Move testing outside Docker, simplify Dockerfile

.github/workflows/test-build.yaml

@@ -23,25 +23,17 @@ jobs:
           --health-retries 5
 
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-
-      - name: Build test image
-        uses: docker/build-push-action@v2
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: pipx install poetry
+      - uses: actions/setup-python@v4
         with:
-          context: .
-          file: docker/Dockerfile
-          push: false
-          target: "development"
-          tags: ghcr.io/${{ github.repository }}:${{ github.sha }}
-
+          python-version: "3.10"
+          cache: "poetry"
+      - name: Install dependencies
+        run: poetry install
       - name: Run tests
-        run: |-
-          docker run --rm \
-          -e CTMS_DB_URL \
-          -e CTMS_SECRET_KEY \
-          ghcr.io/${{ github.repository }}:${{ github.sha }} \
-          ./docker/test.sh
+        run: bin/test.sh
         env:
           CTMS_DB_URL: postgresql://postgres:postgres@172.17.0.1:5432/postgres
           CTMS_SECRET_KEY: secret_${{ github.sha }}

.secrets.baseline

@@ -131,14 +131,14 @@
         "filename": ".github/workflows/test-build.yaml",
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_verified": false,
-        "line_number": 46
+        "line_number": 38
       },
       {
         "type": "Secret Keyword",
         "filename": ".github/workflows/test-build.yaml",
         "hashed_secret": "a2490b1a07aa4a72606afe91f2de20f8c524d779",
         "is_verified": false,
-        "line_number": 47
+        "line_number": 39
       }
     ],
     "bin/lint.sh": [
@@ -165,7 +165,7 @@
         "filename": "docs/developer_setup.md",
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_verified": false,
-        "line_number": 208
+        "line_number": 203
       }
     ],
     "tests/unit/test_acoustic_service.py": [
@@ -203,5 +203,5 @@
       }
     ]
   },
-  "generated_at": "2022-11-29T20:27:29Z"
+  "generated_at": "2023-01-11T16:11:56Z"
 }

Makefile

@@ -17,14 +17,14 @@ help:
 	@echo ""
 	@echo "CTMS make rules:"
 	@echo ""
-	@echo "  build   - build docker containers"
-	@echo "  lint    - lint check for code"
-	@echo "  setup   - (re)create the database"
-	@echo "  start   - run the API service"
-	@echo ""
-	@echo "  test        - run test suite"
-	@echo "  shell       - open a shell in the web container"
-	@echo "  db-only     - run PostgreSQL server"
+	@echo "  build          - build docker containers"
+	@echo "  db-only        - run PostgreSQL server"
+	@echo "  lint           - lint check for code"
+	@echo "  setup          - (re)create the database"
+	@echo "  shell          - open a shell in the web container"
+	@echo "  start          - run the API service"
+	@echo "  test           - run test suite"
+	@echo "  update-secrets - scan repository for secrets and update baseline file, if necessary"
 	@echo ""
 	@echo "  help    - see this text"
 
@@ -72,11 +72,15 @@ start: .env
 	docker-compose up
 
 .PHONY: test
-test: .env
-	docker-compose run --rm ${MK_WITH_SERVICE_PORTS} tests
-ifneq (1, ${MK_KEEP_DOCKER_UP})
+test: .env $(INSTALL_STAMP)
+	docker-compose up --wait postgres
+	bin/test.sh
+ifneq (1, ${MK_KEEP_DOCKER_UP})	
 	# Due to https://github.com/docker/compose/issues/2791 we have to explicitly
 	# rm all running containers
 	docker-compose down
 endif
 
+.PHONY: update-secrets
+update-secrets:
+	bin/update_baseline.sh

README.md

@@ -20,6 +20,8 @@ for this project to ensure correct environment setup.
 
