chore: trigger release process

.github/labeler.yml

@@ -0,0 +1,63 @@
+version: "1"
+labels:
+  - label: "size-XS"
+    size:
+      exclude-files: ["poetry.lock"]
+      below: 10
+  - label: "size-S"
+    size:
+      exclude-files: ["poetry.lock"]
+      above: 9
+      below: 100
+  - label: "size-M"
+    size:
+      exclude-files: ["poetry.lock"]
+      above: 100
+      below: 500
+  - label: "size-L"
+    size:
+      exclude-files: ["poetry.lock"]
+      above: 499
+      below: 1000
+  - label: "size-XL"
+    size:
+      exclude-files: ["poetry.lock"]
+      above: 999
+  - label: "airflow"
+    files:
+      - "^src/airflow/.*"
+  - label: "Documentation"
+    files:
+      - "^docs/.*"
+  - label: "Dataset"
+    files:
+      - "^src/gentropy/dataset/.*"
+  - label: "Method"
+    files:
+      - "^src/gentropy/method/.*"
+  - label: "Datasource"
+    files:
+      - "^src/gentropy/datasource/.*"
+  - label: "Step"
+    files:
+      - "^src/gentropy/[a-zA-Z]\\w+\\.py"
+  - label: "Feature"
+    title: "^feat.*"
+  - label: "Bug"
+    title: "^fix.*"
+  - label: "Refactor"
+    title: "^refactor.*"
+  - label: "Chore"
+    title: "^chore.*"
+  - label: "CI"
+    title: "^ci.*"
+  - label: "Test"
+    title: "^test.*"
+  - label: "Documentation"
+    title: "^docs.*"
+  - label: "Performance"
+    title: "^perf.*"
+  - label: "Build"
+    title: "^build.*"
+  - label: "Revert"
+    title: "^revert.*"

.github/pull_request_template.md

@@ -0,0 +1,28 @@
+## ✨ Context
+
+<!---
+Congratulations! You've made it this far!
+Once merged, your PR is going to appear in the release notes with the title you set, so make sure it's a great title that fully reflects the extent of your contribution.
+What's the context for the changes? If the changes are related to a specific issue, please [link](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue) to it:
+-->
+
+## 🛠 What does this PR implement
+
+<!--- _Detailed description of the changes introduced, Give examples of the changes you've made in this pull request, include an itemized list if you can and
+add diagrams or images if necessary. It'll help the reviewer_ -->
+
+## 🙈 Missing
+
+<!--- If there are things that are requested in the task and were not implemented, list them here -->
+
+## 🚦 Before submitting
+
+- [ ] Do these changes cover one single feature (one change at a time)?
+- [ ] Did you read the [contributor guideline](https://opentargets.github.io/gentropy/development/contributing/#contributing-checklist)?
+- [ ] Did you make sure to update the documentation with your changes?
+- [ ] Did you make sure there is no commented out code in this PR?
+- [ ] Did you follow [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) standards in PR title and commit messages?
+- [ ] Did you make sure the branch is up-to-date with the `dev` branch?
+- [ ] Did you write any new necessary tests?
+- [ ] Did you make sure the changes pass local tests (`make test`)?
+- [ ] Did you make sure the changes pass pre-commit rules (e.g `poetry run pre-commit run --all-files`)?

.github/workflows/labeler.yml

@@ -0,0 +1,14 @@
+name: Label PRs
+
+"on":
+  - pull_request
+  - issues
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: srvaroa/labeler@master
+        env:
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.pre-commit-config.yaml

@@ -1,9 +1,12 @@
+default_language_version:
+  python: python3.10
 ci:
   autoupdate_commit_msg: "chore: pre-commit autoupdate"
   autofix_commit_msg: "chore: pre-commit auto fixes [...]"
+  skip: [poetry-lock]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.0
     hooks:
       - id: ruff
         args:
@@ -99,3 +102,10 @@ repos:
     rev: 0.4.1
     hooks:
       - id: pydoclint
+
+  - repo: https://github.com/python-poetry/poetry
+    rev: "1.8.2"
+    hooks:
+      - id: poetry-check
+      - id: poetry-lock
+        args: ["--no-update"]

config/datasets/ot_gcp.yaml

@@ -39,7 +39,6 @@ thurman: ${datasets.static_assets}/thurman2012/genomewideCorrs_above0.7_promoter
 target_index: ${datasets.release_folder}/targets # OTP 23.12 data
 
 gene_interactions: ${datasets.release_folder}/interaction # OTP 23.12 data
-eqtl_catalogue_paths_imported: ${datasets.inputs}/preprocess/eqtl_catalogue/tabix_ftp_paths_imported.tsv
 finngen_finemapping_results_path: ${datasets.inputs}/Finngen_susie_finemapping_r10/full
 finngen_finemapping_summaries_path: ${datasets.inputs}/Finngen_susie_finemapping_r10/Finngen_susie_credset_summary_r10.tsv
 

config/step/ot_eqtl_catalogue.yaml

@@ -1,6 +1,10 @@
 defaults:
   - eqtl_catalogue
 
-eqtl_catalogue_paths_imported: ${datasets.eqtl_catalogue_paths_imported}
-eqtl_catalogue_study_index_out: ${datasets.eqtl_catalogue_study_index_out}
-eqtl_catalogue_summary_stats_out: ${datasets.eqtl_catalogue_summary_stats_out}
+eqtl_catalogue_paths_imported: ???
+eqtl_catalogue_study_index_out: ???
+eqtl_catalogue_credible_sets_out: ???
+mqtl_quantification_methods_blacklist: []
+session:
+  extended_spark_conf:
+    "spark.sql.shuffle.partitions": "3200"

docs/python_api/datasources/eqtl_catalogue/_eqtl_catalogue.md

@@ -2,10 +2,6 @@
 title: eQTL Catalogue
 ---
 
-The [eQTL Catalogue](https://www.ebi.ac.uk/eqtl/) aims to provide uniformly processed gene expression and splicing Quantitative Trait Loci (QTLs) from all available public studies on humans.
+The [eQTL Catalogue](https://www.ebi.ac.uk/eqtl/) aims to provide unified gene, protein expression and splicing Quantitative Trait Loci (QTLs) from all available human public studies.
 
-It serves as the ultimate resource of eQTLs that we use for colocalization and target prioritization.
-
-We utilize data from the following study within the eQTL Catalogue:
-
-1. **GTEx v8**, 49 tissues
+It serves as the ultimate resource of molecular QTLs that we use for colocalization and target prioritization.

docs/python_api/datasources/eqtl_catalogue/finemapping.md

@@ -0,0 +1,5 @@
+---
+title: Fine mapping results
+---
+
+::: gentropy.datasource.eqtl_catalogue.finemapping.EqtlCatalogueFinemapping

docs/python_api/steps/eqtl_catalogue.md

@@ -1,5 +1,5 @@
 ---
-title: eqtl_catalogue
+title: eQTL Catalogue
 ---
 
 ::: gentropy.eqtl_catalogue.EqtlCatalogueStep