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chore: trigger release process #718

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⚠️ This PR requires a MERGE COMMIT (Don't squash!)

@project-defiant
feat: expose summary statistics qc and locus breaker steps to hydra c…
ea80fbf 
…li (#716)

* feat: expose summary statistics qc to hydra cli

* feat: expose locus breaker clumping step

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@github-actions github-actions bot added documentation Improvements or additions to documentation size-S Step Chore labels Jul 29, 2024
pre-commit-ci bot and others added 2 commits July 30, 2024 09:33
@pre-commit-ci
chore: pre-commit autoupdate (#715)
897ae12 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.5](astral-sh/ruff-pre-commit@v0.5.2...v0.5.5)
- [github.com/pre-commit/mirrors-mypy: v1.10.1 → v1.11.0](pre-commit/mirrors-mypy@v1.10.1...v1.11.0)
- [github.com/jsh9/pydoclint: 0.5.4 → 0.5.6](jsh9/pydoclint@0.5.4...0.5.6)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@dependabot @project-defiant
build(deps-dev): bump pymdown-extensions from 10.8.1 to 10.9 (#720)
397f1e9 
Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.8.1 to 10.9.
- [Release notes](https://github.com/facelessuser/pymdown-extensions/releases)
- [Commits](facelessuser/pymdown-extensions@10.8.1...10.9)

---
updated-dependencies:
- dependency-name: pymdown-extensions
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
dependabot bot and others added 2 commits August 8, 2024 09:47
@dependabot
build(deps-dev): bump deptry from 0.17.0 to 0.18.0 (#723)
0b9af70 
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.17.0 to 0.18.0.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.17.0...0.18.0)

---
updated-dependencies:
- dependency-name: deptry
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@Daniel-Considine
feat: notebook for locus breaker and susie finemapping benchmark (#717)
ae734a8 
* feat: notebook for locus breaker and susie finemapping benchmark

* fix: won't pass tests with matplotlib imported

* feat: ukb_ppp_fm benchmark notebook

* fix: check for nulls as well as nans

* fix: removing matplotlib

* fix: update notebooks

* chore: re-run ukb ppp notebook

* chore: rerun notebook
@github-actions github-actions bot added size-XL and removed size-S labels Aug 8, 2024
Daniel-Considine and others added 4 commits August 8, 2024 15:37
@Daniel-Considine
fix: updating config paths and fine-mapping methods (#725)
5b5b408 
* fix: updating config paths and fine-mapping methods

* Update ot_locus_to_gene_train.yaml
@Daniel-Considine
docs: macos fix for some functions (#729)
e45f295 
* docs: macos fix for some functions

* docs: formatting
@dependabot @d0choa @Daniel-Considine
build(deps-dev): bump ruff from 0.5.1 to 0.6.1 (#732)
f49a5c5 
* build(deps-dev): bump ruff from 0.5.1 to 0.6.1

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.5.1 to 0.6.1.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.5.1...0.6.1)

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

Signed-off-by: dependabot[bot] <[email protected]>

* fix: linting issues associated with ruff 0.6

* chore: fixing imports for notebooks

* chore: removing old notebook

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
Co-authored-by: Daniel Considine <[email protected]>
@pre-commit-ci @d0choa
chore: pre-commit autoupdate (#724)
4169b81 
* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.5 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.5...v0.6.1)
- [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.1](pre-commit/mirrors-mypy@v1.11.0...v1.11.1)

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
dependabot bot and others added 4 commits August 22, 2024 14:07
@dependabot @d0choa
build(deps-dev): bump deptry from 0.18.0 to 0.19.1 (#728)
02b006d 
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.18.0 to 0.19.1.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.18.0...0.19.1)

---
updated-dependencies:
- dependency-name: deptry
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
@dependabot
build(deps-dev): bump lxml from 5.2.2 to 5.3.0 (#727)
5984de9 
Bumps [lxml](https://github.com/lxml/lxml) from 5.2.2 to 5.3.0.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](lxml/lxml@lxml-5.2.2...lxml-5.3.0)

---
updated-dependencies:
- dependency-name: lxml
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot @project-defiant @d0choa
build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0 (#719)
4db64a3 
* build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0

Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.7.1 to 3.8.0.
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v3.7.1...v3.8.0)

---
updated-dependencies:
- dependency-name: pre-commit
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix: update lock

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: David Ochoa <[email protected]>
Co-authored-by: David Ochoa <[email protected]>
@ireneisdoomed @pre-commit-ci @project-defiant
feat(variant_index): changes for a successful run (#735)
dc8c9dc 
* feat: update variant sources for variant idx and drop rsid mapping

* chore: remove variant_index step from etl dag

* chore: move gnomad annotation from dev to static assets

* chore: change gentropy docker image

* feat(convert_to_vcf): write data partitioned

* feat: add vcf merging step

* chore: assert merge is succesful

* fix: remove non canonical variants from vcfs

* chore: pass vcf types to merging rule

* fix: match vep parser order of columns to variant index schema

* fix: ditch `assign_variant_id` in favour of `hash_long_variant_ids`

* chore: update `test_as_vcf_df_without_variant_id`

* fix: correct test mock data

* chore: pre-commit auto fixes [...]