 The project is structured with the following in mind:
 
+- [bin/*](bin/)
+    - Some scripts that have proven useful within the CTMS ecosystem
 - [docs/*](docs/)
     - Documentation to guide others around the project interactions
 - [ctms/*](ctms/)
@@ -30,8 +32,6 @@ The project is structured with the following in mind:
         - Pydantic Models for Data Modeling and Contract Validation
 - [migrations/*](migrations/)
     - Alembic migrations that act as a changelog or version control system for implementing DB changes in an ordered fashion
-- [scripts/*](scripts/)
-    - Some scripts that have proven useful within the CTMS ecosystem
 - [tests/unit/*](test/unit/)
     - Test suite using pytest
 

bin/test.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -euo pipefail
+
+POETRY_RUN="poetry run"
+
+CURRENT_DIR=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
+BASE_DIR="$(dirname "$CURRENT_DIR")"
+
+# without this, some tests fail because of off-by-timezone errors.
+export TZ=UTC
+
+$POETRY_RUN coverage run --rcfile "${BASE_DIR}/pyproject.toml" -m pytest
+$POETRY_RUN coverage report --rcfile "${BASE_DIR}/pyproject.toml" -m --fail-under 80
+$POETRY_RUN coverage html --rcfile "${BASE_DIR}/pyproject.toml"

bin/update_and_install_system_packages.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -euo pipefail
+# Tell apt-get we're never going to be able to give manual 
+# feedback:
+export DEBIAN_FRONTEND=noninteractive
+
+apt-get update
+# Install security updates
+apt-get -y upgrade
+# Install packages
+apt-get -y install --no-install-recommends $@
+# Delete cached files we don't need anymore
+apt-get clean
+rm -rf /var/lib/apt/lists/*

bin/update_baseline.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+set -euo pipefail
+
+detect-secrets scan . \
+--baseline .secrets.baseline \
+--exclude-files "(poetry.lock$)|(htmlcov/)"

docker-compose.yaml

@@ -4,12 +4,9 @@ services:
     build:
       context: .
       dockerfile: docker/Dockerfile
-      target: development
     image: web
-    volumes:
-      - type: bind
-        source: .
-        target: /app
+    volumes: 
+      - .:/app
     ports:
       - ${PORT:-8000}:${PORT:-8000}
     # Let the init system handle signals for us.
@@ -43,16 +40,3 @@ services:
     ports:
       - 8080:8080
 
-  tests:
-    image: web
-    depends_on:
-      web:
-        condition: service_started
-      postgres:
-          condition: service_healthy
-    command: ["bash", "./docker/test.sh"]
-    profiles: [test]
-    init: true
-    env_file:
-      - docker/config/local_dev.env
-      - .env

docker/Dockerfile

@@ -1,91 +1,44 @@
-# Dockerfile
-# Uses multi-stage builds requiring Docker 17.05 or higher
-# See https://docs.docker.com/develop/develop-images/multistage-build/
+FROM python:3.10.6 as python-base
 
-# Creating a python base with shared environment variables
-FROM python:3.10.6-slim as python-base
-ENV PYTHONPATH=/app \
-    PYTHONUNBUFFERED=1 \
-    PYTHONDONTWRITEBYTECODE=1 \
-    PIP_NO_CACHE_DIR=off \
+ENV PIP_DEFAULT_TIMEOUT=100 \
     PIP_DISABLE_PIP_VERSION_CHECK=on \
-    PIP_DEFAULT_TIMEOUT=100 \
-    POETRY_HOME="/opt/poetry" \
-    POETRY_VIRTUALENVS_IN_PROJECT=true \
+    PIP_NO_CACHE_DIR=off \
+    POETRY_HOME=/opt/poetry\
     POETRY_NO_INTERACTION=1 \
-    PYSETUP_PATH="/opt/pysetup" \
-    VENV_PATH="/opt/pysetup/.venv" \
-    PORT=8000
-
-ENV PATH="$VENV_PATH/bin:$POETRY_HOME/bin:$PATH"
-
-# Set up user and group
-ARG userid=10001
-ARG groupid=10001
-WORKDIR /app
-RUN groupadd --gid $groupid app && \
-    useradd -g app --uid $userid --shell /usr/sbin/nologin --create-home app
-
-RUN mkdir -p $POETRY_HOME && \
-    chown app:app /opt/poetry && \
-    mkdir -p $PYSETUP_PATH && \
-    chown app:app $PYSETUP_PATH && \
-    mkdir -p /app && \
-    chown app:app /app
-
-RUN apt-get update && \
-    apt-get install --assume-yes apt-utils && \
-    echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
-    apt-get install --no-install-recommends -y \
-      libpq5
-
-# builder-base is used to build dependencies
-FROM python-base as builder-base
-RUN apt-get install --no-install-recommends -y \
-      build-essential \
-      libpq-dev
+    POETRY_VIRTUALENVS_IN_PROJECT=true \
+    PYSETUP_PATH="/opt/pysetup"
 
