From 3d31edd6ce141db9a258120df37f5a53b14c73e9 Mon Sep 17 00:00:00 2001 From: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Date: Tue, 28 Jan 2025 10:58:31 +0100 Subject: [PATCH] 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 630c0c970d128c42e02721727b61497fe989a135. * chore: update dependencies * Revert "Revert "chore: fix doctest syntax"" This reverts commit 18c66b1d1d9c4833e3dbfc406ba3440577a119a5. * 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 Co-authored-by: Szymon Szyszkowski Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .github/labeler.yml | 10 +- .github/pull_request_template.md | 2 +- .github/workflows/artifact.yml | 15 +- .github/workflows/pr.yaml | 34 +- .github/workflows/release.yaml | 28 +- .gitignore | 2 + .pre-commit-config.yaml | 11 +- .python-version | 1 - Dockerfile | 25 +- Makefile | 55 +- docs/development/contributing.md | 16 +- docs/development/troubleshooting.md | 35 +- poetry.lock | 6373 ----------------- pyproject.toml | 140 +- src/gentropy/common/spark_helpers.py | 32 +- src/gentropy/common/utils.py | 8 +- src/gentropy/config.py | 6 +- src/gentropy/dataset/variant_index.py | 2 +- src/gentropy/datasource/ensembl/vep_parser.py | 10 +- .../datasource/gwas_catalog/associations.py | 45 +- .../datasource/gwas_catalog/study_index.py | 4 +- src/gentropy/method/colocalisation.py | 12 +- .../gentropy/step/test_colocalisation_step.py | 3 +- utils/clean_status.sh | 11 + utils/install_dependencies.sh | 39 +- utils/install_dependencies_on_cluster.sh | 27 +- uv.lock | 4077 +++++++++++ 27 files changed, 4350 insertions(+), 6673 deletions(-) delete mode 100644 .python-version delete mode 100644 poetry.lock create mode 100755 utils/clean_status.sh create mode 100644 uv.lock diff --git a/.github/labeler.yml b/.github/labeler.yml index fdb0e58b6..5f65b4915 100644 --- 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 index aca51c6ea..880289418 100644 --- 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 index be6439e92..161d2767a 100644 --- 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 index d32a3b28e..abf464785 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -4,11 +4,15 @@ 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: @@ -16,35 +20,27 @@ jobs: - 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 index 9c166432f..961f0bef5 100644 --- 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/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 diff --git a/.gitignore b/.gitignore index b62418654..8e4ee8af9 100644 --- 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 index ddcee97c4..a1a022b1d 100644 --- 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 deleted file mode 100644 index 36435ac69..000000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.10.8 diff --git a/Dockerfile b/Dockerfile index 6a66c53ef..b710bba93 100644 --- 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 index 4e6a7463f..6b6418d10 100644 --- 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 diff --git a/docs/development/contributing.md b/docs/development/contributing.md index acbb8f2a7..99b199de1 100644 --- a/docs/development/contributing.md +++ b/docs/development/contributing.md @@ -18,11 +18,13 @@ For Google Cloud configuration: Check that you have the `make` utility installed, and if not (which is unlikely), install it using your system package manager. -Check that you have `java` installed. To be able to use all features including hail support use java 11. +!!! note "Java support" + + Check that you have `java` installed. To be able to use all features including hail support use java 11 (for handling multiple java versions, consider using [`sdkman`](https://sdkman.io/)). ## Environment configuration -Run `make setup-dev` to install/update the necessary packages and activate the development environment. You need to do this every time you open a new shell. +Run `make setup-dev` to install/update the necessary packages (including required python version for development) and activate the development environment. You need to do it just once. It is recommended to use VS Code as an IDE for development. @@ -30,15 +32,15 @@ It is recommended to use VS Code as an IDE for development. All gentropy steps can be invoked after successful environment configuration by running -```python -poetry run gentropy step= +```bash +uv run gentropy step= ``` 1. Create a new step config in the `src/gentropy/config.py` that inherits from `StepConfig` class. 