* chore: merge from dev

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
project-defiant and others added 4 commits August 28, 2024 10:18
@project-defiant
fix: update cluster creation command (#739)
348b6f0 
Co-authored-by: Szymon Szyszkowski <[email protected]>
@project-defiant
fix: revert recursiveFileLookup to False (#738)
b6746fb 
Co-authored-by: Szymon Szyszkowski <[email protected]>
@project-defiant @pre-commit-ci @DSuveges
feat: Finngen r11 ingestion (#733)
cf1ec24 
* feat: finngen r11 study index paths

* feat: simplification of finngen susie finemapping ingestion

* feat: efos in finngne study index

* docs: updated docstring

* fix: pass spark_session not gentropy session to step

* fix: read uploaded file  requires file:///

* fix: parallelize csv from url

* fix: typo in docstring

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Daniel Suveges <[email protected]>
@Daniel-Considine
fix: using h4 instead of log2(h4/h3) (#740)
2612aa7
addramir and others added 26 commits September 3, 2024 11:44
@addramir
fix: adding carma_tau parameter to susie_finemapper (#743)
93a6e60 
* fix: adding carma_tau parameter to susie_finemapper

* fix: changing default

* fix: defaults
@DSuveges @d0choa
@pre-commit-ci @project-defiant
feat: logic and airflow pipeline for validation (#730)
bb8558c 
* refactor: generalised validation logic

* refactor: generalised validation logic

* fix(airflow): fine-tuning DAG for data validation

* fix(validation): study locus uniqueness fixed

* feat: add invalid/valid dataset generation in validation steps/dag (#734)

* fix: does not belong in this PR

* refactor: to be moved to orchestration repo

* docs: respective docs pages for the steps

* docs: ammend docstrings

* revert: maintain dag for now but it should be removed eventually

* feat: validate study_locus dataset to produce valid or invalid df

* feat: adjust DAG to parametrise dataset validation

* fix: duplicated row

* feat: increase abstraction of Dataset validation of rows

* docs: increase clarity of what the function does

* fix: error message

* revert: unintended change

* test: testing dataset filtering by quality flag

---------

Co-authored-by: DSuveges <[email protected]>

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: David Ochoa <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
@DSuveges @project-defiant
feat(variant index): improved data structure (#710)
1a7b0d7 
* feat(variant index): upating schema and logic

* feat(variant index): vep transcript annotation improved with consequence score + transcript index

* refactor: removed hardcoded schema definition from parser

* fix(test): fixing mock variant index

* fix: schema extraction fixed

* fix: doctest issue resolved

* fix: updating vep command in the DAG

* fix: removing un-used sequence ontology terms

* fix: adding example to sorter method + changing variable names

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@project-defiant
fix: remove finngen prefix from credible set (#746)
3ea47a9
@project-defiant @ireneisdoomed
fix(finngen_r11): preserve all studyIds (#747)
12ff35b 
* fix(finngen_r11): preserve all studyIds

Preserve all studyIds, even if EFO mapping is missing, so mapping
between studyIndex and StudyLocus is by studyId column is accurate.

* fix: typo in docstring

Co-authored-by: Irene López Santiago <[email protected]>

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Irene López Santiago <[email protected]>
@Daniel-Considine @project-defiant
feat: adding finemapping method to studylocusid hash (#744)
15a058e 
* feat: adding finemapping method to studylocusid hash

* chore: updating function in needed files

* test: update doc test

* fix: mistakes

* fix: tidying logic

* chore: adding studyLocusId recalculation to pics finemapping method

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@dependabot @project-defiant
build(deps-dev): bump ipython from 8.26.0 to 8.27.0 (#741)
3c1e81a 
Bumps [ipython](https://github.com/ipython/ipython) from 8.26.0 to 8.27.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.26.0...8.27.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
@dependabot @project-defiant
build(deps-dev): bump deptry from 0.19.1 to 0.20.0 (#742)
151b4ec 
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.19.1 to 0.20.0.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.19.1...0.20.0)

---
updated-dependencies:
- dependency-name: deptry
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
@project-defiant
fix: validation name mapping (#753)
0b216f6 
* fix: use mapping instead of enum values in valid_rows

