Gene type column and improved demo files

[1.10]

Added

• An additional Gene Biotype (build 37) or Gene type (build 38) column when downloading genes to file. This allows downloading of non-coding genes

Changed

• Demo files genes_37.tsv and genes_38.tsv to reflect latest changes in genes downloaded files
• Demo files contain now lines from the following genes: MTHFR, DHFR, FOLR1, SLC46A1, MT-TP (better integration with chanjo tests)

Retry streaming files chunks and simpler Swagger docs

[1.9]

Changed

• Added retry logic to stream_resource to handle failed chunk downloads with a configurable number of attempts and error handling.
• Commented out in the code all endpoints that are not yet functioning.

Missing exons workaround and deprecate Python 3.8

[1.7]

Changed

• Do not download duplicated lines from Ensembl BioMart
• Update Python version to v3.12 in Dockerfile
• Update Python version in pyproject.toml

Fixed

• Download data from Ensembl BioMart chromosome-wise, to avoid missing exons, for instance (see issue #74)

Missing build 38 exons using Ensembl v.113: using v.112 instead

[1.6.2]

Fixed

• Some exons are missing when downloading build 38 data using Ensembl v.113 (Oct 2024). Using v.112 (May 2024) until the problem is fixed. Build 37 not affected.

Updated starlette, fastapi, urllib3 and certifi libs

[1.6.1]

Fixed

• Security issue related to starlette version by updating fastapi, starlette and some dependencies
• Updated urlib to v.2.2.3 to address the urllib3's Proxy-Authorization request header isn't stripped during cross-origin redirects issue
• Updated certifi to v.2024.7.4 to address the Certifi removes GLOBALTRUST root certificate issue

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 to schug.load.ensembl.fetch_ensembl_exons
• Upgraded Python version from 3.8 to 3.11 in Dockerfile
• Updated several python libraries in poetry.lock