2. Register new step configuration to `ConfigStore`. -3. Create a step class that holds the business logic in new file in the `src/gentropy`. +3. Create a step class that holds the business logic in new file in the `src/gentropy/{your_step_name}.py`. ## Contributing checklist @@ -78,3 +80,7 @@ For more details on each of these steps, see the sections below. ### Airflow dags - Upstream of version 2.0.0 airflow orchestration layer was moved to the [orchestration repository](https://github.com/opentargets/orchestration) + +### Support for python versions + +As of version 2.1.X gentropy supports multiple python versions. To ensure compatibility with all supported versions, unit tests are run for each of the minor python release from 3.10 to 3.12. Make sure your changes are compatible with all supported versions. diff --git a/docs/development/troubleshooting.md b/docs/development/troubleshooting.md index 498ee3b86..762d40dd0 100644 --- a/docs/development/troubleshooting.md +++ b/docs/development/troubleshooting.md @@ -8,25 +8,17 @@ title: Troubleshooting If you see errors related to BLAS/LAPACK libraries, see [this StackOverflow post](https://stackoverflow.com/questions/69954587/no-blas-lapack-libraries-found-when-installing-scipy) for guidance. -## Pyenv and Poetry +## UV -If you see various errors thrown by Pyenv or Poetry, they can be hard to specifically diagnose and resolve. In this case, it often helps to remove those tools from the system completely. Follow these steps: +The default python version and gentropy dependencies are managed by [uv](https://docs.astral.sh/uv/). To perform a fresh installation run `make setup-dev`. -1. Close your currently activated environment, if any: `exit` -2. Uninstall Poetry: `curl -sSL https://install.python-poetry.org | python3 - --uninstall` -3. Clear Poetry cache: `rm -rf ~/.cache/pypoetry` -4. Clear pre-commit cache: `rm -rf ~/.cache/pre-commit` -5. Switch to system Python shell: `pyenv shell system` -6. Edit `~/.bashrc` to remove the lines related to Pyenv configuration -7. Remove Pyenv configuration and cache: `rm -rf ~/.pyenv` +## Adding new dependencies or updating existing ones -After that, open a fresh shell session and run `make setup-dev` again. +To add new dependencies or update existing ones, you need to update the `pyproject.toml` file. This can be done automatically with `uv add ${package}` command. Refer to the [uv documentation](https://docs.astral.sh/uv/) for more information. ## Java -Officially, PySpark requires Java version 8 (a.k.a. 1.8) or above to work. However, if you have a very recent version of Java, you may experience issues, as it may introduce breaking changes that PySpark hasn't had time to integrate. For example, as of May 2023, PySpark did not work with Java 20. - -If you are encountering problems with initialising a Spark session, try using Java 11. +Officially, PySpark requires Java version 8, or 11, 17. To support hail (gentropy dependency) it is recommended to use Java 11. ## Pre-commit @@ -38,8 +30,6 @@ Another solution which helps is to remove Node, NodeJS, and npm from your system On Ubuntu, this can be done using `sudo apt remove node nodejs npm`, followed by `sudo apt autoremove`. But in some cases, depending on your existing installation, you may need to also manually remove some files. See [this StackOverflow answer](https://stackoverflow.com/a/41057802) for guidance. -After running these commands, you are advised to open a fresh shell, and then also reinstall Pyenv and Poetry to make sure they pick up the changes (see relevant section above). - ## MacOS Some functions on