_executable, cmd_args, files),
     stderr = path_stderr, stdout = path_stdout, env = env

R/utils.R

@@ -85,3 +85,17 @@ git_init <- function(path = ".") {
     core.autocrlf = "true"
   )
 }
+
+
+#' Read the refs corresponding to a hooks repo
+#' @keywords internal
+rev_read <- function(path = ".pre-commit-config.yaml", repo = hooks_repo) {
+  config <- yaml::read_yaml(path)
+  idx <- purrr::map_chr(config$repos, ~ .x$repo) %>%
+    grep(repo, ., fixed = TRUE)
+  config$repos[[idx]]$rev
+}
+
+rev_as_pkg_version <- function(rev) {
+  package_version(gsub("^v", "", rev))
+}

cran-comments.md

@@ -1,3 +1,6 @@
+This is a re-submission to fix problems related to end of line encoding
+in R devel on windows related to the new UCRT toolchain (https://github.com/lorenzwalthert/precommit/issues/320).
+
 ## Test environments
 
 * ubuntu 18.04 (on GitHub Actions): R 4.1.2

inst/WORDLIST

@@ -195,10 +195,12 @@ tibble
 tidelift
 Tidelift
 tidyverse
+toolchain
 trailingOnly
 travis
 tryCatch
 ubuntu
+UCRT
 uninitialised
 Uninstallation
 unlist