release renv 1.0.0 (#1526)

* polish NEWS * Add GitHub links to DESCRIPTION * remove MRAN; update URLs * update copyright * update 2023-07-06 18:51:52.609604 * try to resolve revdep check issues * remove reference to removed vignette * jetpack expects lockfile structure from status * more tweaks for jetpack * pkgdown fixups * Update R/status.R Co-authored-by: Hadley Wickham <[email protected]> * tweaks + snapshot update * update NEWS * remove unneeded function * Polish news * bring back dependency inference on snapshot --------- Co-authored-by: Hadley Wickham <[email protected]>
rstudio · Jul 7, 2023 · 8f6763e · 8f6763e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,7 +14,7 @@ Description: A dependency management toolkit for R. Using 'renv', you can create
     a 'lockfile', and later restore your library as required. Together, these
     tools can help make your projects more isolated, portable, and reproducible.
 License: MIT + file LICENSE
-URL: https://rstudio.github.io/renv/
+URL: https://rstudio.github.io/renv/, https://github.com/rstudio/renv
 BugReports: https://github.com/rstudio/renv/issues
 Imports: utils
 Suggests: BiocManager, cli, covr, cpp11, devtools, gitcreds, jsonlite, knitr, miniUI,

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright 2021 RStudio, PBC
+Copyright 2023 Posit Software, PBC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,148 +1,144 @@
 
-# renv 0.18.0  (UNRELEASED)
+# renv 1.0.0
 
-* `renv::checkout()` gains the `actions` argument, allowing you choose whether
-  a lockfile is generated from the provided repositories ("snapshot"), or
-  whether packages are installed from the provided repositories ("restore").
+## New features
 
-* `renv::status()` gets new, more compact, display when packages have some
-  inconsistent combination of being installed, used, and recorded.
+* New `renv::checkout()` installings the latest-available packages from a 
+  repository. For example, `renv::checkout(date = "2023-02-08")` will install 
+  the packages available on 2023-02-08 from the Posit 
+  [Package Manager](https://packagemanager.rstudio.com/) repository. 
+  The `actions` argument allows you choose whether a lockfile is generated from 
+  the provided repositories ("snapshot"), or whether packages are installed 
+  from the provided repositories ("restore").
 
-* `renv::init()` now prompts the user to select a snapshot type, for projects
-  containing a top-level DESCRIPTION file. (#1485)
+* `renv::deactivate()` gains a `clean` argument: when `TRUE` it will delete
+  all renv files/directories, leaving the project the way it was found.
 
-* `renv::load()` makes the loading message a little more prominent, and we fixed a 
-  bug that prevented out-of-sync repos from being reported.
+* `renv::init()` now uses [Posit Public Package Manager](https://packagemanager.posit.co)
+  by default, for new projects where the repositories have not already been
+  configured externally. See the options `renv.config.ppm.enabled`,
+  `renv.config.ppm.default`, and `renv.config.ppm.url` in `?config` for more
+  details (#430).
 
-* `renv::dependencies()` now discovers R dependencies inside jupyter notebooks (#929).
+* `renv::lockfile_create()`, `renv::lockfile_read()`, `renv::lockfile_write()`
+  and `renv::lockfile_modify()` provide a small family of functions for 
+  interacting with renv lockfiles programmatically (#1438).
 
-* `renv::install(type = "source")` now ensures source repositories are used
-  in projects using [PPM](https://packagemanager.posit.co/). (#927)
-
-* `renv::restore()` now emits an error if called in a project that
-  does not contain a lockfile. (#1474)
+* Handling of development dependencies has been refined. `renv::snapshot()` 
+  and `renv::status()` no longer track development dependencies, while
+  `install()` continues to install them (#1019). `Suggested` packages listed in 
+  `DESCRIPTION` files are declared as development dependencies regardless of 
+  whether or not they're a "package" project.
 
-* If `renv::config$user.profile()` is `TRUE`, the packages it uses are now included
-  in the development dependencies, which means that they will be installed 
-  by `install()` but not recorded in the snapshot.
+* MRAN integration is now disabled by default, pending the upcoming shutdown
+  of Microsoft's MRAN service. Users who require binaries of older R packages
+  on Windows + macOS can consider using the instance of CRAN mirrored by the
+  [Posit Public Package Manager](https://packagemanager.posit.co) (#1343).
 
-* renv now attempts to infer remote dependencies for GitHub packages that
-  appear to be installed from sources; that is, for packages without a
-  recognizable remote source encoded in its DESCRIPTION file. (#841)
+## Bug fixes and minor improvements
 
-* `renv::load()` gives a more informative message if a lockfile is present but 
-  no packages are installed (#353).
+* Development versions of renv are now tracked using the Git SHA of the 
+  current commit, rather than a version number that's incremented on every
+  change (#1327). This shouldn't have any user facing impact, but makes
+  renv maintenance a little easier.
 
