From 4bc3aeeaaa6d3bbffd997d6615bd805ffe8ab9a4 Mon Sep 17 00:00:00 2001 From: github-actions Date: Sun, 14 Jul 2024 07:37:36 +0000 Subject: [PATCH] 1.5.0 Automatically generated by python-semantic-release --- CHANGELOG.md | 146 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 2 +- 2 files changed, 146 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 56af50ced..da0ea3a40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,10 +8,85 @@ -## v1.4.0 (2024-06-14) +## v1.5.0 (2024-07-14) ### ✨ Feature +- full orchestration of the variant index dag (#678) [\@Irene López Santiago](mailto:45119610+ireneisdoomed@users.noreply.github.com) + + +- \[**studyLocus validation**\] adding validation logic to studyLocus dataset (#686) [\@Daniel Suveges](mailto:daniel.suveges@protonmail.com) + + +- artifacts versionned by release (#692) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) + +### 🐛 Fix + + +- moving hl.init (#687) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + +### 👷‍♂️ Ci + + +- revert semantic-release update (#694) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) + + +- prevent user from rebasing in minimal way (#691) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) + +### 🚀 Chore + + +- \[**study_index**\] improve study definition for the eQTL Catalogue and Finngen (#693) [\@Irene López Santiago](mailto:45119610+ireneisdoomed@users.noreply.github.com) + +## v1.4.0 (2024-07-12) +### ✨ Feature + + +- \[**variant index**\] calculate hash as variant id for long variants (#665) [\@Daniel Suveges](mailto:daniel.suveges@protonmail.com) + + +- \[**StudyIndex**\] validation for study type, disease, target etc (#672) [\@Daniel Suveges](mailto:daniel.suveges@protonmail.com) + + +- \[**docker**\] image update for new orchestration (#683) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) + + +- credible set quality control step (#681) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + + +- adding sanity filter to GWASCatalogSumstatsPreprocessStep (#677) [\@Yakov](mailto:yt4@sanger.ac.uk) + + +- add qc step (#675) [\@Yakov](mailto:yt4@sanger.ac.uk) + + +- locus_breaker_clumping (#655) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + + +- vep annotation (dockerised + google batch + airflow) (#608) [\@David Ochoa](mailto:ochoa@ebi.ac.uk) + + +- \[**datasets**\] adding new variant index model (#641) [\@Daniel Suveges](mailto:daniel.suveges@protonmail.com) + + +- implement UKB PPP (EUR) ingestion & harmonisation (#652) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- \[**l2g**\] better l2g training, evaluation, and integration (#576) [\@Irene López](mailto:45119610+ireneisdoomed@users.noreply.github.com) + + +- \[**stydyLocus**\] adding new locus collection using boundaries (#644) [\@Yakov](mailto:yt4@sanger.ac.uk) + + +- \[**ld_annotator**\] optional r2 threshold (#648) [\@Irene López](mailto:45119610+ireneisdoomed@users.noreply.github.com) + + +- exclude region for StudyLocus object (#646) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + + +- \[**SusieFineMapperStep**\] add new function with boundaries (#645) [\@Yakov](mailto:yt4@sanger.ac.uk) + + - \[**config**\] 24.06 data release fixes (#639) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) @@ -44,6 +119,33 @@ ### 🐛 Fix +- fixed selection of major ancestry for finemapper (#685) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + + +- reconcile changes in the finemapping step with config (#682) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- improving locus_breaker_step logic (#679) [\@Daniel-Considine](mailto:113430683+Daniel-Considine@users.noreply.github.com) + + +- leaving only five ancestries in LD (#680) [\@Yakov](mailto:yt4@sanger.ac.uk) + + +- \[**finemapping**\] link configuration and step classes (#669) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- make extended_spark_conf an empty dict instead of None (#668) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- typo in `cs_lbf_thr` parameter name (#667) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- \[**SusieFineMapperStep**\] adding filtering of NANs in LD (#654) [\@Yakov](mailto:yt4@sanger.ac.uk) + + +- remove check merge conflict from pre-commit (#661) [\@David Ochoa](mailto:ochoa@ebi.ac.uk) + + - \[**L2GPrediction**\] schema validation (#642) [\@Szymon Szyszkowski](mailto:69353402+project-defiant@users.noreply.github.com) @@ -67,9 +169,32 @@ - \[**spark helpers**\] sorter function updated to avoid crash (#613) [\@Daniel Suveges](mailto:daniel.suveges@protonmail.com) +### ♻️ Refactor + + +- delete unnecessary config files (#647) [\@David Ochoa](mailto:ochoa@ebi.ac.uk) + ### 🏗 Build +- \[**deps-dev**\] bump ipython from 8.25.0 to 8.26.0 (#662) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- \[**deps-dev**\] bump google-cloud-dataproc from 5.9.3 to 5.10.1 (#684) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- \[**deps**\] bump skops from 0.9.0 to 0.10.0 (#673) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- \[**deps-dev**\] bump ruff from 0.4.10 to 0.5.1 (#674) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- \[**deps-dev**\] bump pydoclint from 0.4.1 to 0.5.1 (#658) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- remove python-semantic-release as project dependency (#650) [\@David Ochoa](mailto:ochoa@ebi.ac.uk) + + - \[**deps-dev**\] bump dbldatagen from 0.3.5 to 0.4.0 (#637) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) @@ -90,6 +215,25 @@ - \[**deps**\] use pandas[gcp, parquet] (#626) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) +### 👷‍♂️ Ci + + +- pre-commit update with pydoclint adjustments (#660) [\@David Ochoa](mailto:ochoa@ebi.ac.uk) + +### 🚀 Chore + + +- pre-commit autoupdate (#676) [\@pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]@users.noreply.github.com) + + +- \[**deps**\] bump python-semantic-release/python-semantic-release (#656) [\@dependabot[bot]](mailto:49699333+dependabot[bot]@users.noreply.github.com) + + +- remove the locus_radius parameter (#659) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + + +- enable Jupyter Notebook gateway for the Dataproc cluster (#651) [\@Kirill Tsukanov](mailto:tskir@users.noreply.github.com) + ## v1.3.0 (2024-05-17) ### ✨ Feature diff --git a/pyproject.toml b/pyproject.toml index 36617bafb..bfb31658d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "gentropy" # !! version is managed by semantic_release -version = "1.4.0" +version = "1.5.0" description = "Open Targets python framework for post-GWAS analysis" authors = ["Open Targets core team"] license = "Apache-2.0"