Updated GitHub repo and package infrastructure

phgrosjean · phgrosjean · commit 19dc72840921 · 2025-08-02T20:32:37.000+02:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,21 +1,22 @@
 Package: data.io
 Type: Package
 Version: 1.6.0
-Title: Read and Write Data in Different Formats
+Title: 'SciViews::R' - Read and Write Data in Different Formats
 Description: Read or write data from many different formats (tabular datasets,
   from statistic software ...) into R objects. Add labels and units in
   different languages.
-Authors@R: c(person("Philippe", "Grosjean", role = c("aut", "cre"),
-  email = "phgrosjean@sciviews.org",
-  comment = c(ORCID = "0000-0002-2694-9471")))
+Authors@R: c(
+  person("Philippe", "Grosjean", role = c("aut", "cre"),
+    email = "phgrosjean@sciviews.org",
+    comment = c(ORCID = "0000-0002-2694-9471")))
 Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
 Depends:
     R (>= 4.2.0)
 Imports:
     data.table (>= 1.15.4),
     data.trame (>= 0.9.0),
     Hmisc (>= 5.0.1),
-    lifecycle (>= 1.0.3),
+    lifecycle (>= 1.0.0),
     utils (>= 4.2.0),
     R.utils (>= 2.13.0),
     readr (>= 2.1.4),
@@ -35,15 +36,16 @@ Suggests:
     readxl (>= 1.4.2),
     writexl (>= 1.4.2),
     WriteXLS (>= 6.4.0),
+    covr (>= 3.5.0),
     knitr (>= 1.42),
     rmarkdown (>= 2.21),
     spelling (>= 2.2.1),
     testthat (>= 3.0.0)
 Remotes:
     SciViews/data.trame,
     SciViews/svBase
-License:  MIT + file LICENSE
-URL: https://github.com/SciViews/data.io, https://www.sciviews.org/data.io/
+License: MIT + file LICENSE
+URL: https://github.com/SciViews/data.io, https://www.sciviews.org/data.io/, https://sciviews.r-universe.dev/data.io
 BugReports: https://github.com/SciViews/data.io/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -44,6 +44,7 @@ importFrom(data.trame,data.trame)
 importFrom(data.trame,is.data.trame)
 importFrom(lifecycle,badge)
 importFrom(lifecycle,deprecate_soft)
+importFrom(lifecycle,deprecated)
 importFrom(readr,default_locale)
 importFrom(readr,read_lines)
 importFrom(rlang,quos)
diff --git a/R/data.io-package.R b/R/data.io-package.R
@@ -18,16 +18,18 @@
 #'   object, to be used while pretty printing a table or plot.
 #'
 
