Merge pull request bcgov#306 from poissonconsulting/dev

.Rbuildignore

@@ -20,3 +20,4 @@
 
 ^COMPLIANCE\.yaml$
 ^CRAN-SUBMISSION$
+^CODE_OF_CONDUCT\.md$

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

@@ -11,20 +11,24 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     runs-on: ${{ matrix.config.os }}
-    timeout-minutes: 60
+
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
+          # 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: 'oldrel-2'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-    branches: main
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -13,13 +13,14 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     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@v3
 

.github/workflows/coverage.yaml → .github/workflows/test-coverage.yaml

@@ -2,15 +2,14 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main, master]
   pull_request:
-    branches: main
+    branches: [main, master]
 
-name: coverage
+name: test-coverage
 
 jobs:
-  coverage:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
+  test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/CODE_OF_CONDUCT.md → CODE_OF_CONDUCT.md

@@ -6,8 +6,8 @@ We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
 identity and expression, level of experience, education, socio-economic status,
-nationality, personal appearance, race, religion, or sexual identity and
-orientation.
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
 
 We pledge to act and interact in ways that contribute to an open, welcoming,
 diverse, inclusive, and healthy community.
@@ -21,25 +21,25 @@ community include:
 * Being respectful of differing opinions, viewpoints, and experiences
 * Giving and gracefully accepting constructive feedback
 * Accepting responsibility and apologizing to those affected by our mistakes,
-and learning from the experience
+  and learning from the experience
 * Focusing on what is best not just for us as individuals, but for the overall
-community
+  community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
-advances of any kind
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
 * Trolling, insulting or derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or email
-address, without their explicit permission
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
 * Other conduct which could reasonably be considered inappropriate in a
-professional setting
+  professional setting
 
 ## Enforcement Responsibilities
 
-Community leaders are responsible for clarifying and enforcing our standards
-of acceptable behavior and will take appropriate and fair corrective action in
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
 response to any behavior that they deem inappropriate, threatening, offensive,
 or harmful.
 
@@ -50,17 +50,17 @@ decisions when appropriate.
 
 ## Scope
 
-This Code of Conduct applies within all community spaces, and also applies
-when an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official e-mail
-address, posting via an official social media account, or acting as an appointed
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
 representative at an online or offline event.
 
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at [INSERT CONTACT
-METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+reported to the community leaders responsible for enforcement at .github/. 
+All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.
@@ -114,15 +114,13 @@ community.
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 2.0,
-available at https://www.contributor-covenant.org/version/2/0/
-code_of_conduct.html.
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
 
-Community Impact Guidelines were inspired by [Mozilla's code of conduct
-enforcement ladder](https://github.com/mozilla/diversity).
-
-[homepage]: https://www.contributor-covenant.org
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at https://
-www.contributor-covenant.org/translations.
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -2,11 +2,11 @@ Package: ssdtools
 Title: Species Sensitivity Distributions
 Version: 1.0.6.9000
 Authors@R: c(
-    person("Joe", "Thorley", , "[email protected]", role = c("aut", "cre", "ctr"),
+    person("Joe", "Thorley", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7683-4592")),
-    person("Carl", "Schwarz", role = c("aut", "ctr")),
-    person("Rebecca", "Fisher", role = "ctb"),
-    person("David", "Fox", role = "ctb"),
+    person("Carl", "Schwarz", role = "aut"),
+    person("Rebecca", "Fisher", , "[email protected]", role = "aut"),
+    person("David", "Fox", , "[email protected]", role = "aut"),
     person("Angeline", "Tillmanns", role = "ctb"),
     person("Ali", "Azizishirazi", role = "ctb"),
     person("Kathleen", "McTavish", role = "ctb"),
@@ -20,11 +20,14 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-3658-4517")),
     person("Emilie", "Doussantousse", role = "ctb"),
     person("Stephanie", "Hazlitt", role = "ctb"),
-    person("Nadine", "Hussein", role = "ctb"),
+    person("Nadine", "Hussein", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0003-4470-8361")),
     person("Nan-Hung", "Hsieh", role = "ctb"),
     person("Sergio", "Ibarra Espinosa", role = "ctb"),
-    person("Province of British Columbia", role = "cph"),
-    person("Environment and Climate Change Canada", role = "cph")
+    person("Hadley", "Wickham", role = "ctb"),
+    person("Province of British Columbia", role = c("fnd", "cph")),
+    person("Environment and Climate Change Canada", role = c("fnd", "cph")),
+    person("Australian Government Department of Climate Change, Energy, the Environment and Water", role = c("fnd", "cph"))
   )
 Description: Species sensitivity distributions are cumulative probability
     distributions which are fitted to toxicity concentrations for
@@ -36,7 +39,7 @@ Description: Species sensitivity distributions are cumulative probability
     on hazard concentrations and proportions are produced by parametric
     bootstrapping.
 License: Apache License (== 2.0) | file LICENSE
-URL: https://github.com/bcgov/ssdtools
+URL: https://github.com/bcgov/ssdtools, https://bcgov.github.io/ssdtools/
 BugReports: https://github.com/bcgov/ssdtools/issues
 Depends:
     R (>= 4.1)

