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[maintenance] requirements upgrades (#1502)
upgrade to latest Fake and redis packages (replaces faulty PR #1501) both in packages and services/web/server upgrades api/tests requirements and Makefile upgrades missing requirements from non-packages/services folders (e.g. coverage, pytest)
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‎README.md

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# osparc-simcore platform
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**WARNING** This application is **still under development**.
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<p align="center">
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<img src="https://user-images.githubusercontent.com/32800795/61083844-ff48fb00-a42c-11e9-8e63-fa2d709c8baf.png" width="700">
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</p>
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<!-- NOTE: when branched replace `master` in urls -->
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[`master`](https://github.com/itisfoundation/osparc-simcore/tree/master)
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<!---------------------------->
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## Contributing
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The SIM-CORE, named **o<sup>2</sup>S<sup>2</sup>PARC** – **O**pen **O**nline **S**imulations for **S**timulating **P**eripheral **A**ctivity to **R**elieve **C**onditions – is one of the three integrative cores of the SPARC program’s Data Resource Center (DRC).
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The aim of o<sup>2</sup>S<sup>2</sup>PARC is to establish a comprehensive, freely accessible, intuitive, and interactive online platform for simulating peripheral nerve system neuromodulation/ stimulation and its impact on organ physiology in a precise and predictive manner.
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To achieve this, the platform will comprise both state-of-the art and highly detailed animal and human anatomical models with realistic tissue property distributions that make it possible to perform simulations ranging from the molecular scale up to the complexity of the human body.
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Would you like to make a change or add something new? Please read the [contributing guidelines](CONTRIBUTING.md).
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## Getting Started
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## Overview
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simcore-stack when deployed locally:
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![](docs/img/.stack-simcore-version.yml.png)
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## Usage
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This is the common workflow to build and deploy locally:
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```bash
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# clone repo
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# display swarm configuration
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make info-swarm
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# open browser in:
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# open front-end in the browser
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# localhost:9081 - simcore front-end site
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#
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xdg-open http://localhost:9081/
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make down
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```
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## Requirements
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Services are deployed in two stacks:``simcore-stack`` comprises all core-services in the framework
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and ``ops-stack`` is a subset of services from [ITISFoundation/osparc-ops](https://github.com/ITISFoundation/osparc-ops) used
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for operations during development. This is a representation of ``simcore-stack``:
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![](docs/img/.stack-simcore-version.yml.png)
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### Requirements
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To verify current base OS, Docker and Python build versions have a look at:
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- Travis CI [config](.travis.yml)
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This project works and is developed under **linux (Ubuntu recommended)**.
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##### Other OSes setup
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##### Setting up Other Operating Systems
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When developing on these platforms you are on your own.
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## Releases
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**WARNING** This application is **still under development**.
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- [Git release workflow](ops/README.md)
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- Public [releases](https://github.com/ITISFoundation/osparc-simcore/releases)
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- Production in https://osparc.io
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- [Staging instructions](docs/staging-instructions.md)
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- [User Manual](https://itisfoundation.github.io/osparc-manual/)
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## Contributing
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Would you like to make a change or add something new? Please read the [contributing guidelines](CONTRIBUTING.md).
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## License
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This project is licensed under the terms of the [MIT license](LICENSE).
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<!-- ADD REFERENCES BELOW AND KEEP THEM IN ALPHABETICAL ORDER -->

‎api/tests/Makefile

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ROOT_DIR = $(abspath $(CURDIR)/../../)
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VENV_DIR ?= $(abspath $(ROOT_DIR)/.venv)
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UPGRADE_OPTION := $(if $(upgrade),--upgrade-package $(upgrade),--upgrade)
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.PHONY: all
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all: install tests
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.PHONY: reqs
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requirements.txt: requirements.in
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# pip compiling $<
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@$(VENV_DIR)/bin/pip-compile --output-file $@ $<
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@$(VENV_DIR)/bin/pip-compile $(UPGRADE_OPTION) --build-isolation --output-file $@ $<
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reqs: requirements.txt ## alias to compile requirements.txt
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‎api/tests/requirements.in

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# testing
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coverage==4.5.1 # TODO: Downgraded because of a bug https://github.com/nedbat/coveragepy/issues/716
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pytest~=5.3.5 # Bug in pytest-sugar https://github.com/Teemu/pytest-sugar/issues/187
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coverage
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pytest
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pytest-cov
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pytest-aiohttp
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pytest-instafail
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pytest-sugar
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# fixtures
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aiohttp
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openapi-core

