Merge pull request #961 from opentargets/dev

chore: trigger release process

.github/labeler.yml

@@ -2,26 +2,26 @@ version: 1
 labels:
   - label: "size-XS"
     size:
-      exclude-files: ["poetry.lock"]
+      exclude-files: ["uv.lock"]
       below: 10
   - label: "size-S"
     size:
-      exclude-files: ["poetry.lock"]
+      exclude-files: ["uv.lock"]
       above: 9
       below: 100
   - label: "size-M"
     size:
-      exclude-files: ["poetry.lock"]
+      exclude-files: ["uv.lock"]
       above: 100
       below: 500
   - label: "size-L"
     size:
-      exclude-files: ["poetry.lock"]
+      exclude-files: ["uv.lock"]
       above: 499
       below: 1000
   - label: "size-XL"
     size:
-      exclude-files: ["poetry.lock"]
+      exclude-files: ["uv.lock"]
       above: 999
   - label: "airflow"
     files:

.github/pull_request_template.md

@@ -25,4 +25,4 @@ add diagrams or images if necessary. It'll help the reviewer_ -->
 - [ ] 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`)?
+- [ ] Did you make sure the changes pass pre-commit rules (e.g `uv run pre-commit run --all-files`)?

.github/workflows/artifact.yml

@@ -1,16 +1,19 @@
 name: Build and Push to Artifact Registry
 
 "on":
+  workflow_dispatch:
   push:
-    branches: ["*"]
-    tags: ["*"]
+    branches:
+      - "*"
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+-*"
 
 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"
+  PYTHON_VERSION_DEFAULT: "3.11.11"
 
 jobs:
   build-push-artifact:
@@ -37,7 +40,7 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: "Docker auth"
-        run: |-
+        run: |
           gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
 
       - name: Quick Docker build (gentropy only, AMD64 only, with layer cache)
@@ -50,36 +53,43 @@ jobs:
           cache-from: type=gha
           cache-to: type=gha,mode=max
 
-      - name: Build and push gentropy image
+      # skip the `v` at the beginning of the tag for docker image tags
+      - name: Create a docker tag
         if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
+        id: docker-tag
+        shell: bash
+        env:
+          TAG: ${{ github.ref_name }}
+        run: |
+          TAG=$(echo $TAG | sed 's/^v//')
+          echo "TAG=$TAG" >> $GITHUB_ENV
+          echo "The tag for this build is $TAG"
+
+      - name: Build and push gentropy image
+        if: steps.docker-tag.outcome == 'success'
         uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64,linux/arm64
           push: true
-          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}"
+          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ env.TAG }}"
           context: .
 
       - name: Build and push VEP image
-        if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
+        if: steps.docker-tag.outcome == 'success'
         uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64
           push: true
-          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/custom_ensembl_vep:${{ github.ref_name }}"
+          tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/custom_ensembl_vep:${{ env.TAG }}"
           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: Install uv
+        uses: astral-sh/setup-uv@v5
 
       - name: Build and push spark cluster dependencies
-        run: |
-          make build
+        run: make build

.github/workflows/pr.yaml

@@ -4,47 +4,43 @@ name: Checks
   pull_request:
 
 env:
-  PYTHON_VERSION_DEFAULT: "3.10.8"
+  PYTHON_VERSION_DEFAULT: "3.11.11"
 
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+      fail-fast: false
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 1
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.10.8
+          python-version: ${{ matrix.python-version }}
       - name: Set up Java
         uses: actions/setup-java@v4
         with:
-          java-version: "8"
+          java-version: "11"
           distribution: "temurin"
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
       - name: Load cached venv
-        id: cached-poetry-dependencies
+        id: cached-uv-dependencies
         uses: actions/cache@v4
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ env.PYTHON_VERSION_DEFAULT }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Validate project dependencies
-        run: poetry check
+          key: venv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/uv.lock') }}
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
-      - name: Install library
-        run: poetry install --no-interaction
+        if: steps.cached-uv-dependencies.outputs.cache-hit != 'true'
+        run: uv sync --all-groups
       - name: Check dependencies
-        run: poetry run deptry .
+        run: uv run deptry .
       - name: Run tests
-        run: poetry run pytest
+        run: uv run pytest
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         with:

.github/workflows/release.yaml

@@ -2,14 +2,14 @@ name: Release
 
 "on":
   push:
-    branches: ["main", "release/**"]
+    branches: ["main", "release/**", "dev"]
 
 concurrency:
   group: deploy
   cancel-in-progress: false # prevent hickups with semantic-release
 
 env:
-  PYTHON_VERSION_DEFAULT: "3.10.8"
+  PYTHON_VERSION_DEFAULT: "3.11.11"
 
 jobs:
   release:
@@ -40,9 +40,7 @@ jobs:
 
       - name: Python Semantic Release
         id: semrelease
-        # 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
+        uses: python-semantic-release/python-semantic-release@v9.16.1
         with:
           github_token: ${{ steps.trigger-token.outputs.token }}
 
@@ -121,25 +119,19 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.PYTHON_VERSION_DEFAULT }}
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
       - name: Load cached venv
-        id: cached-poetry-dependencies
+        id: cached-dependencies
         uses: actions/cache@v4
         with:
           path: .venv
           key: |
             venv-${{ runner.os }}-\
             ${{ env.PYTHON_VERSION_DEFAULT }}-\
-            ${{ hashFiles('**/poetry.lock') }}
+            ${{ hashFiles('**/uv.lock') }}
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
-      - name: Install library
-        run: poetry install --without tests --no-interaction
+        if: steps.cached-dependencies.outputs.cache-hit != 'true'
+        run: uv sync --group docs
       - name: Publish docs
-        run: poetry run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.gitignore

@@ -14,3 +14,5 @@ site/
 .coverage*
 wandb/
 hail*.log
+.python-version
+.idea

.pre-commit-config.yaml

@@ -1,9 +1,8 @@
 default_language_version:
-  python: python3.10
+  python: python3.11
 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: v0.7.4
@@ -46,7 +45,7 @@ repos:
       - id: python-check-blanket-noqa
 
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
       - id: pycln
         args: [--all]
@@ -101,10 +100,7 @@ repos:
     rev: 0.5.9
     hooks:
       - id: pydoclint
-
-  - repo: https://github.com/python-poetry/poetry
-    rev: "1.8.0"
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.5.22
     hooks:
-      - id: poetry-check
-      - id: poetry-lock
-        args: ["--no-update"]
+      - id: uv-lock

Dockerfile

@@ -1,27 +1,20 @@
 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/*
+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
+ENV JAVA_HOME=/usr
 
-RUN pip install poetry==1.7.1
+RUN pip install uv
 WORKDIR /app
 
-COPY pyproject.toml poetry.lock ./
+COPY pyproject.toml uv.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
+RUN uv sync
 
 COPY src ./src
 
-RUN poetry install --without dev,docs,tests
-
-ENTRYPOINT ["poetry", "run", "gentropy"]
+ENTRYPOINT ["uv", "run", "gentropy"]