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teemukatajateemukataja
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Merge pull request #160 from CSCfi/dependabot
Create dependabot.yml
2 parents d894eec + 8b3eb42 commit 0f8a94f

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‎.github/dependabot.yml

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

‎.github/workflows/int.yml

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

‎.github/workflows/s2i-build.yml

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

‎.github/workflows/unit.yml

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

‎Dockerfile

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

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

‎requirements.txt

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

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