…utation is False (opentargets#627)

* fix(susie_finemapper): fix in the FMer in case ss_imp=False

* fix: small fix in docs

* fix(SummaryStatistics): fix in sanity_filter

* fix: adding prune of inf values

* fix(dataset): removal of inf values from beta and stderr

* fix: fix in test and sanity filter

---------

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

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

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

…on (opentargets#628)

* feat(clumping): lower p-value significance threshold for clumping step
* feat(config): extract gwas_significance to config
* feat(config): synced p-value in association parsing

---------

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

* feat(airflow): drop finngen PICS results from etl
* feat(l2g): allow to publish feature matrix
* fix(types): typo in types
* chore(data_release): bumped release date

---------

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

…s#632)

Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.11.0 to 4.12.1.
- [Release notes](https://github.com/python/typing_extensions/releases)
- [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md)
- [Commits](python/typing_extensions@4.11.0...4.12.1)

---
updated-dependencies:
- dependency-name: typing-extensions
  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>
Co-authored-by: Szymon Szyszkowski <[email protected]>

)

Bumps [pep8-naming](https://github.com/PyCQA/pep8-naming) from 0.13.3 to 0.14.1.
- [Release notes](https://github.com/PyCQA/pep8-naming/releases)
- [Changelog](https://github.com/PyCQA/pep8-naming/blob/main/CHANGELOG.rst)
- [Commits](PyCQA/pep8-naming@0.13.3...0.14.1)

---
updated-dependencies:
- dependency-name: pep8-naming
  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>

…rgets#630)

* chore: prototype ingestion of sceqtls

* chore: use credible sets from ftp

* feat(study_index): rename tissuefromsourceid to biosamplefromsourceid to accommodate cell type ids

* chore: update output paths to final destination

)

* feat(spark-helpers): enforce schema of returned objects by other function

* fix: fixing docstring

* test: adding test for array sorter

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

* fix: addressing a typo

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

* fix: removing duplicated rows

* fix: addressing review comments

* fix: adding StructType hint

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* feat(schema): adding locus start/end position to the study locus schema

* feat(clumping) adding clumping logic + docs

* test(clumpin): adding tests for locus breaker method

* test(clumping): adding semantic tests for locus breaker clumping

* fix(config): reverting gwas significance threshold

Bumps [wandb](https://github.com/wandb/wandb) from 0.16.2 to 0.17.0.
- [Release notes](https://github.com/wandb/wandb/releases)
- [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md)
- [Commits](wandb/wandb@v0.16.2...v0.17.0)

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

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

Bumps [ipython](https://github.com/ipython/ipython) from 8.24.0 to 8.25.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.24.0...8.25.0)

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

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.4.0 to 1.5.0.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.4.0...1.5.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  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>

* feat: enable interface with gcp secrets manager

* chore: add google-cloud-secret-manager

* chore: merge

* feat: credible set quality filtering

* fix: purity threshold

Bumps [dbldatagen](https://github.com/databrickslabs/data-generator) from 0.3.5 to 0.4.0.
- [Release notes](https://github.com/databrickslabs/data-generator/releases)
- [Changelog](https://github.com/databrickslabs/dbldatagen/blob/master/CHANGELOG.md)
- [Commits](databrickslabs/dbldatagen@release/v0.3.5...release/v0.4.0)

---
updated-dependencies:
- dependency-name: dbldatagen
  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>

* feat(config): typos fix
* fix(config): moved ld_index dataset to static assets

---------

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

* feat(dataset): schema mismatch issue
* feat(L2GPrediction): schema unification
* fix: swapped data types

---------

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

…ets#645)

* feat(SusieFineMapperStep): add new fucntion that takes boundaries as input

* fix: typo in function

* refactor: remove ot_pics

* refactor: gwas_catalog_sumstat_preprocess config removed

* refactor: ot_finngen_studies removed

* refactor: ot_finngen_studies removed

* refactor: window_based_clumping cleanup

…ets#650)

