v0.1.0-rc.2

What's Changed

✨ Feature

• not fail CI if codecov error (#416) @David Ochoa
• flex python version to make all 3.10 versions compatible (#406) @David Ochoa
• [l2g] limit l2g predictions to gwas-derived associations (#408) @Irene López
• remove ukbiobank and overlaps steps (#404) @David Ochoa
• application configuration (#386) @David Ochoa
• [l2g] add coloc based features (#400) @Irene López
• adding logic to flag gwas catalog studies based on curation (#347) @Daniel Suveges
• [colocalisation] new step runs ecaviar on credible sets (#396) @Irene López
• [eqtl_catalogue] study index improvements (#369) @Irene López
• carma outlier detection method (#281) @David Ochoa
• [study_locus] remove statistics after conditioning from schema (#383) @Irene López
• [l2g] add features based on predicted variant consequences (#360) @Irene López
• [pics] remove variants from locus when PICS cannot be applied (#361) @Irene López
• Finngen R10 harmonisation and preprocessing (#370) @David Ochoa

🐛 Fix

• changelog template (#424) @David Ochoa
• deprecate version in init.py (#421) @David Ochoa
• some of the details of the curation logic needed some fix (#418) @Daniel Suveges
• release action (#417) @David Ochoa
• updating finngen sumstats ingestion (#401) @Daniel Suveges
• release build using poetry (#387) @David Ochoa
• incorrect parsing of app_name in makefile (#367) @Irene López
• [l2g] calculate_feature_missingness_rate counts features annotated with 0 as incomplete (#364) @Irene López

📖 Documentation

• corrected and added documentation to datasource (#362) @Yakov

♻️ Refactor

• rename genetics_etl_python to gentropy (#422) @David Ochoa
• rename otg to gentropy (#405) @David Ochoa

✅ Test

• [study_locus] add semantic test for find_overlaps (#407) @Irene López
• generalise cli test for easier maintainance (#403) @David Ochoa

🏗 Build

• [deps-dev] bump lxml from 4.9.3 to 5.1.0 (#412) @dependabot[bot]
• [deps] bump hail from 0.2.126 to 0.2.127 (#413) @dependabot[bot]
• [deps] bump wandb from 0.16.1 to 0.16.2 (#410) @dependabot[bot]
• [deps-dev] bump pytest from 7.4.3 to 7.4.4 (#415) @dependabot[bot]
• [deps-dev] bump mkdocstrings-python from 1.7.5 to 1.8.0 (#414) @dependabot[bot]
• [deps-dev] bump pymdown-extensions from 10.5 to 10.7 (#390) @dependabot[bot]
• [deps-dev] bump ipykernel from 6.27.1 to 6.28.0 (#389) @dependabot[bot]
• [deps-dev] bump apache-airflow-providers-google (#392) @dependabot[bot]
• [deps-dev] bump mkdocs-material from 9.5.2 to 9.5.3 (#391) @dependabot[bot]
• [deps-dev] bump mkdocs-git-committers-plugin-2 from 2.2.2 to 2.2.3 (#393) @dependabot[bot]
• [deps-dev] bump ipython from 8.18.1 to 8.19.0 (#377) @dependabot[bot]
• [deps-dev] bump mkdocs-git-revision-date-localized-plugin (#376) @dependabot[bot]
• [deps-dev] bump python-semantic-release from 8.5.1 to 8.7.0 (#375) @dependabot[bot]
• [deps-dev] bump mypy from 1.7.1 to 1.8.0 (#374) @dependabot[bot]
• [deps-dev] bump apache-airflow from 2.7.3 to 2.8.0 (#373) @dependabot[bot]
• [deps] bump pyspark from 3.3.3 to 3.3.4 (#358) @dependabot[bot]

👷‍♂️ Ci

• remove unnecessary steps (#428) @David Ochoa
• more complex setup with independent jobs (#427) @David Ochoa
• pypi and testpypi functionalities (#423) @David Ochoa
• reorder commit types in release notes template (#419) @Irene López
• set codecov default branch to dev (#368) @Irene López
• new changelog and release notes templates (#357) @David Ochoa

🚀 Chore

• merge dev @David Ochoa
• updaing configs to the propsed release folder structure (#425) @Daniel Suveges
• update pre-commit hook versions (#411) @David Ochoa
• [studylocus] rename logABF statistics to logBF (#402) @Irene López
• [deps] bump python-semantic-release/python-semantic-release (#388) @dependabot[bot]
• change picsed finngen outputh path (#385) @Irene López
• [deps] bump python-semantic-release/python-semantic-release (#372) @dependabot[bot]
• set cluster delete TTL (#379) @Kirill Tsukanov
• [study_index] change numeric columns from long to integers (#371) @Irene López
• [deps] bump python-semantic-release/python-semantic-release (#359) @dependabot[bot]