Merge pull request #132 from sanger/develop

Merge develop into master

.dockerignore

@@ -1,7 +1,22 @@
+.coverage
+.dockerignore
+.DS_Store
+.editorconfig
+.env
 .env.example
 .git
 .github
 .gitignore
+.mypy_cache
+.pytest_cache
+.release-version
+coverage.xml
+docker-compose.yml
 Dockerfile
+forlint.sh
+htmlcov
 LICENSE
+mypy.ini
+pyproject.toml
 README.md
+setup.cfg

.editorconfig

@@ -0,0 +1,15 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.yml,Dockerfile}]
+indent_size = 2

.env.example

@@ -1,13 +1,2 @@
-DB_DBNAME=baracoda_dev
-DB_HOST=localhost
-DB_PASSWORD=postgres
-DB_PORT=5432
-DB_USER=postgres
-FLASK_APP=baracoda
-FLASK_ENV=development
-SEQUENCE_NAME=heron
-SEQUENCE_START=200000
-SLACK_API_TOKEN=xoxb-123
-SLACK_CHANNEL_ID=Cxxx
-SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://postgres:postgres@localhost:5432/baracoda_dev"
-SETTINGS_PATH=config/defaults.py
+# path to the settings file which flask will use
+SETTINGS_PATH=config/development.py

.flaskenv

@@ -0,0 +1,12 @@
+# use publicly acessible env variables in this file
+#   https://flask.palletsprojects.com/en/1.1.x/cli/#environment-variables-from-dotenv
+
+# https://flask.palletsprojects.com/en/1.1.x/cli/#application-discovery
+FLASK_APP=baracoda
+
+# https://flask.palletsprojects.com/en/1.1.x/cli/#setting-command-options
+FLASK_RUN_HOST=0.0.0.0
+FLASK_RUN_PORT=8000
+
+# https://flask.palletsprojects.com/en/1.1.x/config/#environment-and-debug-features
+FLASK_ENV=development

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "07:00"
+    timezone: Europe/London
+  open-pull-requests-limit: 10

.github/workflows/automated_release_and_build.yml

@@ -5,14 +5,12 @@ on:
     branches:
       - develop
       - master
-    paths-ignore:
-      - "README.md"
-
+
 env:
   IMAGE_NAME: ${{ github.repository }}/${{ github.event.repository.name }}
 
 jobs:
-  build_and_test_job:
+  build_test_release_push:
     runs-on: ubuntu-18.04
     services:
       postgres:
@@ -30,46 +28,55 @@ jobs:
           --health-retries 5
     steps:
       - uses: actions/checkout@v2
-      - name: Set release tag
-        # Generate a release tag name in the format:
-        # devel/YYYY-MM-DD/HHMMSS
-        # Writes this out to the environment file for use downstream
-        run: |
-          echo "RELEASE_TAG=$([ ${GITHUB_REF##*/} = "develop" ] && printf '%s\n' $(cat .release-version)_develop || printf '%s\n' $(cat .release-version))" >> $GITHUB_ENV
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
-        with:
-          tag_name: ${{ env.RELEASE_TAG }}
-          release_name: ${{ env.RELEASE_TAG }}
-          draft: false
-          prerelease: ${{ !(github.ref == 'refs/heads/master') }}
-      - name: Build the Docker image
+
+      - name: Build and tag the image for testing
         run: >-
           docker build .
           --file Dockerfile
-          --tag docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
-      - name: Run mypy against the image
-        run: >-
-          docker run
-          --network host
-          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
-          mypy .
+          --tag docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
+
       - name: Run tests against the image
         run: >-
           docker run
           --network host
-          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
-          python -m  pytest -vsx
-      - name: Login to regitry
+          --env SETTINGS_PATH=config/test.py
+          --entrypoint=""
+          docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
+          python -m pytest --no-cov -vx
+
+      - name: Set release tag
+        # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
+        run: echo "RELEASE_VERSION=$([ ${GITHUB_REF##*/} = "develop" ] && printf '%s\n' $(cat .release-version)-develop || printf '%s\n' $(cat .release-version))" >> $GITHUB_ENV
+
+      - name: Create release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: v${{ env.RELEASE_VERSION }}
+          release_name: ${{ env.RELEASE_VERSION }}
+          draft: false
+          prerelease: ${{ !(github.ref == 'refs/heads/master') }}
+
+      - name: Login to registry
         run: >-
           docker login
           -u ${{ github.actor }}
           -p ${{ secrets.GITHUB_TOKEN }}
           docker.pkg.github.com
-      - name: Publish image with image tag being either develop-timestamp or release-version
+
+      - name: Tag image with release version
         run: >-
-          docker push
-          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
+          docker tag
+          docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
+          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }}
+
+      - name: Push release tag image to registry
+        run: >-
+          docker push docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }}
+
+      - name: Remove the oldest package
+        uses: actions/delete-package-versions@v1
+        with:
+          package-name: "${{ github.event.repository.name }}"

.github/workflows/check_release_name_bump.yml

@@ -1,4 +1,5 @@
-name: Check release bump
+# Checks that the .release-version file has been updated
+name: Check release version
 
 on:
   pull_request:
@@ -8,20 +9,31 @@ on:
 
 jobs:
   check:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
+
+      - name: Set excluded release types
+        run: >-
+          if [ "${{ github.base_ref }}" = "master" ]; then
+            echo "exclude_types=draft|prerelease" >> $GITHUB_ENV
+          elif [ "${{ github.base_ref }}" = "develop" ]; then
+            echo "exclude_types=draft" >> $GITHUB_ENV
+          else
+            exit 1;
+          fi
+
+      - name: Get the latest release
+        id: last_release
+        uses: InsonusK/[email protected]
+        with:
+          myToken: ${{ github.token }}
+          exclude_types: ${{ env.exclude_types }}
+          view_top: 1
 
-    - name: get latest-release
-      id: last_release
-      uses: InsonusK/[email protected]
-      with:
-        myToken: ${{ github.token }}
-        view_top: 1
-
-    - name: Compare release names
-      run: |
-        if [ "${{ steps.last_release.outputs.tag_name }}" = "$(printf '%s\n' $(cat .release-version)_develop)" ] ||
-        [ "${{ steps.last_release.outputs.tag_name }}" = "$(printf '%s\n' $(cat .release-version))" ]; then exit 1; fi
+      - name: Compare releases
+        run: >-
+          if [ "${{ steps.last_release.outputs.tag_name }}" = "$(printf 'v%s-develop\n' $(cat .release-version))" ] ||
+          [ "${{ steps.last_release.outputs.tag_name }}" = "$(printf 'v%s\n' $(cat .release-version))" ]; then
+            exit 1;
+          fi

.github/workflows/ci.yml

@@ -0,0 +1,124 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - develop
+      - master
+  pull_request:
+    branches:
+      - develop
+      - master
+
+jobs:
+  black:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install pipenv
+        run: |
+          pip install pipenv
+      - name: Install dependencies
+        run: |
+          pipenv sync --dev --system
+      - name: Check format with black
+        run: |
+          # stop the build if there are black formatting errors
+          python -m black --check .
+  flake8:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install pipenv
+        run: |
+          pip install pipenv
+      - name: Install dependencies
+        run: |
+          pipenv sync --dev --system
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8
+  mypy:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install pipenv
+        run: |
+          pip install pipenv
+      - name: Install dependencies
+        run: |
+          pipenv sync --dev --system
+      - name: Run mypy
+        run: |
+          python -m mypy .
+  test:
+    runs-on: ubuntu-18.04
+    services:
+      postgres:
+        image: postgres:9.6
+        ports:
+          - 5432:5432
+        env:
+          POSTGRES_USER: "postgres"
+          POSTGRES_PASSWORD: "postgres"
+          POSTGRES_DB: "baracoda_test"
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 20s
+          --health-timeout 10s
+          --health-retries 5
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install pipenv
+        run: |
+          python -m pip install --upgrade pip
+          pip install pipenv
+      - name: Install dependencies
+        run: |
+          pipenv sync --dev --system
+      - name: Test with pytest
+        run: |
+          SETTINGS_PATH=config/test.py python -m pytest -vsx
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1