From 8ab48edb8cbae3f85f996614a50a2fe69fb9add2 Mon Sep 17 00:00:00 2001 From: William Ridgeway <10358980+wrridgeway@users.noreply.github.com> Date: Thu, 16 May 2024 13:13:52 -0500 Subject: [PATCH 1/3] Bump renv versions (#48) --- .pre-commit-config.yaml | 2 +- renv.lock | 10 +- renv/activate.R | 646 +++++++++++++++++++++------------------- 3 files changed, 349 insertions(+), 309 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c49377b..58c9364 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # R specific hooks: https://github.com/lorenzwalthert/precommit repos: - repo: https://github.com/lorenzwalthert/precommit - rev: v0.3.2.9027 + rev: v0.4.2 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] diff --git a/renv.lock b/renv.lock index 11f532e..b48223d 100644 --- a/renv.lock +++ b/renv.lock @@ -1,10 +1,10 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.0", "Repositories": [ { "Name": "CRAN", - "URL": "https://cran.rstudio.com" + "URL": "https://cloud.r-project.org" } ] }, @@ -1265,13 +1265,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.3", + "Version": "1.0.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "41b847654f567341725473431dd0d5ab" + "Hash": "397b7b2a265bc5a7a06852524dabae20" }, "rlang": { "Package": "rlang", @@ -1705,4 +1705,4 @@ "Hash": "d98c94dacb7e0efcf83b0a133a705504" } } -} +} \ No newline at end of file diff --git a/renv/activate.R b/renv/activate.R index cb5401f..017de50 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.7" attr(version, "sha") <- NULL # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -31,6 +33,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -50,9 +60,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -74,24 +97,24 @@ local({ if ("renv" %in% loadedNamespaces()) unloadNamespace("renv") - # load bootstrap tools + # load bootstrap tools `%||%` <- function(x, y) { if (is.null(x)) y else x } - + catf <- function(fmt, ..., appendLF = TRUE) { - + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) if (quiet) return(invisible()) - + msg <- sprintf(fmt, ...) cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") - + invisible(msg) - + } - + header <- function(label, ..., prefix = "#", @@ -102,22 +125,37 @@ local({ n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) if (n <= 0) return(paste(prefix, label)) - + tail <- paste(rep.int(suffix, n), collapse = "") paste0(prefix, " ", label, " ", tail) - + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + } - + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } - + bootstrap <- function(version, library) { - + friendly <- renv_bootstrap_version_friendly(version) section <- header(sprintf("Bootstrapping renv %s", friendly)) catf(section) - + # attempt to download renv catf("- Downloading renv ... ", appendLF = FALSE) withCallingHandlers( @@ -129,7 +167,7 @@ local({ ) catf("OK") on.exit(unlink(tarball), add = TRUE) - + # now attempt to install catf("- Installing renv ... ", appendLF = FALSE) withCallingHandlers( @@ -140,174 +178,174 @@ local({ } ) catf("OK") - + # add empty line to break up bootstrapping from normal output catf("") - + return(invisible()) } - + renv_bootstrap_tests_running <- function() { getOption("renv.tests.running", default = FALSE) } - + renv_bootstrap_repos <- function() { - + # get CRAN repository cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") - + # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) if (!is.na(repos)) { - + # check for RSPM; if set, use a fallback repository for renv rspm <- Sys.getenv("RSPM", unset = NA) if (identical(rspm, repos)) repos <- c(RSPM = rspm, CRAN = cran) - + return(repos) - + } - + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - + # retrieve current repos repos <- getOption("repos") - + # ensure @CRAN@ entries are resolved repos[repos == "@CRAN@"] <- cran - + # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") extra <- getOption("renv.bootstrap.repos", default = default) repos <- c(repos, extra) - + # remove duplicates that might've snuck in dupes <- duplicated(repos) | duplicated(names(repos)) repos[!dupes] - + } - + renv_bootstrap_repos_lockfile <- function() { - + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") if (!file.exists(lockpath)) return(NULL) - + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) if (inherits(lockfile, "error")) { warning(lockfile) return(NULL) } - + repos <- lockfile$R$Repositories if (length(repos) == 0) return(NULL) - + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) names(vals) <- keys - + return(vals) - + } - + renv_bootstrap_download <- function(version) { - + sha <- attr(version, "sha", exact = TRUE) - + methods <- if (!is.null(sha)) { - + # attempting to bootstrap a development version of renv c( function() renv_bootstrap_download_tarball(sha), function() renv_bootstrap_download_github(sha) ) - + } else { - + # attempting to bootstrap a release version of renv c( function() renv_bootstrap_download_tarball(version), function() renv_bootstrap_download_cran_latest(version), function() renv_bootstrap_download_cran_archive(version) ) - + } - + for (method in methods) { path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - + stop("All download methods failed") - + } - + renv_bootstrap_download_impl <- function(url, destfile) { - + mode <- "wb" - + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 fixup <- Sys.info()[["sysname"]] == "Windows" && substring(url, 1L, 5L) == "file:" - + if (fixup) mode <- "w+b" - + args <- list( url = url, destfile = destfile, mode = mode, quiet = TRUE ) - + if ("headers" %in% names(formals(utils::download.file))) args$headers <- renv_bootstrap_download_custom_headers(url) - + do.call(utils::download.file, args) - + } - + renv_bootstrap_download_custom_headers <- function(url) { - + headers <- getOption("renv.download.headers") if (is.null(headers)) return(character()) - + if (!is.function(headers)) stopf("'renv.download.headers' is not a function") - + headers <- headers(url) if (length(headers) == 0L) return(character()) - + if (is.list(headers)) headers <- unlist(headers, recursive = FALSE, use.names = TRUE) - + ok <- is.character(headers) && is.character(names(headers)) && all(nzchar(names(headers))) - + if (!ok) stop("invocation of 'renv.download.headers' did not return a named character vector") - + headers - + } - + renv_bootstrap_download_cran_latest <- function(version) { - + spec <- renv_bootstrap_download_cran_latest_find(version) type <- spec$type repos <- spec$repos - + baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -317,36 +355,36 @@ local({ ".tgz" name <- sprintf("renv_%s%s", version, ext) url <- paste(baseurl, name, sep = "/") - + destfile <- file.path(tempdir(), name) status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (inherits(status, "condition")) return(FALSE) - + # report success and return destfile - + } - + renv_bootstrap_download_cran_latest_find <- function(version) { - + # check whether binaries are supported on this system binary <- getOption("renv.bootstrap.binary", default = TRUE) && !identical(.Platform$pkgType, "source") && !identical(getOption("pkgType"), "source") && Sys.info()[["sysname"]] %in% c("Darwin", "Windows") - + types <- c(if (binary) "binary", "source") - + # iterate over types + repositories for (type in types) { for (repos in renv_bootstrap_repos()) { - + # retrieve package database db <- tryCatch( as.data.frame( @@ -355,89 +393,89 @@ local({ ), error = identity ) - + if (inherits(db, "error")) next - + # check for compatible entry entry <- db[db$Package %in% "renv" & db$Version %in% version, ] if (nrow(entry) == 0) next - + # found it; return spec to caller spec <- list(entry = entry, type = type, repos = repos) return(spec) - + } } - + # if we got here, we failed to find renv fmt <- "renv %s is not available from your declared package repositories" stop(sprintf(fmt, version)) - + } - + renv_bootstrap_download_cran_archive <- function(version) { - + name <- sprintf("renv_%s.tar.gz", version) repos <- renv_bootstrap_repos() urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - + for (url in urls) { - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (identical(status, 0L)) return(destfile) - + } - + return(FALSE) - + } - + renv_bootstrap_download_tarball <- function(version) { - + # if the user has provided the path to a tarball via # an environment variable, then use it tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) if (is.na(tarball)) return() - + # allow directories if (dir.exists(tarball)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } - + # bail if it doesn't exist if (!file.exists(tarball)) { - + # let the user know we weren't able to honour their request fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) - + # bail return() - + } - + catf("- Using local tarball '%s'.", tarball) tarball - + } - + renv_bootstrap_download_github <- function(version) { - + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") if (!identical(enabled, "TRUE")) return(FALSE) - + # prepare download options pat <- Sys.getenv("GITHUB_PAT") if (nzchar(Sys.which("curl")) && nzchar(pat)) { @@ -453,25 +491,25 @@ local({ options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) } - + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (!identical(status, 0L)) return(FALSE) - + renv_bootstrap_download_augment(destfile) - + return(destfile) - + } - + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we # can use renv::install() to fully capture metadata. renv_bootstrap_download_augment <- function(destfile) { @@ -479,13 +517,13 @@ local({ if (is.null(sha)) { return() } - + # Untar tempdir <- tempfile("renv-github-") on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) untar(destfile, exdir = tempdir) pkgdir <- dir(tempdir, full.names = TRUE)[[1]] - + # Modify description desc_path <- file.path(pkgdir, "DESCRIPTION") desc_lines <- readLines(desc_path) @@ -499,170 +537,173 @@ local({ paste("RemoteSha: ", sha) ) writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) - + # Re-tar local({ old <- setwd(tempdir) on.exit(setwd(old), add = TRUE) - + tar(destfile, compression = "gzip") }) invisible() } - + # Extract the commit hash from a git archive. Git archives include the SHA1 # hash as the comment field of the tarball pax extended header # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) # For GitHub archives this should be the first header after the default one # (512 byte) header. renv_bootstrap_git_extract_sha1_tar <- function(bundle) { - + # open the bundle for reading # We use gzcon for everything because (from ?gzcon) # > Reading from a connection which does not supply a 'gzip' magic # > header is equivalent to reading from the original connection conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) on.exit(close(conn)) - + # The default pax header is 512 bytes long and the first pax extended header # with the comment should be 51 bytes long # `52 comment=` (11 chars) + 40 byte SHA1 hash len <- 0x200 + 0x33 res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) - + if (grepl("^52 comment=", res)) { sub("52 comment=", "", res) } else { NULL } } - + renv_bootstrap_install <- function(version, tarball, library) { - + # attempt to install it into project library dir.create(library, showWarnings = FALSE, recursive = TRUE) output <- renv_bootstrap_install_impl(library, tarball) - + # check for successful install status <- attr(output, "status") if (is.null(status) || identical(status, 0L)) return(status) - + # an error occurred; report it header <- "installation of renv failed" lines <- paste(rep.int("=", nchar(header)), collapse = "") text <- paste(c(header, lines, output), collapse = "\n") stop(text) - + } - + renv_bootstrap_install_impl <- function(library, tarball) { - + # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" R <- file.path(bin, exe) - + args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", "-l", shQuote(path.expand(library)), shQuote(path.expand(tarball)) ) - + system2(R, args, stdout = TRUE, stderr = TRUE) - + } - + renv_bootstrap_platform_prefix <- function() { - + # construct version prefix version <- paste(R.version$major, R.version$minor, sep = ".") prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") - + # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) devel <- identical(R.version[["status"]], "Under development (unstable)") || identical(R.version[["nickname"]], "Unsuffered Consequences") - + if (devel) prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") - + # build list of path components components <- c(prefix, R.version$platform) - + # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() if (!is.na(prefix) && nzchar(prefix)) components <- c(prefix, components) - + # build prefix paste(components, collapse = "/") - + } - + renv_bootstrap_platform_prefix_impl <- function() { - + # if an explicit prefix has been supplied, use it prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) if (!is.na(prefix)) return(prefix) - + # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) - + # empty string on failure "" - + } - + renv_bootstrap_platform_prefix_auto <- function() { - + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) if (inherits(prefix, "error") || prefix %in% "unknown") { - + msg <- paste( "failed to infer current operating system", "please file a bug report at https://github.com/rstudio/renv/issues", sep = "; " ) - + warning(msg) - + } - + prefix - + } - + renv_bootstrap_platform_os <- function() { - + sysinfo <- Sys.info() sysname <- sysinfo[["sysname"]] - + # handle Windows + macOS up front if (sysname == "Windows") return("windows") else if (sysname == "Darwin") return("macos") - + # check for os-release files for (file in c("/etc/os-release", "/usr/lib/os-release")) if (file.exists(file)) return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) - + # check for redhat-release files if (file.exists("/etc/redhat-release")) return(renv_bootstrap_platform_os_via_redhat_release()) - + "unknown" - + } - + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { - + # read /etc/os-release release <- utils::read.table( file = file, @@ -672,13 +713,13 @@ local({ comment.char = "#", stringsAsFactors = FALSE ) - + vars <- as.list(release$Value) names(vars) <- release$Key - + # get os name os <- tolower(sysinfo[["sysname"]]) - + # read id id <- "unknown" for (field in c("ID", "ID_LIKE")) { @@ -687,7 +728,7 @@ local({ break } } - + # read version version <- "unknown" for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { @@ -696,17 +737,17 @@ local({ break } } - + # join together paste(c(os, id, version), collapse = "-") - + } - + renv_bootstrap_platform_os_via_redhat_release <- function() { - + # read /etc/redhat-release contents <- readLines("/etc/redhat-release", warn = FALSE) - + # infer id id <- if (grepl("centos", contents, ignore.case = TRUE)) "centos" @@ -714,73 +755,73 @@ local({ "redhat" else "unknown" - + # try to find a version component (very hacky) version <- "unknown" - + parts <- strsplit(contents, "[[:space:]]")[[1L]] for (part in parts) { - + nv <- tryCatch(numeric_version(part), error = identity) if (inherits(nv, "error")) next - + version <- nv[1, 1] break - + } - + paste(c("linux", id, version), collapse = "-") - + } - + renv_bootstrap_library_root_name <- function(project) { - + # use project name as-is if requested asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") if (asis) return(basename(project)) - + # otherwise, disambiguate based on project's path id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) paste(basename(project), id, sep = "-") - + } - + renv_bootstrap_library_root <- function(project) { - + prefix <- renv_bootstrap_profile_prefix() - + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) if (!is.na(path)) return(paste(c(path, prefix), collapse = "/")) - + path <- renv_bootstrap_library_root_impl(project) if (!is.null(path)) { name <- renv_bootstrap_library_root_name(project) return(paste(c(path, prefix, name), collapse = "/")) } - + renv_bootstrap_paths_renv("library", project = project) - + } - + renv_bootstrap_library_root_impl <- function(project) { - + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) if (!is.na(root)) return(root) - + type <- renv_bootstrap_project_type(project) if (identical(type, "package")) { userdir <- renv_bootstrap_user_dir() return(file.path(userdir, "library")) } - + } - + renv_bootstrap_validate_version <- function(version, description = NULL) { - + # resolve description file # # avoid passing lib.loc to `packageDescription()` below, since R will @@ -788,122 +829,121 @@ local({ # this function should only be called after 'renv' is loaded # https://github.com/rstudio/renv/issues/1625 description <- description %||% packageDescription("renv") - + # check whether requested version 'version' matches loaded version of renv sha <- attr(version, "sha", exact = TRUE) valid <- if (!is.null(sha)) renv_bootstrap_validate_version_dev(sha, description) else renv_bootstrap_validate_version_release(version, description) - + if (valid) return(TRUE) - + # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } - + # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] - ) - - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" + sha = if (dev) description[["RemoteSha"]] ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) - + FALSE - + } - + renv_bootstrap_validate_version_dev <- function(version, description) { expected <- description[["RemoteSha"]] is.character(expected) && startswith(expected, version) } - + renv_bootstrap_validate_version_release <- function(version, description) { expected <- description[["Version"]] is.character(expected) && identical(expected, version) } - + renv_bootstrap_hash_text <- function(text) { - + hashfile <- tempfile("renv-hash-") on.exit(unlink(hashfile), add = TRUE) - + writeLines(text, con = hashfile) tools::md5sum(hashfile) - + } - + renv_bootstrap_load <- function(project, libpath, version) { - + # try to load renv from the project library if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) return(FALSE) - + # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) - + # execute renv load hooks, if any hooks <- getHook("renv::autoload") for (hook in hooks) if (is.function(hook)) tryCatch(hook(), error = warnify) - + # load the project renv::load(project) - + TRUE - + } - + renv_bootstrap_profile_load <- function(project) { - + # if RENV_PROFILE is already set, just use that profile <- Sys.getenv("RENV_PROFILE", unset = NA) if (!is.na(profile) && nzchar(profile)) return(profile) - + # check for a profile file (nothing to do if it doesn't exist) path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) if (!file.exists(path)) return(NULL) - + # read the profile, and set it if it exists contents <- readLines(path, warn = FALSE) if (length(contents) == 0L) return(NULL) - + # set RENV_PROFILE profile <- contents[[1L]] if (!profile %in% c("", "default")) Sys.setenv(RENV_PROFILE = profile) - + profile - + } - + renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) return(file.path("profiles", profile, "renv")) } - + renv_bootstrap_profile_get <- function() { profile <- Sys.getenv("RENV_PROFILE", unset = "") renv_bootstrap_profile_normalize(profile) } - + renv_bootstrap_profile_set <- function(profile) { profile <- renv_bootstrap_profile_normalize(profile) if (is.null(profile)) @@ -911,25 +951,25 @@ local({ else Sys.setenv(RENV_PROFILE = profile) } - + renv_bootstrap_profile_normalize <- function(profile) { - + if (is.null(profile) || profile %in% c("", "default")) return(NULL) - + profile - + } - + renv_bootstrap_path_absolute <- function(path) { - + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( substr(path, 1L, 1L) %in% c(letters, LETTERS) && substr(path, 2L, 3L) %in% c(":/", ":\\") ) - + } - + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") root <- if (renv_bootstrap_path_absolute(renv)) NULL else project @@ -937,50 +977,50 @@ local({ components <- c(root, renv, prefix, ...) paste(components, collapse = "/") } - + renv_bootstrap_project_type <- function(path) { - + descpath <- file.path(path, "DESCRIPTION") if (!file.exists(descpath)) return("unknown") - + desc <- tryCatch( read.dcf(descpath, all = TRUE), error = identity ) - + if (inherits(desc, "error")) return("unknown") - + type <- desc$Type if (!is.null(type)) return(tolower(type)) - + package <- desc$Package if (!is.null(package)) return("package") - + "unknown" - + } - + renv_bootstrap_user_dir <- function() { dir <- renv_bootstrap_user_dir_impl() path.expand(chartr("\\", "/", dir)) } - + renv_bootstrap_user_dir_impl <- function() { - + # use local override if set override <- getOption("renv.userdir.override") if (!is.null(override)) return(override) - + # use R_user_dir if available tools <- asNamespace("tools") if (is.function(tools$R_user_dir)) return(tools$R_user_dir("renv", "cache")) - + # try using our own backfill for older versions of R envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") for (envvar in envvars) { @@ -988,7 +1028,7 @@ local({ if (!is.na(root)) return(file.path(root, "R/renv")) } - + # use platform-specific default fallbacks if (Sys.info()[["sysname"]] == "Windows") file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") @@ -996,109 +1036,109 @@ local({ "~/Library/Caches/org.R-project.R/R/renv" else "~/.cache/R/renv" - + } - + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { sha <- sha %||% attr(version, "sha", exact = TRUE) parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) paste(parts, collapse = "") } - + renv_bootstrap_exec <- function(project, libpath, version) { if (!renv_bootstrap_load(project, libpath, version)) renv_bootstrap_run(version, libpath) } - + renv_bootstrap_run <- function(version, libpath) { - + # perform bootstrap bootstrap(version, libpath) - + # exit early if we're just testing bootstrap if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) return(TRUE) - + # try again to load if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { return(renv::load(project = getwd())) } - + # failed to download or load renv; warn the user msg <- c( "Failed to find an renv installation: the project will not be loaded.", "Use `renv::activate()` to re-initialize the project." ) - + warning(paste(msg, collapse = "\n"), call. = FALSE) - + } - + renv_json_read <- function(file = NULL, text = NULL) { - + jlerr <- NULL - + # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - - json <- catch(renv_json_read_jsonlite(file, text)) + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) - + jlerr <- json - + } - + # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) - + # report an error if (!is.null(jlerr)) stop(jlerr) else stop(json) - + } - + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } - + renv_json_read_default <- function(file = NULL, text = NULL) { - + # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - + # if any are found, replace them with placeholders replaced <- text strings <- character() replacements <- character() - + if (!identical(c(locs), -1L)) { - + # get the string values starts <- locs ends <- locs + attr(locs, "match.length") - 1L strings <- substring(text, starts, ends) - + # only keep those requiring escaping strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - + # compute replacements replacements <- sprintf('"\032%i\032"', seq_along(strings)) - + # replace the strings mapply(function(string, replacement) { replaced <<- sub(string, replacement, replaced, fixed = TRUE) }, strings, replacements) - + } - + # transform the JSON into something the R parser understands transformed <- replaced transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) @@ -1106,38 +1146,38 @@ local({ transformed <- gsub("[]}]", ")", transformed, perl = TRUE) transformed <- gsub(":", "=", transformed, fixed = TRUE) text <- paste(transformed, collapse = "\n") - + # parse it json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - + # construct map between source strings, replaced strings map <- as.character(parse(text = strings)) names(map) <- as.character(parse(text = replacements)) - + # convert to list map <- as.list(map) - + # remap strings in object - remapped <- renv_json_remap(json, map) - + remapped <- renv_json_read_remap(json, map) + # evaluate eval(remapped, envir = baseenv()) - + } - - renv_json_remap <- function(json, map) { - + + renv_json_read_remap <- function(json, map) { + # fix names if (!is.null(names(json))) { lhs <- match(names(json), names(map), nomatch = 0L) rhs <- match(names(map), names(json), nomatch = 0L) names(json)[rhs] <- map[lhs] } - + # fix values if (is.character(json)) return(map[[json]] %||% json) - + # handle true, false, null if (is.name(json)) { text <- as.character(json) @@ -1148,16 +1188,16 @@ local({ else if (text == "null") return(NULL) } - + # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } - + json - + } # load the renv profile, if any @@ -1177,4 +1217,4 @@ local({ invisible() -}) +}) \ No newline at end of file From 14aabe44691c80a5fc62c32b499bdf733df39259 Mon Sep 17 00:00:00 2001 From: William Ridgeway <10358980+wrridgeway@users.noreply.github.com> Date: Tue, 28 May 2024 09:52:42 -0500 Subject: [PATCH 2/3] Remove common area specific valuation (#47) * Remove common area code * Bump renv and R versions, renv repo * add renv reqs * Bump pre-commit renv version --- params.yaml | 4 ---- pipeline/02-assess.R | 12 +----------- pipeline/05-finalize.R | 1 - pipeline/07-export.R | 5 ----- renv/activate.R | 5 ----- 5 files changed, 1 insertion(+), 26 deletions(-) diff --git a/params.yaml b/params.yaml index 0ab1227..4612772 100644 --- a/params.yaml +++ b/params.yaml @@ -337,10 +337,6 @@ model: # Parameters used in the assess stage to finalize the intial model predictions pv: - # For nonlivable units, anything below this value gets the same value as the - # prior year - nonlivable_threshold: 1000 - # Cap the proportion of the PIN's total value dedicated to land. This is # necessary since sometimes the model provides low predictions relative to the # land rates created by Valuations diff --git a/pipeline/02-assess.R b/pipeline/02-assess.R index 9020de9..50449b5 100644 --- a/pipeline/02-assess.R +++ b/pipeline/02-assess.R @@ -105,17 +105,7 @@ assessment_data_bldg <- assessment_data_pred %>% na.rm = TRUE ), pred_pin_final_fmv = bldg_total_value_livable * - (adj_pro_rate / bldg_total_proration_rate_livable), - # For certain units (common areas), we want to have a consistent low value - # across time (usually $10) - pred_pin_final_fmv = case_when( - meta_modeling_group == "NONLIVABLE" & - (meta_mailed_tot * 10) <= params$pv$nonlivable_threshold ~ - meta_mailed_tot * 10, - meta_modeling_group == "NONLIVABLE" & - is.na(meta_mailed_tot) ~ 10, - TRUE ~ pred_pin_final_fmv - ) + (adj_pro_rate / bldg_total_proration_rate_livable) ) %>% ungroup() diff --git a/pipeline/05-finalize.R b/pipeline/05-finalize.R index 9b3f85d..bbe182c 100644 --- a/pipeline/05-finalize.R +++ b/pipeline/05-finalize.R @@ -97,7 +97,6 @@ metadata <- tibble::tibble( cv_no_improve = params$cv$no_improve, cv_split_prop = params$cv$split_prop, cv_best_metric = params$cv$best_metric, - pv_nonlivable_threshold = params$pv$nonlivable_threshold, pv_land_pct_of_total_cap = params$pv$land_pct_of_total_cap, pv_round_break = list(params$pv$round_break), pv_round_to_nearest = list(params$pv$round_to_nearest), diff --git a/pipeline/07-export.R b/pipeline/07-export.R index 82425f1..d145625 100644 --- a/pipeline/07-export.R +++ b/pipeline/07-export.R @@ -110,11 +110,6 @@ assessment_pin_prepped <- assessment_pin %>% ", ", loc_property_zip ), meta_pin10 = str_sub(meta_pin, 1, 10), - flag_common_area = replace_na( - as.logical(as.numeric(flag_prior_near_to_pred_unchanged)) & - prior_near_tot <= params$pv$nonlivable_threshold, - 0 - ), across( ends_with("added_later") & where(is.logical), ~ as.numeric(.x) diff --git a/renv/activate.R b/renv/activate.R index 017de50..4bfe543 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -650,7 +650,6 @@ local({ auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) if (is.na(auto) && getRversion() >= "4.4.0") auto <- "TRUE" - if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -847,13 +846,11 @@ local({ paste("rstudio/renv", description[["RemoteSha"]], sep = "@") else paste("renv", description[["Version"]], sep = "@") - # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], sha = if (dev) description[["RemoteSha"]] ) - fmt <- heredoc(" renv %1$s was loaded from project library, but this project is configured to use renv %2$s. - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. @@ -1080,7 +1077,6 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1159,7 +1155,6 @@ local({ # remap strings in object remapped <- renv_json_read_remap(json, map) - # evaluate eval(remapped, envir = baseenv()) From 2a066b51017ee649b280417c757db2aacaa302d7 Mon Sep 17 00:00:00 2001 From: Jean Cochrane Date: Tue, 28 May 2024 13:41:39 -0500 Subject: [PATCH 3/3] Fix file permissions error in `style-files` pre-commit hook (#49) * Fix file permissions error in `style-files` pre-commit hook by requiring serial execution * Switch to ccao-data/actions/pre-commit action in pre-commit workflow * Temporarily pin pre-commit action to time-pre-commit branch * Revert "Fix file permissions error in `style-files` pre-commit hook by requiring serial execution" This reverts commit f079810997e3a0e9027ead6ff30e2b88f9d55681. * Reapply "Fix file permissions error in `style-files` pre-commit hook by requiring serial execution" This reverts commit bc23e2d3520c45289edd55ebb7c1e39575689c9e. * Revert "Temporarily pin pre-commit action to time-pre-commit branch" This reverts commit f572f30ce59dff5199cc80bb487e092688606f69. --- .github/workflows/pre-commit.yaml | 28 +++------------------------- .pre-commit-config.yaml | 3 ++- 2 files changed, 5 insertions(+), 26 deletions(-) diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml index 51ff54d..f1b6fd2 100644 --- a/.github/workflows/pre-commit.yaml +++ b/.github/workflows/pre-commit.yaml @@ -10,29 +10,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - - name: Setup python - uses: actions/setup-python@v4 - with: - python-version: 3.x - - - name: Install pre-commit - run: python -m pip install pre-commit - shell: bash - - - name: Freeze dependencies - run: python -m pip freeze --local - shell: bash - - - name: Cache pre-commit environment - uses: actions/cache@v3 - with: - path: | - ~/.cache/pre-commit - ~/.cache/R - key: pre-commit-3-${{ env.pythonLocation }}-${{ hashFiles('.pre-commit-config.yaml') }} - - - name: Run pre-commit - run: pre-commit run --show-diff-on-failure --color=always --all-files - shell: bash + - name: Run pre-commit checks + uses: ccao-data/actions/pre-commit@main diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 58c9364..7a998d9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,6 +6,7 @@ repos: hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] + require_serial: true - id: lintr - id: readme-rmd-rendered exclude: reports/README.md @@ -25,4 +26,4 @@ repos: name: Don't commit common R artifacts entry: Cannot commit .Rhistory, .RData, .Rds or .rds. language: fail - files: '\.(Rhistory|RData|Rds|rds)$' \ No newline at end of file + files: '\.(Rhistory|RData|Rds|rds)$'