Merge pull request #49 from nutriverse/dev

update repo; fix #46; fix #47; fix #48

Author: ernestguevarra

.Rbuildignore

@@ -23,3 +23,5 @@
 ^pkgdown$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
+^CODE_OF_CONDUCT\.md$
+^codecov\.yml$

.github/CODE_OF_CONDUCT.md

@@ -1,48 +1,126 @@
-# Contributor Code of Conduct
+# Contributor Covenant Code of Conduct
 
-As contributors and maintainers of this project, and in the interest of
-fostering an open and welcoming community, we pledge to respect all people who
-contribute through reporting issues, posting feature requests, updating
-documentation, submitting pull requests or patches, and other activities.
+## Our Pledge
 
-We are committed to making participation in this project a harassment-free
-experience for everyone, regardless of level of experience, gender, gender
-identity and expression, sexual orientation, disability, personal appearance,
-body size, race, ethnicity, age, religion, or nationality.
+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, caste, color, religion, or sexual
+identity and orientation.
 
-Examples of unacceptable behavior by participants include:
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
-* The use of sexualized language or imagery
-* Personal attacks
-* Trolling or insulting/derogatory comments
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* 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
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* 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 other's private information, such as physical or electronic
-  addresses, without explicit permission
-* Other unethical or unprofessional conduct
+* 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
+
+## Enforcement Responsibilities
+
+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.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
 
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
+## Scope
 
-By adopting this Code of Conduct, project maintainers commit themselves to
-fairly and consistently applying these principles to every aspect of managing
-this project. Project maintainers who do not follow or enforce the Code of
-Conduct may be permanently removed from the project team.
+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.
 
-This Code of Conduct applies both within project spaces and in public spaces
-when an individual is representing the project or its community.
+## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting a project maintainer at contact@guevarra.io. All 
-complaints will be reviewed and investigated and will result in a response that 
-is deemed necessary and appropriate to the circumstances. Maintainers are 
-obligated to maintain confidentiality with regard to the reporter of an incident.
+reported to the community leaders responsible for enforcement at ernest@guevarra.io. 
+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.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 1.3.0, available at
-[http://contributor-covenant.org/version/1/3/0/][version]
+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/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>.
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/3/0/
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 ## Bugs
 
-* Submit an issue on the [issues page](https://github.com/como-ph/oxcgrt/issues)
+* Submit an issue on the [issues page](https://github.com/nutriverse/nipnTK/issues)
 
 ## Code contributions
 
@@ -11,14 +11,14 @@
 * Clone your version on your account down to your machine from your account 
 
 ```
-git clone https://github.com/<yourgithubusername>/oxcgrt.git
+git clone https://github.com/<yourgithubusername>/nipnTK.git
 ```
 
-* Make sure to track progress upstream i.e., on our version of `oxcgrt` 
-at `oxcgrt/covidphdata`, by doing 
+* Make sure to track progress upstream i.e., on our version of `nipnTK` 
+at `nutriverse/nipnTK`, by doing 
 
 ```
-git remote add upstream https://github.com/como-ph/oxcgrt.git
+git remote add upstream https://github.com/nutriverse/nipnTK.git
 ```
 
 * Before making changes make sure to pull changes in from `upstream` by doing 
@@ -32,4 +32,4 @@ documentation
 
 * Push up changes to your account
 
-* Submit a pull request at `como-ph/oxcgrt`
+* Submit a pull request at `nutriverse/nipnTK`

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

@@ -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'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.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

DESCRIPTION

@@ -30,11 +30,12 @@ Suggests:
     knitr,
     rmarkdown,
     tufte,
-    spelling
+    spelling,
+    covr
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 URL: https://nutriverse.io/nipnTK/, https://github.com/nutriverse/nipnTK
 BugReports: https://github.com/nutriverse/nipnTK/issues

NEWS.md

@@ -1,18 +1,26 @@
-## nipnTK 0.1.1.9000
+# nipnTK 0.1.1.9000
 
 Second release of `nipnTK`. This is a GitHub-only development release. In this
 release:
 
-### General updates
+## General updates
 
 * remove `appveyor.yml` and the Appveyor ci/cd workflow
 
 * update GitHub Actions workflow to latest 5 system standard check
 
+* update GitHub Actions workflow for coverage testing
 
-## nipnTK 0.1.0
+* change default git branch name from master to main
 
-This is the first [CRAN](https://cran.r-project.org) release of `nipnTK`.
+* add CITATION
+
+* update CONTRIBUTOR guidelines
+
+* upgrade website to bootstrap 5
 
 
+# nipnTK 0.1.0
+
+This is the first [CRAN](https://cran.r-project.org) release of `nipnTK`.
 

README.Rmd

@@ -21,16 +21,15 @@ library(nipnTK)
 
 <!-- Badges start here -->
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN](https://img.shields.io/cran/v/nipnTK.svg)](https://cran.r-project.org/package=nipnTK)
 [![cran checks](https://cranchecks.info/badges/summary/nipnTK)](https://cran.r-project.org/web/checks/check_results_nipnTK.html)
 [![CRAN](https://img.shields.io/cran/l/nipnTK.svg)](https://CRAN.R-project.org/package=nipnTK)
 [![CRAN](http://cranlogs.r-pkg.org/badges/nipnTK)](https://cran.r-project.org/package=nipnTK)
 [![CRAN](http://cranlogs.r-pkg.org/badges/grand-total/nipnTK)](https://cran.r-project.org/package=nipnTK)
-[![R build status](https://github.com/nutriverse/nipnTK/workflows/R-CMD-check/badge.svg)](https://github.com/nutriverse/nipnTK/actions)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/nutriverse/nipnTK?branch=master&svg=true)](https://ci.appveyor.com/project/nutriverse/nipnTK)
-[![R build status](https://github.com/nutriverse/nipnTK/workflows/test-coverage/badge.svg)](https://github.com/nutriverse/nipnTK/actions)
-[![codecov](https://codecov.io/gh/nutriverse/nipnTK/branch/master/graph/badge.svg)](https://codecov.io/gh/nutriverse/nipnTK)
+[![R-CMD-check](https://github.com/nutriverse/nipnTK/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nutriverse/nipnTK/actions/workflows/R-CMD-check.yaml)
+[![test-coverage](https://github.com/nutriverse/nipnTK/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/nutriverse/nipnTK/actions/workflows/test-coverage.yaml)
+[![Codecov test coverage](https://codecov.io/gh/nutriverse/nipnTK/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nutriverse/nipnTK?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/nutriverse/nipntk/badge)](https://www.codefactor.io/repository/github/nutriverse/nipntk)
 [![DOI](https://zenodo.org/badge/118171028.svg)](https://zenodo.org/badge/latestdoi/118171028)
 <!-- Badges end here -->
@@ -88,6 +87,14 @@ These activities and a proposed order in which they should be performed are show
 knitr::include_graphics("man/figures/nipnWorkflow.png")
 ```
 
+## Citation
+
+If you find the `nipnTK` package useful, please cite using the suggested citation provided by a call to the `citation` function as follows:
+
+```{r cite}
+citation("nipnTK")
+```
+
 ## Community guidelines
 
 Feedback, bug reports and feature requests are welcome; file issues or seek support [here](https://github.com/nutriverse/nipnTK/issues). If you would like to contribute to the package, please see our [contributing guidelines](https://nutriverse.io/nipnTK/CONTRIBUTING.html).