chore: multiple python version support with latest pyspark and hail (#…

…974) * chore(pyspark): update to 3.5.X * chore: fix doctest syntax * chore: bump temurin version to 11 * feat: allow multiple python versions * feat: python matrix for gha * chore: pre-commit auto fixes [...] * chore: typos * chore: fix python version in setup dev script * fix: attempt to fix the 3.11 tests * fix: set the session correctly in variant_index_config * Revert "chore: fix doctest syntax" This reverts commit 630c0c9. * chore: update dependencies * Revert "Revert "chore: fix doctest syntax"" This reverts commit 18c66b1. * chore: bump image to 2.2 * chore: update lock files * build: poetry cleanup * build: uv checks droped * chore: fix dockerfile and install test deps * build(uv): add all dependencies to run tests * chore: fix test issue with rounding error * chore: fix dependency version lower bounds * chore: add .python-version file to ignored * build: new setup * build: new setup * build: new setup * build: new setup * build: new setup * revert: bring back initialization actions * chore: align variable name * chore: update pre-commit python version * chore: docs update * feat: more complex uv installation * feat: notify to source shellrc file when installing uv * fix: checks * chore: debug gha * chore: debug gha * feat: debug gha * feat: debug gha * feat: debug gha * feat: force user shell * feat: gha debug * feat: gha debug * feat: gha debug * feat: gha debug --------- Co-authored-by: project-defiant <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
opentargets · Jan 28, 2025 · 3d31edd · 3d31edd
1 parent aa00959
commit 3d31edd
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diff --git a/.github/labeler.yml b/.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:

diff --git a/.github/pull_request_template.md b/.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`)?
diff --git a/.github/workflows/artifact.yml b/.github/workflows/artifact.yml
@@ -1,6 +1,7 @@
 name: Build and Push to Artifact Registry
 
 "on":
+  workflow_dispatch:
   push:
     branches:
       - "*"
@@ -12,7 +13,7 @@ env:
   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:
@@ -54,6 +55,7 @@ jobs:
 
       # 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:
@@ -86,13 +88,8 @@ 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: Build and push spark cluster dependencies
-        run: |
-          make build
+        run: make build
diff --git a/.github/workflows/pr.yaml b/.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:

diff --git a/.github/workflows/release.yaml b/.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/[email protected]
+        uses: python-semantic-release/[email protected]
         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
diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,5 @@ site/
 .coverage*
 wandb/
 hail*.log
+.python-version
+.idea
diff --git a/.pre-commit-config.yaml b/.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
@@ -101,9 +100,7 @@ repos:
     rev: 0.5.9
     hooks:
       - id: pydoclint
-
-  - repo: https://github.com/python-poetry/poetry
-    rev: "2.0.0"
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.5.22
     hooks:
-      - id: poetry-check
-      - id: poetry-lock
+      - id: uv-lock
diff --git a/.python-version b/.python-version
diff --git a/Dockerfile b/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>=2.0.0
+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"]
diff --git a/Makefile b/Makefile
@@ -1,7 +1,8 @@
+SHELL := /bin/bash
 PROJECT_ID ?= open-targets-genetics-dev
 REGION ?= europe-west1
 APP_NAME ?= $$(cat pyproject.toml | grep -m 1 "name" | cut -d" " -f3 | sed  's/"//g')
-PACKAGE_VERSION ?= $$(poetry version --short)
+PACKAGE_VERSION ?= $(shell grep -m 1 'version = ' pyproject.toml | sed 's/version = "\(.*\)"/\1/')
 # NOTE: git rev-parse will always return the HEAD if it sits in the tag,
 # this way we can distinguish the tag vs branch name
 ifeq ($(shell git rev-parse --abbrev-ref HEAD),HEAD)
@@ -11,7 +12,7 @@ else
 endif
 
 CLEAN_PACKAGE_VERSION := $(shell echo "$(PACKAGE_VERSION)" | tr -cd '[:alnum:]')
-BUCKET_NAME=gs://genetics_etl_python_playground/initialisation/${APP_NAME}/${REF}
+BUCKET_NAME=gs://genetics_etl_python_playground/initialisation
 
 .PHONY: $(shell sed -n -e '/^$$/ { n ; /^[^ .\#][^ ]*:/ { s/:.*$$// ; p ; } ; }' $(MAKEFILE_LIST))
 
@@ -23,43 +24,55 @@ help: ## This is help
 clean: ## Clean up prior to building
 	@rm -Rf ./dist
 
