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chore: trigger release process #595

Merged
merged 95 commits into from
May 17, 2024
Merged

chore: trigger release process #595

merged 95 commits into from
May 17, 2024

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

DSuveges and others added 30 commits February 27, 2024 17:00
@DSuveges
chore: small updates to accomodate GWAS Catalog for feb release
ba956c7
@DSuveges
fix: updating cohort parser to new GWAS Catalog format
655a5f3
@DSuveges
fix: updating study index generation from gwas flat files
d4dd97e
@ireneisdoomed
Merge branch 'dev' into ds_gwas_update
97bf3f0
@DSuveges
chore: resolve merge commit
c2e3e91
@DSuveges
chore: bumping for 24.03 release
9b64cf8
@DSuveges
fix: reverting some changes
9ee712a
@ireneisdoomed
chore: add tuqtl features to L2Gfeaturematrix schema
6e62c4b
@ireneisdoomed
chore: add sqtl, tuqtl, pqtl features to l2g inclusion list
fda650b
@DSuveges
Merge pull request #529 from opentargets/il-l2g-config-changes
4dcf542 
chore(l2g): update inclusion features list with newer QTLs
@ireneisdoomed @DSuveges
feat: extract credible sets and studies from all eQTL Catalogue finem…
02dc66f 
…apping results (#518)

* feat: dataflow decompress prototype (#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
fix: fixing merge conflict
0b0db5e
@d0choa @DSuveges
revert: make setup dev not to update pre-commits (#524)
8f91f3a
@d0choa @DSuveges
chore: update ruff pre-commit and rules (#522)
af16331 
* chore: update ruff pre-commit and rules

* refactor: to address None type and remove typeignore

---------

Co-authored-by: Daniel Suveges <[email protected]>
@d0choa @DSuveges
fix: pr labeller patterns (#523)
f6e0ad0 
* fix: pr labeler patterns

* fix: change bug for fix

* revert: as per reviewers will
@DSuveges
fix: fixing merge conflict
8257ea3
@xyg123 @d0choa @DSuveges
feat(coloc): single SNP case (#511)
d70a8ef 
* 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
fix: sorting out merge conflicts
4d72946
@DSuveges
fix: removing fsspec from dependencies
45750c5
@DSuveges
Merge branch 'dev' into ds_gwas_update
4da9462
@DSuveges
fix: fixing lock file
50af4d2
@DSuveges
fix: updating gwas catalog test files following schema changes
a7c919a
@DSuveges
Merge pull request #507 from opentargets/ds_gwas_update
fa938fd 
chore: small updates to accomodate GWAS Catalog for feb release
@dependabot
build(deps-dev): bump ruff from 0.2.0 to 0.3.2 (#531)
8f0c6d5 
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.2.0 to 0.3.2.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.2.0...v0.3.2)

---
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>
@dependabot
build(deps-dev): bump mypy from 1.8.0 to 1.9.0 (#532)
317a09c 
Bumps [mypy](https://github.com/python/mypy) from 1.8.0 to 1.9.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.8.0...1.9.0)

---
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>
@louwenjjr
fix: pin version of commitlint (#533)
5cd4602
@DSuveges
Merge branch 'dev' into ds_3238_update_ETL_DAG
f12d4ea
@louwenjjr
fix: read function for thurman data to include first line (#534)
06c6117
@addramir @ireneisdoomed
feat(sumstat imputation): adding class for sumstat imputation (#490)
43dd479 
* feat(sumstat imputation): adding class for sumstat imputation

* feat: added test

* docs: update summary statistics imputation description

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update docs/python_api/methods/sumstat_imputation.md

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* fix: changes according to comment

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* Update src/gentropy/method/sumstat_imputation.py

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

* fix: fixing tests

---------

Co-authored-by: Irene López <[email protected]>
@DSuveges
Merge branch 'dev' into ds_3238_update_ETL_DAG
088895a
dependabot bot and others added 9 commits April 29, 2024 16:34
@dependabot @d0choa
build(deps-dev): bump deptry from 0.14.0 to 0.16.1 (#570)
d163215 
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.14.0 to 0.16.1.
- [Release notes](https://github.com/fpgmaas/deptry/releases)
- [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md)
- [Commits](fpgmaas/deptry@0.14.0...0.16.1)

---
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 @d0choa
build(deps-dev): bump lxml from 5.1.0 to 5.2.1 (#569)
1c341c2 
Bumps [lxml](https://github.com/lxml/lxml) from 5.1.0 to 5.2.1.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](lxml/lxml@lxml-5.1.0...lxml-5.2.1)

---
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>
Co-authored-by: David Ochoa <[email protected]>
@pre-commit-ci @d0choa
chore: pre-commit autoupdate (#561)
dce499f 
* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.4.1](astral-sh/ruff-pre-commit@v0.3.3...v0.4.1)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0)
- [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.13.0 → v9.15.0](alessandrojcm/commitlint-pre-commit-hook@v9.13.0...v9.15.0)
- [github.com/econchick/interrogate: 1.5.0 → 1.7.0](econchick/interrogate@1.5.0...1.7.0)

* fix: poetry lock is not up-to-date

---------

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]>
@dependabot @d0choa
build(deps-dev): bump pre-commit from 3.6.0 to 3.7.0 (#559)
e58ad7f 
Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.6.0 to 3.7.0.
- [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@v3.6.0...v3.7.0)

---
updated-dependencies:
- dependency-name: pre-commit
  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 @d0choa
build(deps-dev): bump pytest-cov from 4.1.0 to 5.0.0 (#560)
60c0003 
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v4.1.0...v5.0.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-type: direct:development
  update-type: version-update:semver-major
...

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 python-semantic-release from 9.1.0 to 9.4.1 (#571)
c468fe0 
Bumps [python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 9.1.0 to 9.4.1.
- [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@v9.1.0...v9.4.1)

---
updated-dependencies:
- dependency-name: python-semantic-release
  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>
@pre-commit-ci @d0choa
chore: pre-commit autoupdate (#593)
23a5fae 
* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.2](astral-sh/ruff-pre-commit@v0.4.1...v0.4.2)
- [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.15.0 → v9.16.0](alessandrojcm/commitlint-pre-commit-hook@v9.15.0...v9.16.0)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](pre-commit/mirrors-mypy@v1.9.0...v1.10.0)

* chore: it bumps poetry version

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: David Ochoa <[email protected]>
@addramir
feat: add purity qc metrics to fine-mapping (#592)
690d158 
* feat: add purity qc metrics to fine-mapping

* fix: adding cs_lbf_thr to susie_finemapper_one_studylocus_row

* fix: schema
@Daniel-Considine
feat: check for if no overlapping variants in LD index (#594)
962b79c 
* feat: check for if no overlapping variants in LD index

* fix: removing unnecessary else statement
@pre-commit-ci
chore: pre-commit autoupdate (#601)
85c3aa8 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3](astral-sh/ruff-pre-commit@v0.4.2...v0.4.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
dependabot bot and others added 10 commits May 7, 2024 16:57
@dependabot @ireneisdoomed
build(deps-dev): bump pymdown-extensions from 10.7 to 10.8.1 (#600)
a9ef7c0 
Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.7 to 10.8.1.
- [Release notes](https://github.com/facelessuser/pymdown-extensions/releases)
- [Commits](facelessuser/pymdown-extensions@10.7...10.8.1)

---
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 <[email protected]>
@dependabot
build(deps-dev): bump interrogate from 1.5.0 to 1.7.0 (#599)
d34b7d7 
Bumps [interrogate](https://github.com/econchick/interrogate) from 1.5.0 to 1.7.0.
- [Release notes](https://github.com/econchick/interrogate/releases)
- [Changelog](https://github.com/econchick/interrogate/blob/master/docs/changelog.rst)
- [Commits](econchick/interrogate@1.5.0...1.7.0)

---
updated-dependencies:
- dependency-name: interrogate
  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
build(deps-dev): bump pytest from 8.1.0 to 8.2.0 (#598)
7af1cbc 
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.1.0 to 8.2.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.1.0...8.2.0)

---
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>
@dependabot
build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1 (#597)
9f6e6b9 
Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 3.5.0 to 3.6.1.
- [Release notes](https://github.com/pytest-dev/pytest-xdist/releases)
- [Changelog](https://github.com/pytest-dev/pytest-xdist/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-xdist@v3.5.0...v3.6.1)

---
updated-dependencies:
- dependency-name: pytest-xdist
  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
build(deps-dev): bump ruff from 0.3.2 to 0.4.3 (#596)
d89ec86 
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.3.2 to 0.4.3.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.3.2...v0.4.3)

---
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>
@ireneisdoomed
feat(airflow): include COLOC as a node in the DAG (#530)
bc1a112 
* feat: split colocalisation step into two nodes: coloc and ecaviar

* feat: filter credible sets to be colocalised based on method

* fix(dag): update coloc dependencies

* revert(config): revert colocalisation output location

* feat(coloc): _get_colocalisation_class to import methods dynamically

* refactor(step): remove method enum

* refactor(step): do not hardcode method value

* fix(config): typo in static_assets

* refactor(dag): uncomment steps
@dependabot @ireneisdoomed
build(deps): bump typing-extensions from 4.10.0 to 4.11.0 (#602)
1576cf4 
Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.10.0 to 4.11.0.
- [Release notes](https://github.com/python/typing_extensions/releases)
- [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md)
- [Commits](python/typing_extensions@4.10.0...4.11.0)

---
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: Irene López <[email protected]>
@dependabot
build(deps-dev): bump ipython from 8.22.1 to 8.24.0 (#603)
8bc09c8 
Bumps [ipython](https://github.com/ipython/ipython) from 8.22.1 to 8.24.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.22.1...8.24.0)

---
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>
@dependabot
build(deps-dev): bump mypy from 1.9.0 to 1.10.0 (#604)
c066327 
Bumps [mypy](https://github.com/python/mypy) from 1.9.0 to 1.10.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@1.9.0...v1.10.0)

---
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>
@DSuveges @d0choa
refactor: moving all variant coordinates to GnomAD (#566)
bb9f9c6 
* refactor: removing gnomAD variant id. GonomadID is the variant id

* refactor: converting ld index coordinates to gnomad

* refactor: movig GWAS Catalog to gnomad coordinates

* test: fixing doctest

* refactor: touching DAG for preparing GnomAD dataset

* fix: adding updated lockfile

* fix: replace hyphens with underscores in variant identifiers

* fix: removing commented line

---------

Co-authored-by: David Ochoa <[email protected]>
@d0choa d0choa merged commit b0f8903 into main May 17, 2024
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@d0choa @DSuveges @ireneisdoomed @xyg123 @louwenjjr @addramir @Daniel-Considine