Coverage and devops

.devcontainer/Dockerfile

@@ -6,8 +6,16 @@ RUN apt update && apt-get install -y --no-install-recommends \
   # sodium
   libsodium-dev \
   # RPostgres
-  libpq-dev libssl-dev postgresql-client
+  libpq-dev libssl-dev postgresql-client \
+  # R_X11
+  libxt-dev
 
 RUN pip install watchdog[watchmedo]
 
 ENV RENV_CONFIG_SANDBOX_ENABLED=FALSE
+
+# Install database migration tool
+RUN curl -L https://packagecloud.io/golang-migrate/migrate/gpgkey | apt-key add - && \
+  echo "deb https://packagecloud.io/golang-migrate/migrate/ubuntu/ focal main" > /etc/apt/sources.list.d/migrate.list && \
+  apt-get update && \
+  apt-get install -y migrate

.devcontainer/docker-compose.yml

@@ -41,9 +41,7 @@ services:
       - "5454:80"
 
   db:
-    build:
-      context: ..
-      dockerfile: Dockerfile.postgres
+    image: ghcr.io/ttscience/postgres-temporal-tables/postgres-temporal-tables:latest
     restart: unless-stopped
     volumes:
       - postgres-data:/var/lib/postgresql/data

.github/workflows/document.yaml

@@ -0,0 +1,42 @@
+# 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:
+    paths: ["R/**"]
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# 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: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,79 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      POSTGRES_DB: postgres
+      POSTGRES_HOST: 127.0.0.1
+      POSTGRES_PORT: 5432
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+
+    services:
+      postgres:
+        image: ghcr.io/ttscience/postgres-temporal-tables/postgres-temporal-tables:latest
+        env:
+          POSTGRES_PASSWORD: postgres
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      - 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: Install migrate
+        run: |
+          curl -L https://packagecloud.io/golang-migrate/migrate/gpgkey | \
+            sudo apt-key add - && \
+          echo "deb https://packagecloud.io/golang-migrate/migrate/ubuntu/ focal main" | \
+            sudo tee /etc/apt/sources.list.d/migrate.list && \
+          sudo apt-get update && \
+          sudo apt-get install -y migrate
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "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

DESCRIPTION

@@ -47,5 +47,5 @@ RdMacros: mathjaxr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://ttscience.github.io/unbiased/

Dockerfile

@@ -9,7 +9,14 @@ RUN apt update && apt-get install -y --no-install-recommends \
   # sodium
   libsodium-dev \
   # RPostgres
-  libpq-dev libssl-dev postgresql-client
+  libpq-dev libssl-dev postgresql-client \
+  curl gnupg2
+
+# Install database migration tool
+RUN curl -L https://packagecloud.io/golang-migrate/migrate/gpgkey | apt-key add - && \
+  echo "deb https://packagecloud.io/golang-migrate/migrate/ubuntu/ focal main" > /etc/apt/sources.list.d/migrate.list && \
+  apt-get update && \
+  apt-get install -y migrate
 
 ENV RENV_CONFIG_SANDBOX_ENABLED=FALSE
 
@@ -33,5 +40,4 @@ EXPOSE 3838
 ARG github_sha
 ENV GITHUB_SHA=${github_sha}
 
-CMD ["R", "-e", "unbiased::run_unbiased()"]
-
+CMD ["R", "-e", "unbiased::run_unbiased()"]

NAMESPACE

@@ -1,11 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
-export(list_studies)
+export(create_db_connection_pool)
 export(randomize_minimisation_pocock)
 export(randomize_simple)
-export(read_study_details)
 export(run_unbiased)
-export(study_exists)
 import(checkmate)
 import(dplyr)
 import(mathjaxr)