chore: trigger release process by github-actions[bot] · Pull Request #4 · thehyve/gentropy

github-actions · 2024-11-28T16:22:56Z

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

* 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] <support@github.com> * fix: update lock --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: David Ochoa <dogcaesar@gmail.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>

* 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 <69353402+project-defiant@users.noreply.github.com>

Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

* 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 <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>

* fix: adding carma_tau parameter to susie_finemapper * fix: changing default * fix: defaults

* 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 (opentargets#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 <daniel.suveges@protonmail.com> * chore: pre-commit auto fixes [...] --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

* 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 <69353402+project-defiant@users.noreply.github.com>

* 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 <45119610+ireneisdoomed@users.noreply.github.com> --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: Irene López Santiago <45119610+ireneisdoomed@users.noreply.github.com>

* 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 <69353402+project-defiant@users.noreply.github.com>

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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

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](osprey-oss/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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

* fix: use mapping instead of enum values in valid_rows * fix: typos * fix: swap valid and invalid paths --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

* 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 <69353402+project-defiant@users.noreply.github.com> --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

* 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

* 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

…#757) * feat(validation): adding logic to validate credible sets against variant index * fix: tidying docstrings

* refactor: drop gentropy config * feat(airflow): removal of airflow orchestration BREAKING CHANGE: see https://github.com/opentargets/orchestration --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

…targets#749)

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

…rgets#766) * 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 <69353402+project-defiant@users.noreply.github.com>

* 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 <69353402+project-defiant@users.noreply.github.com>

…gets#762) * 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

* 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

…gets#939) * feat(prediction): add `model` as instance attribute * feat: added `convert_map_type_to_columns` spark util * feat(prediction): new method `explain` returns shapley values * feat(prediction): `explain` returns predictions with shapley values * chore: compute `shapleyValues` in the l2g step * refactor: use pandas udf instead * refactor: forget about udfs and get shaps single threaded * chore: remove reference to chromatin interaction data in HF card * fix(l2g_prediction): methods that return new instance preserve attribute * feat(dataset): `filter` method preserves all instance attributes * feat(l2gmodel): add features_list as model attribute and load it from the hub metadata * fix: pass correct order of features to shapley explainer * feat(l2g): predict mode to extract feature list from model, not from config * feat(l2g): pass default features list if model is loaded from a path * feat(l2gmodel): add features_list as model attribute and load it from the hub metadata * feat(l2g): predict mode to extract feature list from model, not from config * feat(l2gprediction): add `model` as attribute * feat(l2gmodel): add features_list as model attribute and load it from the hub metadata * feat(l2g): predict mode to extract feature list from model, not from config * feat(l2gprediction): add `model` as attribute * chore: fix typo * chore: remove `convert_map_type_to_columns` * feat(l2gprediction): refactor feature annotation and change schema * chore: pre-commit auto fixes [...] * feat: report as log odds * feat: calculate scaled probabilities * chore(l2gprediction): remove shapBaseProbability * chore: correct typo in add_features and make schemas non nullable * fix: rename columns in pandas df after pivoting * fix: add raw shap contributions * fix(model): when saving create directory if not exists * feat(l2g): bundle model and training data in hf * feat(model): include data when loading model * feat: final version of shap explanations * fix: do not infer features_list from df * fix: get_features_list_from_metadata returned cols that were not features * refactor(model): read training data in the local filesystem w pandas * chore: successful run, remove test

…3.0,>=2.12.6 to >=2.12.6,<2.24.0 (opentargets#994) * build(deps): update google-cloud-secret-manager requirement --- updated-dependencies: - dependency-name: google-cloud-secret-manager dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * chore(uv): update uv.lock --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.4 → v0.9.6](astral-sh/ruff-pre-commit@v0.7.4...v0.9.6) - [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.18.0 → v9.21.0](alessandrojcm/commitlint-pre-commit-hook@v9.18.0...v9.21.0) - [github.com/pre-commit/mirrors-mypy: v1.13.0 → v1.15.0](pre-commit/mirrors-mypy@v1.13.0...v1.15.0) - [github.com/jsh9/pydoclint: 0.5.9 → 0.6.2](jsh9/pydoclint@0.5.9...0.6.2) - [github.com/astral-sh/uv-pre-commit: 0.5.22 → 0.6.1](astral-sh/uv-pre-commit@0.5.22...0.6.1) * chore: pre-commit auto fixes [...] * chore(docstring): added assertion errors to the docstrings --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

…ata filename (opentargets#997) * fix(model): typo in filename when uploading training data to hub * fix(l2g): direct model to hf repo when path is none * fix: run_train to keep GS and geneId * chore: pre-commit auto fixes [...] --------- Co-authored-by: xyg123 <xiangyuge123@hotmail.co.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…entargets#998)

…rgets#1001)

…ex (opentargets#1003) * fix: remove certain methods from variantEffect struct generation * fix: remove fields from vep output schema

* fix: bump gentropy base image * fix: qemu version bump * chore: dump version of github action runner to temp fix QEMU bug * chore: revert base docker image update * test: check gha no cache build * fix: pin chemu build * test: revert the change in CI pipeline for testing artifact workflow --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>

* fix: change posterior filter * fix: adjust test

updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.9.9](astral-sh/ruff-pre-commit@v0.9.6...v0.9.9) - [github.com/astral-sh/uv-pre-commit: 0.6.1 → 0.6.3](astral-sh/uv-pre-commit@0.6.1...0.6.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…argets#1011) Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 3.4.0 to 3.6.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](docker/setup-qemu-action@v3.4.0...v3.6.0) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

…#1010) Bumps [python-semantic-release/publish-action](https://github.com/python-semantic-release/publish-action) from 9.19.1 to 9.21.0. - [Release notes](https://github.com/python-semantic-release/publish-action/releases) - [Changelog](https://github.com/python-semantic-release/publish-action/blob/main/releaserc.toml) - [Commits](python-semantic-release/publish-action@v9.19.1...v9.21.0) --- updated-dependencies: - dependency-name: python-semantic-release/publish-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

…14.0 to >=2.14.0,<3.2.0 (opentargets#1009) * build(deps): update google-cloud-storage requirement Updates the requirements on [google-cloud-storage](https://github.com/googleapis/python-storage) to permit the latest version. - [Release notes](https://github.com/googleapis/python-storage/releases) - [Changelog](https://github.com/googleapis/python-storage/blob/main/CHANGELOG.md) - [Commits](googleapis/python-storage@v2.14.0...v3.1.0) --- updated-dependencies: - dependency-name: google-cloud-storage dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * chore: update uv lock --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <ss60@sanger.ac.uk>

* chore(l2g): make shap optional * chore(l2g): make shap optional * refactor: make order of operations more explicit

…pentargets#1014)

…s#1015)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.9 → v0.9.10](astral-sh/ruff-pre-commit@v0.9.9...v0.9.10) - [github.com/astral-sh/uv-pre-commit: 0.6.3 → 0.6.5](astral-sh/uv-pre-commit@0.6.3...0.6.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…added when `curation_table` is None (opentargets#1020) * fix: reorder such that necessary columns are added * fix: make missed tests run --------- Co-authored-by: Florian Franz <florian.franz@boehringer-ingelheim.com>

* feat(l2g): make wandb optional * chore: debug * test(l2g): add training tests * test(l2g): add training tests * chore: update test * fix(l2g): remove defaults for hf parameters * chore: init wandb only if requested --------- Co-authored-by: Irene Lopez <irenelopez@qdjrxw0myw.windows.ebi.ac.uk>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.10 → v0.11.0](astral-sh/ruff-pre-commit@v0.9.10...v0.11.0) - [github.com/adrienverge/yamllint.git: v1.35.1 → v1.36.2](https://github.com/adrienverge/yamllint.git/compare/v1.35.1...v1.36.2) - [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.21.0 → v9.22.0](alessandrojcm/commitlint-pre-commit-hook@v9.21.0...v9.22.0) - [github.com/astral-sh/uv-pre-commit: 0.6.5 → 0.6.6](astral-sh/uv-pre-commit@0.6.5...0.6.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.0 → v0.11.2](astral-sh/ruff-pre-commit@v0.11.0...v0.11.2) - [github.com/adrienverge/yamllint.git: v1.36.2 → v1.37.0](https://github.com/adrienverge/yamllint.git/compare/v1.36.2...v1.37.0) - [github.com/astral-sh/uv-pre-commit: 0.6.6 → 0.6.9](astral-sh/uv-pre-commit@0.6.6...0.6.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

opentargets#1016) Updates the requirements on [shap](https://github.com/shap/shap) to permit the latest version. - [Release notes](https://github.com/shap/shap/releases) - [Changelog](https://github.com/shap/shap/blob/master/docs/release_notes.rst) - [Commits](shap/shap@v0.46.0...v0.47.0) --- updated-dependencies: - dependency-name: shap dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Irene López Santiago <45119610+ireneisdoomed@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

…hey can be specified in orchestration (opentargets#1030) * fix: parameterise the overlap cutoff for coloc * feat: adjusting the NA logBF value * Revert "feat: adjusting the NA logBF value" This reverts commit 863738b. * feat: changing default overlap/pp values for coloc * test: updating tests to reflect changes to code * Update src/gentropy/method/colocalisation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix: removing unneeded class attributes --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

dependabot bot and others added 30 commits August 23, 2024 12:29

fix: update cluster creation command (opentargets#739)

348b6f0

Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

fix: revert recursiveFileLookup to False (opentargets#738)

b6746fb

Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>

fix: using h4 instead of log2(h4/h3) (opentargets#740)

2612aa7

fix: adding carma_tau parameter to susie_finemapper (opentargets#743)

93a6e60

* fix: adding carma_tau parameter to susie_finemapper * fix: changing default * fix: defaults

fix: remove finngen prefix from credible set (opentargets#746)

3ea47a9

fix: validation name mapping (opentargets#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 <ss60@mib117351s.internal.sanger.ac.uk>

fix: removing old functions (opentargets#752)

010c881

Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>

refactor: generalise the harmonisation pipeline (opentargets#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

feat(validation): adding credible set variant validation (opentargets…

6469bf5

…#757) * feat(validation): adding logic to validate credible sets against variant index * fix: tidying docstrings

fix: multiple fixes after debugging and test runs (opentargets#760)

d6364f8

build(deps-dev): bump mkdocstrings-python from 1.10.5 to 1.11.1 (open…

34aaaf5

…targets#749)

fix: add condition to eQTL study index and schema (opentargets#770)

d84d43b

feat: flag all top-hits from GWAS catalog curation (opentargets#775)

785dad0

ireneisdoomed and others added 29 commits February 19, 2025 15:17

chore(shap): sample background dataset to make explanation faster (op…

a56f2d0

…entargets#998)

feat: local dataproc cluster settings udpate (opentargets#999)

c5e686c

fix: dev release process (opentargets#992)

6d4109d

fix: foldx column name fix (opentargets#1005)

997993a

chore(trainer): sample train set to base model importances on (openta…

24d2226

…rgets#1001)

fix: solve NULLs found in variantEffect struct of the variant ind…

a3a51f6

…ex (opentargets#1003) * fix: remove certain methods from variantEffect struct generation * fix: remove fields from vep output schema

fix: change posterior filter (opentargets#1006)

e25dedd

* fix: change posterior filter * fix: adjust test

chore(l2g): make shap optional (opentargets#1012)

ea8df77

* chore(l2g): make shap optional * chore(l2g): make shap optional * refactor: make order of operations more explicit

feat(l2g): update params after fine tuning for the new training data (o…

c3675ea

…pentargets#1014)

feat(model): parametrise model version in load_from_hub (opentarget…

d6b8575

…s#1015)

fix: addressing #3800 and #3799 (opentargets#1017)

556a7f9

chore: offline check uv lock (opentargets#1024)

5ce4325

chore: skip uv-lock on pre-commit ci (opentargets#1027)

016266d

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chore: trigger release process#4

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