Merge branch 'master' into implicit-return

.dev/CRAN_Release.cmd

@@ -18,9 +18,7 @@ potools::check_untranslated_src(message_db)
 potools::po_extract(custom_translation_functions = dt_custom_translators)
 
 # 2) Open a PR with the new templates & contact the translators
-#   * zh_CN: @hongyuanjia
-#   * pt_BR: @rffontenelle
-#   * es: @rikivillalba
+#    using @Rdatatable/<lang>, e.g. @Rdatatable/chinese
 ## Translators to submit commits with translations to this PR
 ##   [or perhaps, if we get several languages, each to open
 ##    its own PR and merge to main translation PR]

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,35 @@
+As contributors and maintainers of this project, and in the interest of fostering an open and welcoming community, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic addresses, without explicit permission
+* Other unethical or unprofessional conduct
+
+Project members with the Committer role have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project members commit themselves to fairly and consistently apply these principles to every aspect of managing this project. Project maintainers who do not follow or enforce the Code of Conduct may be permanently removed from the project team.
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community.
+
+
+## Reporting
+
+Project members with the Committer role or the CRAN Maintainer role are pledged to promptly address any reported issues. Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to any individual with this role.
+
+Those who prefer to report in a way that is independent of the current Committers and Maintainer may instead contact the Community Engagement Coordinator by e-mailing [r.data.table\@gmail.com](mailto:[email protected]). Messages sent to this e-mail address will be visible only to the current Community Engagement Coordinator, a position always held by an individual who is not a Committer or CRAN Maintainer of the package.
+
+The current Committers are Toby Dylan Hocking (@tdhock), Matt Dowle (@mattdowle), Arun Srinivasan (@arunsrinivasan), Jan Gorecki (@jangorecki), Michael Chirico (@MichaelChirico), and Benjamin Schwendinger (@ben-schwen).
+
+The current CRAN Maintainer is Tyson Barrett (@tysonstanley).
+
+The current Community Engagement Coordinator is Kelly Bodwin (@kbodwin).
+
+All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. Complaint respondents are obligated to maintain confidentiality with regard to the reporter of an incident.
+
+This Code of Conduct is adapted from the [Contributor Covenant, version 1.3.0](https://www.contributor-covenant.org/version/1/3/0/code-of-conduct/), available at [https://www.contributor-covenant.org/version/1/3/0/](https://www.contributor-covenant.org/version/1/3/0/), and the Swift Code of Conduct.

GOVERNANCE.md

@@ -72,6 +72,14 @@ Functionality that is out of current scope:
 * How to obtain this role: (1) merge into master a PR adding role="cre" to DESCRIPTION, and (2) submit updated package to CRAN (previous CRAN Maintainer will have to confirm change by email to CRAN). 
 * How this role is recognized: credited via role="cre" in DESCRIPTION, so they appear as Maintainer on CRAN. 
 
+## Community Engagement Coordinator
+
+* Definition: An individual who is involved in the project but does **not** also occupy the Committer or CRAN Maintainer role.  In charge of maintaining The Raft blog, preparing Seal of Approval Applications, addressing Code of Conduct violations, and planning social or community events.
+
+* How to obtain this role: At the discretion of the current Community Engagement Coordinator(s) in conversation with the current Committers.
+
+* How this role is recognized: Holds the Owner role in the [rdatatable-community organization](https://github.com/orgs/rdatatable-community/people) on GitHub.
+
 # Decision-making processes
 
 ## Definition of Consensus
@@ -98,19 +106,35 @@ There is no special process for changing this document. Submit a PR and ask for
 
 Please also make a note in the change log under [`# Governance history`](#governance-history)
 
-# Code of conduct
+# Finances and Funding
+
+There is currently no mechanism for the data.table project to receive funding as an entity.  
+
+Funding support for this project therefore may come in two forms:
+
+## Individual external funding
 
-As contributors of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+Any individual developer or community member of data.table may apply for and receive funding for their work on the project.  Individuals or groups seeking funding support are strongly encouraged to consult directly with the data.table Project Members (by initiating an Issue on GitHub) to ensure funds are used meaningfully. Formally, however, decisions about use of funds are governed by the individual grantee(s) and their contract with the funding agency. 
 
-We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion, etc.
+There is no guarantee that funded work will be incorporated into the data.table package; any contributions, whether funded or unfunded, are subject to the same review process as outlined above.
 
-Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+## Direct donations
 
-Committers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. A person with special roles who does not follow the Code of Conduct may have their roles revoked.
+Direct donations to the project may be made via GitHub Sponsorships, which allow individuals to fund a specific developer.  If the current CRAN Maintainer offers a personal sponsorship option, donations may be made to them to support the project in general.
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or emailing one or more of the Committers.
+## Decision-making for future opportunities
 
-This Code of Conduct is adapted from Tidyverse code of conduct.
+We here outline a procedure for disbursing funds, should this project in the future become a directly fundable entity (e.g. an LLC or a subsidiary of an umbrella LLC).
+
+Funds acquired by the data.table project will be disbursed at the discretion of the **Committers**, defined as above.  The **CRAN Maintainer** will have authority to make final decisions in the event that no consensus is reached among committers prior to deadlines for use of funds, and will be responsible for disbursement logistics.
+
+# Code of conduct
+
+The full Code of Conduct can be found [here](CODE_OF_CONDUCT.md), including details for reporting violations.
+
+## Reporting Responsibility
+
+Committers and the Community Engagement Coordinator pledge to address any publicly posted issues or privately sent messages regarding Code of Conduct violations in a respectful and timely manner.
 
 # Version numbering
 
@@ -124,6 +148,8 @@ data.table Version line in DESCRIPTION typically has the following meanings
 
 # Governance history
 
+Feb 2025: add Finances and Funding section, update Code of Conduct section to be a brief summary and reference the broader CoC document.
+
 Jan 2025: clarify that edits to governance should notify all committers, and that role names are proper nouns (i.e., upper-case) throughout.
 
 Feb 2024: change team name/link maintainers to committers, to be consistent with role defined in governance.

NAMESPACE

@@ -206,3 +206,6 @@ S3method(format_list_item, data.frame)
 
 export(fdroplevels, setdroplevels)
 S3method(droplevels, data.table)
+
+# sort_by added in R 4.4.0, #6662, https://stat.ethz.ch/pipermail/r-announce/2024/000701.html
+if (getRversion() >= "4.4.0") S3method(sort_by, data.table)  

NEWS.md

@@ -2,7 +2,9 @@
 
 # data.table [v1.17.99](https://github.com/Rdatatable/data.table/milestone/35)  (in development)
 
+## NEW FEATURES
 
+1. New `sort_by()` method for data.tables, [#6662](https://github.com/Rdatatable/data.table/issues/6662). It uses `forder()` to improve upon the data.frame method and also match `DT[order(...)]` behavior with respect to locale. Thanks @rikivillalba for the suggestion and PR.
 
 # data.table [v1.17.0](https://github.com/Rdatatable/data.table/milestone/34)  (20 Feb 2025)
 
@@ -20,7 +22,7 @@ rowwiseDT(
   a=,b=,c=,  d=,
   1, 2, "a", 2:3,
   3, 4, "b", list("e"),
-  5, 6, "c", ~a+b,
+  5, 6, "c", ~a+b
 )
 #>        a     b      c      d
 #>    <num> <num> <char> <list>

R/data.table.R

@@ -2454,7 +2454,7 @@ split.data.table = function(x, f, drop = FALSE, by, sorted = FALSE, keep.by = TR
     # same as split.data.frame - handling all exceptions, factor orders etc, in a single stream of processing was a nightmare in factor and drop consistency
     # evaluate formula mirroring split.data.frame #5392. Mimics base::.formula2varlist.
     if (inherits(f, "formula"))
-        f = eval(attr(terms(f), "variables"), x, environment(f))
+        f = formula_vars(f, x)
     # be sure to use x[ind, , drop = FALSE], not x[ind], in case downstream methods don't follow the same subsetting semantics (#5365)
     return(lapply(split(x = seq_len(nrow(x)), f = f, drop = drop, ...), function(ind) x[ind, , drop = FALSE]))
   }
@@ -2526,6 +2526,18 @@ split.data.table = function(x, f, drop = FALSE, by, sorted = FALSE, keep.by = TR
   }
 }
 
+sort_by.data.table <- function(x, y, ...)
+{
+  if (!cedta()) return(NextMethod()) # nocov
+  if (inherits(y, "formula"))
+    y <- formula_vars(y, x)
+  if (!is.list(y))
+    y <- list(y)
+  # use forder instead of base 'order'
+  o <- do.call(forder, c(unname(y), list(...)))
+  x[o, , drop=FALSE]
+}
+
 # TO DO, add more warnings e.g. for by.data.table(), telling user what the data.table syntax is but letting them dispatch to data.frame if they want
 
 copy = function(x) {

R/print.data.table.R

@@ -86,6 +86,7 @@ print.data.table = function(x, topn=getOption("datatable.print.topn"),
     if (show.indices) toprint = cbind(toprint, index_dt)
   }
   require_bit64_if_needed(x)
+  classes = classes1(toprint)
   toprint=format.data.table(toprint, na.encode=FALSE, timezone = timezone, ...)  # na.encode=FALSE so that NA in character cols print as <NA>
 