-* renv now provides a small family of functions for interacting with renv
-  lockfiles -- see `?lockfile` for more details. (#1438)
+* Fixed an issue causing "restarting interrupted promise evaluation" warnings
+  to be displayed when querying available packages failed. (#1260)
 
-* renv now activates the Bioconductor repositories when installing a package
-  from a remote (e.g. GitHub) which declares a Bioconductor dependency (via
-  a non-empty 'biocViews' field). (#934)
+* `renv::activate()` uses a three option menu that hopefully make your choices 
+  more clear (#1372).
 
-* renv no longer attempts to query package repositories when checking
-  if a project is synchronized on startup. (#812)
+* `renv::dependencies()` now discovers R package dependencies inside Jupyter
+  notebooks (#929).
 
-* `renv::update()` can now update packages installed from GitLab (#136) and 
-  BitBucket (#1194).
+* `renv::dependencies()` includes packages used by user profile (`~/.Rprofile`)
+  if `renv::config$user.profile()` is `TRUE`. They are set as development 
+  dependencies, which means that they will be installed by `install()` but not
+  recorded in the snapshot.
 
-* `renv::snapshot()` now standardises pak metadata so CRAN packages installed via
-  pak look the same as CRAN packages installed with renv or `install.packages()`
-  (#1239).
-
-* `renv::install()` now keeps source when installing packages from source (#522).
+* `renv::dependencies()` only extracts dependencies from text in YAML
+  headers that looks like valid R code (#1288).
 
-* `renv::install()` now validates that binary packages can be loaded after
-  installation, in a manner similar to source packages. (#1275)
+* `renv::dependencies()` no longer treats `box::use(module/file)` as using
+  package `module` (#1377).
 
-* `renv::snapshot()` and `renv::status()` no longer track development dependencies.
-  `install()` will continue to install them (#1019).
+* `renv::init()` now prompts the user to select a snapshot type if the project
+  contains a top-level DESCRIPTION file (#1485).
 
-* `renv::install()` respects the project snapshot type, if set.
+* `renv::install(type = "source")` now ensures source repositories are used
+  in projects using [PPM](https://packagemanager.posit.co/). (#927)
 
-* `renv::dependencies()` now marks `Suggested` packages listed in `DESCRIPTION` files
-  as development dependencies regardless of whether or not they're a "package" 
-  project.
+* `renv::install()` activates Bioconductor repositories when installing a 
+  package from a remote (e.g. GitHub) which declares a Bioconductor dependency 
+  (via a non-empty 'biocViews' field) (#934).
 
-* `renv::settings$package.dependency.fields()` now only affects packages installed
-  directly by the user, not downstream dependencies of those packages.
+* `renv::install()` respects the project snapshot type, if set.
 
-* Fixed an issue where `renv::snapshot(exclude = <...>)` could warn when
-  attempting to exclude a package which was not already installed. (#1396)
+* `renv::install()` now keeps source when installing packages from source (#522).
 
-* If `renv::snapshot()` finds missing packages, a new prompt allows you to 
-  install them before continuing (#1198).
+* `renv::install()` now validates that binary packages can be loaded after
+  installation, in a manner similar to source packages (#1275).
 
-* When prompting to activate a project, you now get three options that hopefully
-  make your choices more clear.
-
-* `renv::dependencies()` no longer treats `box::use(module/file)` as using
-  package `module` (#1377).
+* `renv::install()` now supports Bioconductor remotes of the form
+  `bioc::<BiocVersion>/<Package>`, for installing packages from
+  a particular version of Bioconductor. Aliases like 'release' and
+  'devel' are also supported (#1195).
 
 * `renv::install()` now requires interactive confirmation that you want to 
   install packages (#587).
 
-* Fixed an issue where `renv::restore()` could fail to restore packages
-  downloaded and installed from [r-universe](https://r-universe.dev/). (#1359)
+* `renv::load()` gives a more informative message if a lockfile is present but 
+  no packages are installed (#353).
 
-* `renv::deactivate()` gains a `clean` argument: when `TRUE` it will delete
-  all renv files/directories, leaving the project the way it was found.
+* `renv::load()` no longer attempts to query package repositories when checking
+  if a project is synchronized (#812).
 
-* `renv::status()` now works more like `renv::restore()` when package versions
-  are different (#675).
+* `renv::load()` no longer duplicates entries on the `PATH` environment variable
+  (#1095).
 
