From 6496c9117d3c6dfec985d1667369ea79a8309121 Mon Sep 17 00:00:00 2001
From: "Adam H. Sparks" <adamhsparks@gmail.com>
Date: Thu, 7 May 2020 13:38:53 +1000
Subject: [PATCH] Revert "Remove GitHub Actions since all seem to be borked"

This reverts commit 39555467df8e863fa9562ae723eaf78bd0614d00.
---
 .github/.gitignore                    |  1 +
 .github/workflows/R-CMD-check.yaml    | 92 +++++++++++++++++++++++++++
 .github/workflows/pkgdown.yaml        | 45 +++++++++++++
 .github/workflows/publish_docker.yaml | 13 ++++
 4 files changed, 151 insertions(+)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 .github/workflows/publish_docker.yaml

diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..0817c23
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,92 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - 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: 'devel'}
+          - {os: macOS-latest,   r: '4.0'}
+          - {os: windows-latest, r: '4.0'}
+          - {os: ubuntu-18.04,   r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..45281da
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,45 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages("remotes")
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+        
+      - name: XQuartz
+        run: |
+          brew cask install xquartz
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-1-
+      - name: Install dependencies
+        run: |
+          install.packages("ggplot2")
+          remotes::install_deps(dependencies = TRUE, type = "binary")
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}
\ No newline at end of file
diff --git a/.github/workflows/publish_docker.yaml b/.github/workflows/publish_docker.yaml
new file mode 100644
index 0000000..2796334
--- /dev/null
+++ b/.github/workflows/publish_docker.yaml
@@ -0,0 +1,13 @@
+name: Publish Docker
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@master
+      with:
+        name: adamhsparks/chickpea_asco_dispersal
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}