MacOS may throw a java error: @@ -54,14 +44,17 @@ This can be resolved by adding the follow line to your `~/.zshrc`: To start dataproc cluster in the development mode run -``` +```bash make create-dev-cluster ``` -The command above will prepare 3 different resources: +!!! note "Tip" +This command will work, provided you have fully commited and pushed all your changes to the remote repository. + +The command will create a new dataproc cluster with the following configuration: -- gentropy package -- cli script -- cluster setup script +- package installed from the current branch you are checkout on (for example `dev` or `feature/xxx`) +- uv installed in the cluster (to speed up the installation and dependency resolution process) +- cli script to run gentropy steps -and based on the branch ref (for example `dev`) will create a namespaced folder under GCS (`gs://genetics_etl_python_playground/initialisation/gentropy/dev`) with the three files described above. These files will be then used to create the cluster environment. +This process requires gentropy to be installable by git repository - see VCS support in [pip documentation](https://pip.pypa.io/en/stable/topics/vcs-support/). diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 9044db42a..000000000 --- a/poetry.lock +++ /dev/null @@ -1,6373 +0,0 @@ -# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. - -[[package]] -name = "aiodns" -version = "2.0.0" -description = "Simple DNS resolver for asyncio" -optional = false -python-versions = "*" -groups = ["main"] -files = [ - {file = "aiodns-2.0.0-py2.py3-none-any.whl", hash = "sha256:aaa5ac584f40fe778013df0aa6544bf157799bd3f608364b451840ed2c8688de"}, - {file = "aiodns-2.0.0.tar.gz", hash = "sha256:815fdef4607474295d68da46978a54481dd1e7be153c7d60f9e72773cd38d77d"}, -] - -[package.dependencies] -pycares = ">=3.0.0" - -[[package]] -name = "aiohappyeyeballs" -version = "2.4.4" -description = "Happy Eyeballs for asyncio" -optional = false -python-versions = ">=3.8" -groups = ["main"] -files = [ - 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"pyspark (==3.3.4)", - "scipy (>=1.11.4, <1.12.0)", - "hydra-core (>=1.3.2, <1.4.0)", - "pyliftover (>=0.4, <0.5)", - "numpy (>=1.26.2, <1.27.0)", - "hail (==0.2.127)", - "wandb (>=0.19.0, <0.20.0)", - "google (>=3.0.0, <3.1.0)", - "omegaconf (>=2.3.0, <2.4.0)", - "typing-extensions (>=4.9.0, <4.13.0)", - "scikit-learn (>=1.6.0, <1.7.0)", - "pandas[gcp,parquet] (>=2.2.2, <2.3.0)", - "skops (>=0.11, <0.12)", - "google-cloud-secret-manager (>=2.20.0, <2.22.0)", - "shap (>=0.46.0, <0.47.0)", - "matplotlib (>=3.7.3, <3.8.0)" + "pyspark (>=3.5.0, <3.6)", + "hail (>=0.2.133, <0.3.0)", + "scipy (>=1.11.4, <1.12.0)", + "hydra-core (>=1.3.2, <1.4.0)", + "pyliftover (>=0.4.1, <0.5.0)", + "numpy (>=1.26.4, <1.27.0)", + "wandb (>=0.19.4, <0.20.0)", + "omegaconf (>=2.3.0, <2.4.0)", + "typing-extensions (>=4.12.2, <4.13.0)", + "scikit-learn (>=1.6.1, <1.7.0)", + "pandas[gcp,parquet] (>=2.2.3, <2.3.0)", + "skops (>=0.11.0, <0.12.0)", + "shap (>=0.46, <0.47)", + "matplotlib (>=3.10.0, <3.11.0)", + "google-cloud-secret-manager (>=2.12.6, <2.13.0)", + "google-cloud-storage (>=2.14.0, <2.15.0)", +] +classifiers = [ + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] - [project.urls] Source = "https://github.com/opentargets/gentropy" "Bug Tracker" = "http://github.com/opentargets/issues" @@ -40,53 +39,55 @@ Documentation = "https://opentargets.github.io/gentropy/" [project.scripts] gentropy = "gentropy.cli:main" -[tool.poetry.group.docs.dependencies] -mkdocs = ">=1.5.3, <1.6.0" -mkdocstrings-python = ">=1.12.2, <1.13.0" -mkdocs-material = "*" -mkdocs-section-index = ">=0.3.4, <0.4.0" -mkdocs-git-revision-date-localized-plugin = ">=1.2.2, <1.4.0" -mkdocs-autolinks-plugin = ">=0.7.1, <0.8.0" -mkdocs-awesome-pages-plugin = ">=2.9.2, <3.0.0" -mkdocs-exclude = ">=1.0.2, <1.1.0" -mkdocs-git-committers-plugin-2 = ">=2.2.3, <2.5.0" -lxml = ">=5.1.0, <5.4.0" -pymdown-extensions = ">=10.7, <10.13" - - -[tool.poetry.group.tests.dependencies] -pytest-cov = ">=4.1,<7.0" -pytest-sugar = ">=0.9.5,<1.1.0" -dbldatagen = ">=0.3.1,<0.5.0" -pyparsing = ">=3.1.1, <3.3.0" -pytest = ">=7.4.4,<9.0.0" -pytest-xdist = ">=3.5.0, <3.7.0" - - -[tool.poetry.group.dev.dependencies] -ipython = ">=8.19.0, <8.31.0" -ipykernel = ">=6.28.0, <6.30.0" -google-cloud-dataproc = ">=5.8.0, <5.16.0" -pydoclint = ">=0.3.8,<0.6.0" -prettier = ">=0.0.7, <0.1.0" -deptry = ">=0.22.0, <0.23.0" -yamllint = ">=1.33.0, <1.36.0" -pre-commit = ">=4.0.0, <4.1.0" -mypy = ">=1.13, <1.14" -pep8-naming = ">=0.14.1, <0.15.0" -interrogate = ">=1.7.0, <1.8.0" -isort = ">=5.13.2, <5.14.0" -darglint = ">=1.8.1, <1.9.0" -ruff = ">=0.8.1, <0.9.0" +[dependency-groups] +docs = [ + "mkdocs >=1.5.3, <1.6.0", + "mkdocstrings-python >=1.12.2, <1.13.0", + "mkdocs-material", + "mkdocs-section-index >=0.3.4, <0.4.0", + "mkdocs-git-revision-date-localized-plugin >=1.2.2, <1.4.0", + "mkdocs-autolinks-plugin >=0.7.1, <0.8.0", + "mkdocs-awesome-pages-plugin >=2.9.2, <3.0.0", + "mkdocs-exclude >=1.0.2, <1.1.0", + "mkdocs-git-committers-plugin-2 >=2.2.3, <2.5.0", + "lxml >=5.1.0, <5.4.0", + "pymdown-extensions >=10.7, <10.13", +] +test = [ + "pytest-cov >=4.1,<7.0", + "pytest-sugar >=0.9.5,<1.1.0", + "dbldatagen >=0.3.1,<0.5.0", + "pyparsing >=3.1.1, <3.3.0", + "pytest >=7.4.4,<9.0.0", + "pytest-xdist >=3.5.0, <3.7.0", +] +dev = [ + "ipython >=8.19.0, <8.31.0", + "ipykernel >=6.28.0, <6.30.0", + "pydoclint >=0.3.8,<0.6.0", + "prettier >=0.0.7, <0.1.0", + "deptry >=0.22.0, <0.23.0", + "yamllint >=1.33.0, <1.36.0", + "pre-commit >=4.0.0, <4.1.0", + "mypy >=1.13, <1.14", + "pep8-naming >=0.14.1, <0.15.0", + "interrogate >=1.7.0, <1.8.0", + "isort >=5.13.2, <5.14.0", + "darglint >=1.8.1, <1.9.0", + "ruff >=0.8.1, <0.9.0", +] [tool.semantic_release] logging_use_named_masks = true -build_command = "pip install poetry && poetry build" +build_command = "pip install uv && uv build" assets = [] -version_toml = ["pyproject.toml:tool.poetry.version"] +version_toml = ["pyproject.toml:project.version"] upload_to_pypi = false upload_to_release = true +[tool.hatch.build.targets.wheel] +packages = ["src/gentropy"] + [tool.semantic_release.branches.main] match = "(main|master)" prerelease = false @@ -109,9 +110,14 @@ match = "(build|chore|ci|docs|feat|fix|perf|style|refactor|test)" prerelease = true prerelease_token = "alpha" +[tool.semantic_release.branches."dev"] +match = "dev" +prerelease = true +prerelease_token = "dev" + [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" [tool.deptry] extend_exclude = ["src/conftest.py", "src/utils"] @@ -126,7 +132,7 @@ color = true exclude = ["dist"] [tool.pytest.ini_options] -addopts = "-n auto --doctest-modules --cov=src/ --cov-report=xml" +addopts = "-n auto --doctest-modules --cov=src/ --cov-report=xml --cache-clear" pythonpath = ["."] testpaths = ["tests/gentropy", "src/gentropy"] markers = ["step_test"] diff --git a/src/gentropy/common/spark_helpers.py b/src/gentropy/common/spark_helpers.py index fd84a9810..08bbe069c 100644 --- a/src/gentropy/common/spark_helpers.py +++ b/src/gentropy/common/spark_helpers.py @@ -119,7 +119,7 @@ def pvalue_to_zscore(pval_col: Column) -> Column: | t3| 0.05| 1.959964| | t4| 1e-300| 37.537838| | t5|1e-1000| 37.537838| - | t6| NA| null| + | t6| NA| NULL| +---+-------+----------+ @@ -149,7 +149,7 @@ def nullify_empty_array(column: Column) -> Column: +---------+---------+ | value| new| +---------+---------+ - | []| null| + | []| NULL| |[1, 2, 3]|[1, 2, 3]| +---------+---------+ @@ -472,8 +472,8 @@ def map_column_by_dictionary(col: Column, mapping_dict: dict[str, Any]) -> Colum | label| id| +--------------------+---------+ | consequence_1|SO:000000| - |unmapped_consequence| null| - | null| null| + |unmapped_consequence| NULL| + | NULL| NULL| +--------------------+---------+ """ @@ -604,7 +604,7 @@ def rename_all_columns(df: DataFrame, prefix: str) -> DataFrame: +-----------+-----------+-----------+ | a| 1.2| true| | b| 0.0| false| - | c| null| null| + | c| NULL| NULL| +-----------+-----------+-----------+ """ @@ -649,7 +649,7 @@ def safe_array_union( |[a, b]| | [c]| | [d]| - | null| + | NULL| +------+ >>> schema="arr2: array>, arr: array>" @@ -752,7 +752,7 @@ def create_empty_column_if_not_exists( +----+----+----+ |col1|col2|col3| +----+----+----+ - | 1| 2|null| + | 1| 2|NULL| +----+----+----+ """ @@ -782,8 +782,8 @@ def get_standard_error_from_confidence_interval(lower: Column, upper: Column) -> | standard_error| +-------------------+ |0.25510204081632654| - | null| - | null| + | NULL| + | NULL| +-------------------+ """ @@ -866,13 +866,13 @@ def calculate_harmonic_sum(input_array: Column) -> Column: ... Row([0.7, 0.2, 0.9]), ... ], ["input_array"] ... ) - >>> df.select("*", calculate_harmonic_sum(f.col("input_array")).alias("harmonic_sum")).show() - +---------------+------------------+ - | input_array| harmonic_sum| - +---------------+------------------+ - |[0.3, 0.8, 1.0]|0.7502326177269538| - |[0.7, 0.2, 0.9]|0.6674366756805108| - +---------------+------------------+ + >>> df.select("*", f.round(calculate_harmonic_sum(f.col("input_array")), 2).alias("harmonic_sum")).show() + +---------------+------------+ + | input_array|harmonic_sum| + +---------------+------------+ + |[0.3, 0.8, 1.0]| 0.75| + |[0.7, 0.2, 0.9]| 0.67| + +---------------+------------+ """ return f.aggregate( diff --git a/src/gentropy/common/utils.py b/src/gentropy/common/utils.py index 91b002fe2..517fff8b0 100644 --- a/src/gentropy/common/utils.py +++ b/src/gentropy/common/utils.py @@ -50,7 +50,7 @@ def calculate_confidence_interval( |pvalue_mantissa|pvalue_exponent|beta|standard_error|betaConfidenceIntervalLower|betaConfidenceIntervalUpper| +---------------+---------------+----+--------------+---------------------------+---------------------------+ | 2.5| -10| 0.5| 0.2| 0.10799999999999998| 0.892| - | 3.0| -5| 1.0| null| 0.5303663900832607| 1.4696336099167393| + | 3.0| -5| 1.0| NULL| 0.5303663900832607| 1.4696336099167393| | 1.5| -8|-0.2| 0.1| -0.396| -0.00400000000000...| +---------------+---------------+----+--------------+---------------------------+---------------------------+ @@ -98,9 +98,9 @@ def convert_odds_ratio_to_beta( |beta|oddsRatio|standardError| beta|standardError| +----+---------+-------------+-------------------+-------------+ | 0.1| 1.1| 0.1| 0.1| 0.1| - |null| 1.1| 0.1|0.09531017980432493| null| - | 0.1| null| 0.1| 0.1| 0.1| - | 0.1| 1.1| null| 0.1| null| + |NULL| 1.1| 0.1|0.09531017980432493| NULL| + | 0.1| NULL| 0.1| 0.1| 0.1| + | 0.1| 1.1| NULL| 0.1| NULL| +----+---------+-------------+-------------------+-------------+ diff --git a/src/gentropy/config.py b/src/gentropy/config.py index 7d924f3fe..b4748a090 100644 --- a/src/gentropy/config.py +++ b/src/gentropy/config.py @@ -436,7 +436,11 @@ class _ConsequenceToPathogenicityScoreMap(TypedDict): label: str score: float - session: SessionConfig = SessionConfig() + session: Any = field( + default_factory=lambda: { + "start_hail": False, + } + ) vep_output_json_path: str = MISSING variant_index_path: str = MISSING gnomad_variant_annotations_path: str | None = None diff --git a/src/gentropy/dataset/variant_index.py b/src/gentropy/dataset/variant_index.py index 649b9f3ff..184f03711 100644 --- a/src/gentropy/dataset/variant_index.py +++ b/src/gentropy/dataset/variant_index.py @@ -94,7 +94,7 @@ def hash_long_variant_ids( |v_short |v_short | |v_looooooong|OTVAR_23_23_3749d019d645894770c364992ae70a05| |no_chrom |OTVAR_41acfcd7d4fd523b33600b504914ef25 | - |null |null | + |NULL |NULL | +------------+--------------------------------------------+ """ diff --git a/src/gentropy/datasource/ensembl/vep_parser.py b/src/gentropy/datasource/ensembl/vep_parser.py index b0a2e50a2..c5c985f3f 100644 --- a/src/gentropy/datasource/ensembl/vep_parser.py +++ b/src/gentropy/datasource/ensembl/vep_parser.py @@ -192,7 +192,7 @@ def _colocated_variants_to_rsids(colocated_variants: Column) -> Column: |rsIds | +---------------+ |[rs1, rs2, rs3]| - |[null] | + |[NULL] | +---------------+ """ @@ -380,8 +380,8 @@ def _get_max_alpha_missense(transcripts: Column) -> Column: +-----------------------------------------------------+ |am | +-----------------------------------------------------+ - |{AlphaMissense, assessment 1, 0.4, null, gene1, null}| - |{AlphaMissense, null, null, null, gene1, null} | + |{AlphaMissense, assessment 1, 0.4, NULL, gene1, NULL}| + |{AlphaMissense, NULL, NULL, NULL, gene1, NULL} | +-----------------------------------------------------+ """ @@ -513,8 +513,8 @@ def _parser_amino_acid_change(amino_acids: Column, protein_end: Column) -> Colum |amino_acid_change| +-----------------+ | A1B| - | null| - | null| + | NULL| + | NULL| +-----------------+ """ diff --git a/src/gentropy/datasource/gwas_catalog/associations.py b/src/gentropy/datasource/gwas_catalog/associations.py index 31238e425..2a2d795d3 100644 --- a/src/gentropy/datasource/gwas_catalog/associations.py +++ b/src/gentropy/datasource/gwas_catalog/associations.py @@ -120,9 +120,9 @@ def _normalise_pvaluetext(p_value_text: Column) -> Column: | European Ancestry| [EA]| | African ancestry| [AA]| |Alzheimer’s Disease| [AD]| - | (progression)| null| - | | null| - | null| null| + | (progression)| NULL| + | | NULL| + | NULL| NULL| +-------------------+----------+ @@ -297,9 +297,7 @@ def _map_variants_to_gnomad_variants( "position", ) - return gwas_associations.join( - fully_mapped_associations, on="rowId", how="left" - ) + return gwas_associations.join(fully_mapped_associations, on="rowId", how="left") @staticmethod def _compare_rsids(gnomad: Column, gwas: Column) -> Column: @@ -423,7 +421,7 @@ def _check_concordance( | A| T| G| true| | A| C| G| false| | A| A| ?| true| - | null| null| A| true| + | NULL| NULL| A| true| +----------+---------------+---------------+------------+ @@ -481,7 +479,7 @@ def _get_reverse_complement(allele_col: Column) -> Column: | AC| GT| |GTaatc| GATTAC| | ?| ?| - | null| null| + | NULL| NULL| +------+-------------+ @@ -551,7 +549,7 @@ def _are_alleles_palindromic( | AG| AT| false| | AT| AT| true| | CATATG| CATATG| true| - | null| -| false| + | NULL| -| false| +---------+---------+--------------+ @@ -653,7 +651,7 @@ def _harmonise_odds_ratio( | 0.5|false| 0.5| | 0.5| true| 2.0| | 0.0|false| 0.0| - | 0.0| true| null| + | 0.0| true| NULL| +------+-----+----------+ """ @@ -693,7 +691,7 @@ def _concatenate_substudy_description( |association_trait|mapped_trait_uri |pvalue_text |substudy_description | +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+ |Height |http://www.ebi.ac.uk/efo/EFO_0000001,http://www.ebi.ac.uk/efo/EFO_0000002|European Ancestry|Height|EA|EFO_0000001/EFO_0000002 | - |Schizophrenia |http://www.ebi.ac.uk/efo/MONDO_0005090 |null |Schizophrenia|no_pvalue_text|MONDO_0005090| + |Schizophrenia |http://www.ebi.ac.uk/efo/MONDO_0005090 |NULL |Schizophrenia|no_pvalue_text|MONDO_0005090| +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+ """ @@ -803,9 +801,9 @@ def _qc_genomic_location( +----------------------------+----------+--------+ |qc |chromosome|position| +----------------------------+----------+--------+ - |[Incomplete genomic mapping]|null |null | - |[Incomplete genomic mapping]|1 |null | - |[Incomplete genomic mapping]|null |1 | + |[Incomplete genomic mapping]|NULL |NULL | + |[Incomplete genomic mapping]|1 |NULL | + |[Incomplete genomic mapping]|NULL |1 | |[] |1 |1 | +----------------------------+----------+--------+ @@ -867,8 +865,8 @@ def _qc_unmapped_variants(qc: Column, alternate_allele: Column) -> Column: +----------------+----+--------------------+ |alternate_allele| qc| new_qc| +----------------+----+--------------------+ - | A|null| []| - | null|null|[No mapping in Gn...| + | A|NULL| []| + | NULL|NULL|[No mapping in Gn...| +----------------+----+--------------------+ @@ -940,7 +938,7 @@ def _get_effect_type(ci_text: Column) -> Column: |95% CI: [0.1-0.2] |odds_ratio | |95% CI: [0.1-0.2] increase|beta | |95% CI: [0.1-0.2] decrease|beta | - |null |null | + |NULL |NULL | +--------------------------+-----------+ @@ -994,11 +992,11 @@ def harmonise_association_effect_to_beta( +-------------------------+---------------+---------------+----------+--------------------+-------------------+--------------------+ |STRONGEST SNP-RISK ALLELE|referenceAllele|alternateAllele|OR or BETA| 95% CI (TEXT)| beta| standardError| +-------------------------+---------------+---------------+----------+--------------------+-------------------+--------------------+ - | rs123-T| A| T| 0.1|[0.08-0.12] unit ...| null| null| + | rs123-T| A| T| 0.1|[0.08-0.12] unit ...| NULL| NULL| | rs123-C| G| T| 0.1|[0.08-0.12] unit ...| -0.1|0.010204081404574064| | rs123-T| C| T| 0.1|[0.08-0.12] unit ...| 0.1|0.010204081404574064| - | rs123-T| C| T| 0.1| [0.08-0.12]|-2.3025850929940455| null| - | rs123-C| G| T| 0.1| [0.08-0.12]| 2.302585092994046| null| + | rs123-T| C| T| 0.1| [0.08-0.12]|-2.3025850929940455| NULL| + | rs123-C| G| T| 0.1| [0.08-0.12]| 2.302585092994046| NULL| +-------------------------+---------------+---------------+----------+--------------------+-------------------+--------------------+ """ @@ -1108,7 +1106,8 @@ def from_source( return StudyLocusGWASCatalog( _df=gwas_associations.withColumn( # temporary column - "rowId", f.monotonically_increasing_id().cast(StringType()) + "rowId", + f.monotonically_increasing_id().cast(StringType()), ) .transform( # Map/harmonise variants to variant annotation dataset: @@ -1140,9 +1139,7 @@ def from_source( # Adding study-locus id: .withColumn( "studyLocusId", - StudyLocus.assign_study_locus_id( - ["studyId", "variantId"] - ), + StudyLocus.assign_study_locus_id(["studyId", "variantId"]), ) .select( # INSIDE STUDY-LOCUS SCHEMA: diff --git a/src/gentropy/datasource/gwas_catalog/study_index.py b/src/gentropy/datasource/gwas_catalog/study_index.py index 8630d31f6..d43261d5b 100644 --- a/src/gentropy/datasource/gwas_catalog/study_index.py +++ b/src/gentropy/datasource/gwas_catalog/study_index.py @@ -219,7 +219,7 @@ def parse_cohorts(raw_cohort: Column) -> Column: |parsedCohorts | +--------------------------------------+ |[BioME, CaPS, Estonia, FHS, UKB, GERA]| - |null | + |NULL | +--------------------------------------+ """ @@ -655,7 +655,7 @@ def add_no_sumstats_flag(self: StudyIndexGWASCatalog) -> StudyIndexGWASCatalog: """ self.df = self.df.withColumn( "qualityControls", - f.array(f.lit(StudyQualityCheck.SUMSTATS_NOT_AVAILABLE.value)) + f.array(f.lit(StudyQualityCheck.SUMSTATS_NOT_AVAILABLE.value)), ) return self diff --git a/src/gentropy/method/colocalisation.py b/src/gentropy/method/colocalisation.py index c20f4909c..c05b26187 100644 --- a/src/gentropy/method/colocalisation.py +++ b/src/gentropy/method/colocalisation.py @@ -51,8 +51,8 @@ def get_tag_variant_source(statistics: Column) -> Column: | a| b|source| +----+----+------+ | a| b| both| - |null| b| right| - | a|null| left| + |NULL| b| right| + | a|NULL| left| +----+----+------+ """ @@ -181,8 +181,8 @@ def colocalise( .withColumn("colocalisationMethod", f.lit(cls.METHOD_NAME)) .join( overlapping_signals.calculate_beta_ratio(), - on=["leftStudyLocusId", "rightStudyLocusId","chromosome"], - how="left" + on=["leftStudyLocusId", "rightStudyLocusId", "chromosome"], + how="left", ) ), _schema=Colocalisation.get_schema(), @@ -386,8 +386,8 @@ def colocalise( .withColumn("colocalisationMethod", f.lit(cls.METHOD_NAME)) .join( overlapping_signals.calculate_beta_ratio(), - on=["leftStudyLocusId", "rightStudyLocusId","chromosome"], - how="left" + on=["leftStudyLocusId", "rightStudyLocusId", "chromosome"], + how="left", ) ), _schema=Colocalisation.get_schema(), diff --git a/tests/gentropy/step/test_colocalisation_step.py b/tests/gentropy/step/test_colocalisation_step.py index 95ceaf976..2d2a43707 100644 --- a/tests/gentropy/step/test_colocalisation_step.py +++ b/tests/gentropy/step/test_colocalisation_step.py @@ -282,9 +282,8 @@ def test_colocalise( coloc_dataset = Colocalisation.from_parquet( session, self.coloc_path, recursiveFileLookup=True ) - for column in expected_data: + for column, expected_values in expected_data.items(): values = [c[column] for c in coloc_dataset.df.collect()] - expected_values = expected_data[column] for v, e in zip(values, expected_values): if isinstance(e, float): assert ( diff --git a/utils/clean_status.sh b/utils/clean_status.sh new file mode 100755 index 000000000..583bb881c --- /dev/null +++ b/utils/clean_status.