Releases: Clinical-Genomics/schug
Releases · Clinical-Genomics/schug
Updated dependencies
[1.6]
Changed
- Updated a number of libraries to address security alerts
Fix Docker RuntimeError: can't start new thread
[1.5.1]
Fixed
- Revert to python 3.8 in Dockerfile to avoid
RuntimeError: can't start new thread
issue
Updates and deprecated code removal
[1.5]
Changed
- Updated version of external images used in GitHub actions
- Updated Python version to v3.11 in tests GitHub action
- Removed pytest from the package dependencies
Fixed
- Converted deprecated Pydantic validators and Config into Pydantic 2 format
Support Python >=3.8 and upgrade Pydantic to v2
[1.4]
Changed
- Updated Pydantic(^2.5.2) library and other dependencies
- Support Python>=3.8
Python 3.11 in Dockerfile plus fixes and lib updates
[1.3]
Fixed
- Typo in instructions to download genes in README document
Changed
- Code formatted with black and black check GitHub action
- Renamed
schug.load.ensembl.fetch_ensembl_exon_lines
function toschug.load.ensembl.fetch_ensembl_exons
- Upgraded Python version from 3.8 to 3.11 in Dockerfile
- Updated several python libraries in poetry.lock
Include Mane transcripts info and support official genome build names
[1.2]
Added
- Include also
mane_plus_clinical
andmane_select
columns in transcripts file downloaded from Ensembl
Changed
- Updated Uvicorn library
- Accept also
GRCh37
andGRCh38
as build values when downloading resources
Fixed PyPI push action and demo instance to use a memory database
[1.1]
Changed
- Move the
schug
directory up in root dir folder
Fixed
- Use a memory database as default database in demo instance
- Issues flagged by SonarCloud
Publish to PyPI
GitHub action
Proxy endpoints to Ensembl genes, exons and transcripts
[1.0.0]
Added
- Endpoint to Ensembl genes download
- Endpoint to Ensembl transcripts download
- Endpoint to Ensembl exons download
- Dockerfile and docker-compose files
- Push to Docker Hub -prod and stage- GitHub actions
- Publish to PyPI GitHub actions
- Run tests GitHub action
- CHANGELOG file
Changed
- Run the app with Python>=3.8
Fixed
- Typing errors in
fetch_ensembl_exons
andfetch_genes_to_hpo_to_disease
that prevented the app from starting