From f82e337511a89ebea14616eb19ccc49b77e6ba1f Mon Sep 17 00:00:00 2001
From: MikkoVihtakari <mikko.vihtakari@hi.no>
Date: Fri, 26 Jan 2024 14:19:14 +0100
Subject: [PATCH] Add .github folder

---
 .github/.gitignore                 |  1 +
 .github/workflows/R-CMD-check.yaml | 72 ++++++++++++++++++++++++++++++
 .github/workflows/gh-pages.yml     | 35 +++++++++++++++
 3 files changed, 108 insertions(+)
 create mode 100755 .github/.gitignore
 create mode 100755 .github/workflows/R-CMD-check.yaml
 create mode 100755 .github/workflows/gh-pages.yml

diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100755
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 100755
index 0000000..3488e85
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,72 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - 'v*'
+  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: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+          - {os: ubuntu-latest, r: 'oldrel-2'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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-pandoc@v2
+
+      # TMB binary package is complaining about Matrix inconsistency & failing to compile with
+      # /Users/runner/work/_temp/Library/TMB/include/TMB.hpp:78:10: fatal error: 'Eigen/Dense' file not found
+      - name: Install TMB
+        run: install.packages('TMB', type = 'source')
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck any::mfdb
+          needs: check
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          # NB: The model compilations should in theory work on windows, but github actions hangs
+          _R_CHECK_DONTTEST_EXAMPLES_: ${{ runner.os != 'Windows' && 'true' || 'false' }}
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: ${{ !success() }}
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
new file mode 100755
index 0000000..27762b3
--- /dev/null
+++ b/.github/workflows/gh-pages.yml
@@ -0,0 +1,35 @@
+# Based on:-
+# * https://ropenscilabs.github.io/actions_sandbox/websites-using-pkgdown-bookdown-and-blogdown.html#action-to-deploy-a-bookdown-site
+# * https://github.com/peaceiris/actions-gh-pages
+on:
+  push:
+     branches:
+       - master
+
+name: Render documentation
+
+jobs:
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          publish_branch: gh-pages
+          publish_dir: ./docs