Simpler ci test

.github/workflows/cml.yml

@@ -0,0 +1,22 @@
+name: update comment
+on: [pull_request]
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: comment
+        env:
+          TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          ISSUES_API=https://api.github.com/repos/$GITHUB_REPOSITORY/issues
+          CURL='curl -L -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2026-03-10"'
+          PR_API=$ISSUES_API/$PR_NUMBER/comments
+          FIRST_COMMENT_ID=$($CURL $PR_API?per_page=1 | grep '"id"' | head -1 | sed s/[^0-9]//g)
+          if [ "$FIRST_COMMENT_ID" == "" ]; then CMD=$PR_API; else CMD=$ISSUES_API/comments/$FIRST_COMMENT_ID; fi; echo $CMD
+          IURL=$(curl -F "file=@README-figure.png" -F "visibility=unlisted" https://picrd.com/api/upload | sed 's/.*image_url":"//' | sed 's/",".*//')
+          echo "[![tests-preview-facet.png]($IURL)](https://github.com) is the first comment from json" > comment.md
+          MD=$(sed 's/"/\\"/g' comment.md | awk '$1=$1' ORS='\\n')
+          echo '{"body":"'$MD'"}' > pr-comment.json
+          $CURL -X PATCH -H "Authorization: Bearer $TOKEN" $CMD -d "@pr-comment.json"

DESCRIPTION

@@ -1,12 +1,14 @@
 Package: atime
 Type: Package
 Title: Asymptotic Timing
-Version: 2026.5.29
+Version: 2026.5.30
 Depends: R (>= 3.5.0)
 Authors@R: c(
-    person("Toby", "Hocking",
-     email="toby.hocking@r-project.org",
-     role=c("aut", "cre")))
+ person("Toby", "Hocking",
+        email="toby.hocking@r-project.org",
+        role=c("aut", "cre"),
+        comment = c(ORCID="0000-0002-3146-0865"))
+    )
 Description: Computing and visualizing comparative
  asymptotic timings of different algorithms and code versions.
  Also includes functionality for comparing empirical timings with
@@ -17,7 +19,8 @@ Description: Computing and visualizing comparative
 License: GPL-3
 URL: https://github.com/tdhock/atime, https://atime-docs.netlify.app
 BugReports: https://github.com/tdhock/atime/issues
-Imports: data.table, bench, lattice, git2r, utils, stats, grDevices
+Imports: data.table, bench, lattice, gert, utils, stats, grDevices
+SystemRequirements: git command line program
 Suggests: 
     directlabels,
     ggplot2,

NEWS

@@ -1,3 +1,12 @@
+Changes in version 2026.5.30
+
+- switched from git2r to gert for running git from R.
+- atime_pkg() now works with repos that have sub-modules, via system("git submodule update --init --recursive").
+- atime_pkg() now uses label "install" instead of "CRAN" when installed version does not match CRAN version.
+- .ci/atime/tests.R can define base.ref="main" for repos where the default branch is not named master.
+- .ci/atime/tests.R can define remove.units="kilobytes" for repos where memory benchmarking results should be hidden.
+- atime_pkg_test_info() bugfix when pkg is not on CRAN.
+
 Changes in version 2026.5.29
 
 - atime_pkg() now uses only a common subset of columns of the measurements table from each test, so that each test can have different units to analyze.

