Merge branch 'styling' into vignette-branch-name

.Rbuildignore

@@ -1,17 +1,22 @@
+# checklist
+^_pkgdown.yml$
 ^.*\.Rproj$
-^\.Rproj\.user$
-^\.github$
-^codemeta\.json$
 ^.zenodo\.json$
-^man-roxygen$
-^pkgdown$
-^_pkgdown.yml$
-^docs$
-^cran-comments\.md$
-# checklist
+^\.github$
+^\.httr-oauth$
+^\.Rproj\.user$
+^\.zenodo\.json$
 ^checklist.yml$
+^CITATION\.cff$
 ^codecov.yml$
-^LICENSE.md$
-^\.httr-oauth$
+^codecov\.yml$
+^codemeta\.json$
+^cran-comments\.md$
+^data-raw$
 ^doc$
+^docs$
+^LICENSE.md$
+^man-roxygen$
 ^Meta$
+^pkgdown$
+^README\.Rmd$

.github/workflows/check_on_branch.yml

@@ -1,6 +1,7 @@
 on:
   push:
     branches-ignore:
+      - main
       - master
       - ghpages
 
@@ -10,8 +11,10 @@ jobs:
   check-package:
     runs-on: ubuntu-latest
     name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
     steps:
       - uses: inbo/actions/check_pkg@master
         with:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+          token: ${{ secrets.PAT }}

.github/workflows/check_on_different_r_os.yml

@@ -1,12 +1,14 @@
 on:
   push:
     branches:
+      - main
       - master
   pull_request:
     branches:
+      - main
       - master
 
-name: R-CMD-check
+name: R-CMD-check-OS
 
 jobs:
   R-CMD-check:
@@ -21,10 +23,11 @@ jobs:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-20.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      _R_CHECK_SYSTEM_CLOCK_: false
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
@@ -61,6 +64,7 @@ jobs:
           Rscript -e "remotes::install_github('r-hub/sysreqs')"
           sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
           sudo -s eval "$sysreqs"
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
@@ -77,7 +81,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
@@ -91,3 +95,4 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+          retention-days: 5

.github/workflows/check_on_main.yml

@@ -0,0 +1,21 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  schedule:
+    - cron: '6 0 15 * *'
+
+name: "check package on main"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+    steps:
+      - uses: inbo/actions/check_pkg@master
+        with:
+          token: ${{ secrets.PAT }}

.github/workflows/release.yml

@@ -0,0 +1,30 @@
+on:
+  push:
+    tags:
+      - 'v*'
+
+name: Create Release
+
+jobs:
+  build:
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Get tag message
+        run: |
+          TAG_BODY=$(git tag --contains ${{ github.sha }} -n100 | awk '(NR>1)')
+          echo "::set-output name=TAG_BODY::$TAG_BODY"
+        id: tag-body
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          body: ${{ steps.tag-body.outputs.TAG_BODY }}
+          draft: false
+          prerelease: false

.gitignore

@@ -1,9 +1,10 @@
-.Rproj.user
-.Rhistory
+.httr-oauth
 .RData
+.Rhistory
+.Rproj.user
 .Ruserdata
-inst/doc
-docs
-.httr-oauth
+*.html
 doc
+docs
+inst/doc
 Meta

.zenodo.json

@@ -0,0 +1,46 @@
+{
+  "title": "git2rdata: Store and Retrieve Data.frames in a Git Repository",
+  "version": "0.4.0",
+  "description": "The git2rdata package is an R package for writing and reading dataframes as plain text files. A metadata file stores important information. 1) Storing metadata allows to maintain the classes of variables. By default, git2rdata optimizes the data for file storage. The optimization is most effective on data containing factors. The optimization makes the data less human readable. The user can turn this off when they prefer a human readable format over smaller files. Details on the implementation are available in vignette(\"plain_text\", package = \"git2rdata\"). 2) Storing metadata also allows smaller row based diffs between two consecutive commits. This is a useful feature when storing data as plain text files under version control. Details on this part of the implementation are available in vignette(\"version_control\", package = \"git2rdata\"). Although we envisioned git2rdata with a git workflow in mind, you can use it in combination with other version control systems like subversion or mercurial. 3) git2rdata is a useful tool in a reproducible and traceable workflow. vignette(\"workflow\", package = \"git2rdata\") gives a toy example. 4) vignette(\"efficiency\", package = \"git2rdata\") provides some insight into the efficiency of file storage, git repository size and speed for writing and reading.",
+  "creators": [
+    {
+      "name": "Onkelinx, Thierry",
+      "orcid": "https://orcid.org/0000-0001-8804-4216"
+    }
+  ],
+  "upload_type": "software",
+  "access_right": "open",
+  "license": "GPL-3.0",
+  "communities": [
+    {
+      "identifier": "inbo"
+    }
+  ],
+  "contributors": [
+    {
+      "name": "Vanderhaeghe, Floris",
+      "type": "ProjectMember",
+      "orcid": "https://orcid.org/0000-0002-6378-6229"
+    },
+    {
+      "name": "Desmet, Peter",
+      "type": "ProjectMember",
+      "orcid": "https://orcid.org/0000-0002-8442-8025"
+    },
+    {
+      "name": "Lommelen, Els",
+      "type": "ProjectMember",
+      "orcid": "https://orcid.org/0000-0002-3481-5684"
+    },
+    {
+      "name": "Research Institute for Nature and Forest",
+      "type": "RightsHolder"
+    },
+    {
+      "name": "Onkelinx, Thierry",
+      "type": "ContactPerson",
+      "orcid": "https://orcid.org/0000-0001-8804-4216"
+    }
+  ],
+  "language": "en"
+}