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
 ## usethis namespace: start
 #' @importFrom data.table fread fwrite
 #' @importFrom data.trame data.trame as.data.trame is.data.trame
-#' @importFrom tibble tibble tribble as_tibble is_tibble add_column
-#' @importFrom tsibble as_tsibble
-#' @importFrom utils .DollarNames data download.file
+#' @importFrom lifecycle badge deprecated deprecate_soft
 #' @importFrom R.utils gunzip
 #' @importFrom readr default_locale read_lines
 #' @importFrom rlang quos
 #' @importFrom svBase default_dtx
-#' @importFrom lifecycle badge deprecate_soft
+#' @importFrom tibble tibble tribble as_tibble is_tibble add_column
+#' @importFrom tsibble as_tsibble
+#' @importFrom utils .DollarNames data download.file
 ## usethis namespace: end
 "_PACKAGE"
diff --git a/README.Rmd b/README.Rmd
@@ -0,0 +1,68 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include=FALSE}
+knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
+  fig.path = "man/figures/README-", out.width = "100%")
+```
+
+# 'SciViews::R' - Read and Write Data in Different Formats <a href="https://www.sciviews.org/data.io"><img src="man/figures/logo.png" align="right" height="138" /></a>
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/SciViews/data.io/graph/badge.svg?token=Ei9DhKMdnO)](https://codecov.io/gh/SciViews/data.io)
+[![CRAN Status](https://www.r-pkg.org/badges/version/data.io)](https://cran.r-project.org/package=data.io)
+[![r-universe status](https://sciviews.r-universe.dev/badges/data.io)](https://sciviews.r-universe.dev/data.io)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable))
+<!-- badges: end -->
+
+{data.io} main functions are `read()` and `write()`. They are made super-easy to import and export data in various formats in an unified way (they use functions from other packages under the hood like {haven}, {readr}, {readxl}, {writexl} ...). They care about metadata, in particular, meaningful labels and units for the variables. Also, a mechanism to preprocess data sets using sidecar files, and to translate them into various languages are provided for a subset of R packages data sets.
+
+## Installation
+
+{data.io} is not available from CRAN yet. You should install it from the [SciViews R-Universe](https://sciviews.r-universe.dev). To install this package and its dependencies, run the following command in R:
+
+```{r, eval=FALSE}
+install.packages('data.io', repos = c('https://sciviews.r-universe.dev',
+  'https://cloud.r-project.org'))
+```
+
+You can also install the latest development version. Make sure you have the {remotes} R package installed:
+
+``` r
+install.packages("remotes")
+```
+
+Use `install_github()` to install the {data.io} package from Github (source from **main** branch will be recompiled on your machine):
+
+``` r
+remotes::install_github("SciViews/data.io")
+```
+
+R should install all required dependencies automatically, and then it should compile and install {data.io}.
+
+## Further explore {data.io}
+
+You can get further help about this package this way. Make the {data.io} package available in your R session:
+
+``` r
+library("data.io")
+```
+
+Get help about this package:
+
+``` r
+library(help = "data.io")
+help("data.io-package")
+vignette("data-io") # None is installed with install_github()
+```
+
+For further instructions, please, refer to these help pages at <https://www.sciviews.org/data.io/>.
+
+## Code of Conduct
+
+Please note that the {data.io} package is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
diff --git a/README.md b/README.md
@@ -1,39 +1,63 @@
-# Read and Write Data in Different Formats <a href='https://www.sciviews.org/data.io'><img src='man/figures/logo.png' align='right' height='139'/></a>
 
-<!-- badges: start -->
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# ‘SciViews::R’ - Read and Write Data in Different Formats <a href="https://www.sciviews.org/data.io"><img src="man/figures/logo.png" align="right" height="138" /></a>
 
-[![R-CMD-check](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/SciViews/data.io/branch/main/graph/badge.svg)](https://app.codecov.io/gh/SciViews/data.io?branch=main) [![CRAN Status](https://www.r-pkg.org/badges/version/data.io)](https://cran.r-project.org/package=data.io) [![r-universe status](https://sciviews.r-universe.dev/badges/data.io)](https://sciviews.r-universe.dev/data.io) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable))
+<!-- badges: start -->
 
+[![R-CMD-check](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SciViews/data.io/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/SciViews/data.io/graph/badge.svg?token=Ei9DhKMdnO)](https://codecov.io/gh/SciViews/data.io)
+[![CRAN
+Status](https://www.r-pkg.org/badges/version/data.io)](https://cran.r-project.org/package=data.io)
+[![r-universe
+status](https://sciviews.r-universe.dev/badges/data.io)](https://sciviews.r-universe.dev/data.io)
+[![License:
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Lifecycle:
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable))
 <!-- badges: end -->
 
-{data.io} main functions are `read()` and `write()`. They are made super-easy to import and export data in various formats in an unified way (they use functions from other packages under the hood like {haven}, {readr}, {readxl}, {writexl} ...). They care about metadata, in particular, meaningful labels and units for the variables. Also, a mechanism to preprocess data sets using sidecar files, and to translate them into various languages are provided for a subset of R packages data sets.
+{data.io} main functions are `read()` and `write()`. They are made
+super-easy to import and export data in various formats in an unified
+way (they use functions from other packages under the hood like {haven},
+{readr}, {readxl}, {writexl} …). They care about metadata, in
+particular, meaningful labels and units for the variables. Also, a
+mechanism to preprocess data sets using sidecar files, and to translate
+them into various languages are provided for a subset of R packages data
+sets.
 
