SECURITY-59: Add GHA workflows

.github/codeql.yml

@@ -0,0 +1,52 @@
+name: "Code scanning - action"
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 19 * * 0'
+
+jobs:
+  CodeQL-Build:
+
+    # CodeQL runs on ubuntu-latest and windows-latest
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      # Override language selection by uncommenting this and choosing your languages
+      # with:
+      #   languages: go, javascript, csharp, python, cpp, java
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3

.github/dependabot.yml

@@ -0,0 +1,23 @@
+version: 2
+updates:
+
+  # Docker
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25
+
+  # Python
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 25

.github/workflows/pr_build.yml

@@ -0,0 +1,43 @@
+---
+name: Pull Request Build, Tag, & Push
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+jobs:
+  build-develop-open:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build.yml@main
+    secrets: inherit
+  build-develop-merge:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: pr-${{ github.event.number }},latest
+    secrets: inherit
+  build-main-open:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }}
+    secrets: inherit
+  build-main-merge:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }},latest-rc
+    secrets: inherit
+  trivy-scans:
+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit

.github/workflows/release-main.yml

@@ -0,0 +1,25 @@
+---
+name: Release - Build & Push Image
+on:
+  release:
+    branches:
+      - main
+      - master
+    types: [ published ]
+jobs:
+  check-source-branch:
+    uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
+    with:
+      build_branch: '${{ github.event.release.target_commitish }}'
+  validate-release-tag:
+    needs: check-source-branch
+    uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
+    with:
+      release_tag: '${{ github.event.release.tag_name }}'
+  build-push:
+    needs: validate-release-tag
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: '${{ github.event.release.tag_name }},latest'
+    secrets: inherit

.github/workflows/test-pull-request.yml → .github/workflows/test.yml

@@ -1,35 +1,50 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Run tests
+name: Run search_api2 tests
 
 on:
   pull_request:
-    branches: [ "*" ]
+    types:
+    - opened
+    - reopened
+    - synchronize
+    - ready_for_review
+  push:
+    # run workflow when merging to main or develop
+    branches:
+      - main
+      - master
+      - develop
+  workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7]
+
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - name: Check out GitHub repo
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.9.19
+
     - name: Pip installation
       run: python -m pip install --upgrade pip poetry
+
     - name: Poetry installation
-      run: poetry install
+      run: poetry install --no-root
+
     - name: Create test image
-      run: docker-compose build
+      run: docker compose build
+
     - name: Run tests
       run: scripts/run_tests
-    - name: Codecov
-      uses: codecov/codecov-action@v1
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
         fail_ci_if_error: true

CHANGELOG.md

@@ -5,6 +5,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+- Standard GitHub Actions workflows
+
+### Changed
+- Upgraded Python to version 3.9.19 in test workflows and Dockerfile
+- Updated integration tests README file
+
+### Fixed
+- Container/service shutdown issues; all unit and integration tests now pass locally
+
+### Security
+- Vendored `kbase-jsonrpcbase` 0.3.0a6 and `jsonrpc11base` to resolve dependency conflicts
 
 ## [1.0.0] - 2021-04-20
 ### Fixed

Dockerfile

@@ -1,10 +1,10 @@
-FROM python:3.7-alpine
+FROM python:3.9.19-alpine
 
 # Dockerize related args
 ARG BUILD_DATE
 ARG VCS_REF
 ARG BRANCH=develop
 ENV DOCKERIZE_VERSION v0.6.1
 
 # Install dockerize
 RUN apk --update add --no-cache --virtual build-dependencies curl tar gzip && \
@@ -27,9 +27,9 @@
 # Install dependencies
 COPY pyproject.toml poetry.lock /app/
 RUN apk --update add --no-cache --virtual build-dependencies libffi-dev libressl-dev musl-dev python3-dev build-base git rust cargo && \
-    pip install --upgrade pip poetry==1.0.9 && \
+    pip install --upgrade pip poetry==2.1.2 && \
     poetry config virtualenvs.create false && \
-    poetry install --no-dev --no-interaction --no-ansi && \
+    poetry install --no-root --without dev --no-interaction --no-ansi && \
     apk del --no-cache build-dependencies
 
 COPY . /app

docker-compose.yaml

@@ -1,5 +1,3 @@
-version: '3'
-
 # This docker-compose is for developer convenience, not for running in production.
 
 services: