Gentropy

What's Changed



🐛 Fix

- logo css [\David Ochoa](mailto:ochoaebi.ac.uk)


📖 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)








🚀 Chore

- merge dev [\David Ochoa](mailto:dogcaesargmail.com)
- 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)

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)


🐛 Fix

- 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

- 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)


👷‍♂️ 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

- merge dev [\David Ochoa](mailto:dogcaesargmail.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)

Build

* build(deps-dev): bump ruff from 0.1.7 to 0.1.8 (341)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.7 to 0.1.8.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/v0.1.7...v0.1.8)

---
updated-dependencies:
- dependency-name: ruff
dependency-type: direct:development
update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <supportgithub.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]users.noreply.github.com> ([`3643f64`](https://github.com/opentargets/genetics_etl_python/commit/3643f649c5b1afc555249caa086fd26853daa4f1))

* build(deps-dev): bump isort from 5.13.1 to 5.13.2 (342)

Bumps [isort](https://github.com/pycqa/isort) from 5.13.1 to 5.13.2.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pycqa/isort/compare/5.13.1...5.13.2)

---
updated-dependencies:
- dependency-name: isort
dependency-type: direct:development
update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <supportgithub.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]users.noreply.github.com> ([`a96793a`](https://github.com/opentargets/genetics_etl_python/commit/a96793af5d0d91209b12113a2097f92fe705efba))

* build(deps-dev): bump python-semantic-release from 8.3.0 to 8.5.1 (343)

Bumps [python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 8.3.0 to 8.5.1.
- [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases)
- [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python-semantic-release/python-semantic-release/compare/v8.3.0...v8.5.1)

---
updated-dependencies:
- dependency-name: python-semantic-release
dependency-type: direct:development
update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <supportgithub.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]users.noreply.github.com>
Co-authored-by: David Ochoa <ochoaebi.ac.uk> ([`817d8f0`](https://github.com/opentargets/genetics_etl_python/commit/817d8f07cd621f13db7933bdb14369f846ba076c))

Feature

* feat: semantic release gh action (354) ([`c7b0dca`](https://github.com/opentargets/genetics_etl_python/commit/c7b0dca11aef068451d57883ef5f1fa295122444))

* feat: upload release (353) ([`0c00e50`](https://github.com/opentargets/genetics_etl_python/commit/0c00e50328a64c77c4eaf7e99ea6c180451102b1))

* feat: activate release process (352)

* feat: serious release

* revert: no tests within release workflow ([`2a40dca`](https://github.com/opentargets/genetics_etl_python/commit/2a40dca883f7d7bdb3a3ea2b0bf25b1c9cddc86b))

Unknown

* revert: dispatch (355) ([`721a8b1`](https://github.com/opentargets/genetics_etl_python/commit/721a8b1cab48d74e63fbd0476ba7b84eddce86a0))

The dawn of time.

Note: Mock release just to setup the CI/CD release pipeline