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Deployment to Production Mode (#46)
* adds all deployment changes * removes colocarpy requirement * adds init file * fixes import * updates python config * one more time * updates config * manually add path * edit django config * update requirements * change project name * move eb extensions * update settings * shifting folders around * fix static files * collects all statics * updates settings once more * remove ds store * updates readme
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‎.DS_Store

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‎.gitignore

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# Pyre type checker
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.pyre/
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neuvueDB
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# Elastic Beanstalk Files
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.elasticbeanstalk/*
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!.elasticbeanstalk/*.cfg.yml
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!.elasticbeanstalk/*.global.yml

‎.gitmodules

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[submodule "neuvue-client"]
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path = neuvue_project/deps/neuvue-client
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url = https://github.com/aplbrain/neuvue-client.git

‎Neuvue_Blueprint.png

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‎README.md

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# neuvue
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MICrONS Proofreading App
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## How to run the app locally
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- create a virtual environment using the requirements.txt file
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- activate the environment
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- check for django updates:
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- run `python3 manage.py makemigrations`
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- run `python3 manage.py migrate`
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- run `python3 manage.py runserver localhost:8000`
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- navigate to [http://127.0.0.1:8000/]( http://127.0.0.1:8000/) in your browser
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<h3 align=center>Neuvue</h3>
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<h6 align=center>Proofreading web-app and task management system</h6>
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## Installation
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Create a python3 virtual environment and install the requirements in neuvue_project/requirements.txt.
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```shell
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python -m venv venv
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source venv/bin/activate
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pip install -r neuvue_project/requirements.txt
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```
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## Running a development environment
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For development purposes, there is a included neuvueDB.sqlite3 database file containing the tables needed to run the Django app. By default, the settings are configured for production which uses a cloud-enabled MySQL datatbase server. Here are the steps to enable development mode.
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1. Open `neuvue_project/neuvue/settings.py` and set `DEBUG=True`
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2. In the same file, modify `NEUVUE_QUEUE_ADDR` variable to the Nuevue-Queue endpoint you would like to use.
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3. Get the recent migrations to the database by running
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`python manage.py migrate`
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4. (OPTIONAL) Create a superuser to modify the app in your development environment.
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`python manage.py createsuperuser`
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5. Run the app with the `runserver` command to start a development instance. Run on the localhost:8000 address and port to allow OAuth client to properly authenticate user.
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`python manage.py runserver localhost:8000`
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6. Open your app on http://localhost:8000
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## Deploying to production
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We use AWS Elastic Beanstalk to deploy Neuvue. To re-deploy after changes are made to the production branch, follow the instructions below.
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1. Update your AWS credentials in `~/.aws/credentials` file with a long-lived token generated on cloudmanager.jhuapl.edu.
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2. Install the elastic beanstalk CLI and restart the terminal.
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`sudo pip install --upgrade awsebcli`
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3. Change directories to `neuvue_project` and run `eb init`. This will connect to the current deployment environment.
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```bash
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cd neuvue_project
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eb init
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```
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4. (OPTIONAL) Run `eb health` to check the current status of the app.
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5. Run `eb deploy` to upload your local environment to the production system. You do not have to run `manage.py collectstatic`, elastic beanstalk will do this for you.
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Modifications to the elastic beanstalk environment (database, instance types, error logs, etc) are best handled directly throught the AWS console.
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## OAuth Set-up
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The included development database is preconfigured to allow OAuth to authetnticate user accounts from `localhost:8000`. For a more complete guide on how this was done, refer to this link:
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https://www.section.io/engineering-education/django-google-oauth/
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We use `django-allauth` to connect Google OAuth to the Django environment. Users also have the option to log in through the base allauth login/signup page:
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http://localhost:8000/accounts/login/
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Django users, OAuth settings, and site configuration can be modified in the admin console.
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http://localhost:8000/admin
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## Cloud Blueprint
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<img src="Neuvue_Blueprint.png" style="background-color: rgb(300, 300, 300);">

‎django/neuvueDB

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‎neuvue_project/.ebextensions/django.config

