What's Changed
✨ Feature
- not fail CI if codecov error (416) [\David Ochoa](mailto:ochoaebi.ac.uk)
- flex python version to make all 3.10 versions compatible (406) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**l2g**\] limit l2g predictions to gwas-derived associations (408) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- remove ukbiobank and overlaps steps (404) [\David Ochoa](mailto:ochoaebi.ac.uk)
- application configuration (386) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**l2g**\] add coloc based features (400) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- adding logic to flag gwas catalog studies based on curation (347) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**colocalisation**\] new step runs ecaviar on credible sets (396) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**eqtl_catalogue**\] study index improvements (369) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- carma outlier detection method (281) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**study_locus**\] remove statistics after conditioning from schema (383) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**l2g**\] add features based on predicted variant consequences (360) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**pics**\] remove variants from `locus` when PICS cannot be applied (361) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- Finngen R10 harmonisation and preprocessing (370) [\David Ochoa](mailto:ochoaebi.ac.uk)
- semantic release gh action (354) [\David Ochoa](mailto:ochoaebi.ac.uk)
- upload release (353) [\David Ochoa](mailto:ochoaebi.ac.uk)
- activate release process (352) [\David Ochoa](mailto:ochoaebi.ac.uk)
🐛 Fix
- logo css [\David Ochoa](mailto:ochoaebi.ac.uk)
- changelog template (424) [\David Ochoa](mailto:ochoaebi.ac.uk)
- deprecate __version__ in __init__.py (421) [\David Ochoa](mailto:ochoaebi.ac.uk)
- some of the details of the curation logic needed some fix (418) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- release action (417) [\David Ochoa](mailto:ochoaebi.ac.uk)
- updating finngen sumstats ingestion (401) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- release build using poetry (387) [\David Ochoa](mailto:ochoaebi.ac.uk)
- incorrect parsing of `app_name` in makefile (367) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**l2g**\] `calculate_feature_missingness_rate` counts features annotated with 0 as incomplete (364) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
📖 Documentation
- fix step name (438) [\David Ochoa](mailto:ochoaebi.ac.uk)
- docs ammendments (437) [\David Ochoa](mailto:ochoaebi.ac.uk)
- several enhancements on docs including index and installation (433) [\David Ochoa](mailto:ochoaebi.ac.uk)
- release documentation preparation (432) [\Yakov](mailto:yt4sanger.ac.uk)
- update index.md [\David Ochoa](mailto:ochoaebi.ac.uk)
- update README.md (431) [\David Ochoa](mailto:ochoaebi.ac.uk)
- gentropy hero image (430) [\David Ochoa](mailto:ochoaebi.ac.uk)
- documentation link (429) [\David Ochoa](mailto:ochoaebi.ac.uk)
- corrected and added documentation to datasource (362) [\Yakov](mailto:yt4sanger.ac.uk)
♻️ Refactor
- rename genetics_etl_python to gentropy (422) [\David Ochoa](mailto:ochoaebi.ac.uk)
- rename otg to gentropy (405) [\David Ochoa](mailto:ochoaebi.ac.uk)
✅ Test
- \[**study_locus**\] add semantic test for find_overlaps (407) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- generalise cli test for easier maintainance (403) [\David Ochoa](mailto:ochoaebi.ac.uk)
🏗 Build
- \[**deps-dev**\] bump lxml from 4.9.3 to 5.1.0 (412) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump hail from 0.2.126 to 0.2.127 (413) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump wandb from 0.16.1 to 0.16.2 (410) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest from 7.4.3 to 7.4.4 (415) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocstrings-python from 1.7.5 to 1.8.0 (414) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pymdown-extensions from 10.5 to 10.7 (390) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipykernel from 6.27.1 to 6.28.0 (389) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump apache-airflow-providers-google (392) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocs-material from 9.5.2 to 9.5.3 (391) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocs-git-committers-plugin-2 from 2.2.2 to 2.2.3 (393) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.18.1 to 8.19.0 (377) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocs-git-revision-date-localized-plugin (376) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump python-semantic-release from 8.5.1 to 8.7.0 (375) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mypy from 1.7.1 to 1.8.0 (374) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump apache-airflow from 2.7.3 to 2.8.0 (373) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump pyspark from 3.3.3 to 3.3.4 (358) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ruff from 0.1.7 to 0.1.8 (341) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump isort from 5.13.1 to 5.13.2 (342) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump python-semantic-release from 8.3.0 to 8.5.1 (343) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
👷♂️ Ci
- remove unnecessary steps (428) [\David Ochoa](mailto:ochoaebi.ac.uk)
- more complex setup with independent jobs (427) [\David Ochoa](mailto:ochoaebi.ac.uk)
- pypi and testpypi functionalities (423) [\David Ochoa](mailto:ochoaebi.ac.uk)
- reorder commit types in release notes template (419) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- set codecov default branch to dev (368) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- new changelog and release notes templates (357) [\David Ochoa](mailto:ochoaebi.ac.uk)
🚀 Chore
- improvements to generate 2401 data release (436) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- tidying up gwas catalog ingestion and process configuration (426) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- updaing configs to the propsed release folder structure (425) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- update pre-commit hook versions (411) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**studylocus**\] rename logABF statistics to logBF (402) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**deps**\] bump python-semantic-release/python-semantic-release (388) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- change picsed finngen outputh path (385) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**deps**\] bump python-semantic-release/python-semantic-release (372) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- set cluster delete TTL (379) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- \[**study_index**\] change numeric columns from long to integers (371) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**deps**\] bump python-semantic-release/python-semantic-release (359) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)