0.4.5 release candidate

.github/workflows/R-CMD-check.yaml

@@ -8,9 +8,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,20 +26,22 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
 
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -56,3 +59,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -4,7 +4,9 @@ on:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -13,8 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -50,8 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: corrr
 Title: Correlations in R
-Version: 0.4.4.9000
+Version: 0.4.5
 Authors@R: c(
     person("Max", "Kuhn", , "[email protected]", role = c("aut", "cre")),
     person("Simon", "Jackson", role = "aut"),
@@ -40,5 +40,5 @@ VignetteBuilder:
 Config/Needs/website: tidyverse/tidytemplate
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1.9000
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,6 @@
-# corrr (development version)
+# corrr 0.4.5
+
+- Maintenance release for broken code links. 
 
 # corrr 0.4.4
 

R/output.R

@@ -79,7 +79,7 @@ fashion.default <- function(x, decimals = 2, leading_zeros = FALSE, na_print = "
 #'   that can be coerced to one (see \code{\link{as_cordf}}).
 #' @param legend Boolean indicating whether a legend mapping the colors to the
 #'   correlations should be displayed.
-#' @param shape \code{\link{geom_point}} aesthetic.
+#' @param shape [ggplot2::geom_point()] aesthetic.
 #' @param print_cor Boolean indicating whether the correlations should be
 #'   printed over the shapes.
 #' @param colours,colors Vector of colors to use for n-color gradient.

README.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/tidymodels/corrr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidymodels/corrr/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/corrr)](https://cran.r-project.org/package=corrr)
-[![Codecov test coverage](https://codecov.io/gh/tidymodels/corrr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/corrr?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/tidymodels/corrr/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/corrr)
 <!-- badges: end -->
 
 corrr is a package for exploring **corr**elations in **R**. It focuses on creating and working with **data frames** of correlations (instead of matrices) that can be easily explored via corrr functions or by leveraging tools like those in the [tidyverse](https://www.tidyverse.org/). This, along with the primary corrr functions, is represented below:
@@ -134,7 +134,7 @@ datasets::airquality %>%
 
 This project 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.
 
-- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on RStudio Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
+- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on RStudio Community](https://forum.posit.co/new-topic?category_id=15&tags=tidymodels,question).
 
 - If you think you have encountered a bug, please [submit an issue](https://github.com/tidymodels/corrr/issues).
 

README.md

@@ -8,7 +8,7 @@
 [![R-CMD-check](https://github.com/tidymodels/corrr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidymodels/corrr/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/corrr)](https://cran.r-project.org/package=corrr)
 [![Codecov test
-coverage](https://codecov.io/gh/tidymodels/corrr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/corrr?branch=main)
+coverage](https://codecov.io/gh/tidymodels/corrr/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/corrr)
 <!-- badges: end -->
 
 corrr is a package for exploring **corr**elations in **R**. It focuses
@@ -22,13 +22,13 @@ corrr functions, is represented below:
 
 You can install:
 
--   the latest released version from CRAN with
+- the latest released version from CRAN with
 
 ``` r
 install.packages("corrr")
 ```
 
--   the latest development version from GitHub with
+- the latest development version from GitHub with
 
 ``` r
 # install.packages("remotes") 
@@ -42,10 +42,10 @@ base correlation function `cor()`. It differs by defaulting to pairwise
 deletion, and returning a correlation data frame (`cor_df`) of the
 following structure:
 
--   A `tbl` with an additional class, `cor_df`
--   An extra “term” column
--   Standardized variances (the matrix diagonal) set to missing values
-    (`NA`) so they can be ignored.
+- A `tbl` with an additional class, `cor_df`
+- An extra “term” column
+- Standardized variances (the matrix diagonal) set to missing values
+  (`NA`) so they can be ignored.
 
 ### API
 
@@ -57,19 +57,19 @@ purposes:
 
 Internal changes (`cor_df` out):
 
--   `shave()` the upper or lower triangle (set to NA).
--   `rearrange()` the columns and rows based on correlation strengths.
+- `shave()` the upper or lower triangle (set to NA).
+- `rearrange()` the columns and rows based on correlation strengths.
 
 Reshape structure (`tbl` or `cor_df` out):
 
--   `focus()` on select columns and rows.
--   `stretch()` into a long format.
+- `focus()` on select columns and rows.
+- `stretch()` into a long format.
 
 Output/visualizations (console/plot out):
 
--   `fashion()` the correlations for pretty printing.
--   `rplot()` the correlations with shapes in place of the values.
--   `network_plot()` the correlations in a network.
+- `fashion()` the correlations for pretty printing.
+- `rplot()` the correlations with shapes in place of the values.
+- `network_plot()` the correlations in a network.
 
 ## Databases and Spark
 
@@ -167,6 +167,7 @@ rplot(x)
 ![](man/figures/README-combination-1.png)<!-- -->
 
 ``` r
+
 datasets::airquality %>% 
   correlate() %>% 
   network_plot(min_cor = .2)
@@ -183,18 +184,18 @@ This project 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.
 
--   For questions and discussions about tidymodels packages, modeling,
-    and machine learning, please [post on RStudio
-    Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
+- For questions and discussions about tidymodels packages, modeling, and
+  machine learning, please [post on RStudio
+  Community](https://forum.posit.co/new-topic?category_id=15&tags=tidymodels,question).
 
--   If you think you have encountered a bug, please [submit an
-    issue](https://github.com/tidymodels/corrr/issues).
+- If you think you have encountered a bug, please [submit an
+  issue](https://github.com/tidymodels/corrr/issues).
 
--   Either way, learn how to create and share a
-    [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
-    (a minimal, reproducible example), to clearly communicate about your
-    code.
+- Either way, learn how to create and share a
+  [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
+  (a minimal, reproducible example), to clearly communicate about your
+  code.
 
--   Check out further details on [contributing guidelines for tidymodels
-    packages](https://www.tidymodels.org/contribute/) and [how to get
-    help](https://www.tidymodels.org/help/).
+- Check out further details on [contributing guidelines for tidymodels
+  packages](https://www.tidymodels.org/contribute/) and [how to get
+  help](https://www.tidymodels.org/help/).

vignettes/using-corrr.Rmd

@@ -121,4 +121,4 @@ d %>%
 
 ## Other Resources
 
-For other resources about how to use `corrr`, you'll find plenty of posts explaining functions at [blogR](https://drsimonj.svbtle.com/), or keep up to date with these on Twitter by following [\@drsimonj](https://twitter.com/drsimonj).
+For other resources about how to use `corrr`, you'll find plenty of posts explaining functions at [blogR](https://drsimonj.svbtle.com/).