Merge pull request #8 from inbo/more_work

Version 0.1.1

.Rbuildignore

@@ -3,4 +3,8 @@
 ^checklist.yml$
 ^Dockerfile$
 ^.dockerignore$
-^entrypoint.sh$
+^entrypoint_package.sh$
+^entrypoint_source.sh$
+^.github$
+^README\.Rmd$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check_on_branch.yml

@@ -0,0 +1,14 @@
+on:
+  push:
+    branches-ignore:
+      - master
+      - ghpages
+
+name: "check package"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    steps:
+      - uses: inbo/actions/check_pkg@master

.github/workflows/check_on_different_r_os.yaml

@@ -0,0 +1,93 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/check_on_master.yml

@@ -0,0 +1,15 @@
+on:
+  push:
+    branches:
+      - master
+  schedule:
+    - cron: '6 0 * * 1'
+
+name: "check package on master"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    steps:
+      - uses: inbo/actions/check_pkg@master

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: checklist
 Title: A Thorough and Strict Set of Checks for R Packages
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: 
     c(person(given = "Thierry",
              family = "Onkelinx",
@@ -13,13 +13,19 @@ Authors@R:
              email = "[email protected]"))
 Description: An opinated set of rules for R packages and code.
 License: GPL-3
+Imports:
+    assertthat,
+    devtools,
+    git2r,
+    lintr,
+    R6,
+    rcmdcheck,
+    rmarkdown,
+    usethis,
+    yaml
+Suggests: 
+    testthat
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
-Imports:
-  assertthat,
-  lintr,
-  rcmdcheck,
-  R6,
-  yaml

Dockerfile

@@ -59,6 +59,9 @@ RUN  apt-get update \
     libxml2-dev \
   && Rscript --no-save --no-restore -e 'remotes::install_cran("devtools")'
 
+## install git2r
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("git2r")'
+
 ## install hunspell
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'
 
@@ -68,15 +71,27 @@ RUN Rscript --no-save --no-restore -e 'remotes::install_cran("lintr")'
 ## install microbenchmark
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("microbenchmark")'
 
+## install pillar
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("pillar")'
+
+## install Rcpp
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("Rcpp")'
+
 ## install rcmdcheck
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("rcmdcheck")'
 
+## install rlang
+RUN Rscript --no-save --no-restore -e 'remotes::install_cran("rlang")'
+
 ## install R6
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("R6")'
 
 ## install spelling
 RUN Rscript --no-save --no-restore -e 'remotes::install_cran("spelling")'
 
+## install tibble
+RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("tibble")'
+
 ## install tidyverse
 RUN  Rscript --no-save --no-restore -e 'remotes::install_cran("tidyverse")'
 
@@ -90,5 +105,6 @@ RUN Rscript --no-save --no-restore -e 'install.packages("INLA", repos = c(getOpt
 COPY . /checklist/
 RUN Rscript --no-save --no-restore -e 'remotes::install_local("checklist", dependencies = FALSE)'
 
-COPY entrypoint.sh /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
+COPY entrypoint_package.sh /entrypoint_package.sh
+COPY entrypoint_package.sh /entrypoint_source.sh
+ENTRYPOINT ["/entrypoint_package.sh"]

NAMESPACE

@@ -1,19 +1,44 @@
 # Generated by roxygen2: do not edit by hand
 
 export(check_cran)
+export(check_description)
+export(check_documentation)
+export(check_filename)
 export(check_lintr)
 export(check_package)
+export(check_source)
 export(checklist)
-export(checklist_template)
+export(is_workdir_clean)
 export(read_checklist)
+export(write_checklist)
+export(yesno)
 importFrom(R6,R6Class)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_name)
 importFrom(assertthat,is.flag)
 importFrom(assertthat,is.string)
 importFrom(assertthat,noNA)
+importFrom(devtools,document)
+importFrom(git2r,branch_target)
+importFrom(git2r,branches)
+importFrom(git2r,commits)
+importFrom(git2r,in_repository)
+importFrom(git2r,ls_tree)
+importFrom(git2r,repository)
+importFrom(git2r,repository_head)
+importFrom(git2r,reset)
+importFrom(git2r,sha)
+importFrom(git2r,status)
+importFrom(lintr,lint_dir)
 importFrom(lintr,lint_package)
 importFrom(rcmdcheck,rcmdcheck)
+importFrom(rmarkdown,github_document)
+importFrom(rmarkdown,render)
+importFrom(stats,na.omit)
+importFrom(usethis,use_tidy_description)
 importFrom(utils,file_test)
+importFrom(utils,head)
+importFrom(utils,menu)
+importFrom(utils,tail)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)

