Merge pull request #80 from ttscience/devel

Release candidate

.Rbuildignore

@@ -1,3 +1,10 @@
 ^renv$
 ^renv\.lock$
 ^\.github$
+^unbiased\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes/articles$

.devcontainer/Dockerfile

@@ -0,0 +1,21 @@
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.2
+
+RUN apt update && apt-get install -y --no-install-recommends \
+  # httpuv
+  libz-dev \
+  # sodium
+  libsodium-dev \
+  # RPostgres
+  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/devcontainer.json

@@ -0,0 +1,42 @@
+{
+  "name": "R unbiased",
+  "dockerComposeFile": "docker-compose.yml",
+  "service": "app",
+  "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
+  "features": {
+    "ghcr.io/rocker-org/devcontainer-features/renv-cache:0": {},
+    "ghcr.io/rocker-org/devcontainer-features/rstudio-server:0": {
+      "singleUser": true,
+      "version": "stable"
+    }
+  },
+  "postCreateCommand": "R -q -e 'renv::restore()'",
+  // "postAttachCommand": {
+  //   "rstudio-start": "rserver"
+  // },
+  "forwardPorts": [
+    8787,
+    5454
+  ],
+  "portsAttributes": {
+    "8787": {
+      "label": "RStudio IDE"
+    },
+    "5454": {
+      "label": "PGAdmin"
+    }
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "RDebugger.r-debugger"
+      ],
+      "settings": {
+        "terminal.integrated.shell.linux": "/bin/bash",
+        "r.rterm.linux": "/usr/local/bin/radian",
+        "r.bracketedPaste": true,
+        "r.plot.useHttpgd": true
+      }
+    }
+  }
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,57 @@
+version: '3.8'
+
+services:
+  app:
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+
+    volumes:
+      - ../..:/workspaces:cached
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: sleep infinity
+
+    # Runs app on the same network as the database container, allows "forwardPorts" in devcontainer.json function.
+    network_mode: service:db
+
+    # Use "forwardPorts" in **devcontainer.json** to forward an app port locally.
+    # (Adding the "ports" property to this file will not forward from a Codespace.)
+
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_DB: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_HOST: db
+
+  pgadmin:
+    image: dpage/pgadmin4
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_DB: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_HOST: db
+      PGADMIN_DEFAULT_EMAIL: [email protected]
+      PGADMIN_DEFAULT_PASSWORD: pgadmin
+    volumes:
+      - pga-data:/tmp/dev/pga/data
+    depends_on:
+      - db
+    ports:
+      - "5454:80"
+
+  db:
+    image: ghcr.io/ttscience/postgres-temporal-tables/postgres-temporal-tables:latest
+    restart: unless-stopped
+    volumes:
+      - postgres-data:/var/lib/postgresql/data
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_DB: postgres
+      POSTGRES_PASSWORD: postgres
+    # Add "forwardPorts": ["5432"] to **devcontainer.json** to forward PostgreSQL locally.
+    # (Adding the "ports" property to this file will not forward from a Codespace.)
+
+volumes:
+  postgres-data:
+  pga-data:

.github/workflows/docker-publish.yml

@@ -1,26 +1,25 @@
-name: Docker
+name: Build and Publish Docker Images
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
 
 on:
-  schedule:
-    - cron: '15 0 * * *'
   push:
-    branches: [ "main" ]
+    branches: [ "main", "devel" ]
     # Publish semver tags as releases.
     tags: [ 'v*.*.*' ]
   pull_request:
-    branches: [ "main" ]
+    branches: [main, devel]
   workflow_dispatch:
 
 env:
   # Use docker.io for Docker Hub if empty
   REGISTRY: ghcr.io
   # github.repository as <account>/<repo>
   IMAGE_NAME: ${{ github.repository }}
+  BRANCH_TAG: ${{ github.ref == 'refs/heads/devel' && 'unbiased-dev' || 'latest' }}
 
 
 jobs:

.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/pkgdown.yaml

@@ -0,0 +1,51 @@
+# 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@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          install-pandoc: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs