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chore: trigger release process #1

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

dependabot bot and others added 22 commits February 26, 2024 09:31
Bumps [ipython](https://github.com/ipython/ipython) from 8.21.0 to 8.22.1.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.21.0...8.22.1)

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

Signed-off-by: dependabot[bot] <[email protected]>
…ython-8.22.1

build(deps-dev): bump ipython from 8.21.0 to 8.22.1
…#506)

Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.9.0 to 4.10.0.
- [Release notes](https://github.com/python/typing_extensions/releases)
- [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md)
- [Commits](https://github.com/python/typing_extensions/commits)

---
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>
…3.0 (opentargets#505)

Bumps [mkdocs-git-committers-plugin-2](https://github.com/ojacques/mkdocs-git-committers-plugin-2) from 2.2.3 to 2.3.0.
- [Release notes](https://github.com/ojacques/mkdocs-git-committers-plugin-2/releases)
- [Commits](ojacques/mkdocs-git-committers-plugin-2@2.2.3...2.3.0)

---
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]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* feat: include single snp overlaps in coloc calcs

* chore: added unit test for coloc

* feat: include single snp overlaps in coloc calcs

* chore: added unit test for coloc

* fix: check for differences in test results

* fix: revert changes to single snp coloc tests for other pr

* fix: revert single snp change

* chore: restructure test folder

* fix: compare differences in results rather than exact match

* chore: test description
…ng results (opentargets#514)

* feat: dataflow decompress prototype (opentargets#501)

* chore: commit susie results gist

* feat(study_index): add `tissueFromSourceId` to schema and make `traitFromSource` nullable

* fix: bug and linting fixes in new eqtl ingestion step

* perf: config bugfixes and performance improvements

* perf: remove data persistance to avoid executor failure

* perf: load susie results for studies of interest only

* perf: collect locus for leads only and optimise partitioning cols

* feat: parametrise methods to include

* feat: run full dag

* test: add tests

* fix: reorder test inputs

* docs: update eqtl catalogue docs

* fix: correct typos in tests docstrings

* fix: correct typos in tests docstrings

* test: fix

* revert: revert unwanted change in studyId definition

* test: final fix

---------

Co-authored-by: David Ochoa <[email protected]>
* ci: pull request labeler

* fix: adjust capitalisation

* refactor: add size to make clear what the letters are about

* feat: trigger on issues

* revert: mergeable does not seem to work
* ci: pull request template

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* Update .github/pull_request_template.md

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

* refactor: il-suggestion

---------

Co-authored-by: Irene López <[email protected]>
* fix: adding missing gentropy

* fix: allowing for scope to be there

* feat: step label added
* feat(CARMA): adding time limited CARMA

* feat: correct the function

* feat(CARMA): added tests

* chore: small fix of varaible types

* chore: fix of test descriptions
…apping results (opentargets#518)

* feat: dataflow decompress prototype (opentargets#501)

* chore: commit susie results gist

* feat(study_index): add `tissueFromSourceId` to schema and make `traitFromSource` nullable

* fix: bug and linting fixes in new eqtl ingestion step

* perf: config bugfixes and performance improvements

* perf: remove data persistance to avoid executor failure

* perf: load susie results for studies of interest only

* perf: collect locus for leads only and optimise partitioning cols

* feat: parametrise methods to include

* feat: run full dag

* test: add tests

* fix: reorder test inputs

* docs: update eqtl catalogue docs

* fix: correct typos in tests docstrings

* refactor: change mqtl_quantification_methods to mqtl_quantification_methods_blacklist

* feat: studyId is based on measured trait and not on gene

* feat: credible set lead is the variant with highest pip

* feat(studies): change logic in _identify_study_type to extract qtl type based on quantization method

* refactor: externalise reading logic to source classes

* chore: add mqtl_quantification_methods_blacklist to yaml config

* docs: update docs

* fix(dag): pass bucket name to GCSDeleteBucketOperator

* refactor(coloc): move get_logsum function to common utils

* feat(studylocus): add calculate_credible_set_log10bf and use it for eqtlcat credible sets

* fix: credible sets dataset is too large and cant be broadcasted

* fix(dag): use GCSDeleteObjectsOperator instead of GCSDeleteBucketOperator

* fix: correct typo

* fix: correct typo
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.1 to 8.1.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.0.1...8.1.0)

---
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>
Co-authored-by: David Ochoa <[email protected]>
* chore: update ruff pre-commit and rules

* refactor: to address None type and remove typeignore

---------

Co-authored-by: Daniel Suveges <[email protected]>
* fix: pr labeler patterns

* fix: change bug for fix

* revert: as per reviewers will
* ci: precommit poetry checks for toml and lock

* test: add poetry lock to ensure this is working

* fix: specify python version in pre-commit config

* fix: skip poetry lock in remote
* feat: include single snp overlaps in coloc calcs

* chore: added unit test for coloc

* feat: include single snp overlaps in coloc calcs

* chore: added unit test for coloc

* fix: check for differences in test results

* fix: revert changes to single snp coloc tests for other pr

* fix: revert single snp change

* chore: restructure test folder

* fix: compare differences in results rather than exact match

* chore: test description

* fix: allow for coloc when only one snp is overlapping

* chore: include tests for h0 and h1/2

* fix: added pseudocount variable to coloc

* fix: pseudocount as a Coloc attribute

---------

Co-authored-by: David Ochoa <[email protected]>
DSuveges and others added 7 commits March 7, 2024 23:36
…nges

chore(l2g): update inclusion features list with newer QTLs
…apping results (opentargets#518)

* feat: dataflow decompress prototype (opentargets#501)

* chore: commit susie results gist

* feat(study_index): add `tissueFromSourceId` to schema and make `traitFromSource` nullable

* fix: bug and linting fixes in new eqtl ingestion step

* perf: config bugfixes and performance improvements

* perf: remove data persistance to avoid executor failure

* perf: load susie results for studies of interest only

* perf: collect locus for leads only and optimise partitioning cols

* feat: parametrise methods to include

* feat: run full dag

* test: add tests

* fix: reorder test inputs

* docs: update eqtl catalogue docs

* fix: correct typos in tests docstrings

* refactor: change mqtl_quantification_methods to mqtl_quantification_methods_blacklist

* feat: studyId is based on measured trait and not on gene

* feat: credible set lead is the variant with highest pip

* feat(studies): change logic in _identify_study_type to extract qtl type based on quantization method

* refactor: externalise reading logic to source classes

* chore: add mqtl_quantification_methods_blacklist to yaml config

* docs: update docs

* fix(dag): pass bucket name to GCSDeleteBucketOperator

* refactor(coloc): move get_logsum function to common utils

* feat(studylocus): add calculate_credible_set_log10bf and use it for eqtlcat credible sets

* fix: credible sets dataset is too large and cant be broadcasted

* fix(dag): use GCSDeleteObjectsOperator instead of GCSDeleteBucketOperator

* fix: correct typo

* fix: correct typo
DSuveges and others added 21 commits March 14, 2024 10:23
…L_DAG

feat(dag): add data transfer task group for release process
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.12.0 to 0.14.0.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.12.0...0.14.0)

---
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>
…rgets#549)

Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.8.0 to 1.9.0.
- [Release notes](https://github.com/mkdocstrings/python/releases)
- [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md)
- [Commits](mkdocstrings/python@1.8.0...1.9.0)

---
updated-dependencies:
- dependency-name: mkdocstrings-python
  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>
* refactor(l2g): select features of interest in data outside trainer

* chore(l2g): log annotated gold standards in w&b

* fix: update test_train
* refactor(l2g): streamline coloc feature factory

* perf(l2g): make joins in _get_vep_features lighter

* fix(l2g): use weighted scores for _get_vep_features

* refactor(l2g): minor improvements

* perf(l2g): adapt session to set partition number for shuffling to 800

---------

Co-authored-by: Daniel Suveges <[email protected]>
* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3)
- [github.com/python-poetry/poetry: 1.8.2 → 1.8.0](python-poetry/poetry@1.8.2...1.8.0)

* fix: poetry lock adjustments

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
* refactor(l2g): streamline coloc feature factory

* perf(l2g): make joins in _get_vep_features lighter

* fix(l2g): use weighted scores for _get_vep_features

* refactor(l2g): minor improvements

* perf(l2g): adapt session to set partition number for shuffling to 800

* feat(l2g): distance features based on weighted score

* docs: update docs

* refactor(l2g): select features of interest in data outside trainer

* chore(l2g): log annotated gold standards in w&b

* fix: update test_train

* fix(l2g): typo in _get_tss_distance_features with no consequences
* perf: refactored window based clumping

* fix: gwas catalog clump step adjusted

* fix: broadcast logic

* revert: coalesce instruction

* fix: add alias

* docs: enhance docs

* test: accidentally removed test

* test: rescue missing test

* chore: remove unused step

* refactor: increased modularisation

* feat: restructure data model

* test: structural test for annotate function

* fix: prevent locus column could be duplicated

* chore: up-to-date with pre-commit
* feat: notebook to run qc metrics each release

* feat: added additional checks as discussed

* feat: additional checks

* fix: remove matplotlib from dependencies

* fix: address comments
* fix: pytest for coloc unit tests

* fix: removed unused coloc tests

* test(coloc): add coloc semantic test (opentargets#538)

* test(coloc): define fixtures and parametrise coloc tests

* test(coloc): compare dfs with assert_frame_equal

* fix: remove unused threshold variable

---------

Co-authored-by: Irene López <[email protected]>
Co-authored-by: David Ochoa <[email protected]>
opentargets#553)

* perf(l2g): rewrite ColocalisationFactory._get_max_coloc_per_credible_set

* perf(l2g): more elegant rewrite ColocalisationFactory._get_max_coloc_per_credible_set

* chore: adapt tests to changes

* refactor: import colocalisation attributes
…#556)

* fix(coloc): fillna doesnt fill nested data

* test(coloc): added test_coloc_no_logbf (semantic)

* revert(ecaviar): revert accidental changes
* feat: add the step class for fine-mapping

* test: adding test for susie to studylocus converter

* chore: fix the class description

* chore: answering comments

---------

Co-authored-by: Daniel Suveges <[email protected]>
…ets#463)

* test: adding test for pairwiseLD

* feat: adding ld matrix extraction

* chore: merge from dev

* feat: index and block matrix extraction for studyLocus

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* chore: updating some test files to gentropy

* chore: updating tests

* chore: updating pairwise_ld_schema for tests

* chore: updating pairwise_ld tests

* chore: fix ld_pairwise tests

* chore: fix pairwise_ld tests

* chore: fix tests

* chore: fix tests

* chore: fixing typing for tests

* chore: fixing tests

* chore: fixing ld tests

* Update src/gentropy/dataset/study_index.py

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

* feat: moving functions to their appropriate locations and improving logic

* fix: optimise conversion of BM to NumPy

* feat: updating get_locus_index to allow for just chromosome and position inputs

* fix: suggested changes

* Update study_index.py

* fix: changes to datasource/gnomad/ld.py

* feat: updated method for ld_index extraction

* fix: sorting idx in hail

---------

Co-authored-by: Daniel Suveges <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* test: adding test for pairwiseLD

* feat: adding ld matrix extraction

* chore: merge from dev

* feat: index and block matrix extraction for studyLocus

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* chore: updating some test files to gentropy

* chore: updating tests

* chore: updating pairwise_ld_schema for tests

* chore: updating pairwise_ld tests

* chore: fix ld_pairwise tests

* chore: fix pairwise_ld tests

* chore: fix tests

* chore: fix tests

* chore: fixing typing for tests

* chore: fixing tests

* chore: fixing ld tests

* Update src/gentropy/dataset/study_index.py

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

* feat: moving functions to their appropriate locations and improving logic

* fix: optimise conversion of BM to NumPy

* feat: updating get_locus_index to allow for just chromosome and position inputs

* fix: suggested changes

* Update study_index.py

* fix: changes to datasource/gnomad/ld.py

* feat: add the draft of finemapper fucntion

* feat: updated method for ld_index extraction

* fix: changing input

* fix: adding fillter by studyId

* fix: sorting idx in hail

* feat: add fine-mapping of one study_locus_row

* fix: small fix in majpop

* fix: small fixes in function

* fix: using more spark before converting to pandas

* fix: fix in test

---------

Co-authored-by: Daniel Suveges <[email protected]>
Co-authored-by: Daniel Considine <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Daniel-Considine <[email protected]>
* feat: susie_finemapper_ss_gathered()

* fix: docstring updates
* feat: add fm step with carma and sumstat imputation

* fix: adding log

* fix: fixing carma

* fix: resolving conflict

* fix: resolve conflicts with dev v2

* fix: siliencing FutureWarning in Carma
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