Setup GitHub worflows (#97)

* Add pyproject.toml

* Remove setup files

* Remove unnecessary tables in the pyproject.toml

* Move tox config to pyproject.toml

* Add build workflow

* Add Pipfile

* Update aidbox launch config

* Skip aiohttp.request mocking tests

Fix once #93 is done

* Remove pytest-mock

* Add mised import to test

* Update build workflow config

* Remove python required version in Pipfile

* Add docker services to build workflow

* Pass env vars for Aidbox container

* Fix typo in the build config

* Fix typoes

* Disable aidbox healthcheck service

* Remove services description

* Move test command to the shell script

* Remove setup python step

.env.tpl

@@ -0,0 +1 @@
+AIDBOX_LICENSE=

.github/workflows/build.yaml

@@ -0,0 +1,34 @@
+name: fhirpy
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - python-version: 3.8
+          - python-version: 3.9
+          - python-version: "3.10"
+          - python-version: "3.11"
+    env:
+      PYTHON: ${{ matrix.python-version }}
+      AIDBOX_LICENSE: ${{ secrets.AIDBOX_LICENSE}}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run tests
+        run: ./run_test.sh
+        shell: bash
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     env_vars: PYTHON
+    #     fail_ci_if_error: true
+    #     files: ./coverage.xml
+    #     flags: unittests
+    #     name: codecov-umbrella
+    #     verbose: true

Dockerfile

@@ -0,0 +1,16 @@
+ARG PYTHON_VERSION
+FROM python:$PYTHON_VERSION
+RUN pip install pipenv
+
+RUN mkdir /app
+WORKDIR /app
+
+COPY Pipfile Pipfile.lock ./
+RUN pipenv install --dev
+
+# SQLAlchemy vulnerability - https://pyup.io/v/51668/742
+# Remove ignore option once fix is released or upgrade to version 2
+# RUN pipenv check -i 51668
+COPY . .
+
+EXPOSE 8081

Pipfile

@@ -0,0 +1,17 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+
+[dev-packages]
+requests = "==2.25.1"
+pytest = ">=6.2.4"
+pytest-cov = "==2.12.0"
+aiohttp = "==3.7.4"
+pytest-asyncio = "==0.15.1"
+responses = "==0.13.3"
+pytz = "==2021.1"
+black = "==22.10.0"
+pre-commit = "==2.20.0"

devbox/run_devbox.sh

@@ -1,15 +1,12 @@
 #!/bin/sh
-
-if [ -z "${AIDBOX_LICENSE_KEY_TESTS}" ]; then
-    echo "AIDBOX_LICENSE_KEY_TESTS is required to run tests"
-    exit 1
+if [ -f ".env" ]; then
+    export `cat .env`
 fi
 
-if [ -z "${AIDBOX_LICENSE_ID_TESTS}" ]; then
-    echo "AIDBOX_LICENSE_ID_TESTS is required to run tests"
+if [ -z "${AIDBOX_LICENSE}" ]; then
+    echo "AIDBOX_LICENSE is required to run tests"
     exit 1
 fi
 
-docker-compose -f docker-compose.tests.yaml pull
-docker-compose -f docker-compose.tests.yaml run dockerize
+docker compose -f docker-compose.tests.yaml up --exit-code-from devbox devbox
 exit $?

docker-compose.tests.yaml

@@ -0,0 +1,47 @@
+services:
+  devbox:
+    image: "healthsamurai/aidboxone:edge"
+    depends_on:
+      - devbox-db
+    ports:
+      - 8080:8080
+    links:
+      - "devbox-db:database"
+    env_file:
+      - env_tests
+    environment:
+      AIDBOX_LICENSE: ${AIDBOX_LICENSE}
+  devbox-db:
+    image: healthsamurai/aidboxdb:14.5
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: devbox
+  devbox-healthcheck:
+    image: curlimages/curl
+    entrypoint: /bin/sleep 10000
+    links:
+      - devbox
+    depends_on:
+      - devbox
+    healthcheck:
+      test: curl --fail http://devbox:8080/__healthcheck || exit 1
+      interval: 1s
+      timeout: 20s
+      retries: 100
+  app:
+    build:
+      context: .
+      args:
+        PYTHON_VERSION: ${PYTHON:-3.11}
+    command: ["pipenv", "run", "pytest"]
+    depends_on:
+      devbox-healthcheck:
+        condition:
+          service_healthy
+    links:
+     - devbox
+    ports:
+     - "8081:8081"
+    volumes:
+     - .:/app

pyproject.toml

@@ -0,0 +1,99 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "fhirpy"
+description = "FHIR client for python"
+readme = "README.md"
+license = { file = "LICENSE.md" }
+keywords = ["fhir"]
+dynamic = ["version"]
+authors = [{ name = "beda.software", email = "[email protected]" }]
+dependencies = ["requests>=2.25.1", "aiohttp>=3.6.3", "pytz"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Web Environment",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Internet :: WWW/HTTP",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+requires-python = ">=3.8"
+
+[project.optional-dependencies]
+test = ["pytest>=6.2.4", "pytest-asyncio>=0.15.1", "responses>=0.13.3"]
+
+[project.urls]
+Homepage = "https://github.com/beda-software/fhir-py"
+Documentation = "https://github.com/beda-software/fhir-py#readme"
+Source = "https://github.com/beda-software/fhir-py.git"
+
+[tool.tox]
+legacy_tox_ini = """
+    [pytest]
+    addopts=--tb=short
+
+    [tox]
+    envlist =
+        py38
+        py39
+        py310
+        py311
+    skip_missing_interpreters = true
+    requires =
+        virtualenv>=16.7.8
+        pip>=19.3.1
+
+    [gh-actions]
+    python =
+        3.8: py38
+        3.9: py39
+        3.10: py310
+        3.11: py311
+
+    [testenv]
+    passenv =
+        TOXENV
+        CI
+        CODECOV_*
+    commands =
+        pytest --doctest-modules --cov=./fhirpy tests
+    setenv =
+        PYTHONDONTWRITEBYTECODE=1
+        PYTHONWARNINGS=once
+    deps =
+        -r requirements.txt
+"""
+
+[tool.black]
+line-length = 100
+target-version = ['py311']
+exclude = '''
+(
+  /(
+    | \.git
+    | \.pytest_cache
+    | pyproject.toml
+    | dist
+  )/
+)
+'''
+
+[tool.isort]
+profile = "black"
+line_length = 100
+skip = [".gitignore"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -q --color=yes"
+testpaths = ["tests"]
+log_cli = true
+log_cli_level = "INFO"

run_test.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker compose -f docker-compose.tests.yaml up --quiet-pull --exit-code-from app app

tests/config.py

@@ -2,7 +2,7 @@
 from aiohttp import BasicAuth
 
 
-FHIR_SERVER_URL = os.environ.get("FHIR_SERVER_URL", "http://localhost:8080/fhir")
+FHIR_SERVER_URL = os.environ.get("FHIR_SERVER_URL", "http://devbox:8080/fhir")
 FHIR_SERVER_AUTHORIZATION = os.environ.get(
     "FHIR_SERVER_AUTHORIZATION", BasicAuth("root", "secret").encode()
 )