Major release 3.0

[northwestwitch]

[3.0]

Changed

• Updated several libraries including schug (now v1.7)
• Update project's Python version to 3.9
• BREAKING CHANGE: modified the structure of the database table genes, converting the ensembl_id string field to ensembl_ids: an array of strings. This change addresses recent changes in the MySQL: https://bugs.mysql.com/bug.php?id=114838

Fixed

• The MariaDB healthcheck step in docker-compose-mysql.yml, preventing the demo app to start

Review

• Tests executed by CR
• "Merge and deploy" approved by

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.22%. Comparing base (6fcdf37) to head (ce6e065).
Report is 21 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #396      +/-   ##
==========================================
- Coverage   92.60%   92.22%   -0.38%     
==========================================
  Files          31       31              
  Lines        1514     1531      +17     
==========================================
+ Hits         1402     1412      +10     
- Misses        112      119       +7     

Flag	Coverage Δ
unittests	92.22% <100.00%> (-0.38%)	⬇️

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[northwestwitch]

Hi @Jakob37, I'm about to release a major on chanjo2. It's a major because it contains a breaking change, see the changelog.

Next time you want to update the tables (genes, transcripts, exons) unfortunately you'd need to drop and recreate the database first. This is because I had to change the field named ensembl_id of the genes table (previously a string) to an array of strings, which is now named genes.ensembl_ids. Due to this change of the database schema I had to introduce many changes in the code, but I haven't touched the functions responsible for calculating the stats, which return exactly the same numbers (tested on our staging server). Sorry for the inconvenience! 🙏🏻

[Jakob37]

Hi @Jakob37, I'm about to release a major on chanjo2. It's a major because it contains a breaking change, see the changelog.

Next time you want to update the tables (genes, transcripts, exons) unfortunately you'd need to drop and recreate the database first. This is because I had to change the field named ensembl_id of the genes table (previously a string) to an array of strings, which is now named genes.ensembl_ids. Due to this change of the database schema I had to introduce many changes in the code, but I haven't touched the functions responsible for calculating the stats, which return exactly the same numbers (tested on our staging server). Sorry for the inconvenience! 🙏🏻

No worries, thanks for letting me know!