Merge pull request #1 from ttscience/devel

CI/CD and overall API structure

.Rbuildignore

@@ -0,0 +1,3 @@
+^renv$
+^renv\.lock$
+^\.github$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,33 @@
+# 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, devel]
+  pull_request:
+    branches: [main, devel]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+
+    name: Ubuntu (latest)
+
+    strategy:
+      fail-fast: false
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Build image
+        run: docker build -t unbiased --build-arg github_sha=${{ github.sha }} .
+
+      - name: Run tests
+        run: docker compose -f "docker-compose.test.yaml" up --abort-on-container-exit --exit-code-from tests --attach tests

.github/workflows/docker-publish.yml

@@ -82,6 +82,9 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
+          provenance: false
+          sbom: false
+          build-args: github_sha=${{ github.sha }}
 
       # Sign the resulting Docker image digest except on PRs.
       # This will only write to the public Rekor transparency log when the Docker

Dockerfile

@@ -1,2 +1,27 @@
-FROM alpine
-CMD ["echo", "Hello TTSI!..."]
+FROM rocker/r-ver:4.3.1
+
+WORKDIR /src/unbiased
+
+# Install system dependencies
+RUN apt update && apt-get install -y --no-install-recommends \
+  # httpuv
+  libz-dev \
+  # sodium
+  libsodium-dev
+
+ENV RENV_CONFIG_SANDBOX_ENABLED=FALSE
+
+COPY ./renv ./renv
+COPY .Rprofile .
+COPY renv.lock .
+
+RUN R -e 'renv::restore()'
+
+COPY api/ ./api
+
+EXPOSE 3838
+
+ARG github_sha
+ENV GITHUB_SHA=${github_sha}
+
+CMD ["R", "-e", "plumber::plumb(dir = 'api') |> plumber::pr_run(host = '0.0.0.0', port = 3838)"]

api/meta.R

@@ -0,0 +1,10 @@
+#* Github commit SHA
+#* 
+#* Each release of the API is based on some Github commit. This endpoint allows
+#* the user to easily check the SHA of the deployed API version.
+#* 
+#* @get /sha
+#* @serializer unboxedJSON
+function() {
+  Sys.getenv("GITHUB_SHA", unset = "")
+}

api/plumber.R

@@ -0,0 +1,9 @@
+#* @plumber
+function(api) {
+  rand_simple <- plumber::pr("randomize-simple.R")
+  meta <- plumber::pr("meta.R")
+
+  api |>
+    plumber::pr_mount("/simple", rand_simple) |>
+    plumber::pr_mount("/meta", meta)
+}

api/randomize-simple.R

@@ -0,0 +1,11 @@
+#* Return hello world
+#* 
+#* @get /hello
+#* @serializer unboxedJSON
+function() {
+  call_hello_world()
+}
+
+call_hello_world <- function() {
+  "Hello TTSI!"
+}

docker-compose.test.yaml

@@ -0,0 +1,24 @@
+version: "3.9"
+services:
+  api:
+    image: unbiased
+    container_name: unbiased_api
+    networks:
+      - test_net
+  tests:
+    image: unbiased
+    container_name: unbiased_tests
+    depends_on:
+      - api
+    environment:
+      - CI=true
+    networks:
+      - test_net
+    volumes:
+      - type: bind
+        source: ./tests
+        target: /src/unbiased/tests
+    command: Rscript tests/testthat.R
+
+networks:
+  test_net: