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/artifact.yml

@@ -0,0 +1,85 @@
+name: Build and Push to Artifact Registry
+
+"on":
+  push:
+    branches: ["*"]
+    tags: ["*"]
+
+env:
+  PROJECT_ID: open-targets-genetics-dev
+  REGION: europe-west1
+  GAR_LOCATION: europe-west1-docker.pkg.dev/open-targets-genetics-dev
+  REPOSITORY: gentropy-app
+  PYTHON_VERSION_DEFAULT: "3.10.8"
+
+jobs:
+  build-push-artifact:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Checkout"
+        uses: "actions/checkout@v3"
+
+      - name: "auth"
+        uses: "google-github-actions/auth@v2"
+        with:
+          credentials_json: "${{ secrets.SERVICE_ACCOUNT_KEY }}"
+
+      - name: "Set up Cloud SDK"
+        uses: "google-github-actions/setup-gcloud@v2"
+
+      - name: "Use gcloud CLI"
+        run: "gcloud info"
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: "Docker auth"
+        run: |-
+          gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
+
+      - name: Quick Docker build (gentropy only, AMD64 only, with layer cache)
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/amd64
+          push: true
+          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}"
+          context: .
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Build and push gentropy image
+        if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}"
+          context: .
+
+      - name: Build and push VEP image
+        if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/amd64
+          push: true
+          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/custom_ensembl_vep:${{ github.ref_name }}"
+          context: .
+          file: "src/vep/Dockerfile"
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION_DEFAULT }}
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Build and push spark cluster dependencies
+        run: |
+          make build

.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 }}"

.github/workflows/pr.yaml

@@ -17,6 +17,11 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.10.8
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          java-version: "8"
+          distribution: "temurin"
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:

.github/workflows/pr_release_trigger.yaml

@@ -15,7 +15,7 @@ jobs:
           source_branch: "dev"
           destination_branch: "main"
           pr_title: "chore: trigger release process"
-          pr_body: ":warning: *This PR requires a MERGE or REBASE COMMIT (Don't squash!)*"
+          pr_body: ":warning: *This PR requires a MERGE COMMIT (Don't squash!)*"
           pr_label: "auto-pr"
           pr_draft: false
           pr_allow_empty: true

.github/workflows/release.yaml

@@ -23,22 +23,35 @@ jobs:
       contents: write
 
     steps:
+      # NOTE: commits using GITHUB_TOKEN does not trigger workflows
+      - uses: actions/create-github-app-token@v1
+        id: trigger-token
+        with:
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           repository: opentargets/gentropy
           token: ${{ secrets.GITHUB_TOKEN }}
+          persist-credentials: false
 
       - name: Python Semantic Release
         id: semrelease
-        uses: python-semantic-release/python-semantic-release@master
+        # v9.6.0 is required due to the python v3.12 in the newer version of semantic release action which
+        # breaks the poetry build command.
+        uses: python-semantic-release/python-semantic-release@v9.6.0
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ steps.trigger-token.outputs.token }}
 
       - name: Publish package to GitHub Release
         uses: python-semantic-release/upload-to-gh-release@main
         if: ${{ steps.semrelease.outputs.released }} == 'true'
         with:
+          # NOTE: allow to start the workflow when push action on tag gets executed
+          # requires using GH_APP to authenitcate, otherwise push authorised with
+          # the GITHUB_TOKEN does not trigger the tag artifact workflow.
+          # see https://github.com/actions/create-github-app-token
           github_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ steps.semrelease.outputs.tag }}
 

.gitignore

@@ -11,3 +11,6 @@ src/airflow/logs/*
 !src/airflow/logs/.gitkeep
 site/
 .env
+.coverage*
+wandb/
+hail*.log

.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: v0.7.1
     hooks:
       - id: ruff
         args:
@@ -12,13 +15,12 @@ repos:
         files: ^((gentropy|utils|tests)/.+)?[^/]+\.py$
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
         exclude: "CHANGELOG.md"
       - id: debug-statements
-      - id: check-merge-conflict
       - id: check-case-conflict
       - id: check-json
         exclude: (.vscode|.devcontainer)
@@ -56,14 +58,14 @@ repos:
         exclude: "CHANGELOG.md"
 
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.11.0
+    rev: v9.18.0
     hooks:
       - id: commitlint
-        additional_dependencies: ["@commitlint/config-conventional"]
+        additional_dependencies: ["@commitlint/config-conventional@18.6.3"]
         stages: [commit-msg]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0"
+    rev: "v1.13.0"
     hooks:
       - id: mypy
         args:
@@ -79,7 +81,7 @@ repos:
           - "--disallow-untyped-defs"
 
   - repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
+    rev: 1.7.0
     hooks:
       - id: interrogate
         args: [--verbose]
@@ -96,6 +98,13 @@ repos:
       - id: beautysh
 
   - repo: https://github.com/jsh9/pydoclint
-    rev: 0.4.1
+    rev: 0.5.9
     hooks:
       - id: pydoclint
+
+  - repo: https://github.com/python-poetry/poetry
+    rev: "1.8.0"
+    hooks:
+      - id: poetry-check
+      - id: poetry-lock
+        args: ["--no-update"]

.vscode/settings.json

@@ -25,5 +25,8 @@
   "python.testing.pytestEnabled": true,
   "mypy-type-checker.severity": {
     "error": "Information"
-  }
+  },
+  "yaml.extension.recommendations": false,
+  "workbench.remoteIndicator.showExtensionRecommendations": false,
+  "extensions.ignoreRecommendations": true
 }

Dockerfile

@@ -0,0 +1,27 @@
+FROM python:3.10-bullseye
+
+RUN apt-get update \
+  && apt-get clean \
+  && apt-get install -y openjdk-11-jdk \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1 \
+    POETRY_CACHE_DIR=/tmp/poetry_cache \
+    JAVA_HOME=/usr
+
+RUN pip install poetry==1.7.1
+WORKDIR /app
+
+COPY pyproject.toml poetry.lock ./
+RUN touch README.md
+
+RUN poetry config installer.max-workers 10
+RUN poetry install --without dev,docs,tests --no-root --no-interaction --no-ansi -vvv && rm -rf $POETRY_CACHE_DIR
+
+COPY src ./src
+
+RUN poetry install --without dev,docs,tests
+
+ENTRYPOINT ["poetry", "run", "gentropy"]