R/test.R

@@ -35,6 +35,11 @@ atime_pkg_plot_files <- function(out.dir, test.info, pkg.results){
   issue <- character()
   for(Test in names(pkg.results)){
     atime.list <- pkg.results[[Test]]
+    if(is.character(test.info$remove.units)){
+      keep <- !atime.list$unit.col.vec %in% test.info$remove.units
+      ## don't use setdiff() here because it drops names.
+      atime.list$unit.col.vec <- atime.list$unit.col.vec[keep]
+    }
     best.list <- atime::references_best(atime.list)
     ref.dt <- best.list$ref[each.sign.rank==1]
     sec.dt <- best.list$meas[unit=="seconds"]
@@ -309,42 +314,49 @@ atime_pkg_test_info <- function(pkg.path=".", tests.dir=NULL){
   pkg.DESC <- file.path(pkg.path, "DESCRIPTION")
   DESC.mat <- read.dcf(pkg.DESC)
   Package <- DESC.mat[,"Package"]
-  repo <- git2r::repository(pkg.path)
-  HEAD.commit <- git2r::revparse_single(repo, "HEAD")
+  HEAD.commit <- gert::git_commit_id("HEAD",pkg.path)
   sha.vec <- c()
-  HEAD.name <- paste0("HEAD=",git2r::repository_head(repo)$name)
-  sha.vec[[HEAD.name]] <- git2r::sha(HEAD.commit)
-  installed_version <- tryCatch(paste(packageVersion(Package)), error=function(e)NULL)
-  if(!is.null(installed_version)){
-    CRAN.name <- paste0("CRAN=", installed_version)
-    sha.vec[[CRAN.name]] <- ""
-  }else{
+  HEAD.name <- paste0("HEAD=", gert::git_branch(pkg.path))
+  sha.vec[[HEAD.name]] <- HEAD.commit
+  installed_version <- tryCatch(paste(packageVersion(Package)), error=function(e)"(not installed)")
+  ap <- utils::available.packages()
+  installed_name <- "installed"
+  if(Package %in% rownames(ap)){
+    CRAN_version <- ap[Package,"Version"]
+    if(identical(CRAN_version, installed_version)){
+      installed_name <- "CRAN"
+    }else{
+      warning(sprintf(
+        "CRAN version=%s but installed version=%s fix via install.packages('%s')",
+        CRAN_version, installed_version, Package))
+    }
+  }
+  if(identical(installed_version, "(not installed)")){
     CRAN.name <- NA_character_
+  }else{
+    CRAN.name <- paste0(installed_name, "=", installed_version)
+    sha.vec[[CRAN.name]] <- ""
   }
-  ap <- utils::available.packages()
-  CRAN_version <- ap[Package,"Version"]
-  if(!identical(CRAN_version, installed_version)){
-    warning(sprintf(
-      "CRAN version=%s but installed version=%s fix via install.packages('%s')",
-      CRAN_version, installed_version, Package))
+  if(is.null(test.env$base.ref)){
+    test.env$base.ref <- Sys.getenv("GITHUB_BASE_REF", "master")
   }
-  base.ref <- Sys.getenv("GITHUB_BASE_REF", "master")
   base.commit <- tryCatch({
-    git2r::revparse_single(repo, base.ref)
+    gert::git_commit_info(test.env$base.ref, pkg.path)$id
   }, error=function(e){
     NULL
   })
-  base.name <- paste0("base=",base.ref)
-  if(git2r::is_commit(base.commit)){
-    add_if_new <- function(name, commit.obj){
-      sha <- git2r::sha(commit.obj)
-      if(!sha %in% sha.vec){
-        sha.vec[[name]] <<- sha
+  base.name <- paste0("base=", test.env$base.ref)
+  if(is.character(base.commit)){
+    maybe.new.list <- list()
+    maybe.new.list[[base.name]] <- base.commit
+    maybe.new.list[["merge-base"]] <- gert::git_merge_find_base(
+      base.commit, "HEAD", pkg.path)
+    for(maybe.new.name in names(maybe.new.list)){
+      maybe.new.sha <- maybe.new.list[[maybe.new.name]]
+      if(!maybe.new.sha %in% sha.vec){
+        sha.vec[[maybe.new.name]] <- maybe.new.sha
       }
     }
-    add_if_new(base.name, base.commit)
-    mb.commit <- git2r::merge_base(HEAD.commit, base.commit)
-    add_if_new("merge-base", mb.commit)
   }
   abbrev2name <- c(
     HEAD=HEAD.name,