‎api/tests/requirements.txt

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async-timeout==3.0.1 # via aiohttp
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attrs==19.3.0 # via aiohttp, jsonschema, openapi-core, pytest
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chardet==3.0.4 # via aiohttp
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coverage==4.5.1 # via -r requirements.in, pytest-cov
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coverage==5.1 # via -r requirements.in, pytest-cov
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idna-ssl==1.1.0 # via aiohttp
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idna==2.9 # via idna-ssl, yarl
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importlib-metadata==1.5.0 # via jsonschema, pluggy, pytest
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importlib-metadata==1.6.0 # via jsonschema, pluggy, pytest
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isodate==0.6.0 # via openapi-schema-validator
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jsonschema==3.2.0 # via openapi-schema-validator, openapi-spec-validator
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lazy-object-proxy==1.4.3 # via openapi-core
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parse==1.15.0 # via openapi-core
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pluggy==0.13.1 # via pytest
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py==1.8.1 # via pytest
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pyparsing==2.4.6 # via packaging
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pyrsistent==0.15.7 # via jsonschema
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pyparsing==2.4.7 # via packaging
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pyrsistent==0.16.0 # via jsonschema
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pytest-aiohttp==0.3.0 # via -r requirements.in
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pytest-cov==2.8.1 # via -r requirements.in
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pytest-instafail==0.4.1.post0 # via -r requirements.in
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pytest-sugar==0.9.2 # via -r requirements.in
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pytest==5.3.5 # via -r requirements.in, pytest-aiohttp, pytest-cov, pytest-instafail, pytest-sugar
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pyyaml==5.3 # via openapi-spec-validator
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pytest-sugar==0.9.3 # via -r requirements.in
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pytest==5.4.2 # via -r requirements.in, pytest-aiohttp, pytest-cov, pytest-instafail, pytest-sugar
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pyyaml==5.3.1 # via openapi-spec-validator
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six==1.14.0 # via isodate, jsonschema, openapi-core, openapi-schema-validator, openapi-spec-validator, packaging
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strict-rfc3339==0.7 # via openapi-schema-validator
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termcolor==1.1.0 # via pytest-sugar
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typing-extensions==3.7.4.1 # via aiohttp
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wcwidth==0.1.8 # via pytest
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werkzeug==1.0.0 # via openapi-core
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typing-extensions==3.7.4.2 # via aiohttp
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wcwidth==0.1.9 # via pytest
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werkzeug==1.0.1 # via openapi-core
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yarl==1.4.2 # via aiohttp
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zipp==3.1.0 # via importlib-metadata
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‎packages/postgres-database/requirements/_migration.in

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# frozen specs
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-r _base.txt
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certifi==2019.11.28 # added contraint to fit pre-installation of jupyter/base-notebook:python-3.7.3 (cannot uninstall)
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urllib3>=1.25.8 # Vulnerability
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alembic

‎packages/postgres-database/requirements/_migration.txt

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# pip-compile --output-file=requirements/_migration.txt requirements/_migration.in
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#
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alembic==1.4.2 # via -r requirements/_migration.in
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certifi==2019.11.28 # via -r requirements/_migration.in, requests
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certifi==2020.4.5.1 # via requests
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chardet==3.0.4 # via requests
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click==7.1.2 # via -r requirements/_migration.in
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docker==4.2.0 # via -r requirements/_migration.in

‎packages/postgres-database/requirements/_test.txt

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astroid==2.4.1 # via pylint
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async-timeout==3.0.1 # via aiohttp
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attrs==19.3.0 # via aiohttp, pytest, pytest-docker
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certifi==2019.11.28 # via -r requirements/_migration.txt, requests
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certifi==2020.4.5.1 # via -r requirements/_migration.txt, requests
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chardet==3.0.4 # via -r requirements/_migration.txt, aiohttp, requests
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click==7.1.2 # via -r requirements/_migration.txt
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coverage==5.1 # via -r requirements/_test.in, coveralls, pytest-cov
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coveralls==2.0.0 # via -r requirements/_test.in
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docker==4.2.0 # via -r requirements/_migration.txt
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docopt==0.6.2 # via coveralls
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faker==4.0.3 # via -r requirements/_test.in
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faker==4.1.0 # via -r requirements/_test.in
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idna-ssl==1.1.0 # via aiohttp
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idna==2.9 # via -r requirements/_migration.txt, requests, yarl
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importlib-metadata==1.6.0 # via pluggy, pytest

‎services/web/server/requirements/_base.txt

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aiohttp==3.6.2 # via -r requirements/../../../../packages/service-library/requirements/_base.in, aiohttp-jinja2, aiohttp-security, aiohttp-session, aiohttp-swagger, aiozipkin
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aiopg[sa]==1.0.0 # via -r requirements/../../../../packages/service-library/requirements/_base.in, -r requirements/_base.in
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aioredis==1.3.1 # via -r requirements/_base.in
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aiormq==3.2.1 # via aio-pika
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aiormq==3.2.2 # via aio-pika
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aiosmtplib==1.1.3 # via -r requirements/_base.in
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aiozipkin==0.6.0 # via -r requirements/../../../../packages/service-library/requirements/_base.in
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amqp==2.5.2 # via kombu

