Passing r cmd check

.Rbuildignore

@@ -4,11 +4,11 @@
 ^\.github$
 ^CODE_OF_CONDUCT\.md$
 ^LICENSE\.md$
-^man/commits_range\.Rd$
-^man/blob_to_file\.Rd$
-^man/install_minio\.Rd$
-^man/sys_tempdir\.Rd$
-^man/sys_tempfile\.Rd$
-^man/as_repo\.Rd$
-^man/as_commit\.Rd$
 ^CITATION\.cff$
+^codemeta.json$
+^.lintr$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^inst/scratch$
+^inst/mc$

.github/workflows/pkgdown.yaml

@@ -3,8 +3,6 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:

.gitignore

@@ -1,7 +1,111 @@
-.Rproj.user
+inst/doc
+inst/scratch
+inst/mc
+docs
+tests/testthat/*.log
+### R ###
+# History files
+*Rhistory
 .Rhistory
-.Rdata
+.Rapp.history
+.Rproj.user
+.RData
+.Ruserdata
+# Session Data files
+# User-specific files
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
-.DS_Store
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
 .quarto
-inst/doc
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+# End of https://www.toptal.com/developers/gitignore/api/r,c++,macos,microsoftoffice
+### C++ ###
+# Prerequisites
+*.d
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+# Precompiled Headers
+*.gch
+*.pch
+# Linker files
+*.ilk
+# Debugger Files
+*.pdb
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+# Fortran module files
+*.mod
+*.smod
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+# Executables
+*.exe
+*.out
+*.app
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+# Icon must end with two \r
+Icon
+# Thumbnails
+._*
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+### MicrosoftOffice ###
+*.tmp
+# Word temporary
+~$*.doc*
+# Word Auto Backup File
+Backup of *.doc*
+# Excel temporary
+~$*.xls*
+# Excel Backup File
+*.xlk
+# PowerPoint temporary
+~$*.ppt*
+# Visio autosave temporary files
+*.~vsd*
+
+
+# Created by https://www.toptal.com/developers/gitignore/api/r,c++,macos,microsoftoffice
+# Edit at https://www.toptal.com/developers/gitignore?templates=r,c++,macos,microsoftoffice

DESCRIPTION

@@ -5,37 +5,42 @@ Authors@R: c(
     person("Noam", "Ross", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2136-0000")),
     person("EcoHealth Alliance", role = c("cph", "fnd"))
-    )
-Description: Tools working with the history of version-controlled projects, 
+  )
+Description: The 'relic' package provides tools for extracting files and
+    objects from the history of a git repository. It is a high-level
+    interface designed to enable comparison of objects in reproducible
+    research workflows, especially pipelines that use the 'targets'
+    package.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Language: en-US
-Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace", "devtag::dev_roclet"))
-RoxygenNote: 7.2.3
+URL: https://ecohealthalliance.github.io/relic,
+    https://ecohealthalliance.r-universe.dev/relic
+BugReports: https://github.com/ecohealthalliance/relic/issues
 Imports: 
-    git2r,
     fs,
+    git2r,
     rlang
 Suggests: 
-    igraph,
+    callr,
+    devtag,
+    glue,
     knitr,
+    lintr,
+    minioclient,
+    pkgcheck,
     rmarkdown,
+    spelling,
     targets,
     testthat (>= 3.0.0),
-    devtag,
-    pkgcheck,
-    lintr,
-    processx,
-    paws,
-    httr,
-    autotest,
-    callr,
-    spelling
+    withr
+VignetteBuilder: 
+    knitr
 Remotes:
-    ropensci/git2r,
-    moodymudskipper/devtag,
-    ropensci-review-tools/pkgcheck
+    cboettig/minioclient#14,
+    ropensci-review-tools/pkgcheck,
+    ropensci/git2r
 Config/testthat/edition: 3
-URL: https://ecohealthalliance.github.io/relic, https://ecohealthalliance.r-universe.dev/relic
-BugReports: https://github.com/ecohealthalliance/relic/issues
-VignetteBuilder: knitr
+Encoding: UTF-8
+Language: en-US
+Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace",
+    "devtag::dev_roclet"))
+RoxygenNote: 7.2.3

NAMESPACE

@@ -1,18 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(relic,git_blob)
-S3method(relic,git_tree)
 export(commits_between)
 export(dir_ls_version)
 export(dir_ls_versions)
 export(file_copy_version)
 export(file_copy_versions)
 export(file_read_version)
 export(file_read_versions)
-export(graph_from_commits)
-export(graph_from_git_repository)
 export(relic)
-export(tar_load_version)
+export(relic_cache)
+export(relic_cache_clear)
+export(tar_exists_version)
+export(tar_exists_version_raw)
+export(tar_meta_version)
+export(tar_read_raw_version)
+export(tar_read_raw_versions)
+export(tar_read_version)
 export(tar_read_versions)
 import(fs)
 import(git2r)

NEWS.md

@@ -1,3 +1,7 @@
 # relic (development version)
 