NEWS.md

@@ -0,0 +1,22 @@
+# checklist 0.1.1
+
+* Added a `NEWS.md` file to track changes to the package.
+* Added a `README.Rmd` file with installation instructions.
+* Rework `checklist_template()` into `write_checklist()`.
+* Add `check_description()`.
+* Add `check_documentation()`.
+* Add `check_filename()`.
+* Add `check_source()`.
+* `check_lintr()` also works on source code repositories.
+* Activate GitHub action `inbo/check_package`.
+
+# checklist 0.1.0
+
+* Initital version.
+* Create `checklist` R6 class.
+* Add `check_cran()`.
+* Add `check_lintr()`.
+* Add `check_package()`.
+* Add `read_checklist()`.
+* Add `checklist_template()`.
+* Add Dockerimage for GitHub actions.

R/check_cran.R

@@ -1,12 +1,18 @@
 #' Run the package checks required by CRAN
 #' @inheritParams read_checklist
 #' @return A `Checklist` object.
+#' @importFrom assertthat assert_that
 #' @importFrom rcmdcheck rcmdcheck
 #' @export
 check_cran <- function(x = ".") {
   if (!inherits(x, "Checklist") || !"checklist" %in% x$get_checked) {
     x <- read_checklist(x = x)
   }
+  assert_that(
+    x$package,
+    msg = "`check_cran()` is only relevant for packages.
+`checklist.yml` indicates this is not a package."
+  )
 
   check_output <- rcmdcheck(
     path = x$get_path,

R/check_description.R

@@ -0,0 +1,70 @@
+#' Check the DESCRIPTION file
+#' @inheritParams read_checklist
+#' @importFrom assertthat has_name
+#' @importFrom git2r branches branch_target commits repository repository_head
+#' reset sha
+#' @importFrom stats na.omit
+#' @importFrom usethis use_tidy_description
+#' @importFrom utils head tail
+#' @export
+check_description <- function(x = ".") {
+  if (!inherits(x, "Checklist") || !"checklist" %in% x$get_checked) {
+    x <- read_checklist(x = x)
+  }
+  assert_that(
+    x$package,
+    msg = "`check_description()` is only relevant for packages.
+`checklist.yml` indicates this is not a package."
+  )
+
+  repo <- repository(x$get_path)
+  description <- file.path(x$get_path, "DESCRIPTION")
+  assert_that(file_test("-f", description), msg = "DESCRIPTION file missing")
+
+  version <- read.dcf(description)[, "Version"]
+  "Incorrect version tag format. Use `0.0`, `0.0.0`"[
+    !grepl("^[0-9]+\\.[0-9]+(\\.[0-9]+)?$", version)
+  ] -> desc_error
+
+  branch_sha <- vapply(branches(repo, "all"), branch_target, character(1))
+  head_sha <- sha(repository_head(repo))
+  current_branch <- head(names(which(branch_sha == head_sha)), 1)
+  if (current_branch == "master") {
+    old_sha <- vapply(
+      tail(commits(repo, ref = "master", n = 2), 1), sha, character(1)
+    )
+    desc_diff <- system2(
+      "git", args = c("diff", old_sha, head_sha, "DESCRIPTION"),
+      stdout = TRUE
+    )
+  } else {
+    desc_diff <- system2(
+      "git", args = c("diff", "origin/master", "--", "DESCRIPTION"),
+      stdout = TRUE
+    )
+  }
+  clean <- is_workdir_clean(repo)
+  use_tidy_description()
+  if (clean && !is_workdir_clean(repo)) {
+    desc_error <- c(
+      desc_error,
+      "DESCRIPTION not tidy. use `usethis::use_tidy_description()`"
+    )
+    reset(repo)
+  }
+  old_version <- desc_diff[grep("\\-Version: ", desc_diff)]
+  old_version <- gsub("-Version: ", "", old_version)
+  version_bump <- ifelse(
+    length(old_version),
+    ifelse(
+      package_version(old_version) < package_version(version),
+      NA,
+      "Package version not increased"
+    ),
+    "Package version not updated"
+  )
+  desc_error <- c(desc_error, na.omit(version_bump))
+
+  x$add_error(desc_error, "DESCRIPTION")
+  return(x)
+}