* feat(ld_annotator): apply r2 threshold

* feat(ld_annotator): apply r2 threshold

* chore(ldannotator): change threshold to 0.5

…argets#644)

* feat(stydyLocus): adding new locus collection using boundaries

* fix: fix in test

* Update tests/gentropy/dataset/test_study_locus.py

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

* 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>

…targets#651)

Sometimes it is very useful to be able to spin up a Jupyter notebook on a Dataproc cluster which has access to Gentropy and all its configured environment. Previously, I already added the “enable_component_gateway” option; however, it doesn't really take any effect unless you also specify the list of components to enable, which is what I'm doing in this PR.

…ets#576)

* chore: checkpoint

* chore: checkpoint

* chore: deprecate spark evaluator

* chore: checkpoint

* chore: resolve conflicts with dev

* chore: resolve conflicts with dev

* chore(model): add parameters class property

* feat: add module to export model to hub

* refactor: make model agnostic of features list

* chore: add wandb to gitignore

* feat: download model from hub

* chore(model): adapt predict method

* feat(trainer): add hyperparameter tuning

* chore: deprecate trainer tests

* refactor: modularise step

* feat: download model from hub by default

* fix: convert omegaconfig defaults to python objects

* fix: write serialised model to disk and then upload to gcs

* fix(matrix): drop goldStandardSet when in predict mode

* chore: pass token to access private model

* chore: pass token to access private model

* fix: pass right schema

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

* chore: fix mypy issues

* build: remove xgboost

* chore: merge

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

* chore: address comments

)

* feat: implement UKB PPP (EUR) ingestion & harmonisation

* fix: correct module name for docs

* fix: definitely correct module name for docs

* test: update output of neglog_pvalue_to_mantissa_and_exponent

* fix: test syntax with <BLANKLINE>

* Update src/gentropy/datasource/ukb_ppp_eur/summary_stats.py

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

* fix: code review updates for docs and version

* fix: syntax for concat_ws

* style: list harmonisation steps in the docstring

* style: rename freq to MAF

* style: use concat_ws

* style: use two distinct parameters for study index and summary stats output paths

---------

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

Code inspection shows that it is not used anymore.

…entargets#656)

Bumps [python-semantic-release/python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 9.6.0 to 9.8.3.
- [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](python-semantic-release/python-semantic-release@v9.6.0...v9.8.3)

---
updated-dependencies:
- dependency-name: python-semantic-release/python-semantic-release
  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>
Co-authored-by: Kirill Tsukanov <[email protected]>

Bumps [pydoclint](https://github.com/jsh9/pydoclint) from 0.4.1 to 0.5.1.
- [Release notes](https://github.com/jsh9/pydoclint/releases)
- [Changelog](https://github.com/jsh9/pydoclint/blob/main/CHANGELOG.md)
- [Commits](jsh9/pydoclint@0.4.1...0.5.1)

---
updated-dependencies:
- dependency-name: pydoclint
  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]>

* fix: remove check merge conflict

* fix: remove line for now

…#654)

* feat(variant annotation): new variant annotation schema + logic to extract from VEP

* fix: typehints in function

* refactor(variant annotation): migrating methods to the new schema

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

* refactor(variant index): sorting out new variant index dataset

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

* feature(vep): adding predictors to vep transcript object

* fix(schema): fixing schema missing fields

* fix(schema): fixing schema missing fields

* fix(schema): fixing schema missing fields

* fix(schema): fixing schema missing fields

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

* fix(annotation): array union under condition

* fix: merging dbxref objects

* feat(variants): updating variants to make more robust

* feat: migrating methods to new variant index

* adjusting variant index methods

* some updates

* rename v2g to variant to gene

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

* adding test

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

* fix(precommit): json file needed to rename to jsonl

* fix(precommit): removing steps depending on old data model

* fix(coftest): fixing variant index mock generation

* fix: typo in package import

* fix: sorting out conftest

* refactor(gwas ingest): Updating GnomAD handling

* refactor(gnomad): variant annotation removed, changed to variant index, steps updated

