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add github workflow
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Zilong-Li committed Aug 16, 2024
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1 change: 1 addition & 0 deletions .github/.gitignore
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*.html
9 changes: 9 additions & 0 deletions .github/CONTRIBUTING.md
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### Contributing to PCAoneR

Please see the file [Contributing](https://github.com/Zilong-Li/PCAoneR/blob/main/Contributing.md) for details on

- how to report an issue: a [Minimally Complete (and) Verifiable Example (MCVE)](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) helps a lot;
- how to submit a pull request: post an issue first, get consensus about _what_ and _how_;
- how to follow our (informal) coding style: simply do as other files do and do not invent a new style;
- how to be nice and [NEWS.Rd](https://github.com/Zilong-Li/PCAoneR/blob/main/NEWS.md)
11 changes: 11 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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### Pull Request Template for PCAoneR

Please explain the changes you want to apply to PCAoneR, preferably in an issue ticket **before** you create a pull request. See the file [Contributing](https://github.com/Zilong-Li/PCAoneR/blob/main/Contributing.md) and the other templates for details.

#### Checklist

- [ ] Code compiles correctly
- [ ] `R CMD check` still passes all tests
- [ ] Preferably, new tests were added which fail without the change
- [ ] Document changes in [NEWS.Rd](https://github.com/Zilong-Li/PCAoneR/blob/main/NEWS.md)
47 changes: 47 additions & 0 deletions .github/workflows/check-release.yaml
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# Run CI for R using https://eddelbuettel.github.io/r-ci/
# This file is a slight variant by running a matrix of containers

name: R-CMD-check

on:
push:
branches: [main, dev]
pull_request:
branches: [main]

jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}

name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3

- 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-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check

- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
95 changes: 95 additions & 0 deletions .github/workflows/rhub.yaml
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# R-hub's generic GitHub Actions workflow file. It's canonical location is at
# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
# You can update this file to a newer version using the rhub2 package:
#
# rhub::rhub_setup()
#
# It is unlikely that you need to modify this file manually.

name: R-hub
run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"

on:
workflow_dispatch:
inputs:
config:
description: 'A comma separated list of R-hub platforms to use.'
type: string
default: 'linux,windows,macos'
name:
description: 'Run name. You can leave this empty now.'
type: string
id:
description: 'Unique ID. You can leave this empty now.'
type: string

jobs:

setup:
runs-on: ubuntu-latest
outputs:
containers: ${{ steps.rhub-setup.outputs.containers }}
platforms: ${{ steps.rhub-setup.outputs.platforms }}

steps:
# NO NEED TO CHECKOUT HERE
- uses: r-hub/actions/setup@v1
with:
config: ${{ github.event.inputs.config }}
id: rhub-setup

linux-containers:
needs: setup
if: ${{ needs.setup.outputs.containers != '[]' }}
runs-on: ubuntu-latest
name: ${{ matrix.config.label }}
strategy:
fail-fast: false
matrix:
config: ${{ fromJson(needs.setup.outputs.containers) }}
container:
image: ${{ matrix.config.container }}

steps:
- uses: r-hub/actions/checkout@v1
- uses: r-hub/actions/platform-info@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/setup-deps@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/run-check@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}

other-platforms:
needs: setup
if: ${{ needs.setup.outputs.platforms != '[]' }}
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.label }}
strategy:
fail-fast: false
matrix:
config: ${{ fromJson(needs.setup.outputs.platforms) }}

steps:
- uses: r-hub/actions/checkout@v1
- uses: r-hub/actions/setup-r@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}
- uses: r-hub/actions/platform-info@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/setup-deps@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}
- uses: r-hub/actions/run-check@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}

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