Update GiHub workflows and README

simisc · Mar 21, 2023 · d81379b · d81379b
1 parent ebdd88b
commit d81379b
Show file tree

Hide file tree

Showing 6 changed files with 770 additions and 79 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml → .github/workflows/check-standard.yaml b/.github/workflows/R-CMD-check.yaml → .github/workflows/check-standard.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
-
-      - 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@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,48 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         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")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        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 dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: whozr
 Type: Package
 Title: Convert Raw Anthrops to WHO Z-Scores
-Version: 1.1.2
+Version: 1.1.3
 Authors@R: person("Simon", "Schoenbuchner",
   email = "[email protected]",
   role = c("aut", "cre"),
@@ -14,7 +14,7 @@ Depends: R (>= 2.10)
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Imports: dplyr (>= 1.0.9), tibble (>= 3.1.8), stats, utils, rlang
+Imports: dplyr (>= 1.0.9), tibble (>= 3.1.8), stats, rlang
 RoxygenNote: 7.2.1
-Suggests: 
+Suggests:
     testthat
diff --git a/README.Rmd b/README.Rmd
@@ -6,19 +6,21 @@ output: github_document
 
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "README-"
+    collapse = TRUE,
+    comment = "#>",
+    fig.path = "README-"
 )
 ```
 
 # whozr
-
-[![R build status](https://github.com/simisc/whozr/workflows/R-CMD-check/badge.svg)](https://github.com/simisc/whozr/actions)
+
+<!-- badges: start -->
+[![check-standard](https://github.com/simisc/whozr/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/simisc/whozr/actions/workflows/check-standard.yaml)
 [![DOI](https://zenodo.org/badge/113995327.svg)](https://zenodo.org/badge/latestdoi/113995327)
 [![Licence](https://img.shields.io/github/license/simisc/whozr)](https://github.com/simisc/whozr/blob/master/LICENSE)
 [![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
 [![codecov](https://codecov.io/gh/simisc/whozr/branch/master/graph/badge.svg?token=OTFYOOXEVC)](https://codecov.io/gh/simisc/whozr)
+<!-- badges: end -->
 
 Convert raw anthropometric measurement (weight, height, length, BMI, MUAC, head circumeference, tricep skinfold and subscapular skinfold) to z-scores, using the WHO growth standards (0-5 years) and/or references (5-19 years).
 
@@ -29,27 +31,30 @@ Also allows the 'reverse' calculation of original anthropometry measures from z-
 You can install whozr from github with:
 
 ```{r gh-installation, eval = FALSE}
-# install.packages("devtools")
-devtools::install_github("simisc/whozr")
+# install.packages("remotes")
+remotes::install_github("simisc/whozr")
 ```
 
 ## Example
 
 ```{r message=FALSE, warning=FALSE}
-library(dplyr) # tibble(), %>%, mutate()
+library(dplyr) # tibble(), mutate()
 library(knitr) # kable()
 library(whozr) # zwa(), zla(), zwl()
 ```
 
 
 ```{r}
-tibble(sex = c("F", "M", "M", "F"),
-       age_days = c(120, 310, 370, 460),
-       weight_kg = c(5.98, 8.09, 8.40, 8.46),
-       length_cm = c(60.2, 70.7, 72.6, 74.9)) %>%
-    mutate(waz = zwa(weight_kg, age_days, sex),
-           laz = zla(length_cm, age_days, sex),
-           wlz = zwl(weight_kg, length_cm, sex)) %>%
+tibble(
+    sex = c("F", "M", "M", "F"),
+    age_days = c(120, 310, 370, 460),
+    weight_kg = c(5.98, 8.09, 8.40, 8.46),
+    length_cm = c(60.2, 70.7, 72.6, 74.9)
+) |>
+    mutate(
+        waz = zwa(weight_kg, age_days, sex),
+        laz = zla(length_cm, age_days, sex),
+        wlz = zwl(weight_kg, length_cm, sex)
+    ) |>
     kable(digits = 3)
 ```
-