Cgbeacon2

Added
- Vulture GitHub action to find unused code with 80% confidence
Fixed
- Freeze PyMongo lib to version<4.0 to keep supporting previous MongoDB versions
Changed
- Scan only changed .py files with Vulture
- Multi-stage Dockerfile for smaller and faster-built image

Added
- Option to provide a custom token when creating a database user
- Example of URI for connecting to a MongoDB replica set
Fixed
- Fixed the command that runs the web app service on docker-compose
Changed
- Replaced the alpine-based MongoDB image used in docker-compose with the official MongodDB image (db version 4.4.9)
- Launch the demo app on port 6000 when it's started via docker-compose
- Build Docker image from local repo when using docker-compose
- Use database port 27013 in docker-compose

Added
- Instructions to run the Beacon cli and web server connected to mongo as a service via Podman
- Inclusive-language check using [woke](https://github.com/get-woke/woke) github action
- Use official Docker github actions to push Docker images to Docker Hub -> Master branch (on release event) and PR branch (on push event)
- Create a demo user with a token for using the API when creating a demo instance
- Github action to deploy docs after a new release is published
Fixed
- Links in docs pages
- Added instructions on how to install bedtools in documentation and readme file
- Build badge link in README page
- Fixed test no longer working after the release of Flask 2.0
- Replaced old docs link www.clinicalgenomics.se/cgbeacon2 with new https://clinical-genomics.github.io/cgbeacon2
- Improved code according to codefactor and Flake8 suggestions
- Indented code in a github action
- Link to docs in the README page
Changed
- Switch to codecov in gihub actions
- Switched coveralls badge with codecov badge
- id param name in create user and create database cli command
- Use list_collection_names() instead of collection_names() that was deprecated in pymongo 3.7
- Use DELETE requests for deleting items from the database

Added
- Create users with randomly generated tokens to use the REST API
- Auth token validation in `add` and `delete` requests
- Updated documentation to add and delete variants using the APIs
Fixed
- Docker action that didn't push 2 tags for a new release, just the "latest"
- Dockerfile faster to build and cleaner code
- Modified jwt.decode params to be compliant to PyJWT v2.0
- Bug when trying to delete variants for samples not in dataset
- Bug when variant samples do not correspond to dataset samples
Changed
- `add` and `delete` API are returning async responses
- Renamed entry point command `cgbeacon2` to `beacon`

Added
- Github action to build and publish Docker image
Changed
- Docker reference to image point to clinicalgenomics Docker Hub
Fixed
- Broken link in the docs and in README

Fixed
- Broken github actions test
Changed
- Removed Codecov and master workflow github action
Added
- Codecov and CodeFactor github actions
- Created deployment WSGI file
- Dockerfile and docker-compose files
- Flake8, Coveralls and Black github actions