 ## Installation
 
-{data.io} is not available from CRAN yet. You should install it from the [SciViews R-Universe](https://sciviews.r-universe.dev). To install this package and its dependencies, run the following command in R:
+{data.io} is not available from CRAN yet. You should install it from the
+[SciViews R-Universe](https://sciviews.r-universe.dev). To install this
+package and its dependencies, run the following command in R:
 
-```{r, eval=FALSE}
+``` r
 install.packages('data.io', repos = c('https://sciviews.r-universe.dev',
   'https://cloud.r-project.org'))
 ```
 
-You can also install the latest development version. Make sure you have the {remotes} R package installed:
+You can also install the latest development version. Make sure you have
+the {remotes} R package installed:
 
 ``` r
 install.packages("remotes")
 ```
 
-Use `install_github()` to install the {data.io} package from Github (source from **main** branch will be recompiled on your machine):
+Use `install_github()` to install the {data.io} package from Github
+(source from **main** branch will be recompiled on your machine):
 
 ``` r
 remotes::install_github("SciViews/data.io")
 ```
 
-R should install all required dependencies automatically, and then it should compile and install {data.io}.
+R should install all required dependencies automatically, and then it
+should compile and install {data.io}.
 
 ## Further explore {data.io}
 
-You can get further help about this package this way. Make the {data.io} package available in your R session:
+You can get further help about this package this way. Make the {data.io}
+package available in your R session:
 