* refactor: shuffling around gnomad logic

* fix: references in tests

* refactor: sorting out gnomad variant dag

* refactor: cleaning configs and tests

* docs(vep): adding datasource description

* test(vep): adding more test to the vep parser

* test(vep): tests are now running

* fix: removing version suffix from pyproject and airflow config

* fix: reverting DAGs - removing temporary modifications I added for testing

* fix: addressing reviewer comments

* refactor: fiddling with variant index annotation logic

* chore: addressing comments

* fix: variant cross-ref snake case

* fix: correcting join strategy

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fix: typo in cs_lbf_thr parameter name

* fix: removing two parameters

---------

Co-authored-by: Yakov Tsepilov <[email protected]>

…ets#668)

As it is, when the susie_finemapper step is triggered, nothing happens because the configuration class is not linked via _target_ to the step class. This commit addresses the problem

…ts#608)

* feat: custom dockerfile to run ensembl vep

* ci: automate vep image build and artifact registry

* chore: update airflow google operators (not required)

* feat: working version of google batch airflow vep job

* feat: working version of google batch airflow vep job

* feat(VEP): adding CADD plugin

* feat: local loftee file

* feat: working with input bucket full of input files

* feat: prevent writing html

* fix: minor adjustments to retry strategy

* feat(airflow): separating mounting points for input/output and cache

* fix: typo in airflow dag

* fix: pre-commit pain

* chore: rename airflow dag file

---------

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

* feat: locus_breaker_clumping

* fix: dosctring

* feat: _process_locus_breaker function

* feat: locus breaker clumping step

* fix: tidying parameters

* feat: option to remove MHC region

* fix: description for LocusBreakerClumpingStep

* fix: removing division of distance

* fix: adding new parameters for wbc distance separate from large_loci_size

* fix: resolving comments

* refactor: refactored code in process_locus_breaker_output

* fix: removing superfluous variable

* fix: persisting sumstats parquet to improve analysis plan

---------

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

* feat: add qc step

* fix: remove .df

* fix: fix in name

* fix: fix v3

* Update src/gentropy/sumstat_qc_step.py

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

* Update src/gentropy/sumstat_qc_step.py

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

* fix: optimisation of code

---------

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

…targets#677)

* feat: adding sanity filter to GWASCatalogSumstatsPreprocessStep

* fix: adding description

* fix: improving locus_breaker_step logic

* fix: updating susie_finemapper.py to deal with new I/O logic

* chore: removing unused log output path

…ts#682)

Two values were recently removed from the step. This brings config in alignment with these changes.

* feat: credible set quality control step

* feat: credible_set_qc.py step

* chore: updating genotropy/config.py to include CredibleSetQCConfig()

* chore: updated LocusBreakerClumpingConfig(StepConfig)

* fix: changing default configs in code

* feat: added jq to the docker image dependencies
* feat: added gsutil to gentropy image
* fix: added missing env vars

---------

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

…ntargets#672)

* chore: snapshot

* feat(StudyIndex): adding valiation methods

* feat(studyIdex): adding disease validation

* fix: typo in test

* fix: moving import under the type checking condition

* fix: some columns might need to be dropped

* fix(study index): preventing [null] arrays in the cohorts object

* fix(study index): more context is provided for disease normalisation

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.4.10 to 0.5.1.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.4.10...0.5.1)

---
updated-dependencies:
- dependency-name: ruff
  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]>

* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.5.1](astral-sh/ruff-pre-commit@v0.4.3...v0.5.1)
- [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](pre-commit/mirrors-mypy@v1.10.0...v1.10.1)
- [github.com/jsh9/pydoclint: 0.4.1 → 0.5.3](jsh9/pydoclint@0.4.1...0.5.3)

* chore: update lock

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
Co-authored-by: David Ochoa <[email protected]>