* fix: typos

* fix: swap valid and invalid paths

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@addramir @project-defiant
fix: removing old functions (#752)
010c881 
Co-authored-by: Szymon Szyszkowski <[email protected]>
@tskir @project-defiant
refactor: generalise per-chromosome processing (#754)
feb9cad 
* refactor: move VA preparation logic into a separate module

* refactor: generalise per-chromosome summary stats ingestion

* Update src/gentropy/common/per_chromosome.py

Co-authored-by: Szymon Szyszkowski <[email protected]>

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@tskir
refactor: generalise the harmonisation pipeline (#755)
d10cc20 
* refactor: move harmonisation into a separate module

* refactor: make column names configurable

* feat: make INFO and A1FREQ columns optional

* docs: expand comments on tmp_variant_annotation_path and variant types
@tskir
feat: ingest FinnGen UKB meta-analysis data (#756)
a49ae9a 
* feat: implement FinnGen UKB meta-analysis ingestion and harmonisation

* chore: remove ot_finngen_ukb_meta.yaml

* chore: remove raw_study_index_path to raw_study_index_path_from_tsv

* fix: use session.write_mode

* style: rename class to FinngenUkbMetaIngestionStep
@DSuveges
feat(validation): adding credible set variant validation (#757)
6469bf5 
* feat(validation): adding logic to validate credible sets against variant index

* fix: tidying docstrings
@project-defiant
feat: drop airflow orchestration layer from gentropy (#758)
d3435bb 
* refactor: drop gentropy config

* feat(airflow): removal of airflow orchestration

BREAKING CHANGE: see https://github.com/opentargets/orchestration

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@tskir
fix: multiple fixes after debugging and test runs (#760)
d6364f8
@dependabot
build(deps-dev): bump mkdocstrings-python from 1.10.5 to 1.11.1 (#749)
34aaaf5
@dependabot
build(deps): bump wandb from 0.17.2 to 0.18.0 (#763)
2e0e326 
Bumps [wandb](https://github.com/wandb/wandb) from 0.17.2 to 0.18.0.
- [Release notes](https://github.com/wandb/wandb/releases)
- [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md)
- [Commits](wandb/wandb@v0.17.2...v0.18.0)

---
updated-dependencies:
- dependency-name: wandb
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@d0choa @project-defiant
fix: prevent multiple credible filters to override spark plan (#766)
6ede736 
* fix: prevent multiple filters to override spark plan

* feat: mhc quality control flag

* fix: prevent multiple filters to override spark plan

* Revert "fix: prevent multiple filters to override spark plan"

This reverts commit a358781.

* revert: wrong commit

* fix: missing changes due to git chaos

* chore: merge dev toml, update lock

* chore: update lock after upgrading poetry to 1.8.3 v 2

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@d0choa
feat: flag MHC credible sets based on lead (#767)
8c4421a 
* fix: prevent multiple filters to override spark plan

* feat: mhc quality control flag

* fix: typo

* docs: genomic region added to docs

* docs: info added to common index (and title)

* docs: fix paths

* Update src/gentropy/study_locus_validation.py

* fix: remove unnecessary comment

---------
Closes opentargets/issues#3469
Co-authored-by: Szymon Szyszkowski <[email protected]>
@vivienho
fix: add condition to eQTL study index and schema (#770)
d84d43b
@DSuveges
fix(effect harmonisation): addressing beta harmonisation bug (#762)
c3651b7 
* fix: turning OR to beta harmonisation on for GWAS Catalog

* fix(ingestion): addressing beta harmonisation bug

* fix(ingestion): addressing beta harmonisation bug

* test: adding test for effect harmonisation

* test: adding doctests for beta harmonisation

* fix: fixing value checking bug: effect value needs to be cast to double type

* fix: typos in gwas ingestion script
@tskir
perf: quickly build a Docker image for every branch (#773)
c292e84 
* perf: cache Docker image layers

* chore: temporary add branch to test

* perf: separate AMD and ARM builds for gentropy

* perf: temporarily test only VEP image separately

* perf: test ARM/AMD gentropy/VEP separately

* perf: introduce quick build for all commits

* perf: quick build for all tags

* fix: use correct syntax for tags

* fix: revert accidental changes for the VEP step
@d0choa
feat: flag all top-hits from GWAS catalog curation (#775)
785dad0
@d0choa @project-defiant
docs: fix broken refs (#768)
018defa 
Co-authored-by: Szymon Szyszkowski <[email protected]>
@d0choa @DSuveges
feat: flag PICS top hits in studies with credset sumstats (#777)
ad3f503 
Co-authored-by: Daniel Suveges <[email protected]>
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@project-defiant @Daniel-Considine @ireneisdoomed @addramir @DSuveges @tskir @d0choa @vivienho