Create dependabot.yml

.github/dependabot.yml

@@ -0,0 +1,26 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "pip dependencies"
+    open-pull-requests-limit: 10
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "github actions"
+    open-pull-requests-limit: 10
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "docker dependencies"
+    open-pull-requests-limit: 0

.github/workflows/int.yml

@@ -1,6 +1,7 @@
 name: Integration Tests
 
-on: [pull_request]
+on:
+  pull_request:
 
 jobs:
   build:
@@ -13,38 +14,52 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     name: Integration Tests
+
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install requirements
       run: |
-        wget https://github.com/openshift/source-to-image/releases/download/v1.2.0/source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
-        tar -xvf source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
-        sudo cp s2i /usr/local/bin
         pip install aiohttp
         pip install requests
-    - name: Build image
-      run:  |
-        s2i build . centos/python-36-centos7 cscfi/beacon-python
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v1
+      with:
+        driver-opts: network=host
+
+    - name: Build
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        push: true
+        file: ./Dockerfile
+        tags: localhost:5000/beacon-python:latest
+        cache-from: localhost:5000/beacon-python:latest
+        cache-to: type=local,dest=/tmp/.buildx-cache
 
     - name: Start Services
       run: |
-        pushd deploy/test
-        docker-compose up -d
+        docker-compose -f deploy/test/docker-compose.yml up -d
         sleep 10
-        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz data/example_metadata.json
-        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
-        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
-        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
+        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata.json
+        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
+        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
+        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
 
     - name: Run Integration test
       run: |
-        pushd deploy/test
-        python run_tests.py
+        python deploy/test/run_tests.py
 
     - name: Collect logs from docker
       if: ${{ failure() }}

.github/workflows/s2i-build.yml

@@ -0,0 +1,26 @@
+name: check s2i build
+
+on: [pull_request]
+
+jobs:
+  build:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    name: Integration Tests
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install requirements
+      run: |
+        wget https://github.com/openshift/source-to-image/releases/download/v1.2.0/source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
+        tar -xvf source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
+        sudo cp s2i /usr/local/bin
+    - name: Build image
+      run:  |
+        s2i build . centos/python-36-centos7 cscfi/beacon-python

.github/workflows/unit.yml

@@ -1,6 +1,9 @@
 name: Python Unit Tests
 
-on: [push]
+on:
+  push:
+  schedule:
+    - cron: '0 7 * * 1'
 
 jobs:
   unit_test:
@@ -27,4 +30,4 @@ jobs:
     - name: Run unit tests
       env:
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-      run: tox -e unit_tests
+      run: tox -e unit_tests

Dockerfile

@@ -1,19 +1,22 @@
-FROM python:3.7-alpine3.9 as BUILD
+FROM python:3.7-alpine3.13 as BUILD
 
 RUN apk add --update \
     && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\
     && apk add --no-cache libressl-dev libffi-dev autoconf bzip2-dev xz-dev\
+    && apk add --no-cache python3-dev rust cargo \
     && rm -rf /var/cache/apk/*
 
 COPY requirements.txt /root/beacon/requirements.txt
 COPY setup.py /root/beacon/setup.py
 COPY beacon_api /root/beacon/beacon_api
 
+ENV CYTHONIZE=1
+
 RUN pip install --upgrade pip && \
     pip install -r /root/beacon/requirements.txt && \
     pip install /root/beacon
 
-FROM python:3.7-alpine3.9
+FROM python:3.7-alpine3.13
 
 RUN apk add --no-cache --update bash
 

deploy/test/docker-compose.yml

@@ -15,9 +15,11 @@ services:
       - ./mate.sql:/docker-entrypoint-initdb.d/mate.sql:ro
   beacon:
     hostname: beacon
-    image: cscfi/beacon-python
+    image: localhost:5000/beacon-python
     volumes:
       - ./auth_test.ini:/auth_test.ini
+      - ../../data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz:/exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz
+      - ../../data/example_metadata.json:/exdata/example_metadata.json
       - ./example_metadata_controlled.json:/exdata/example_metadata_controlled.json
       - ./example_metadata_controlled1.json:/exdata/example_metadata_controlled1.json
       - ./example_metadata_registered.json:/exdata/example_metadata_registered.json
@@ -35,7 +37,7 @@ services:
     restart: on-failure
   mockauth:
     hostname: mockauth
-    image: cscfi/beacon-python
+    image: localhost:5000/beacon-python
     ports:
       - 8000:8000
     volumes:

requirements.txt

@@ -1,15 +1,15 @@
-aiohttp
-aiohttp_cors
-asyncpg
-jsonschema
-Cython
-numpy
+aiohttp==3.7.4
+aiohttp-cors==0.7.0
+asyncpg==0.22.0
+jsonschema==3.2.0
+Cython==0.29.22
 cyvcf2==0.10.1; python_version < '3.7'
 cyvcf2; python_version >= '3.7'
-tox
-uvloop
-aiocache
-ujson
-aiomcache
-authlib
-gunicorn>=20.0.1
+tox==3.23.0
+uvloop==0.14.0; python_version < '3.7'
+uvloop==0.15.2; python_version >= '3.7'
+aiocache==0.11.1
+ujson==4.0.2
+aiomcache==0.6.0
+Authlib==0.15.3
+gunicorn==20.0.4