Patientmatcher

Added
- Software purpose and short description of developers and Stockholm MME node in README
Changed
- Improve docker-compose file with 2 demo connected nodes
- Replaced vepo/mongo with the official MongoDB image mongo:4.4.9 in docker-compose files
- Created a mongo-init script for database authentication in docker-compose `docker-compose_auth_server_with_2_nodes.yml` development file
- Modified docker-compose file to connect to database without authentication
- Modified the `pytest_codecov` GitHub action file to connect to database matrix (MongoDB 3.2, 4.4, 5.0) without authentication
- Some cli commands don't instantiate a complete app object
- Fixed the code to connect to a MongoDB replica set
Fixed
- Removed unused `--ensembl_genes` parameter from `add demodata` command in all docker-compose file

Added
Changed
- Save Ensembl ids for demo patient data genes automatically
- Mock the Ensembl REST API converting gene symbols to Ensembl IDs in tests
- Changed the tests for the gene conversion Ensembl APIs to use mocks APIs
- Do not download resources when testing the update resources command
- Use the requests lib instead of urllib.request to interrogate the Ensembl APIs
- Split cli tests into 4 dedicated files (test_add, test_remove, test_update, test_commands)
Fixed
- Syntax in the disclaimer
- Validate the Ensembl gene ID against the Ensembl API when multiple IDs are returned by converting a HGNC symbol.

Added
- .cff citation file and doi badge on readme page
- GitHub action to publish repo to PyPI when a new release is created
Changed
Fixed
- Fixed in README file the server port used by the web server container launched from docker-compose
- Provide a content type description for long_description in setup file

Added
- A demo docker-compose file with a MME server connected to 2 other nodes under `/containers`
Changed
Fixed
- Assign 2 different ids to the demo connected nodes in docker-compose

Added
- Email logging of errors howto in readme
- Inclusive-language check using [woke](https://github.com/get-woke/woke) github action
Changed
- Removed coveralls badge and added codecov badge
- Required downloading of hp.obo.txt and phenotype_annotation.tab.txt to run a non-test app
- Integrate HPO parsing and handling into the software (decouple from Patient-similarity for HPO)
- Integrate OMIM parsing and handling into the software (decouple from Patient-similarity for OMIM)
- Use app port 9020 instead of 5000 in docker-compose
- Use MongoDB port 27013 instead of 27017 in docker-compose
- Subnet address used in bridge of docker-compose file
- Integrate HPOIC (HPO info content) creation in HPO extensions (decouple from Patient-similarity for HPOIC)
- All collections are removed and recreated on `add demodata` rerun
- Demo client with token `DEMO` is created when `add demodata` command is run
- Remove patient-similarity dependency and replace needed functions with internal code
Fixed
- downloading phenotype_annotation.tab file from Monarch Initiative
- document keys when a demo client is created with the command `pmatcher add demodata`

Added
- Notify admins via email when app crashes
Changed
- Use codecov instead of coveralls in github actions
- Send notification emails using TLS instead of SSL
Fixed