CITATION.cff

@@ -0,0 +1,36 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+- family-names: Onkelinx
+  given-names: Thierry
+  orcid: https://orcid.org/0000-0001-8804-4216
+contact:
+- email: [email protected]
+  family-names: Onkelinx
+  given-names: Thierry
+- email: [email protected]
+  name: Research Institute for Nature and Forest
+title: 'git2rdata: Store and Retrieve Data.frames in a Git Repository'
+version: 0.4.0
+abstract: The git2rdata package is an R package for writing and reading dataframes
+  as plain text files. A metadata file stores important information. 1) Storing metadata
+  allows to maintain the classes of variables. By default, git2rdata optimizes the
+  data for file storage. The optimization is most effective on data containing factors.
+  The optimization makes the data less human readable. The user can turn this off
+  when they prefer a human readable format over smaller files. Details on the implementation
+  are available in vignette("plain_text", package = "git2rdata"). 2) Storing metadata
+  also allows smaller row based diffs between two consecutive commits. This is a useful
+  feature when storing data as plain text files under version control. Details on
+  this part of the implementation are available in vignette("version_control", package
+  = "git2rdata"). Although we envisioned git2rdata with a git workflow in mind, you
+  can use it in combination with other version control systems like subversion or
+  mercurial. 3) git2rdata is a useful tool in a reproducible and traceable workflow.
+  vignette("workflow", package = "git2rdata") gives a toy example. 4) vignette("efficiency",
+  package = "git2rdata") provides some insight into the efficiency of file storage,
+  git repository size and speed for writing and reading.
+license: GPL-3.0
+type: software
+repository-code: https://github.com/ropensci/git2rdata/
+identifiers:
+- type: url
+  value: https://ropensci.github.io/git2rdata/

DESCRIPTION

@@ -1,30 +1,17 @@
 Package: git2rdata
 Title: Store and Retrieve Data.frames in a Git Repository
-Version: 0.3.1
-Authors@R: 
-    c(person(given = "Thierry",
-             family = "Onkelinx",
-             role = c("aut", "cre"),
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0001-8804-4216")),
-      person(given = "Floris",
-             family = "Vanderhaeghe",
-             role = "ctb",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-6378-6229")),
-      person(given = "Peter",
-             family = "Desmet",
-             role = "ctb",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-8442-8025")),
-      person(given = "Els",
-             family = "Lommelen",
-             role = "ctb",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-3481-5684")),
-      person(given = "Research Institute for Nature and Forest",
-             role = c("cph", "fnd"),
-             email = "[email protected]"))
+Version: 0.4.0
+Authors@R: c(
+    person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-8804-4216")),
+    person("Floris", "Vanderhaeghe", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-6378-6229")),
+    person("Peter", "Desmet", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-8442-8025")),
+    person("Els", "Lommelen", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-3481-5684")),
+    person("Research Institute for Nature and Forest", , , "[email protected]", role = c("cph", "fnd"))
+  )
 Description: The git2rdata package is an R package for writing and reading
     dataframes as plain text files.  A metadata file stores important
     information.  1) Storing metadata allows to maintain the classes of
@@ -44,10 +31,10 @@ Description: The git2rdata package is an R package for writing and reading
     traceable workflow.  vignette("workflow", package = "git2rdata") gives
     a toy example.  4) vignette("efficiency", package = "git2rdata")
     provides some insight into the efficiency of file storage, git
-    repository size and speed for writing and reading.  Please cite using
-    <doi:10.5281/zenodo.1485309>.
+    repository size and speed for writing and reading.
 License: GPL-3
-URL: https://ropensci.github.io/git2rdata/
+URL: https://ropensci.github.io/git2rdata/,
+    https://github.com/ropensci/git2rdata/
 BugReports: https://github.com/ropensci/git2rdata/issues
 Depends: 
     R (>= 3.5.0)
@@ -67,9 +54,8 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-GB
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Collate:
     'clean_data_path.R'
     'datahash.R'
@@ -87,3 +73,4 @@ Collate:
     'rename_variable.R'
     'upgrade_data.R'
     'utils.R'
+    'verify_vc.R'

NAMESPACE

@@ -61,6 +61,7 @@ export(repository)
 export(rm_data)
 export(status)
 export(upgrade_data)
+export(verify_vc)
 export(write_vc)
 importFrom(assertthat,"on_failure<-")
 importFrom(assertthat,assert_that)
@@ -81,6 +82,7 @@ importFrom(git2r,workdir)
 importFrom(methods,setOldClass)
 importFrom(stats,setNames)
 importFrom(utils,file_test)
+importFrom(utils,flush.console)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,write.table)

NEWS.md

@@ -1,3 +1,10 @@
+# git2rdata 0.4.0
+
+## Internal changes
+
+* Upgrade to Roxygen2 7.1.2
+* Add `inst/CITATION`, `CITATION.cff`, `.zenodo.json`
+
 # git2rdata 0.3.1
 
 * Use `icuSetCollate()` to define a standardised sorting.

R/clean_data_path.R

@@ -11,9 +11,9 @@
 clean_data_path <- function(root, file, normalize = TRUE) {
   assert_that(is.flag(normalize), noNA(normalize))
   dir_name <- dirname(file)
-  if (length(grep("\\.\\.", dir_name))) {
-    stop("file should not contain '..'")
-  }
+  assert_that(
+    length(grep("\\.\\.", dir_name)) == 0, msg = "file should not contain '..'"
+  )
 
   file <- gsub("\\..*$", "", basename(file))
   if (dir_name == ".") {