Refactor the deployment setup and reorganise the repo (#108)

.dockerignore

@@ -0,0 +1,2 @@
+**/renv
+**/.Rprofile

.env.sample

@@ -0,0 +1,12 @@
+ENV=test
+DATA_VOLUME_PATH=./data/test_data
+
+# For preprocessing
+PREPROCESS_DB_NAME=         # name of the source database
+PREPROCESS_HOST=            # host address for the source database
+PREPROCESS_PORT=            # port on which to connect to the source database
+PREPROCESS_DB_USERNAME=     # username for the source database
+PREPROCESS_DB_PASSWORD=     # password for the source database
+
+# For testing
+TEST_DB_PATH=./data-raw/test_db/eunomia

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

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check.yaml
+name: R-CMD-check
 
 permissions: read-all
 
@@ -18,9 +18,14 @@ concurrency:
 jobs:
   R-CMD-check:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        package_dir: [app, preprocessing]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v4
 
@@ -29,12 +34,16 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ matrix.package_dir }}
 
       - name: Install rcmdcheck
         run: install.packages("rcmdcheck")
         shell: Rscript {0}
+        working-directory: ${{ matrix.package_dir }}
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          working-directory: ${{ matrix.package_dir }}

.github/workflows/docker-build.yml

@@ -3,20 +3,28 @@ name: Build Docker Image
 on:
   push:
     branches: ["main"]
-    paths: ["deploy/**"]
+    paths: ["docker-compose.yml", "app/Dockerfile", "preprocessing/Dockerfile"]
   pull_request:
     branches: ["main"]
-    paths: ["deploy/**"]
+    paths: ["docker-compose.yml", "app/Dockerfile", "preprocessing/Dockerfile"]
   workflow_dispatch:
 
+# Only run actions on the most recent push to a branch
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref }}"
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        image: [omopcat, preprocess]
 
     steps:
       - uses: actions/checkout@v4
-      - name: Add dummy .Renviron file
-        run: touch deploy/.Renviron
       - name: Build the Docker image
-        run: docker compose build
-        working-directory: deploy/
+        run: |
+          cp .env.sample .env
+          docker compose build ${{ matrix.image }}

.github/workflows/lint.yaml

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [main, master]
 
-name: lint.yaml
+name: lint
 
 permissions: read-all
 
@@ -18,6 +18,10 @@ concurrency:
 jobs:
   lint:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        package_dir: [app, preprocessing]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -28,15 +32,19 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ matrix.package_dir }}
 
       - name: Install lintr
         run: install.packages("lintr")
         shell: Rscript {0}
+        working-directory: ${{ matrix.package_dir }}
 
       - name: Lint
         run: |
           pkgload::load_all()
           lintr::lint_package()
         shell: Rscript {0}
+        working-directory: ${{ matrix.package_dir }}
         env:
           LINTR_ERROR_ON_LINT: true

.github/workflows/test-coverage.yaml

@@ -6,13 +6,17 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage.yaml
+name: test-coverage
 
 permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        package_dir: [app, preprocessing]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
@@ -24,10 +28,13 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ matrix.package_dir }}
 
       - name: Install dependencies
         run: install.packages("covr", "xml2")
         shell: Rscript {0}
+        working-directory: ${{ matrix.package_dir }}
 
       - name: Test coverage
         run: |
@@ -38,6 +45,7 @@ jobs:
           )
           covr::to_cobertura(cov)
         shell: Rscript {0}
+        working-directory: ${{ matrix.package_dir }}
 
       - uses: codecov/codecov-action@v4
         with:
@@ -46,13 +54,15 @@ jobs:
           plugin: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
+          directory: ${{ matrix.package_dir }}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
           find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
+        working-directory: ${{ matrix.package_dir }}
 
       - name: Upload test results
         if: failure()

.pre-commit-config.yaml

@@ -7,10 +7,12 @@ repos:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
       - id: roxygenize
+        args: [--root=./app]
         additional_dependencies:
           - bslib
           - config
           - DT
+          - fs
           - ggplot2
           - golem
           - shiny
@@ -35,14 +37,16 @@ repos:
       # codemeta must be above use-tidy-description when both are used
       # -   id: codemeta-description-updated
       - id: use-tidy-description
+        args: [--root=./app]
       # - id: lintr  # disabling lintr hook as it doesn't seem to correctly load the package
       # see also https://github.com/lorenzwalthert/precommit/issues/440
       - id: parsable-R
       - id: no-browser-statement
       - id: no-print-statement
       - id: no-debug-statement
       - id: deps-in-desc
-        exclude: ^scripts/
+        args: [--root=./app]
+        exclude: "^scripts/|^app/dev/"
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
@@ -52,11 +56,6 @@ repos:
         files: '^\.Rbuildignore$'
       - id: end-of-file-fixer
         exclude: '\.Rd'
-  - repo: https://github.com/pre-commit-ci/pre-commit-ci-config
-    rev: v1.6.1
-    hooks:
-      # Only required when https://pre-commit.ci is used for config validation
-      - id: check-pre-commit-ci-config
   - repo: local
     hooks:
       - id: forbid-to-commit