Update all actions

[4.5.1] - 2024-09-04

Fixed

• Bump actions/download-artifact from 2 to 4 in /.github/workflows (recommended by security advisory)
• Update version of other actions
• Broken upload to Codecov step in Tests & Coverage GitHub action

Unfreeze PyMongo lib and support latest MongoDB versions

[4.5] - 2023-11-07

Changed

• Unfreeze PyMongo dependency
• Use MongoDB version 7 in docker-compose.yml
• Execute tests using MongoDB 7

Display connected nodes on index and fixes

[4.4] - 2023-08-14

Added

• Option to display the description of the connected nodes on the index page

Fixed

• Build and publish to Docker Hub stage README page badge
• Parsing of phenotype.hpoa file

Changed

• Updated resource files

Switch to new phenotype file format phenotype.hpoa

[4.3] - 2023-03-16

Changed

• Abort server startup if phenotypes terms are not correctly parse from resource files

Fixed

• Parsing and downloading of the HPO definitions in the new format (phenotype.hpoa)
• Replaced deprecated version of Ubuntu in GitHub actions

Fixed broken link to phenotype_annotation.tab and improved code quality

[4.2] - 2022-09-23

Changed

• Refactor to avoid code smells reported by SonarCloud

Fixed

• Broken link to HPO definitions (phenotype_annotation.tab)
• Security hotspots flagged by SonarCloud
• Decreased vulnerability by removing some server log messages
• Problems flagged as bugs by SonarCloud
• Server startup debug message showing correct number of parsed diseases

Automatic update of phenotype resources

[4.1] - 2022-06-27

Added

• Documentation on how to update phenotype resource files

Changed

• Download automatically phenotype resources when a non-demo app starts

Removed support for async requests and dedicated documentation pages

[4.0] - 2022-05-18

Added

• GitHub action to auto-deploy documentation when a new release is created

Fixed

• Ports used to serve the app in docker-compose howto

Changed

• Removed support for asynchronous requests to the server
• Moved documentation to mkdocs pages (https://clinical-genomics.github.io/patientMatcher)

Improved GitHub actions and updated resource files

[3.4] - 2022-04-29

Added

• Created codecov config file in app's root folder

Fixed

• Updated deprecated codecov action from v1. to v.2
• Upgraded the version of Black lib to latest (22.3.0) in GitHub action
• Link to the GitHub repo on the top-left corner of index page
• Remove HTTP-related security issues

Changed

• Updated resource files (HPO and OMIM definitions)

Database name in crash report email and updated citation reference

[3.3] - 2022-03-09

Changed

• Citation file, pointing to newly published paper

Added

• Name of database in crash report email, to understand if crashed app is stage or prod app
• Citation button on index page
• Double helix favicon to index page

Fixed admin error notifications and landing page's colors and icons

[3.2] - 2022-01-21

Changed

• Colors and icons of landing page

Fixed

• Admin error log email handling and relative test