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chore: trigger release process #858

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

project-defiant and others added 30 commits July 25, 2024 11:26
@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]>
@project-defiant
fix: change config params to match new name (#721)
a5c96b9 
Co-authored-by: Szymon Szyszkowski <[email protected]>
@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
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
@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 @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
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
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
d0choa and others added 24 commits October 11, 2024 08:33
@d0choa
fix: write mode added to validation steps (#826)
c7c602a
@ireneisdoomed
feat(l2g): merge sQTL and tuQTL colocalisation features (#824)
e3d32ba 
* feat: merge tuQTL colocalisation results into sQTL features

* fix: add colocalisation neighbourhood features in the l2g default features list

* fix: minor bug
@DSuveges
fix: adding single point statistics to pics loci (#832)
fb6111d 
* fix: adding single point statistics to pics loci

* fix: patching field update logic

* refactor: simplifying the pics process slightly

* test: for lead statistics propagation

* refactor: udf as decorator

* fix: removing commented rows

* fix: reverting udf decorator - tests would fail otherwise
@DSuveges @d0choa
fix(find_overlap): missing right study type in output (#828)
9f446e8 
* fix: rightStudyType nulls removed

* test: improve testing of peak overlap function

* fix: overlap test

---------

Co-authored-by: David Ochoa <[email protected]>
@d0choa
feat: enhance variant index partitioning (#834)
c4520aa
@addramir @tskir
@Daniel-Considine @DSuveges
feat: adding new LD interface (#759)
e77abf4 
* feat: adding new LD interface

* fix: adding ld_index

* fix: adding csa

* fix: adding fucntion in init

* chore: temporary commit to build the Docker image

* chore: revert temporary GitHub Actions configuration

* chore: committing some restructuring

* chore: committing some changes

* chore: tweaking variable names

* fix: fixing locus index boundaries

* docs: documenting where gnomad ht were sourced from

* fix: adding afr ancestry to panUKBB interface

* fix: fixing arguments for susie_finemapper

* fix: removing unneeded code from panukbb ld

* feat: ancestry mapping

* fix: remove chr from chromosome column + some other bugs

* fix: removing duplicated variants & resolving flipped indels

* chore: committing changes

* Update src/gentropy/datasource/pan_ukbb_ld/ld.py

Co-authored-by: Daniel Suveges <[email protected]>

* Update src/gentropy/method/ld_matrix_interface.py

Co-authored-by: Daniel Suveges <[email protected]>

* Update colocalisation.py

* fix: rightStudyType nulls removed

* test: improve testing of peak overlap function

* fix: overlap test

* fix: changes suggested by ds review

* chore: removing unneeded variants.py

---------

Co-authored-by: Kirill Tsukanov <[email protected]>
Co-authored-by: Daniel Considine <[email protected]>
Co-authored-by: Daniel-Considine <[email protected]>
Co-authored-by: Daniel Suveges <[email protected]>
@ireneisdoomed
ci: configure java v8 (#840)
38d4cb5
@ireneisdoomed
fix(trainer): drop studyLocusId from training sets (#837)
d461e38
@ireneisdoomed
fix(l2g): remove custom session params + other fixes (#841)
6817aad 
* chore: delete l2g custom spark session

* fix: add neighbourhood features in `LocusToGeneFeatureMatrixConfig`

* fix(feature_matrix): use right config for default values
@dependabot @ireneisdoomed
build(deps-dev): bump pymdown-extensions from 10.10.1 to 10.11.2 (#815)
44f05c4 
Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.10.1 to 10.11.2.
- [Release notes](https://github.com/facelessuser/pymdown-extensions/releases)
- [Commits](facelessuser/pymdown-extensions@10.10.1...10.11.2)

---
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: Irene López Santiago <[email protected]>
@dependabot
build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.…
7fa85b2 
…4.1 (#818)

Bumps [mkdocs-git-committers-plugin-2](https://github.com/ojacques/mkdocs-git-committers-plugin-2) from 2.3.0 to 2.4.1.
- [Release notes](https://github.com/ojacques/mkdocs-git-committers-plugin-2/releases)
- [Commits](ojacques/mkdocs-git-committers-plugin-2@2.3.0...2.4.1)