-setup-dev: SHELL:=/bin/bash
-setup-dev: ## Setup development environment
+setup-dev: SHELL := $(shell echo $${SHELL})
+setup-dev:  ## Setup development environment
 	@. utils/install_dependencies.sh
+	@echo "Run . ${HOME}/.$(notdir $(SHELL))rc to finish setup"
 
 check: ## Lint and format code
 	@echo "Linting API..."
-	@poetry run ruff check src/gentropy .
+	@uv run ruff check src/gentropy .
 	@echo "Linting docstrings..."
-	@poetry run pydoclint --config=pyproject.toml src
-	@poetry run pydoclint --config=pyproject.toml --skip-checking-short-docstrings=true tests
+	@uv run pydoclint --config=pyproject.toml src
+	@uv run pydoclint --config=pyproject.toml --skip-checking-short-docstrings=true tests
 
 test: ## Run tests
 	@echo "Running Tests..."
-	@poetry run pytest
+	@uv run pytest
 
 build-documentation: ## Create local server with documentation
 	@echo "Building Documentation..."
-	@poetry run mkdocs serve
+	@uv run mkdocs serve
 
-create-dev-cluster: build ## Spin up a simple dataproc cluster with all dependencies for development purposes
+sync-cluster-init-script: ## Synchronize the cluster inicialisation actions script to google cloud
+	@echo "Syncing install_dependencies_on_cluster.sh to ${BUCKET_NAME}"
+	@gcloud storage cp utils/install_dependencies_on_cluster.sh ${BUCKET_NAME}/install_dependencies_on_cluster.sh
+
+sync-gentropy-cli-script: ## Synchronize the gentropy cli script
+	@echo "Syncing gentropy cli script to ${BUCKET_NAME}"
+	@gcloud storage cp src/gentropy/cli.py ${BUCKET_NAME}/cli.py
+
+create-dev-cluster: sync-cluster-init-script sync-gentropy-cli-script ## Spin up a simple dataproc cluster with all dependencies for development purposes
+	@echo "Making sure the branch is in sync with remote, so cluster can install gentropy dev version..."
+	@./utils/clean_status.sh || (echo "ERROR: Commit and push or stash local changes, to have up to date cluster"; exit 1)
 	@echo "Creating Dataproc Dev Cluster"
-	@gcloud config set project ${PROJECT_ID}
-	@gcloud dataproc clusters create "ot-genetics-dev-${CLEAN_PACKAGE_VERSION}-$(USER)" \
-		--image-version 2.1 \
+	gcloud config set project ${PROJECT_ID}
+	gcloud dataproc clusters create "ot-genetics-dev-${CLEAN_PACKAGE_VERSION}-$(USER)" \
+		--image-version 2.2 \
 		--region ${REGION} \
-		--master-machine-type n1-standard-16 \
-		--initialization-actions=$(BUCKET_NAME)/install_dependencies_on_cluster.sh \
-		--metadata="PACKAGE=$(BUCKET_NAME)/${APP_NAME}-${PACKAGE_VERSION}-py3-none-any.whl" \
+		--master-machine-type n1-standard-2 \
+		--metadata="GENTROPY_REF=${REF}" \
+		--initialization-actions=${BUCKET_NAME}/install_dependencies_on_cluster.sh \
 		--secondary-worker-type spot \
 		--worker-machine-type n1-standard-4 \
+		--public-ip-address \
 		--worker-boot-disk-size 500 \
 		--autoscaling-policy="projects/${PROJECT_ID}/regions/${REGION}/autoscalingPolicies/otg-etl" \
 		--optional-components=JUPYTER \
 		--enable-component-gateway \
 		--max-idle=60m
 
-make update-dev-cluster: build ## Reinstalls the package on the dev-cluster
+update-dev-cluster: build ## Reinstalls the package on the dev-cluster
 	@echo "Updating Dataproc Dev Cluster"
 	@gcloud config set project ${PROJECT_ID}
 	gcloud dataproc jobs submit pig --cluster="ot-genetics-dev-${CLEAN_PACKAGE_VERSION}" \
@@ -68,10 +81,4 @@ make update-dev-cluster: build ## Reinstalls the package on the dev-cluster
 		-e='sh chmod 750 $${PWD}/install_dependencies_on_cluster.sh; sh $${PWD}/install_dependencies_on_cluster.sh'
 
 build: clean ## Build Python package with dependencies
-	@gcloud config set project ${PROJECT_ID}
-	@echo "Packaging Code and Dependencies for ${APP_NAME}-${PACKAGE_VERSION}"
-	@poetry build
-	@echo "Uploading to ${BUCKET_NAME}"
-	@gsutil cp src/${APP_NAME}/cli.py ${BUCKET_NAME}/
-	@gsutil cp ./dist/${APP_NAME}-${PACKAGE_VERSION}-py3-none-any.whl ${BUCKET_NAME}/
-	@gsutil cp ./utils/install_dependencies_on_cluster.sh ${BUCKET_NAME}/
+	@uv build