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Merge pull request #19 from KopfLab/dev
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sebkopf committed Jul 28, 2023
2 parents 9bfd512 + caf4942 commit 01f248b
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83 changes: 18 additions & 65 deletions .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
63 changes: 33 additions & 30 deletions .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
6 changes: 3 additions & 3 deletions DESCRIPTION
Expand Up @@ -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
Expand All @@ -21,7 +21,7 @@ Imports:
scales,
dplyr,
tidyr,
vctrs,
vctrs (>= 0.3.4),
stringi,
stringr
Suggests:
Expand All @@ -34,4 +34,4 @@ License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
RoxygenNote: 7.2.3
10 changes: 1 addition & 9 deletions README.Rmd
Expand Up @@ -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

Expand All @@ -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)
42 changes: 15 additions & 27 deletions README.md
Expand Up @@ -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

Expand Down Expand Up @@ -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)
22 changes: 11 additions & 11 deletions man/check_quantities.Rd

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10 changes: 5 additions & 5 deletions man/closed_system.Rd

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6 changes: 3 additions & 3 deletions man/constants.Rd

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8 changes: 4 additions & 4 deletions man/gas_calculations.Rd

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8 changes: 4 additions & 4 deletions man/metric_scaling.Rd

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