-* renv functions give a clearer error if `renv.lock` has somehow become 
-  corrupted (#1027).
+* `renv::restore()` can now use `pak::pkg_install()` to install packages
+  when `pak` integration is enabled. Set `RENV_CONFIG_PAK_ENABLED = TRUE`
+  in your project's `.Renviron` if you'd like to opt-in to this behavior.
+  Note that this requires a nightly build of `pak` (>= 0.4.0-9000);
+  see https://pak.r-lib.org/dev/reference/install.html for more details.
+
+* `renv::restore()` now emits an error if called within a project that
+  does not contain a lockfile (#1474).
 
-* `renv::init()` now uses [Posit Public Package Manager](https://packagemanager.posit.co)
-  by default, for new projects where the repositories have not already been
-  configured externally. See the options `renv.config.ppm.enabled`,
-  `renv.config.ppm.default`, and `renv.config.ppm.url` in `?config` for more
-  details. (#430)
+* `renv::restore()` correctly restores packages downloaded and installed 
+  from [r-universe](https://r-universe.dev/) (#1359).
 
-* MRAN integration is now disabled by default, pending the upcoming shutdown
-  of Microsoft's MRAN service. Users who require binaries of older R packages
-  on Windows + macOS can consider using the instance of CRAN mirrored by the
-  [Posit Public Package Manager](https://packagemanager.posit.co) (#1343).
+* `renv::snapshot()` now standardises pak metadata so CRAN packages installed via
+  pak look the same as CRAN packages installed with renv or `install.packages()`
+  (#1239).
 
-* `renv::dependencies()` only extracts dependencies from text in YAML
-  headers that looks like valid R code (#1288).
+* If `renv::snapshot()` finds missing packages, a new prompt allows you to 
+  install them before continuing (#1198).
 
 * `renv::snapshot()` no longer requires confirmation when writing the first
   snapshot, since that's an action that can easily be undone (by deleting
   `renv.lock`) (#1281).
 
-* `renv::snapshot()` now shows if the R version changes, even if no packages
+* `renv::snapshot()` reports if the R version changes, even if no packages
   change (#962).
 
-* Development versions of renv are now tracked using the Git SHA of the 
-  current commit, rather than a version number that's incremented on every
-  change (#1327). This shouldn't have any user facing impact, but makes
-  renv maintenance a little easier.
+* `renv::snapshot(exclude = <...>)` no longer warns when attempting to exclude 
+  a package that is not installed (#1396).
 
-* Fixed an issue causing "restarting interrupted promise evaluation" warnings
-  to be displayed when querying available packages failed. (#1260)
+* `renv::status()` now uses a more compact display when packages have some
+  inconsistent combination of being installed, used, and recorded.
 
-* `renv::load()` no longer duplicates entries on the `PATH` environment variable
-  (#1095).
+* `renv::status()` now works more like `renv::restore()` when package versions
+  are different (#675).
 
-* renv gains a new function `renv::checkout()`, for installing the
-  latest-available packages from a repository. For example, one can
-  use `renv::checkout(date = "2023-02-08")` to install the packages available
-  on 2023-02-08 from the Posit [Package Manager](https://packagemanager.rstudio.com/)
-  repository.
-
-* `renv::install()` now supports Bioconductor remotes of the form
-  `bioc::<BiocVersion>/<Package>`, for installing packages from
-  a particular version of Bioconductor. Aliases like 'release' and
-  'devel' are also supported. (#1195)
+* `renv::update()` can now update packages installed from GitLab (#136) and 
+  BitBucket (#1194).
 
-* `renv::restore()` can now use `pak::pkg_install()` to install packages
-  when `pak` integration is enabled. Set `RENV_CONFIG_PAK_ENABLED = TRUE`
-  in your project's `.Renviron` if you'd like to opt-in to this behavior.
-  Note that this requires a nightly build of `pak` (>= 0.4.0-9000);
-  see https://pak.r-lib.org/dev/reference/install.html for more details.
-
+* `renv::settings$package.dependency.fields()` now only affects packages 
+  installed directly by the user, not downstream dependencies of those packages.
+
+* renv functions give a clearer error if `renv.lock` has somehow become 
+  corrupted (#1027).
 
