Add CI/CD

.Rbuildignore

@@ -1,3 +1,6 @@
 ^rphg2\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/check-standard.yaml

@@ -0,0 +1,49 @@
+# 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]
+  pull_request:
+    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: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    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 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

README.md

@@ -0,0 +1,33 @@
+# rPHG2
+
+<!-- badges: start -->
+[![Life Cycle Status](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+<!-- badges: end -->
+
+`rPHG2` is a system to interact with and retrieve information from **version 2** 
+of the Practical Haplotype Graph (PHGv2) - a general, graph-based, computational 
+framework for genotype inference. This is accomplished by leveraging the 
+[Breeding](https://brapi.org/) and 
+[PHG](https://github.com/maize-genetics/phg_v2) APIs.
+
+## Installation
+
+You can install the development version of rphg2 from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("maize-genetics/rPHG2")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(rphg2)
+
+phgCon <- PHGServerCon("localhost", 8080, "http")
+
+phgCon |> readSamples()
+```
+

_pkgdown.yml

@@ -0,0 +1,14 @@
+url: ~
+template:
+  bootstrap: 5
+
+footer:
+  structure:
+    left: acknowledgment
+  components:
+    acknowledgment: <b>rPHG2</b> is an R package developed by <a href="https://www.maizegenetics.net/">The Buckler Lab</a>
+
+home:
+  links:
+  - text: Report a bug
+    href: https://github.com/maize-genetics/rPHG2/issues