README.Rmd

@@ -36,11 +36,10 @@ To install the latest version from [CRAN](https://CRAN.R-project.org/package=ssd
 install.packages("ssdtools")
 ```
 
-To install the latest development version:
-
+To install the latest development version from [GitHub](https://github.com/bcgov/ssdtools)
 ```{r, eval = FALSE}
-# install.packages("devtools")
-devtools::install_github("bcgov/ssdtools")
+# install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
+pak::pak("bcgov/ssdtools")
 ```
 
 ## Introduction
@@ -141,8 +140,7 @@ If you would like to contribute to the package, please see our
 
 ## Code of Conduct
 
-Please note that the ssdtools project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
-By contributing to this project, you agree to abide by its terms.
+Please note that the ssdtools 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.
 
 ## License
 

README.md

@@ -35,11 +35,12 @@ To install the latest version from
 install.packages("ssdtools")
 ```
 
-To install the latest development version:
+To install the latest development version from
+[GitHub](https://github.com/bcgov/ssdtools)
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("bcgov/ssdtools")
+# install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
+pak::pak("bcgov/ssdtools")
 ```
 
 ## Introduction
@@ -213,7 +214,7 @@ guidelines.
 
 Please note that the ssdtools project is released with a [Contributor
 Code of
-Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
+Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
 
 ## License
@@ -238,10 +239,9 @@ limitations under the License.
 ------------------------------------------------------------------------
 
 <a rel="license" href="https://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons Licence"
-style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a><br /><span
-xmlns:dct="http://purl.org/dc/terms/"
-property="dct:title">ssdtools</span> by <span
-xmlns:cc="http://creativecommons.org/ns#"
+style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/"
+property="dct:title">ssdtools</span> by
+<span xmlns:cc="http://creativecommons.org/ns#"
 property="cc:attributionName">the Province of British Columbia and
 Environment and Climate Change Canada </span> is licensed under a
 <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">

_pkgdown.yml

@@ -1 +1,19 @@
-destination: docs
+template:
+  bootstrap: 5
+authors:
+  Joe Thorley:
+    href: "https://github.com/joethorley"
+  Carl Schwarz:
+    href: "https://www.sfu.ca/stat-actsci/department/profiles/carl-schwarz.html"
+  David Fox:
+    href: "https://training.ecotox.science/who-we-are/"
+  Rebecca Fisher:
+    href: "https://www.aims.gov.au/about/our-people/dr-rebecca-fisher"
+  Angeline Tillmans:
+    href: "https://www.linkedin.com/in/angeline-tillmanns-5b7999a/"
+  Province of British Columbia:
+    href: "https://www2.gov.bc.ca/"
+  Environment and Climate Change Canada:
+    href: "https://www.canada.ca/en/environment-climate-change.html"
+  Australian Government Department of Climate Change, Energy, the Environment and Water:
+    href: "https://www.dcceew.gov.au/"

scripts/build.R

@@ -19,9 +19,6 @@ lintr::lint_package()
 devtools::test()
 devtools::document()
 
-rmarkdown::render("README.Rmd", output_format = "md_document")
-pkgdown::build_site()
-demo(ssdtools, ask = FALSE)
+pkgdown::build_home()
 
 devtools::check()
-