+* Started adding tests
+
+# relic 0.0.1
+
 * Initial proof of concept

R/commits_between.R

@@ -13,7 +13,8 @@
 #'
 #' @param from A commit object or revision string. A string of the form
 #'   'from...to' may also be passed, in which case the commits between the two
-#'   revision strings are used and the `to` argument is ignored.
+#'   revision strings are used and the `to` argument is ignored. If a list of commits
+#'   is passed, these commits are used rather than calculating the commits between.
 #' @param to A commit object or reference
 #' @param filter_file The path to a file relative to the git directory. If not NULL,
 #'   only commits modifying this file will be returned. Note that modifying
@@ -24,6 +25,9 @@
 #' @export
 commits_between <- function(from, to = NULL, filter_file = NULL, repo = ".") {
   repo <- as_repo(repo)
+  if (is.list(from) && all(vapply(from, is_commit, logical(1)))) {
+    return(commits)
+  }
   range <- commits_range(from, to, repo)
   if (is.null(range[[2]])) {
     return(list(range[[1]]))
@@ -66,7 +70,7 @@ commits_between <- function(from, to = NULL, filter_file = NULL, repo = ".") {
 }
 
 #' Parse 1 or 2 commits or revision strings into two commits
-#' @dev
+#' @noRd
 commits_range <- function(from, to, repo) {
   if (is.character(from)) {
     refs <- strsplit(from, "...", fixed = TRUE)[[1]]

R/dir_ls_version.R

@@ -1,16 +1,17 @@
 #' List files and folders in a git repository
 #'
 #' @inheritParams file_read_version
-#' @param param all If TRUE hidden files are also returned
+#' @param all If TRUE hidden files are also returned
 #' @param recurse If TRUE recurse fully, if a positive number the number of levels to recurse
 #' @param type One or more of "any", "file", "directory", "symlink", or "submodule"
-#' @param regexp A regular expression (e.g. ⁠[.]csv$⁠) passed on to grep() to filter paths.
-#' @param glob A wildcard aka globbing pattern (e.g. ⁠*.csv⁠) passed on to grep() to filter paths
+#' @param regexp A regular expression (e.g. '\\.csv$'⁠) passed on to grep() to filter paths.
+#' @param glob A wildcard aka globbing pattern (e.g. '*.csv'⁠) passed on to grep() to filter paths
 #' @param invert If TRUE, return paths that do not match the pattern or glob
 #' @return A character vector of paths
 #' @export
-dir_ls_version <- function(path = ".", ref = "HEAD", all = FALSE, recurse = FALSE, type = "any", regexp = NULL, glob = NULL, repo = ".") {
-  tree <- get_obj_at_commit(path, ref, repo)
+dir_ls_version <- function(path = ".", ref = "HEAD", all = FALSE, recurse = FALSE, type = "any", regexp = NULL, glob = NULL, invert = FALSE, repo = ".") {
+  commit <- as_commit(ref, repo)
+  tree <- get_obj_at_commit(path, commit)
   if (!is_tree(tree)) abort("Path is not a directory")
   if (!is.numeric(recurse)) recurse <- if (recurse) Inf else 0
 
@@ -27,7 +28,7 @@ dir_ls_version <- function(path = ".", ref = "HEAD", all = FALSE, recurse = FALS
   if (!all) {
     paths <- path_filter(paths, regexp = "^[^\\.].*$")
   }
-  paths <- path_filter(paths, glob = glob, regexp = regexp)
+  paths <- path_filter(paths, glob = glob, regexp = regexp, invert = invert)
   paths
 }
 

R/example_repo.R

@@ -0,0 +1,62 @@
+#' Set up a testing and example repository
+#'
+#' This function generates a repository with a commit history that can be used
+#' for testing and examples.
+#' @param dir Path to the directory where the repository should be created
+#' @param reporter the reporter to use when building targets with [targets::tar_make()]. Defaults to "silent".
+#' @param s3 Whether the repository should use S3 storage for targets. Note that
+#'   the S3 endpoint and bucket must already be available.
+create_example_repo <- function(dir = fs::file_temp("relic_example_"), reporter = "silent", s3 = TRUE) {
+  check_installed(c("targets", "glue"))
+  if (dir_exists(dir)) dir_delete(dir)
+  dir_create(dir)
+  od <- setwd(dir)
+  on.exit(setwd(od))
+  repo <- git2r::init()
+  # Configure the repository to use a generic user name and email address
+  git2r::config(repo, user.name = "relic-bot", user.email = "[email protected]")
+
+  # Create a minimal _targets.R file
+  write_to_file(
+    "_targets.R",
+    'library(targets)
+    list(
+     tar_target(cars, mtcars, repository = "local"),
+     tar_target(cars_csv, {name <- "cars.csv"; write.csv(cars, name); name}, format = "file", repository = "local")
+    )
+  '
+  )
+
+  stamp("initial-target-file")
+
+  targets::tar_make(reporter = reporter)
+  append_to_file("_targets/.gitignore", c("!objects/\n!objects/*"))
+  stamp("first-targets-run")
+
+  overwrite_at_line(
+    "_targets.R", 3,
+    "tar_target(cars, rbind(mtcars, mtcars)),"
+  )
+  targets::tar_make(reporter = reporter)
+  stamp("longer-cars")
+
+  if(s3) {
+  insert_lines_at(
+    "_targets.R", 2,
+    'Sys.setenv(AWS_ACCESS_KEY_ID="minioadmin", AWS_SECRET_ACCESS_KEY="minioadmin")
+     tar_option_set(
+       resources = tar_resources(
+         aws = tar_resources_aws(
+           bucket = "relic-test",
+           prefix = "_targets",
+           endpoint = "http://localhost:9000"
+        )),
+      repository = "aws"
+       )
+    ')
+  targets::tar_make(reporter = reporter)
+  stamp("setup-s3")
+  }
+
+  dir
+}