---
updated-dependencies:
- dependency-name: mkdocs-git-committers-plugin-2
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
build(deps-dev): bump pyparsing from 3.1.2 to 3.2.0 (#836)
c50f660 
Bumps [pyparsing](https://github.com/pyparsing/pyparsing) from 3.1.2 to 3.2.0.
- [Release notes](https://github.com/pyparsing/pyparsing/releases)
- [Changelog](https://github.com/pyparsing/pyparsing/blob/master/CHANGES)
- [Commits](pyparsing/pyparsing@pyparsing_3.1.2...3.2.0)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
build(deps-dev): bump mkdocstrings-python from 1.11.1 to 1.12.1 (#842)
6da92ce 
Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.11.1 to 1.12.1.
- [Release notes](https://github.com/mkdocstrings/python/releases)
- [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md)
- [Commits](mkdocstrings/python@1.11.1...1.12.1)

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

Signed-off-by: dependabot[bot] <[email protected]>
@addramir @Daniel-Considine @project-defiant
chore: adding priors to coloc step (#830)
e34e0c9 
* chore: adding priors to step

* fix: making specifying the priors optional

* fix: revert optional

---------

Co-authored-by: Daniel Considine <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
@addramir @project-defiant
fix: fix ukbppp studindex (#839)
0a6d57b 
* fix: fix ukbppp studindex

* fix: review

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@d0choa @ireneisdoomed
fix: l2g fixes (#844)
84a7a0d 
* fix: unnecessary session object

* fix: circular dependency

* revert: broadcast

* fix: join

* feat(l2g): persist feature matrix in l2g training plan (#843)

* fix(gold_standard): remove extra columns in `build_feature_matrix`

* fix: uncomment filter overlaps

* feat(feature_matrix): `select_features` returns a new instance

* fix(overlaps): add missing columns in `_convert_to_square_matrix`

* fix(l2g): set `variant_index_path` as optional in step config

* fix(l2g): set `feature_matrix_path` as mandatory in step config

* fix(l2g): set `predictions_path` as optional in step config

* chore(feature_matrix): remove `features_list` default from step

* chore: fix `test_filter_unique_associations` toy data

* chore: fix `test_filter_unique_associations` toy data

---------

Co-authored-by: Irene López Santiago <[email protected]>
Co-authored-by: Irene López <[email protected]>
@addramir
chore: remove h4/h3 ratio (#829)
172cedf 
* chore: remove h3/h4 ratiob

* fix: remove it from schema

* fix: conftest

* fix: h3h4
@Daniel-Considine @addramir
fix: updating the susie_finemapper init (#846)
97a8873 
* fix: updating the susie_finemapper init

* fix: more fixes

* fix: v2

* fix: v2

---------

Co-authored-by: Yakov Tsepilov <[email protected]>
@project-defiant @SzymonSzyszkowski
feat(coloc): step refactoring (#845)
6a059d0 
* feat: prior fix

* refactor: coloc step

* fix: subclasss colocalisation methods on interface

* fix: failing coloc step

* chore(coloc): step tests

* chore: restore old script

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: project-defiant <[email protected]>
@ireneisdoomed
test: skip fetch_coordinates_from_rsids (#850)
9bbbc02
@DSuveges
fix(eqtl): deduplicating credible set loci (#849)
5cbf5ed 
* fix(eqtl): deduplicating credible set loci

* fix: removing
@addramir
chore: adding logging even when no CS in locus (#848)
3ef43a9 
* chore: adding logging even when no CS in locus

* fix: addin CS count to log
@ireneisdoomed
feat(l2g): limit colocalisation neighbourhood to protein coding genes (…
d33f66a 
…#847)

* feat(l2g): wip - limit colocalisation neighbourhood to protein coding genes

* feat: adjust logic in `common_neighbourhood_colocalisation_feature_logic`

* fix: correct logic in `common_neighbourhood_vep_feature_logic`

* chore: adjust tests
@addramir
fix: filter nan in CSs (#855)
9c52397 
* fix: filter nan in CSs

* fix: fix v1
@github-actions github-actions bot added the Chore label Oct 17, 2024
project-defiant and others added 3 commits October 18, 2024 09:53
@project-defiant
feat(susie_finemapper): allow for extraction of the log file from man…
d650a29 
…ifest (#859)

* feat(susie_finemapper): allow for extraction of the log file from manifest

* fix: add missing extension to the log file

* fix: row istead of column

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
@DSuveges @pre-commit-ci
chore(coloc): changing the content of numberColocalisingVariants fi…
333facb 
…eld (#857)

* chore(coloc): chaning the content of numberColocalisingVariants

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

* fix: adjuting for schema and tests

* fix(pics): ensuring locus has variantId

* fix: pics udf test

* fix: udf keys

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@d0choa
fix: susie credible sets with unknown confidence (#862)
f93a9d3
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9 participants
@project-defiant @Daniel-Considine @ireneisdoomed @addramir @DSuveges @tskir @d0choa @vivienho @Tobi1kenobi