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Merge pull request #49 from nutriverse/dev
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update repo; fix #46; fix #47; fix #48
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ernestguevarra authored Jan 5, 2023
2 parents 5d483ca + 21be691 commit 1ed6cf5
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2 changes: 2 additions & 0 deletions .Rbuildignore
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^pkgdown$
^cran-comments\.md$
^CRAN-RELEASE$
^CODE_OF_CONDUCT\.md$
^codecov\.yml$
148 changes: 113 additions & 35 deletions .github/CODE_OF_CONDUCT.md
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@@ -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 [email protected]. 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 [email protected].
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
12 changes: 6 additions & 6 deletions .github/CONTRIBUTING.md
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## 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

Expand All @@ -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
Expand All @@ -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`
4 changes: 2 additions & 2 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -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'}
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R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v2

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60 changes: 31 additions & 29 deletions .github/workflows/test-coverage.yaml
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# 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
5 changes: 3 additions & 2 deletions DESCRIPTION
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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
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16 changes: 12 additions & 4 deletions NEWS.md
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## 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`.

17 changes: 12 additions & 5 deletions README.Rmd
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<!-- 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 -->
Expand Down Expand Up @@ -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).
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