   # FR #353 - add row.names = logical argument to print.data.table
@@ -100,7 +101,6 @@ print.data.table = function(x, topn=getOption("datatable.print.topn"),
       factor = "<fctr>", POSIXct = "<POSc>", logical = "<lgcl>",
       IDate = "<IDat>", integer64 = "<i64>", raw = "<raw>",
       expression = "<expr>", ordered = "<ord>")
-    classes = classes1(x)
     abbs = unname(class_abb[classes])
     if ( length(idx <- which(is.na(abbs))) ) abbs[idx] = paste0("<", classes[idx], ">")
     toprint = rbind(abbs, toprint)

R/utils.R

@@ -212,3 +212,11 @@ rss = function() {  #5515 #5517
   round(ans / 1024.0, 1L)  # return MB
   # nocov end
 }
+
+formula_vars = function(f, x) { # .formula2varlist is not API and seems to have appeared after R-4.2, #6841
+  terms <- terms(f)
+  setNames(
+    eval(attr(terms, "variables"), x, environment(f)),
+    attr(terms, "term.labels")
+  )
+}

Seal_of_Approval.md

@@ -31,3 +31,4 @@ Translates `data.table` syntax to a different syntax, or provides helper functio
 Not necessarily directly connected to `data.table`, but deliberately follows the [core philosophies of `data.table`](https://github.com/Rdatatable/data.table/blob/master/GOVERNANCE.md#the-r-package).
 
 - [collapse](https://github.com/SebKrantz/collapse): Advanced and Fast Data Transformation in R.
+

inst/tests/tests.Rraw

@@ -21042,3 +21042,37 @@ test(2304.100, set(copy(DT), i=2L, j=c("L1", "L2"), value=list(list(NULL), list(
 
 # the integer overflow in #6729 is only noticeable with UBSan
 test(2305, { fread(testDir("issue_6729.txt.bz2")); TRUE })
+
+if (exists("sort_by", "package:base")) {
+  # sort_by.data.table
+  DT1 = data.table(a=c(1, 3, 2, NA, 3), b=4:0)
+  DT2 = data.table(a=c("c", "a", "B")) # data.table uses C-locale and should sort_by if cedta()
+  DT3 = data.table(a=c(1, 2, 3), b=list(c("a", "b", "", NA), c(1, 3, 2, 0), c(TRUE, TRUE, FALSE, NA))) # list column
+
+  # sort_by.data.table: basics
+  test(2306.01, sort_by(DT1, ~a + b), data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+  test(2306.02, sort_by(DT1, ~I(a + b)), data.table(a=c(3, 2, 1, 3, NA), b=c(0L, 2L, 4L, 3L, 1L)))
+  test(2306.03, sort_by(DT2, ~a), data.table(a=c("B", "a", "c")))
+
+  # sort_by.data.table: list columns.
+  # NOTE 1: .formula2varlist works well with list columns.
+  # NOTE 2: 4 elem in DT of 3 row because forderv takes a list column as a DT.
+  test(2306.04, sort_by(DT3, ~b), DT3[order(b)]) # should be consistent.
+
+  # sort_by.data.table: additional C-locale sorting
+  test(2306.10, DT2[, sort_by(.SD, a)], data.table(a=c("B", "a", "c")))
+  test(2306.11, DT2[, sort_by(.SD, ~a)], data.table(a=c("B", "a", "c")))
+
+  # sort_by.data.table: various working interfaces
+  test(2306.20, sort_by(DT1, list(DT1$a, DT1$b)), data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+  test(2306.21, sort_by(DT1, DT1[, .(a, b)]), data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+  test(2306.22, DT1[, sort_by(.SD, .(a, b))], data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+  test(2306.23, DT1[, sort_by(.SD, ~a + b)], data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+  test(2306.24, DT1[, sort_by(.SD, ~.(a, b))], data.table(a=c(1, 2, 3, 3, NA), b=c(4L, 2L, 0L, 3L, 1L)))
+}
+
+DT <- data.table(a = 1:2, b = 2:1)
+setindex(DT, b)
+# make sure that print(DT) doesn't warn due to the header missing index column types, #6806
+# can't use output= here because the print() call is outside withCallingHandlers(...)
+test(2307, { capture.output(print(DT, class = TRUE, show.indices = TRUE)); TRUE })

man/setorder.Rd

@@ -5,6 +5,7 @@
 \alias{fastorder}
 \alias{forder}
 \alias{forderv}
+\alias{sort_by}
 
