Updating master

.github/workflows/build.yml

@@ -0,0 +1,33 @@
+name: Publish Docker image
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ispyb/py-ispyb
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/doc.yml

@@ -0,0 +1,53 @@
+name: Deploy documentation
+on:
+  push:
+    branches:
+      - master
+jobs:
+  build-and-deploy:
+    concurrency: ci-${{ github.ref }}
+    runs-on: ubuntu-latest
+    services:
+      mariadb:
+        image: ispyb/ispyb-pydb:latest
+        ports:
+          - 3306:3306
+        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs
+          pip install mkdocs-material
+
+      - name: Build
+        run: |
+          mkdocs build --strict --verbose
+
+      - name: Create OpenAPI spec
+        env:
+          ISPYB_ENVIRONMENT: ci
+        run: |
+          sudo apt-get update && sudo apt-get install -y libldap2-dev libsasl2-dev
+          pip install -r requirements.txt
+          pip install -e . --no-deps
+          python scripts/generate_apispec.py
+          mkdir public/api
+
+      - name: Run redoc
+        uses: seeebiii/redoc-cli-github-action@v10
+        with:
+          args: "bundle -o public/api/index.html openapi.json"
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4.3.0
+        with:
+          branch: gh-pages
+          folder: public

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on: [push]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
+      - name: Run flake8
+        uses: py-actions/flake8@v2
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run black
+        uses: psf/black@stable
+  security:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run bandit
+        uses: tj-actions/bandit@v5.1
+        with:
+          targets: pyispyb

.github/workflows/tests.yml

@@ -0,0 +1,38 @@
+name: Test
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mariadb:
+        image: ispyb/ispyb-pydb:latest
+        ports:
+          - 3306:3306
+        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y libldap2-dev libsasl2-dev
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          pip install -e . --no-deps
+      - name: Run tests
+        env:
+          ISPYB_ENVIRONMENT: ci
+        run: |
+          pytest --cov=pyispyb --cov-report xml tests/
+      - name: Coverage report
+        uses: codecov/codecov-action@v2
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: true

.gitignore

@@ -2,12 +2,16 @@
 __pycache__/
 *.py[cod]
 *swp
-.vscode*
 
-ispyb_core_config.yml
-ispyb_ssx_config.yml
-ispyb_em_config.yml
+/auth.yml
 
 build/
 dist/
 pyispyb.egg-info/
+
+.tox*
+.DS_Store
+
+.coverage
+coverage.xml
+*.py,cover

.prettierrc

@@ -0,0 +1,16 @@
+{
+  "overrides": [
+    {
+      "files": ["*.yml", "*.yaml"],
+      "options": {
+        "tabWidth": 2
+      }
+    },
+    {
+      "files": "*.json",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}