R/versions.R

@@ -57,11 +57,10 @@ atime_versions_install <- function(Package, pkg.path, new.Package.vec, sha.vec,
     ## on GH actions windows tempfile() gives C:\Users\RUNNER~1\AppData\Local\Temp\Rtmpc9T5Us/working_dir\Rtmpu23suf\file5d41af35765
     tdir <- normalizePath(tempfile(), mustWork=FALSE)
     dir.create(tdir)
-    ## pkg.path may be path/to/repo/pkg
+    ## pkg.path may be in a sub-dir of git repo: path/to/repo/pkg
     norm.pkg.path <- normalizePath(pkg.path)
-    orig.repo <- git2r::repository(norm.pkg.path)
     ## path/to/repo root without trailing /.git
-    orig.repo.path <- normalizePath(dirname(orig.repo$path))
+    orig.repo.path <- normalizePath(gert::git_info(pkg.path)$path)
     ## /pkg
     pkg.suffix.in.repo <- sub(orig.repo.path, "", norm.pkg.path, fixed=TRUE)
     for(new.i in which(new.not.installed)){
@@ -78,14 +77,21 @@ atime_versions_install <- function(Package, pkg.path, new.Package.vec, sha.vec,
       }else{
         new.repo.path <- file.path(tdir, new.Package)
         unlink(new.repo.path, recursive=TRUE, force=TRUE)
-        repo <- git2r::clone(orig.repo.path, new.repo.path, progress=FALSE)
+        gert::git_clone(orig.repo.path, new.repo.path)
+        gert::git_branch_create(#and checkout
+          "atime-versions-testing", sha, repo=new.repo.path)
+        if(TRUE){
+          old.wd <- setwd(new.repo.path)
+          system("git submodule update --init --recursive")
+          setwd(old.wd)
+        }else{
+          submodule_tib <- gert::git_submodule_list(new.repo.path)
+          for(sub.i in seq_along(submodule_tib$name)){
+            gert::git_submodule_init(
+              submodule_tib$name[sub.i], overwrite=TRUE, repo=new.repo.path)
+          }
+        }
         new.pkg.path <- paste0(new.repo.path, pkg.suffix.in.repo)
-        tryCatch(
-          git2r::checkout(repo, branch=sha, force=TRUE),
-          error=function(e)stop(
-            e, " when trying to checkout ", sha))
-        ## before editing and installing, make sure directory has sha
-        ## suffix, for windows checks.
         unlink(file.path(new.pkg.path, "src", "*.o"))
         pkg.edit.fun(
           old.Package=Package, 

man/atime_pkg.Rd

@@ -87,9 +87,8 @@ if(FALSE){
   ## Clone binsegRcpp, and checkout a branch which has performance tests.
   tdir <- tempfile()
   dir.create(tdir)
-  git2r::clone("https://github.com/tdhock/binsegRcpp", tdir)
-  repo <- git2r::repository(tdir)
-  git2r::checkout(repo, "another-branch")
+  gert::git_clone("https://github.com/tdhock/binsegRcpp", tdir)
+  gert::git_branch_checkout("another-branch", repo=tdir)
 
   ## Run one test.
   info.env <- atime::atime_pkg_test_info(tdir)

man/atime_versions.Rd

@@ -53,7 +53,7 @@ atime_versions(
   Each version should be either \code{""} (to use currently installed
   version of package, or if missing, install most recent
   version from CRAN) or a SHA1 hash, which is passed as branch
-  arg to \code{git2r::checkout}; version names used to identify/interpret
+  to git checkout; version names used to identify/interpret
   the output/plots.
 }
 \value{list of class atime with elements \code{seconds.limit} (numeric
@@ -72,7 +72,7 @@ if(FALSE){
 
   tdir <- tempfile()
   dir.create(tdir)
-  git2r::clone("https://github.com/tdhock/binsegRcpp", tdir)
+  gert::git_clone("https://github.com/tdhock/binsegRcpp", tdir)
   atime.list <- atime::atime_versions(
     pkg.path=tdir,
     setup={
@@ -89,7 +89,7 @@ if(FALSE){
 
   gdir <- tempfile()
   dir.create(gdir)
-  git2r::clone("https://github.com/tdhock/grates", gdir)
+  gert::git_clone("https://github.com/tdhock/grates", gdir)
   glist <- atime::atime_versions(
     file.path(gdir,"pkg"),
     current = "1aae646888dcedb128c9076d9bd53fcb4075dcda",