 ``` r
 library("data.io")
@@ -47,8 +71,12 @@ help("data.io-package")
 vignette("data-io") # None is installed with install_github()
 ```
 
-For further instructions, please, refer to these help pages at <https://www.sciviews.org/data.io/>.
+For further instructions, please, refer to these help pages at
+<https://www.sciviews.org/data.io/>.
 
 ## Code of Conduct
 
-Please note that the {data.io} package is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the {data.io} package is released with a [Contributor
+Code of
+Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
+By contributing to this project, you agree to abide by its terms.
diff --git a/inst/figures/data.io.png b/inst/figures/data.io.png
diff --git a/man/data.io-package.Rd b/man/data.io-package.Rd
diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg
@@ -0,0 +1,21 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="126" height="20" role="img" aria-label="lifecycle: deprecated">
+    <title>lifecycle: deprecated</title>
+    <linearGradient id="s" x2="0" y2="100%">
+        <stop offset="0" stop-color="#bbb" stop-opacity=".1" />
+        <stop offset="1" stop-opacity=".1" />
+    </linearGradient>
+    <clipPath id="r">
+        <rect width="126" height="20" rx="3" fill="#fff" />
+    </clipPath>
+    <g clip-path="url(#r)">
+        <rect width="55" height="20" fill="#555" />
+        <rect x="55" width="71" height="20" fill="#fe7d37" />
+        <rect width="126" height="20" fill="url(#s)" />
+    </g>
+    <g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110">
+        <text aria-hidden="true" x="285" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="450">lifecycle</text>
+        <text x="285" y="140" transform="scale(.1)" fill="#fff" textLength="450">lifecycle</text>
+        <text aria-hidden="true" x="895" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="610">deprecated</text>
+        <text x="895" y="140" transform="scale(.1)" fill="#fff" textLength="610">deprecated</text>
+    </g>
+</svg>
diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg
@@ -0,0 +1,21 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="138" height="20" role="img" aria-label="lifecycle: experimental">
+    <title>lifecycle: experimental</title>
+    <linearGradient id="s" x2="0" y2="100%">
+        <stop offset="0" stop-color="#bbb" stop-opacity=".1" />
+        <stop offset="1" stop-opacity=".1" />
+    </linearGradient>
+    <clipPath id="r">
+        <rect width="138" height="20" rx="3" fill="#fff" />
+    </clipPath>
+    <g clip-path="url(#r)">
+        <rect width="55" height="20" fill="#555" />
+        <rect x="55" width="83" height="20" fill="#fe7d37" />
+        <rect width="138" height="20" fill="url(#s)" />
+    </g>
+    <g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110">
+        <text aria-hidden="true" x="285" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="450">lifecycle</text>
+        <text x="285" y="140" transform="scale(.1)" fill="#fff" textLength="450">lifecycle</text>
+        <text aria-hidden="true" x="955" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="730">experimental</text>
+        <text x="955" y="140" transform="scale(.1)" fill="#fff" textLength="730">experimental</text>
+    </g>
+</svg>
diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg
@@ -0,0 +1,29 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="98" height="20" role="img" aria-label="lifecycle: stable">
+    <title>lifecycle: stable</title>
+    <linearGradient id="s" x2="0" y2="100%">
+        <stop offset="0" stop-color="#bbb" stop-opacity=".1" />
+        <stop offset="1" stop-opacity=".1" />
+    </linearGradient>
+    <clipPath id="r">
+        <rect width="98" height="20" rx="3" fill="#fff" />
+    </clipPath>
+    <g clip-path="url(#r)">
+        <rect width="55" height="20" fill="#555" />
+        <rect x="55" width="43" height="20" fill="#4c1" />
+        <rect width="98" height="20" fill="url(#s)" />
+    </g>
+    <g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110">
+        <text aria-hidden="true" x="285" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="450">
+      lifecycle
+    </text>
+        <text x="285" y="140" transform="scale(.1)" fill="#fff" textLength="450">
+      lifecycle
+    </text>
+        <text aria-hidden="true" x="755" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="330">
+      stable
+    </text>
+        <text x="755" y="140" transform="scale(.1)" fill="#fff" textLength="330">
+      stable
+    </text>
+    </g>
+</svg>
diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg
@@ -0,0 +1,21 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="lifecycle: superseded">
+    <title>lifecycle: superseded</title>
+    <linearGradient id="s" x2="0" y2="100%">
+        <stop offset="0" stop-color="#bbb" stop-opacity=".1" />
+        <stop offset="1" stop-opacity=".1" />
+    </linearGradient>
+    <clipPath id="r">
+        <rect width="128" height="20" rx="3" fill="#fff" />
+    </clipPath>
+    <g clip-path="url(#r)">
+        <rect width="55" height="20" fill="#555" />
+        <rect x="55" width="73" height="20" fill="#007ec6" />
+        <rect width="128" height="20" fill="url(#s)" />
+    </g>
+    <g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110">
+        <text aria-hidden="true" x="285" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="450">lifecycle</text>
+        <text x="285" y="140" transform="scale(.1)" fill="#fff" textLength="450">lifecycle</text>
+        <text aria-hidden="true" x="905" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="630">superseded</text>
+        <text x="905" y="140" transform="scale(.1)" fill="#fff" textLength="630">superseded</text>
+    </g>
+</svg>
diff --git a/tests/spelling.R b/tests/spelling.R
@@ -1,3 +1,3 @@
 if (requireNamespace('spelling', quietly = TRUE))
   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
-                             skip_on_cran = TRUE)
+    skip_on_cran = TRUE)
diff --git a/vignettes/data-io.Rmd b/vignettes/data-io.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "Read and Write Data in Different Formats"
+title: "'SciViews::R' - Read and Write Data in Different Formats"
 author: "Philippe Grosjean"
 date: "`r Sys.Date()`"
 output:
@@ -8,7 +8,7 @@ output:
     toc_depth: 3
     fig_caption: yes
 vignette: >
-  %\VignetteIndexEntry{Read and Write Data in Different Formats}
+  %\VignetteIndexEntry{'SciViews::R' - Read and Write Data in Different Formats}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