* build(deps): bump skops from 0.9.0 to 0.10.0

Bumps [skops](https://github.com/skops-dev/skops) from 0.9.0 to 0.10.0.
- [Release notes](https://github.com/skops-dev/skops/releases)
- [Changelog](https://github.com/skops-dev/skops/blob/main/docs/changes.rst)
- [Commits](skops-dev/skops@v0.9.0...v0.10)

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

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

* fix: update `trusted` in load to avoid typeerror

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Irene López <[email protected]>

…ntargets#684)

Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.9.3 to 5.10.1.
- [Release notes](https://github.com/googleapis/google-cloud-python/releases)
- [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md)
- [Commits](googleapis/google-cloud-python@google-cloud-dataproc-v5.9.3...google-cloud-dataproc-v5.10.1)

---
updated-dependencies:
- dependency-name: google-cloud-dataproc
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

…pentargets#665)

* feat(variant index): calculate hash as variant id for variants with long alleles

* fix: adjusting hashing method

* fix: painful iteration to get gnomad running with the new schema + fine tune with variant index

* chore: fixing variant index step

* fix: reverting changes

* fix: minor updates

* feat(variant index): null values of array columns are enforced to be replaced with empty arrays

* fix: array union vs coalese fix

* fix(variant index): annotation logic made more robust

* fix: addressing review comments

* fix: renaming helper function for better readability

* fix(liftover): fixing docstring

Bumps [ipython](https://github.com/ipython/ipython) from 8.25.0 to 8.26.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.25.0...8.26.0)

---
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: David Ochoa <[email protected]>
Co-authored-by: David Ochoa <[email protected]>

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

added tags to the artifact github actions triggers, so the
images produced by gentropy will be versionned by tag name

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

* fix: moving hl.init

* fix: missed a hl.init

* fix: removing the hl.init from notebooks

…nd Finngen (opentargets#693)

* chore: remove finngen prefix from studyIds

* feat(eqtl_catalogue): changes from #3357

* fix: update study table

* fix: update _identify_study_type example

…taset (opentargets#686)

* feat(studyLocus validation): adding validation logic to studyLocus dataset

* feat: making QC more granular

* Update src/gentropy/dataset/study_locus.py

Co-authored-by: David Ochoa <[email protected]>

---------

Co-authored-by: David Ochoa <[email protected]>

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

* feat(session): replace `read_parquet` with more general `load_data`

* chore: checkpoint

* feat(variant_index): overwrite variant id for longer variants

* feat(variant_index): copy vcf from local filesystem to gcs

* build: remove request dependency for urllib

* feat(variant idx): integrate all components into dag

* test: fix `fetch_coordinates` typo

* Update src/airflow/dags/common_airflow.py

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

* refactor: move fetch_coordinates_from_rsids to independent module

* fix: update fetch_coordinates_from_rsids example

---------

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.2](astral-sh/ruff-pre-commit@v0.5.1...v0.5.2)
- [github.com/jsh9/pydoclint: 0.5.3 → 0.5.4](jsh9/pydoclint@0.5.3...0.5.4)

fix(variants): explode loci to generate list of variants + tests

…ate-config

chore: pre-commit autoupdate

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

…s-for-gentropy

…of-the-docker-release-process-for-gentropy

ci: Refactoring of the docker release process for gentropy

…ping-typo

fix(finemapping): typo in "elapsed_time"

…push

feat: allow image push

…ets#706)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.2.2 to 8.3.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.2.2...8.3.1)

---
updated-dependencies:
- dependency-name: pytest
  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>

Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.16.1 to 0.17.0.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.16.1...0.17.0)

---
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>

Bumps [mypy](https://github.com/python/mypy) from 1.10.0 to 1.11.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.10.0...v1.11)

---
updated-dependencies:
- dependency-name: mypy
  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>

…li (opentargets#716)

* feat: expose summary statistics qc to hydra cli

* feat: expose locus breaker clumping step

---------

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

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

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>

…gets#720)

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]>

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>

…ntargets#717)

* 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

* fix: updating config paths and fine-mapping methods

* Update ot_locus_to_gene_train.yaml