updae master

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

@@ -1,83 +1,36 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
-  schedule:
-    - cron: "0 0 * * FRI"
+    branches: [main, 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: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'devel'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
+    runs-on: ubuntu-latest
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - 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-pandoc@v1
-
-      - 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@v2
+      - uses: r-lib/actions/setup-r-dependencies@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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - 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

.github/workflows/pkgdown.yaml

@@ -1,45 +1,48 @@
+# 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: master
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
-        with:
-          r-version: 'release'
-
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: macOS-r-4.0-2-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_dev("pkgdown")
-          remotes::install_github("tidyverse/tidytemplate")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: pkgdown::deploy_to_branch(new_process = FALSE)
-        shell: Rscript {0}
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -2,7 +2,7 @@ Package: microbialkitchen
 Type: Package
 Title: Culture Media Tools
 Description: Package to simplify working with defined culture medium.
-Version: 0.4.2
+Version: 0.4.3
 Authors@R: person("Sebastian", "Kopf", email = "sebastian.kopf@colorado.edu",
     role = c("aut", "cre"))
 URL: https://github.com/kopflab/microbialkitchen
@@ -21,7 +21,7 @@ Imports:
     scales,
     dplyr,
     tidyr,
-    vctrs,
+    vctrs (>= 0.3.4),
     stringi,
     stringr
 Suggests:
@@ -34,4 +34,4 @@ License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3

README.Rmd

@@ -15,13 +15,9 @@ version <- as.character(packageVersion("microbialkitchen"))
 
 # Microbial Kitchen (formerly MediaChemTools)
 
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/microbialkitchen)](https://cran.r-project.org/package=microbialkitchen)
-[![Git_Hub_Version](https://img.shields.io/badge/GitHub-`r version`-orange.svg?style=flat-square)](/commits)
+[![R-CMD-check](https://github.com/KopfLab/microbialkitchen/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/KopfLab/microbialkitchen/actions/workflows/R-CMD-check.yaml)
 [![Documentation](https://img.shields.io/badge/docs-online-green.svg)](https://microbialkitchen.kopflab.org/reference/)
 [![codecov](https://codecov.io/github/KopfLab/microbialkitchen/branch/master/graphs/badge.svg)](https://codecov.io/github/Kopflab/microbialkitchen) 
-[![R build status](https://github.com/KopfLab/microbialkitchen/workflows/R-CMD-check/badge.svg)](https://github.com/KopfLab/microbialkitchen/actions)
-[![Binder](https://img.shields.io/badge/launch-Jupyter-orange.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=lab)
-[![Binder](https://img.shields.io/badge/launch-RStudio-blue.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=rstudio)
 
 ## About
 
@@ -45,7 +41,3 @@ devtools::install_github("KopfLab/microbialkitchen")
     - [equations vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_equations.html)
     - [examples vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_examples.html)
 
-Explore all functionality and vignettes of the **microbialkitchen** package interactively on [binder](https://mybinder.org/):
-
-[![Binder](https://img.shields.io/badge/launch-Jupyter-orange.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=lab)
-[![Binder](https://img.shields.io/badge/launch-RStudio-blue.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=rstudio)

README.md

@@ -3,14 +3,9 @@
 
 # Microbial Kitchen (formerly MediaChemTools)
 
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/microbialkitchen)](https://cran.r-project.org/package=microbialkitchen)
-[![Git\_Hub\_Version](https://img.shields.io/badge/GitHub-0.4.2-orange.svg?style=flat-square)](/commits)
+[![R-CMD-check](https://github.com/KopfLab/microbialkitchen/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/KopfLab/microbialkitchen/actions/workflows/R-CMD-check.yaml)
 [![Documentation](https://img.shields.io/badge/docs-online-green.svg)](https://microbialkitchen.kopflab.org/reference/)
 [![codecov](https://codecov.io/github/KopfLab/microbialkitchen/branch/master/graphs/badge.svg)](https://codecov.io/github/Kopflab/microbialkitchen)
-[![R build
-status](https://github.com/KopfLab/microbialkitchen/workflows/R-CMD-check/badge.svg)](https://github.com/KopfLab/microbialkitchen/actions)
-[![Binder](https://img.shields.io/badge/launch-Jupyter-orange.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=lab)
-[![Binder](https://img.shields.io/badge/launch-RStudio-blue.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=rstudio)
 
 ## About
 
@@ -42,24 +37,17 @@ devtools::install_github("KopfLab/microbialkitchen")
 
 ## Functionality
 
-  - [function
-    reference](https://microbialkitchen.kopflab.org/reference/) for
-    details on all functions
-  - [quantities
-    vignette](https://microbialkitchen.kopflab.org/articles/quantities.html)
-    on built-in chemical quantities
-  - [operations
-    vignette](https://microbialkitchen.kopflab.org/articles/operations.html)
-    on working with quantities
-  - carbonate chemistry vignettes for working with carbonate buffered
-    media systems:
-      - [equations
-        vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_equations.html)
-      - [examples
-        vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_examples.html)
-
-Explore all functionality and vignettes of the **microbialkitchen**
-package interactively on [binder](https://mybinder.org/):
-
-[![Binder](https://img.shields.io/badge/launch-Jupyter-orange.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=lab)
-[![Binder](https://img.shields.io/badge/launch-RStudio-blue.svg)](https://mybinder.org/v2/gh/KopfLab/microbialkitchen/binder?urlpath=rstudio)
+- [function reference](https://microbialkitchen.kopflab.org/reference/)
+  for details on all functions
+- [quantities
+  vignette](https://microbialkitchen.kopflab.org/articles/quantities.html)
+  on built-in chemical quantities
+- [operations
+  vignette](https://microbialkitchen.kopflab.org/articles/operations.html)
+  on working with quantities
+- carbonate chemistry vignettes for working with carbonate buffered
+  media systems:
+  - [equations
+    vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_equations.html)
+  - [examples
+    vignette](https://microbialkitchen.kopflab.org/articles/carbonate_chemistry_examples.html)