 \title{Fast row reordering of a data.table by reference}
 \description{
@@ -32,6 +33,7 @@ setorderv(x, cols = colnames(x), order=1L, na.last=FALSE)
 # optimised to use data.table's internal fast order
 # x[order(., na.last=TRUE)]
 # x[order(., decreasing=TRUE)]
+# sort_by(x, ., na.last=TRUE, decreasing=FALSE)    # R >= 4.4.0
 }
 \arguments{
 \item{x}{ A \code{data.table}. }
@@ -46,7 +48,7 @@ when \code{b} is of type \code{character} as well. }
 \code{order} must be either \code{1} or equal to that of \code{cols}. If
 \code{length(order) == 1}, it is recycled to \code{length(cols)}. }
 \item{na.last}{ \code{logical}. If \code{TRUE}, missing values in the data are placed last; if \code{FALSE}, they are placed first; if \code{NA} they are removed.
-\code{na.last=NA} is valid only for \code{x[order(., na.last)]} and its
+\code{na.last=NA} is valid only for \code{x[order(., na.last)]} and related \code{sort_by(x, .)} (\eqn{\R \ge 4.4.0}) and its
 default is \code{TRUE}. \code{setorder} and \code{setorderv} only accept
 \code{TRUE}/\code{FALSE} with default \code{FALSE}. }
 }
@@ -71,8 +73,8 @@ sets the \code{sorted} attribute.
 
 \code{na.last} argument, by default, is \code{FALSE} for \code{setorder} and
 \code{setorderv} to be consistent with \code{data.table}'s \code{setkey} and
-is \code{TRUE} for \code{x[order(.)]} to be consistent with \code{base::order}.
-Only \code{x[order(.)]} can have \code{na.last = NA} as it is a subset operation
+is \code{TRUE} for \code{x[order(.)]} and \code{sort_by(x, .)} (\eqn{\R \ge 4.4.0}) to be consistent with \code{base::order}.
+Only \code{x[order(.)]} (and related \code{sort_by(x, .)}) can have \code{na.last = NA} as it is a subset operation
 as opposed to \code{setorder} or \code{setorderv} which reorders the data.table
 by reference.
 
@@ -96,6 +98,11 @@ was started in. By contrast, \code{"america" < "BRAZIL"} is always \code{FALSE}
 
 If \code{setorder} results in reordering of the rows of a keyed \code{data.table},
 then its key will be set to \code{NULL}.
+
+Starting from \R 4.4.0, \code{sort_by(x, y, \dots)} is the S3 method for the generic \code{sort_by} for \code{data.table}'s. 
+It uses the same formula or list interfaces as data.frame's \code{sort_by} but internally uses \code{data.table}'s fast ordering, 
+hence it behaves the same as \code{x[order(.)]} and takes the same optional named arguments and their defaults.
+
 }
 \value{
 The input is modified by reference, and returned (invisibly) so it can be used

src/dogroups.c

@@ -535,6 +535,11 @@ SEXP growVector(SEXP x, const R_len_t newlen)
   if (isNull(x)) error(_("growVector passed NULL"));
   PROTECT(newx = allocVector(TYPEOF(x), newlen));   // TO DO: R_realloc(?) here?
   if (newlen < len) len=newlen;   // i.e. shrink
+  if (!len) { // cannot memcpy invalid pointer, #6819
+    keepattr(newx, x);
+    UNPROTECT(1);
+    return newx;
+  }
   switch (TYPEOF(x)) {
   case RAWSXP:  memcpy(RAW(newx),     RAW(x),     len*SIZEOF(x)); break;
   case LGLSXP:  memcpy(LOGICAL(newx), LOGICAL(x), len*SIZEOF(x)); break;

src/utils.c

@@ -222,6 +222,14 @@ SEXP copyAsPlain(SEXP x) {
   }
   const int64_t n = XLENGTH(x);
   SEXP ans = PROTECT(allocVector(TYPEOF(x), n));
+  // aside: unlike R's duplicate we do not copy truelength here; important for dogroups.c which uses negative truelenth to mark its specials
+  if (ALTREP(ans))
+    internal_error(__func__, "copyAsPlain returning ALTREP for type '%s'", type2char(TYPEOF(x))); // # nocov
+  if (!n) { // cannot memcpy invalid pointer, #6819
+    DUPLICATE_ATTRIB(ans, x);
+    UNPROTECT(1);
+    return ans;
+  }
   switch (TYPEOF(x)) {
   case RAWSXP:
     memcpy(RAW(ans),     RAW(x),     n*sizeof(Rbyte));
@@ -250,9 +258,6 @@ SEXP copyAsPlain(SEXP x) {
     internal_error(__func__, "type '%s' not supported in %s", type2char(TYPEOF(x)), "copyAsPlain()"); // # nocov
   }
   DUPLICATE_ATTRIB(ans, x);
-  // aside: unlike R's duplicate we do not copy truelength here; important for dogroups.c which uses negative truelenth to mark its specials
-  if (ALTREP(ans))
-    internal_error(__func__, "copyAsPlain returning ALTREP for type '%s'", type2char(TYPEOF(x))); // # nocov
   UNPROTECT(1);
   return ans;
 }