Basic infrastructure: Add Dockerfile and basic testing for this repository

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.github

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,93 @@
+# 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:
+      - main
+  pull_request:
+    branches:
+      - main
+
+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-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    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: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        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 system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Check testthat
+        if: runner.os != 'Windows'
+        id: check_check
+        run: |
+            error_num=$(Rscript --vanilla '.github/workflows/check_testthat.R')
+            echo "error_num=$error_num" >> $GITHUB_OUTPUT
+
+      - name: Stop if there are errors!
+        if: ${{ steps.check_check.outputs.error_num != '0' }}
+        run: exit 1
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/check_testthat.R

@@ -0,0 +1,31 @@
+# Check up on the testthat results
+# C. Savonen
+# Nov 2023
+
+library(magrittr)
+
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+out_file <- list.files(pattern = "testthat.Rout$|Rout.fail$", file.path(root_dir, "check"),
+ recursive = TRUE, full.names = TRUE)
+
+check_content <- readLines(out_file)
+test_result <- grep("\\[ FAIL", check_content, value = TRUE)[1]
+test_result <- unlist(strsplit(test_result, "\\||\\[|\\]"))
+
+# Format the data into a dataframe
+test_result_df <- data.frame(result = trimws(test_result)) %>%
+  dplyr::filter(result != "") %>%
+  tidyr::separate(result, sep = " ", into = c("test_name", "num")) %>%
+  dplyr::mutate(num = as.numeric(num))
+
+fail_num <- test_result_df %>%
+  dplyr::filter(test_name %in% c("FAIL", "WARN")) %>%
+  dplyr::summarize(total = sum(num))
+
+fail_num <- as.character(fail_num$total)
+
+# Spit the number out
+writeLines(fail_num, con = stdout())

.github/workflows/docker-build.yml

@@ -0,0 +1,74 @@
+# Candace Savonen Jan 2024
+
+name: Build Docker
+
+on:
+  workflow_dispatch:
+    inputs:
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: true
+        default: 'false'
+      tag:
+        description: 'What tag to use?'
+        required: true
+        default: 'none'
+jobs:
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --system --add safe.directory "$GITHUB_WORKSPACE"
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      # Set up Docker build
+      - name: Set up Docker Build
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
+
+      # Build docker image
+      - name: Build Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: false
+          load: true
+          context: docker
+          file: inst/extdata/Dockerfile
+          tags: hutch/gimap
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        run: |
+          docker tag jhudsl/base_ottr:latest jhudsl/base_ottr:$github.event.inputs.tag
+          docker push jhudsl/base_ottr:$github.event.inputs.tag

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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 }}
+    permissions:
+      contents: write
+    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/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/render-vignette.yml

@@ -0,0 +1,49 @@
+
+# Candace Savonen Jan 2024
+
+name: Render vignette with Docker image
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: [ main, staging ]
+  push:
+    branches: [ main, staging ]
+    paths:
+      - R/*
+      - inst/extdata/*
+
+jobs:
+
+  render-vignette:
+    name: Render test
+    runs-on: ubuntu-latest
+    container:
+      image: cansav09/gimap
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
+
+      - name: Run vignette
+        run: Rscript -e "rmarkdown::render('vignettes/getting-started.Rmd')"
+
+      # Commit the rendered bookdown files
+      - name: Commit rendered files
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git add --force docs/*
+          git commit -m 'Render vignette' || echo "No changes to commit"
+          git pull --allow-unrelated-histories --strategy-option=ours
+          git push -u origin main  || echo "No changes to push"

.github/workflows/style-code.yml

@@ -0,0 +1,37 @@
+# Candace Savonen 2024
+
+name: Style Code
+
+on:
+  pull_request:
+    branches: [ main, staging ]
+
+jobs:
+
+  style-code:
+    name: Style code
+    runs-on: ubuntu-latest
+    container:
+      image: cansav09/gimap
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
+
+      - name: Run styler
+        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+
+      - name: Commit styled files
+        run: |
+          git config --system --add safe.directory "$GITHUB_WORKSPACE"
+          git add \*.Rmd
+          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.gitignore

@@ -12,3 +12,4 @@ inst/extdata/cached-secrets/*
 testthat-problems.rds
 .Renviron
 inst/doc
+git_token.txt

CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# CONTRIBUTING
+
+This document describes how to contribute to this R package.
+
+## GitHub Workflow
+
+- File an issue with anything you see that needs to be considered, added or fixed.
+- Assign yourself to an issue that you'd like to work on. If you have any questions about how to go about the issue you've been assigned to, communicate your questions on that issue!
+- Clone this repository locally and create a new branch to work on this issue from.
+- When you feel you have enough to discuss, push the branch and open a pull request. When you do this, you will see a series of checks begin to run:
+
+## Automatic checks
+
+- `R-CMD-checks` - these checks make sure that the R package files are built properly. It will also rebuild the vignette underneath 4 different operating systems:
+  - windows
+  - macOS
+  - ubuntu release
+  - ubuntu dev
+- `docker-build.yml` - handles the docker image associated with this pipeline. Any changes to the docker image will be tested by this GitHub Action by rebuilding it.
+- `style-code.yml` - this will style your code and commit any changes to the pull request
+
+
+## Testing
+
+Whenever appropriate, new functions should be added to:
+  - the `vignette/getting-started.Rmd` if they are a part of the essential workflow.
+  - a unit test using testthat. You can create a new test using `usethis::use_test("name")`. then open up that file in the `tests/testthat` folder and write a test there. See this chapter for how to write tests https://r-pkgs.org/testing-basics.html
+
+
+## Docker image
+
+For reproducibility purposes, this repository has a Docker image. And software requirements should be added to this Docker image as development occurs.