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option_settings:
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aws:elasticbeanstalk:application:environment:
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DJANGO_SETTINGS_MODULE: "neuvue.settings"
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PYTHONPATH: "/var/app/current:$PYTHONPATH"
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aws:elasticbeanstalk:container:python:
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WSGIPath: neuvue.wsgi:application
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NumProcesses: 3
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NumThreads: 20
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aws:elasticbeanstalk:environment:proxy:staticfiles:
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/static: static
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container_commands:
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01_migrate:
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command: "source /var/app/venv/*/bin/activate && python3 manage.py migrate"
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leader_only: true

‎neuvue_project/.ebextensions/https.config

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option_settings:
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aws:elbv2:listener:443:
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SSLCertificateArns: arn:aws:acm:us-east-1:473318664541:certificate/78634bd0-b992-44d1-81f3-da0c52b7ba24
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Protocol: HTTPS
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Resources:
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AWSEBV2LoadBalancerListener:
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Type: 'AWS::ElasticLoadBalancingV2::Listener'
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Properties:
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LoadBalancerArn: { "Ref" : "AWSEBV2LoadBalancer" }
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DefaultActions:
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- RedirectConfig:
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Port: 443
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Protocol: HTTPS
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StatusCode: HTTP_301
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Type: redirect
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Port: 80
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Protocol: HTTP

‎neuvue_project/.ebextensions/packages.config

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packages:
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yum:
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python3-devel: []
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mariadb-devel: []

‎neuvue_project/.gitignore

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# Elastic Beanstalk Files
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.elasticbeanstalk/*
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!.elasticbeanstalk/*.cfg.yml
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!.elasticbeanstalk/*.global.yml

‎neuvue_project/deps/neuvue-client/.gitignore

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# Created by https://www.gitignore.io/api/code,macos,python,jupyternotebook
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### Code ###
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# Visual Studio Code - https://code.visualstudio.com/
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.settings/
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.vscode/
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tsconfig.json
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jsconfig.json
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### JupyterNotebook ###
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.ipynb_checkpoints
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*/.ipynb_checkpoints/*
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# Remove previous ipynb_checkpoints
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# git rm -r .ipynb_checkpoints/
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#
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### macOS ###
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# General
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.DS_Store
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.AppleDouble
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.LSOverride
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# Icon must end with two \r
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Icon
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# Thumbnails
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._*
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# Files that might appear in the root of a volume
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.DocumentRevisions-V100
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.fseventsd
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.Spotlight-V100
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.TemporaryItems
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.Trashes
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.VolumeIcon.icns
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.com.apple.timemachine.donotpresent
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# Directories potentially created on remote AFP share
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.AppleDB
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.AppleDesktop
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Network Trash Folder
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Temporary Items
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.apdisk
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### Python ###
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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### Python Patch ###
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.venv/
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# End of https://www.gitignore.io/api/code,macos,python,jupyternotebook
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### colocarpy ###
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notebooks/

‎neuvue_project/deps/neuvue-client/CHANGELOG.md

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- **0.2.1**
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- Fix infamous `_id` index error when a result has zero rows; now returns an empty dataframe with the correct columns.
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- Add test suite
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- Add `limit` argument when requesting large numbers of results
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- Enable environment-variable authentication
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- Fix unauthorized-access infinite loop

‎neuvue_project/deps/neuvue-client/README.md

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<p align=center><img align=center src='axonolotl.png' width=300 /></p>
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<h3 align=center>neuvue-client</h3>
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<h6 align=center>a python client for neuvuequeue</h6>
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# Installation
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```shell
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pip3 install git+https://github.com/aplbrain/neuvueclient.git
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```
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# Configuration
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Create a configuration file in your home directory `~/.neuvueclient/neuvue-secret.txt` with your Google Oauth token:
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```
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[CONFIG]
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token = <insert token>
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```
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# Usage
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First, create a new neuvuequeue instance:
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```python
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import neuvueclient as Client
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C = Client.NeuvueQueue("http://neuvuequeue-server/")
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```
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Now you can do all that your corazón desires:
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```python
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C.get_tasks(sieve={"namespace": "split"})
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```
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# Implementation Progress
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| Object | POST | GET | LIST | DELETE | PATCH |
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|----------|------|-----|------|--------|-------|
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| Point | ✅ | ✅ | ✅ | ✅ | ⛔
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| Task | ✅ | ✅ | ✅ | ✅ | ✅

‎django/static/images/axonolotl.png ‎neuvue_project/deps/neuvue-client/axonolotl.png

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