 # renv 0.17.3
 

diff --git a/R/activate.R b/R/activate.R
@@ -78,7 +78,7 @@ renv_activate_impl <- function(project,
     renv_imbue_self(project)
 
   # restart session if requested
-  if (restart && !renv_tests_running())
+  if (restart && !is_testing())
     return(renv_restart_request(project, reason = "renv activated"))
 
   if (renv_rstudio_available())

diff --git a/R/cache.R b/R/cache.R
@@ -114,11 +114,11 @@ renv_cache_synchronize <- function(record, linkable = FALSE) {
   if (!file.exists(path))
     return(FALSE)
 
-  # bail if the package source is unknown (assume that packages with an
-  # unknown source are not cacheable)
+  # bail if the package source is unknown
+  # (packages with an unknown source are not cacheable)
   desc <- renv_description_read(path)
   source <- renv_snapshot_description_source(desc)
-  if (identical(source, list(Source = "Unknown")))
+  if (identical(source, list(Source = "unknown")))
     return(FALSE)
 
   # bail if record not cacheable

diff --git a/R/config-defaults.R b/R/config-defaults.R
@@ -303,6 +303,15 @@ config <- list(
     )
   },
 
+  snapshot.inference = function(..., default = TRUE) {
+    renv_config_get(
+      name    = "snapshot.inference",
+      type    = "logical[1]",
+      default = default,
+      args    = list(...)
+    )
+  },
+
   snapshot.validate = function(..., default = TRUE) {
     renv_config_get(
       name    = "snapshot.validate",

diff --git a/R/dependencies.R b/R/dependencies.R
@@ -504,7 +504,7 @@ renv_dependencies_discover_preflight <- function(paths, errors) {
     "A large number of files (%i in total) have been discovered.",
     "It may take renv a long time to crawl these files for dependencies.",
     "Consider using .renvignore to ignore irrelevant files.",
-    "See `?dependencies` for more information.",
+    "See `?renv::dependencies` for more information.",
     "Set `options(renv.config.dependencies.limit = Inf)` to disable this warning.",
     ""
   )
@@ -723,7 +723,7 @@ renv_dependencies_discover_rmd_yaml_header <- function(path, mode) {
   # check for parameterized documents
   status <- catch(renv_dependencies_discover_rmd_yaml_header_params(yaml, deps))
   if (inherits(status, "error"))
-    renv_error_report(status)
+    renv_dependencies_error_push(path, status)
 
   # get list of dependencies
   packages <- deps$data()
@@ -1634,19 +1634,26 @@ renv_dependencies_scope <- function(root = NULL, scope = parent.frame()) {
   defer(the$dependencies_state <- NULL, scope = scope)
 }
 
+renv_dependencies_error_push <- function(path = NULL, error = NULL) {
+
+  state <- renv_dependencies_state()
+  if (is.null(state))
+    return()
+
+  path <- path %||% state$path
+  problem <- list(file = path, error = error)
+  state$problems$push(problem)
+
+}
+
 renv_dependencies_error <- function(path, error = NULL, packages = NULL) {
 
   # if no error, return early
   if (is.null(error))
     return(renv_dependencies_list(path, packages))
 
-  # check for missing state (e.g. if internal method called directly)
-  state <- renv_dependencies_state()
-  if (!is.null(state)) {
-    path <- path %||% state$path
-    problem <- list(file = path, error = error)
-    state$problems$push(problem)
-  }
+  # push the error report
+  renv_dependencies_error_push(path, error)
 
   # return dependency list
   renv_dependencies_list(path, packages)

diff --git a/R/download.R b/R/download.R
@@ -655,7 +655,7 @@ renv_download_report <- function(elapsed, file) {
     return()
 
   info <- renv_file_info(file)
-  size <- if (renv_tests_running())
+  size <- if (is_testing())
     "XXXX bytes"
   else
     structure(info$size, class = "object_size")

diff --git a/R/errors.R b/R/errors.R
@@ -156,8 +156,3 @@ renv_error_tag <- function(e) {
 renv_error_handler_call <- function() {
   as.call(list(renv_error_handler))
 }
-
-renv_error_report <- function(error = NULL) {
-  if (renv_tests_running() && inherits(error, "error"))
-    stop(error)
-}
diff --git a/R/init.R b/R/init.R
@@ -119,11 +119,13 @@ init <- function(project = NULL,
   renv_init_settings(project, settings)
 
   # for bare inits, just activate the project
-  if (bare)
+  if (bare) {
+    renv_imbue_impl(project)
     return(renv_init_fini(project, profile, restart))
+  }
 
   # compute and cache dependencies to (a) reveal problems early and (b) compute once
-  deps <- renv_snapshot_dependencies(project, dev = TRUE)
+  deps <- renv_snapshot_dependencies(project, type = type, dev = TRUE)
 
   # determine appropriate action
   action <- renv_init_action(project, library, lockfile, bioconductor)

diff --git a/R/install.R b/R/install.R
@@ -172,6 +172,10 @@ install <- function(packages = NULL,
     packages <- unique(c(packages, bioc))
   }
 
+  # don't update renv unless it was explicitly requested
+  if (!"renv" %in% names(remotes))
+    packages <- setdiff(packages, "renv")
+
   # start building a list of records; they should be resolved this priority:
   #
   # 1. explicit requests from the user