‎services/web/server/requirements/_test.txt

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aiohttp==3.6.2 # via -r requirements/_base.txt, aiohttp-jinja2, aiohttp-security, aiohttp-session, aiohttp-swagger, aiozipkin, pytest-aiohttp
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aiopg[sa]==1.0.0 # via -r requirements/_base.txt
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aioredis==1.3.1 # via -r requirements/_base.txt
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aiormq==3.2.1 # via -r requirements/_base.txt, aio-pika
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aiormq==3.2.2 # via -r requirements/_base.txt, aio-pika
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aiosmtplib==1.1.3 # via -r requirements/_base.txt
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aiozipkin==0.6.0 # via -r requirements/_base.txt
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amqp==2.5.2 # via -r requirements/_base.txt, kombu
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docker==4.2.0 # via -r requirements/_test.in
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docopt==0.6.2 # via coveralls
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expiringdict==1.2.0 # via -r requirements/_base.txt
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faker==4.0.3 # via -r requirements/_test.in
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faker==4.1.0 # via -r requirements/_test.in
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hiredis==1.0.1 # via -r requirements/_base.txt, aioredis
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idna-ssl==1.1.0 # via -r requirements/_base.txt, aiohttp
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idna==2.9 # via -r requirements/_base.txt, idna-ssl, requests, yarl
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python-socketio==4.5.1 # via -r requirements/_base.txt
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pytz==2020.1 # via -r requirements/_base.txt, celery
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pyyaml==5.3.1 # via -r requirements/_base.txt, aiohttp-swagger, openapi-spec-validator
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redis==3.5.0 # via -r requirements/_test.in
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redis==3.5.1 # via -r requirements/_test.in
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requests==2.23.0 # via codecov, coveralls, docker
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semantic-version==2.8.5 # via -r requirements/_base.txt
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six==1.14.0 # via -r requirements/_base.txt, astroid, cryptography, docker, isodate, jsonschema, openapi-core, openapi-spec-validator, packaging, pyrsistent, python-dateutil, python-engineio, python-socketio, tenacity, websocket-client

‎tests/swarm-deploy/requirements/requirements.in

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aio-pika
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coverage==4.5.1 # TODO: Downgraded because of a bug https://github.com/nedbat/coveragepy/issues/716
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coverage
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pytest
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pytest-aiohttp
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pytest-cov

‎tests/swarm-deploy/requirements/requirements.txt

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#
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aio-pika==6.6.0 # via -r requirements/requirements.in
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aiohttp==3.6.2 # via pytest-aiohttp
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aiormq==3.2.1 # via aio-pika
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aiormq==3.2.2 # via aio-pika
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async-timeout==3.0.1 # via aiohttp
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attrs==19.3.0 # via aiohttp, pytest
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certifi==2019.11.28 # via requests
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certifi==2020.4.5.1 # via requests
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chardet==3.0.4 # via aiohttp, requests
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coverage==4.5.1 # via -r requirements/requirements.in, pytest-cov
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coverage==5.1 # via -r requirements/requirements.in, pytest-cov
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docker==4.2.0 # via -r requirements/requirements.in
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idna-ssl==1.1.0 # via aiohttp
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idna==2.9 # via requests, yarl
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importlib-metadata==1.5.2 # via pluggy, pytest
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importlib-metadata==1.6.0 # via pluggy, pytest
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more-itertools==8.2.0 # via pytest
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multidict==4.7.5 # via aiohttp, yarl
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packaging==20.3 # via pytest, pytest-sugar
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pamqp==2.3.0 # via aiormq
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pluggy==0.13.1 # via pytest
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py==1.8.1 # via pytest
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pyparsing==2.4.6 # via packaging
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pyparsing==2.4.7 # via packaging
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pytest-aiohttp==0.3.0 # via -r requirements/requirements.in
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pytest-cov==2.8.1 # via -r requirements/requirements.in
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pytest-instafail==0.4.1.post0 # via -r requirements/requirements.in
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pytest-mock==2.0.0 # via -r requirements/requirements.in
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pytest-mock==3.1.0 # via -r requirements/requirements.in
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pytest-runner==5.2 # via -r requirements/requirements.in
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pytest-sugar==0.9.2 # via -r requirements/requirements.in
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pytest-sugar==0.9.3 # via -r requirements/requirements.in
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pytest==5.4.2 # via -r requirements/requirements.in, pytest-aiohttp, pytest-cov, pytest-instafail, pytest-mock, pytest-sugar
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pyyaml==5.3.1 # via -r requirements/requirements.in
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requests==2.23.0 # via docker
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six==1.14.0 # via docker, packaging, tenacity, websocket-client
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tenacity==6.1.0 # via -r requirements/requirements.in
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tenacity==6.2.0 # via -r requirements/requirements.in
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termcolor==1.1.0 # via pytest-sugar
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typing-extensions==3.7.4.1 # via aiohttp
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urllib3==1.25.8 # via requests
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typing-extensions==3.7.4.2 # via aiohttp
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urllib3==1.25.9 # via requests
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wcwidth==0.1.9 # via pytest
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websocket-client==0.57.0 # via docker
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yarl==1.4.2 # via aio-pika, aiohttp, aiormq

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