Merge pull request #122 from alan-turing-institute/r-docker-refactor

R docker refactor for lab sessions

.dockerignore

@@ -0,0 +1,6 @@
+README_files
+_reference
+_sidebar*
+_site*
+_extensions
+*.bak

.github/workflows/ci.yaml

@@ -5,8 +5,9 @@ env:
   DOCKER_BUILDKIT: 1
   COMPOSE_DOCKER_CLI_BUILD: 1
   CONDA_ENV_NAME: clim-recal
+  CONDA_ENV_PATH: environment.yml
   MIN_PYTHON_VERSION: 3.9
-  PYTHON_MODULE_FOLDER: /home/jovyan/python/
+  PYTHON_MODULE_FOLDER: python/
   COVERAGE_SVG_FOLDER: docs/assets/
   COVERAGE_SVG_FILE_NAME: coverage.svg
   # replace below with references to previous config lines
@@ -15,12 +16,11 @@ env:
 
 on:
   pull_request:
-    branches: ['main', 'doc-deploy']
+    branches: ['main', 'r-docker-refactor']
     paths-ignore: ['docs/**']
 
   push:
-    branches: ['main', 'doc-deploy']
-    paths-ignore: ['docs/**']
+    branches: ['main', 'r-docker-refactor']
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -45,91 +45,47 @@ jobs:
         uses: pre-commit/action@main
 
       - name: Update pre-commit
-        uses: pre-commit-ci/lite-action@v1.0.1
+        uses: pre-commit-ci/lite-action@main
         if: always()
 
-  # With no caching at all the entire ci process takes 4m 30s to complete!
   pytest:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout Code Repository
         uses: actions/checkout@main
 
-      - name: Build, Test and Save Test Coverage
-        run: |
-          docker compose build
-          docker compose up --detach
-          docker compose exec jupyter bash -c "conda run -n $CONDA_ENV_NAME --cwd python pytest -p no:sugar"
-          export JUPYTER_ID=$(docker compose ps -q jupyter)
-          echo "jupyter_id=$JUPYTER_ID" >> $GITHUB_ENV
-          echo "jupyter_id=$JUPYTER_ID"
-
-      - name: Check accessing saved jupyter_id
+      - name: Build Conda Environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ${{ env.CONDA_ENV_NAME }}
+          environment-file: ${{ env.CONDA_ENV_PATH }}
+          auto-activate-base: false
+          miniforge-version: latest
+
+      - name: Test and Save Test Coverage
+        shell: bash -el {0}
         run: |
-          echo ${{ env.jupyter_id }}
+          mamba run -n ${{ env.CONDA_ENV_NAME }} --cwd python pytest
 
       - name: Copy test coverage results
         run: |
-          docker cp ${{ env.jupyter_id }}:${{ env.PYTHON_MODULE_FOLDER }}${{ env.COVERAGE_SVG_PATH }} ${{ env.COVERAGE_SVG_FOLDER }}
+          cp ${{ env.PYTHON_MODULE_FOLDER }}${{ env.COVERAGE_SVG_PATH }} ${{ env.COVERAGE_SVG_FOLDER }}
 
       - name: Archive coverage svg
         uses: actions/upload-artifact@v3
         with:
           name: coverage-badge
           path: ${{ env.COVERAGE_SVG_PATH }}
 
-      - name: Tear down the Stack
-        run: docker compose down
-
   docs:
     needs: [linter, pytest]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Download coverage svg
         uses: actions/download-artifact@v3
         with:
           name: coverage-badge
           path: ${{ env.GH_PAGE_PATH }}${{ env.COVERAGE_SVG_PATH }}
-
-      # Other options for documentation build for future testing outside docker
-      # - name: Set up conda environment
-      #   uses: conda-incubator/setup-miniconda@v2
-      #   with:
-      #     activate-environment: environment.yml
-      #
-      # From https://github.com/r-lib/actions/tree/v2-branch/setup-r
-      # - name: Setup R
-      #   uses: r-lib/actions/setup-r@v2
-
-      # Potentially necessary for future interactive documentation builds following uatk-spc
-      # - name: Install node
-      #   uses: actions/setup-node@v2
-      #   with:
-      #     node-version: 18.x
-      #     cache: 'npm'
-      #     cache-dependency-path: web/package-lock.json
-      #
-      # - name: Build web app
-      #   run: |
-      #     cd web
-      #     npm ci
-      #     npm run build --if-present
-      #     mv dist ../docs/_book/app
-
-      - name: Build docker quarto
-        run: |
-          # A potentially quicker build option to try in future, requires running in detatched mode
-          # DOCKER_BUILDKIT=1 docker build --no-cache -f compose/docs/Dockerfile --target builder --tag 'clim-recal-docs' .
-          docker compose build
-          docker compose up --detach
-          docker cp $(docker compose ps -q docs):/usr/local/apache2/htdocs/ ${{ env.GH_PAGE_PATH }}
-
-      - name: Publish
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ${{ env.GH_PAGE_PATH }}
-          keep_files: false

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
-exclude: "R|data"
+exclude: "data"
 repos:
   - repo: https://github.com/psf/black
-    rev: "23.9.1"
+    rev: "23.12.1"
     hooks:
       - id: black-jupyter
 
@@ -27,13 +27,13 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.2.2
+    rev: v2.4.0
     hooks:
       - id: pycln
         args: ["python/"]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)