Merge pull request #6 from bento-platform/asyncify

Asyncify with Quart + add Docker container CI building

.dockerignore

@@ -0,0 +1,5 @@
+.coverage
+.github
+.mypy_cache
+.tox
+env

.github/workflows/build.yml

@@ -0,0 +1,32 @@
+name: Build and push bento_service_registry
+on:
+  release:
+    types: [ published ]
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Run Bento build action
+        uses: bento-platform/[email protected]
+        with:
+          registry: ghcr.io
+          registry-username: ${{ github.actor }}
+          registry-password: ${{ secrets.GITHUB_TOKEN }}
+          image-name: ghcr.io/bento-platform/bento_service_registry
+          development-dockerfile: dev.Dockerfile
+          dockerfile: Dockerfile

.github/workflows/lint.yml

@@ -12,8 +12,12 @@ jobs:
       - uses: actions/setup-python@v2
         name: Set up Python
         with:
-          python-version: 3.6
-      - name: Install flake8
-        run: python -m pip install flake8
+          python-version: "3.8"
+      - name: Install poetry
+        run: python -m pip install poetry
+      - name: Install dependencies
+        run: python -m poetry install --only dev
       - name: Run linter
-        run: flake8 ./bento_service_registry ./tests
+        run: python -m flake8 ./bento_service_registry ./tests
+      - name: Run type checker
+        run: python -m mypy bento_service_registry

.github/workflows/test.yml

@@ -9,29 +9,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.6, 3.9 ]
+        python-version: [ "3.8", "3.10" ]
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-python@v2
         name: Set up Python
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install Poetry
+        run: python -m pip install poetry
       - name: Install Python dependencies
-        run: python -m pip install -r requirements.txt
+        run: python -m poetry install
       - name: Test
-        run: pytest -svv --cov=bento_service_registry --cov-branch
+        run: python -m pytest -svv --cov=bento_service_registry --cov-branch
       - name: Codecov
         run: codecov
-  install:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ 3.6, 3.9 ]
-    steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-python@v2
-        name: Set up Python
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install bento_service_registry
-        run: python -m pip install .

.gitignore

@@ -2,6 +2,8 @@
 __pycache__
 env/
 .coverage
+.mypy_cache
+.tox
 htmlcov/
 .idea/workspace.xml
 .idea/dataSources*

Dockerfile

@@ -0,0 +1,29 @@
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-latest
+
+# Use uvicorn (instead of hypercorn) in production since I've found
+# multiple benchmarks showing it to be faster - David L
+RUN pip install --no-cache-dir poetry==1.2.2 "uvicorn[standard]==0.20.0"
+
+# Backwards-compatible with old BentoV2 container layout
+WORKDIR /service-registry
+
+COPY pyproject.toml pyproject.toml
+COPY poetry.toml poetry.toml
+COPY poetry.lock poetry.lock
+
+# Install production dependencies
+# Without --no-root, we get errors related to the code not being copied in yet.
+# But we don't want the code here, otherwise Docker cache doesn't work well.
+RUN poetry install --without dev --no-root
+
+# Manually copy only what's relevant
+# (Don't use .dockerignore, which allows us to have development containers too)
+COPY bento_service_registry bento_service_registry
+COPY entrypoint.sh entrypoint.sh
+COPY LICENSE LICENSE
+COPY README.md README.md
+
+# Install the module itself, locally (similar to `pip install -e .`)
+RUN poetry install --without dev
+
+CMD [ "sh", "./entrypoint.sh" ]

README.md

@@ -6,17 +6,34 @@
 
 **Author:** David Lougheed, Canadian Centre for Computational Genomics
 
-Prototype implementation of GA4GH's [service registry API](https://github.com/ga4gh-discovery/ga4gh-service-registry/)
+Prototype implementation of the GA4GH [service registry API](https://github.com/ga4gh-discovery/ga4gh-service-registry/)
 for the Bento platform.
 
+
 ## Development
 
-### Running the Service
+### Getting set up
+
+1. Create a virtual environment for the project:
+   ```bash
+   virtualenv -p python3 ./env
+   source env/bin/activate
+   ```
+2. Install `poetry`:
+   ```bash
+   pip install poetry
+   ```
+3. Install project dependencies:
+   ```bash
+   poetry install
+   ```
 
-To run the service, use the following command:
+### Running the service locally
+
+To run the service in development mode, use the following command:
 
 ```bash
-FLASK_DEBUG=True FLASK_APP=bento_service_registry.app flask run
+QUART_ENV=development QUART_APP=bento_service_registry.app quart run
 ```
 
 ### Running tests
@@ -27,6 +44,7 @@ To run tests and linting, run Tox:
 tox
 ```
 
+
 ## Configuration
 
 The following environment variables are used to configure the 

bento_service_registry/__init__.py

@@ -1,10 +1,6 @@
-import configparser
-import os
+from importlib import metadata
 
 __all__ = ["name", "__version__"]
 
-config = configparser.ConfigParser()
-config.read(os.path.join(os.path.dirname(os.path.realpath(__file__)), "package.cfg"))
-
-name = config["package"]["name"]
-__version__ = config["package"]["version"]
+name = __package__
+__version__ = metadata.version(__package__)