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +echo "Fetching version changes..." +git fetch +if output=$(git status --porcelain) && [[ -n "$output" ]]; then + exit 1 +fi +echo "Checking if branch is up-to-date with remote..." +if output=$(git push --dry-run --porcelain) && [[ "$output" != *"[up to date]"* ]]; then + exit 1 +fi diff --git a/utils/install_dependencies.sh b/utils/install_dependencies.sh index 4ed3909c3..fcac7d1fc 100644 --- a/utils/install_dependencies.sh +++ b/utils/install_dependencies.sh @@ -1,33 +1,18 @@ -if ! command -v pyenv &>/dev/null; then - echo "Installing Pyenv, a tool to manage multiple Python versions..." - curl -sSL https://pyenv.run | bash - # Add Pyenv configuration to ~/.bashrc. - echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc - echo 'command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc - echo 'eval "$(pyenv init -)"' >> ~/.bashrc - # And also execute it right now. - . <(tail -n3 ~/.bashrc) -fi +readonly SHELL_RC="$HOME/.${SHELL##*/}rc" +readonly PYTHON_VERSION=$(cat .python-version >&/dev/null || echo "3.11.11") -echo "Activating Pyenv environment with a Python version required for the project..." -if [ -f ".python-version" ]; then - PYTHON_VERSION=$(cat .python-version) - pyenv install --skip-existing $PYTHON_VERSION - pyenv shell $PYTHON_VERSION -else - echo ".python-version file not found." - exit 1 +if ! command -v uv &>/dev/null; then + echo "uv was not found, installing uv..." + curl -LsSf https://astral.sh/uv/install.sh | sh + source "$SHELL_RC" fi -if ! command -v poetry &>/dev/null; then - echo "Installing Poetry, a tool to manage Python dependencies..." - curl -sSL https://install.python-poetry.org | python3 - -fi +echo "Installing python version from .python-version..." +uv python install "$PYTHON_VERSION" -echo "Preparing the Poetry environment and installing dependencies..." -poetry env use $PYTHON_VERSION -poetry install --sync +echo "Installing dependencies with UV..." +uv sync --all-groups --frozen echo "Setting up pre-commit..." -poetry run pre-commit install -poetry run pre-commit install --hook-type commit-msg +uv run --no-sync pre-commit install +uv run --no-sync pre-commit install --hook-type commit-msg diff --git a/utils/install_dependencies_on_cluster.sh b/utils/install_dependencies_on_cluster.sh index 849dee0c3..4b1f9ae72 100644 --- a/utils/install_dependencies_on_cluster.sh +++ b/utils/install_dependencies_on_cluster.sh @@ -2,8 +2,8 @@ set -exo pipefail -readonly PACKAGE=$(/usr/share/google/get_metadata_value attributes/PACKAGE || true) - +readonly GENTROPY_REF=$(/usr/share/google/get_metadata_value attributes/GENTROPY_REF || true) +readonly REPO_URI="https://github.com/opentargets/gentropy" function err() { echo "[$(date +'%Y-%m-%dT%H:%M:%S%z')]: $*" >&2 exit 1 @@ -11,7 +11,7 @@ function err() { function run_with_retry() { local -r cmd=("$@") - for ((i = 0; i < 10; i++)); do + for ((i = 0; i < 3; i++)); do if "${cmd[@]}"; then return 0 fi @@ -37,33 +37,22 @@ function install_pip() { run_with_retry apt install python-pip -y } + function main() { # Define a specific directory to download the files - local work_dir="/" - cd "${work_dir}" || err "Failed to change to working directory" - echo "Working directory: $(pwd)" - - # more meaningful errors from hydra echo "export HYDRA_FULL_ERROR=1" | tee --append /etc/profile source /etc/profile - if [[ -z "${PACKAGE}" ]]; then - echo "ERROR: Must specify PACKAGE metadata key" + if [[ -z "${GENTROPY_REF}" ]]; then + echo "ERROR: Must specify GENTROPY_REF metadata key" exit 1 fi install_pip + pip install uv - echo "Downloading package..." - gsutil cp ${PACKAGE} . || err "Failed to download PACKAGE" - PACKAGENAME=$(basename ${PACKAGE}) - - echo "Uninstalling previous version if it exists" pip 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