-# Install Poetry - respects $POETRY_VERSION & $POETRY_HOME
-USER app
 RUN python3 -m venv $POETRY_HOME && \
 $POETRY_HOME/bin/pip install poetry==1.3.1 && \
 $POETRY_HOME/bin/poetry --version
 
-# We copy our Python requirements here to cache them
-# and install only runtime deps using poetry
 WORKDIR $PYSETUP_PATH
-COPY --chown=app:app ./poetry.lock ./pyproject.toml ./
-RUN poetry install --no-dev --no-root
+COPY ./poetry.lock ./pyproject.toml ./
+RUN $POETRY_HOME/bin/poetry install --no-dev --no-root
 
+FROM python:3.10.6-slim as production
 
-# 'development' stage installs all dev deps and can be used to develop code.
-# For example using docker-compose to mount local volume under /app
-FROM python-base as development
-ENV FASTAPI_ENV=development
+COPY bin/update_and_install_system_packages.sh /opt
+RUN opt/update_and_install_system_packages.sh libpq5
 
-# Copying poetry and venv into image
-USER app
-COPY --from=builder-base $POETRY_HOME $POETRY_HOME
-COPY --from=builder-base $PYSETUP_PATH $PYSETUP_PATH
+ENV PATH="/opt/pysetup/.venv/bin:$PATH" \
+    PORT=8000 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONFAULTHANDLER=1 \
+    PYTHONUNBUFFERED=1 \
+    PYTHONPATH=/app \
+    VENV_PATH="/opt/pysetup/.venv"
 
-# venv already has runtime deps installed we get a quicker install
-WORKDIR $PYSETUP_PATH
-RUN poetry install --no-root
+COPY --from=python-base $VENV_PATH $VENV_PATH
 
+# Set up user and group
+ARG userid=10001
+ARG groupid=10001
+RUN groupadd --gid $groupid app && \
+    useradd -g app --uid $userid --shell /usr/sbin/nologin --create-home app
+USER app
 WORKDIR /app
-COPY --chown=app:app . .
-
-EXPOSE $PORT
-CMD ["python", "asgi.py"]
-
-# 'production' stage uses the clean 'python-base' stage and copyies
-# in only our runtime deps that were installed in the 'builder-base'
-FROM python-base as production
-ENV FASTAPI_ENV=production
 
-COPY --from=builder-base $VENV_PATH $VENV_PATH
-
-WORKDIR /app
 COPY --chown=app:app . .
 
 EXPOSE $PORT

docs/developer_setup.md

@@ -20,15 +20,10 @@ curl -sSL https://install.python-poetry.org | python3 -
 ```
 
 ## Setup Dependencies
-Install prod dependencies in pyproject.toml through poetry:
+To set up dependencies necessary for local development, run:
 
 ```sh
-poetry install --no-dev
-```
-
-Install ALL deps including DEV dependencies:
-```sh
-poetry install
+make install
 ```
 
 If these fail with an error like: