diff --git a/.dockerignore b/.dockerignore index d60f37160..92d4aa663 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,2 +1,3 @@ webknossos/testdata webknossos/testoutput +.venv diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 44aca0e09..d31c7eff6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,11 +44,13 @@ jobs: working-directory: cluster_tools steps: - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: ${{ matrix.python-version }} - architecture: "x64" + version: "0.4.19" + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} - name: Build/pull dockered-slurm image if: ${{ matrix.executors == 'slurm' }} run: | @@ -70,9 +72,9 @@ jobs: docker logs c2 # Run setup.py on all three nodes - docker exec -w /cluster_tools slurmctld bash -c "poetry install" & - docker exec -w /cluster_tools c1 bash -c "poetry install" & - docker exec -w /cluster_tools c2 bash -c "poetry install" & + docker exec -w /cluster_tools slurmctld bash -c "uv sync --frozen" & + docker exec -w /cluster_tools c1 bash -c "uv sync --frozen" & + docker exec -w /cluster_tools c2 bash -c "uv sync --frozen" & wait - name: Setup Kubernetes-in-Docker @@ -84,21 +86,18 @@ jobs: ./kind create cluster --config=tests/cluster-config.yaml ./kind export kubeconfig - cp ../requirements.txt . docker build -f tests/Dockerfile -t scalableminds/cluster-tools:latest . ./kind load docker-image scalableminds/cluster-tools:latest - name: Install dependencies (without docker) if: ${{ matrix.executors == 'multiprocessing' }} run: | - pip install -r ../requirements.txt - poetry install + uv sync --frozen - name: Install dependencies (without docker) if: ${{ matrix.executors == 'kubernetes' || matrix.executors == 'dask' }} run: | - pip install -r ../requirements.txt - poetry install --all-extras + uv sync --all-extras --frozen - name: Check typing if: ${{ matrix.executors == 'multiprocessing' && matrix.python-version == '3.11' }} @@ -117,7 +116,7 @@ jobs: run: | cd tests PYTEST_EXECUTORS=multiprocessing,sequential,test_pickling,debug_sequential \ - poetry run python -m pytest -sv test_all.py test_multiprocessing.py + uv run --frozen python -m pytest -sv test_all.py test_multiprocessing.py - name: Run slurm tests if: ${{ matrix.executors == 'slurm' }} @@ -126,22 +125,22 @@ jobs: docker exec \ -w /cluster_tools/tests \ -e PYTEST_EXECUTORS=slurm \ - slurmctld bash -c "poetry run python -m pytest -sv test_all.py test_slurm.py" + slurmctld bash -c "uv run --frozen python -m pytest -sv test_all.py test_slurm.py" docker exec \ -w /cluster_tools/tests \ - slurmctld bash -c "poetry run python test_deref_main.py" + slurmctld bash -c "uv run --frozen python test_deref_main.py" - name: Run kubernetes tests if: ${{ matrix.executors == 'kubernetes' }} run: | cd tests - PYTEST_EXECUTORS=kubernetes poetry run python -m pytest -sv test_all.py test_kubernetes.py + PYTEST_EXECUTORS=kubernetes uv run --frozen python -m pytest -sv test_all.py test_kubernetes.py - name: Run dask tests if: ${{ matrix.executors == 'dask' }} run: | cd tests - PYTEST_EXECUTORS=dask poetry run python -m pytest -sv test_all.py test_dask.py + PYTEST_EXECUTORS=dask uv run --frozen python -m pytest -sv test_all.py test_dask.py webknossos_linux: needs: changes @@ -161,17 +160,16 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - architecture: "x64" - - - name: Install dependencies - run: | - pip install -r ../requirements.txt - poetry install --extras all --with examples --with dev + - name: Install uv + uses: astral-sh/setup-uv@v3 + with: + # Install a specific version of uv. + version: "0.4.19" + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + - name: Check formatting if: ${{ matrix.group == 1 && matrix.python-version == '3.11' }} run: ./format.sh check @@ -192,7 +190,7 @@ jobs: - name: Check if git is dirty run: | - git diff --no-ext-diff --quiet --exit-code + git diff --no-ext-diff --exit-code [[ -z $(git status -s) ]] webknossos_cli_docker: @@ -205,21 +203,20 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: "3.10" - + # Install a specific version of uv. + version: "0.4.19" - name: Write version file run: | - pip install -r requirements.txt pushd webknossos - PKG_VERSION="$(dunamai from git)" + PKG_VERSION="$(uvx dunamai from git)" echo "__version__ = '$PKG_VERSION'" > ./webknossos/version.py - poetry version "$PKG_VERSION" + sed -i 's/version = "0.0.0"/version = "'"${PKG_VERSION}"'"/g' pyproject.toml - popd + popd - name: Build docker image run: docker build -t scalableminds/webknossos-cli:$GITHUB_SHA -f webknossos/Dockerfile . @@ -283,16 +280,11 @@ jobs: with: repository: scalableminds/webknossos path: docs/wk-repo - - name: Set up Python 3.8 - uses: actions/setup-python@v4 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: 3.8 - architecture: "x64" - - - name: Install dependencies - run: | - pip3 install -r requirements.txt - + # Install a specific version of uv. + version: "0.4.19" - name: Build Docs run: | cd docs @@ -325,7 +317,7 @@ jobs: SLACK_HOOK: ${{ secrets.LINK_CHECKER_SLACK_HOOK }} run: | cd docs - poetry run linkchecker --config linkcheckerrc https://docs.webknossos.org > link_status || \ + uv run --frozen linkchecker --config linkcheckerrc https://docs.webknossos.org > link_status || \ curl -X POST --data-urlencode "payload={\"text\": \":warning: Broken Links on doc.webknossos.org :warning:\n"'```'"\n$(cat link_status)\n"'```"}' \ "$SLACK_HOOK" @@ -340,20 +332,18 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - - name: Set up Python 3.8 - uses: actions/setup-python@v4 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: 3.8 - architecture: "x64" - - name: Install dependencies - run: pip3 install -r requirements.txt + # Install a specific version of uv. + version: "0.4.19" - name: Publish python packages env: - POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_PASSWORD }} + UV_PUBLISH_TOKEN: ${{ secrets.PYPI_PASSWORD }} run: _tooling/publish.sh - name: Prepare github release run: | - VERSION="$(dunamai from git)" + VERSION="$(uvx dunamai from git)" _tooling/changelog_for_version.sh $VERSION > Changelog.md - name: Publish github release id: create_release diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml index 5473e1f9e..16636125c 100644 --- a/.github/workflows/nightly.yml +++ b/.github/workflows/nightly.yml @@ -20,16 +20,14 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: ${{ matrix.python-version }} - architecture: 'x64' - - - name: Install dependencies - run: | - pip install poetry - poetry install --extras all --with examples --with dev + version: "0.4.19" + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} - name: Check if git is dirty run: | diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 6c6c1dbdf..604f45380 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -15,15 +15,11 @@ jobs: with: repository: scalableminds/webknossos path: docs/wk-repo - - name: Set up Python 3.10 - uses: actions/setup-python@v1 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: "3.10" - architecture: 'x64' - - - name: Install dependencies - run: | - pip install -r requirements.txt + # Install a specific version of uv. + version: "0.4.19" - name: Build Docs run: | @@ -45,6 +41,6 @@ jobs: SLACK_HOOK: ${{ secrets.LINK_CHECKER_SLACK_HOOK }} run: | cd docs - poetry run linkchecker --config linkcheckerrc https://docs.webknossos.org > link_status || \ + uv run --frozen linkchecker --config linkcheckerrc https://docs.webknossos.org > link_status || \ curl -X POST --data-urlencode "payload={\"text\": \":warning: Broken Links on doc.webknossos.org :warning:\n"'```'"\n$(cat link_status)\n"'```"}' \ "$SLACK_HOOK" diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 739590af5..2b1f92ddd 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -102,15 +102,11 @@ The [WEBKNOSSOS-libs repository](https://github.com/scalableminds/webknossos-lib See below for specifics of the different packages. Let's have a look at the common tooling first: -* [**poetry**](https://python-poetry.org) is used for dependency management and publishing. - Use `poetry install --all-extras` in each package folder to install all dependencies for development. +* [**uv**](https://docs.astral.sh/uv) is used for dependency management and publishing. + Use `uv sync --all-extras` in each package folder to install all dependencies for development. By default, this creates a [virtual environment](https://docs.python.org/3/tutorial/venv.html) for each package. - To run commands inside this package, prefix them with `poetry run`, e.g. `poetry run python myscript.py`, - or enter the virtual environment with `poetry shell`. - The creation of a separate environment can be disabled (e.g. if you want to manage this manually), - [see here for details](https://python-poetry.org/docs/configuration/#virtualenvscreate). - To install the preferred version for this repository, run - [`pip install -f requirements.txt`](https://github.com/scalableminds/webknossos-libs/blob/master/requirements.txt) + To run commands inside this package, prefix them with `uv run`, e.g. `uv run python myscript.py`, + or enter the virtual environment with `source .venv/bin/activate`. To install the dependencies for all sub-projects, run `make install`. diff --git a/Makefile b/Makefile index 0b984a0d4..6a9ce0964 100644 --- a/Makefile +++ b/Makefile @@ -15,14 +15,8 @@ endef list_packages_by_priority: @echo $(packages_by_priority) -update: - $(call in_each_pkg_by_dependency, poetry update --without dev) - -update-internal: - $(call in_each_pkg_by_dependency, poetry update $(packages_by_dependency)) - install: - $(call in_each_pkg_by_dependency, poetry install --all-extras) + $(call in_each_pkg_by_dependency, uv sync --all-extras) format: $(call in_each_code_pkg, ./format.sh) diff --git a/README.md b/README.md index 02e218903..bb7eddbbf 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![Supported Python Versions](https://img.shields.io/pypi/pyversions/webknossos.svg)](https://pypi.python.org/pypi/webknossos) [![Build Status](https://img.shields.io/github/actions/workflow/status/scalableminds/webknossos-libs/.github/workflows/ci.yml?branch=master)](https://github.com/scalableminds/webknossos-libs/actions?query=workflow%3A%22CI%22) [![Documentation](https://img.shields.io/badge/docs-passing-brightgreen.svg)](https://docs.webknossos.org/webknossos-py/index.html) +[![Package Manager](https://img.shields.io/pypi/pyversions/uv.svg)](https://pypi.python.org/pypi/uv) [![Code Style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/) WEBKNOSSOS Logo diff --git a/_tooling/publish.sh b/_tooling/publish.sh index 3e4f419ed..2cff9c52a 100755 --- a/_tooling/publish.sh +++ b/_tooling/publish.sh @@ -9,14 +9,18 @@ for PKG in {cluster_tools,webknossos}/pyproject.toml; do pushd "$PKG" > /dev/null cp pyproject.toml pyproject.toml.bak - PKG_VERSION="$(dunamai from git)" + PKG_VERSION="$(uvx dunamai from git)" echo "__version__ = '$PKG_VERSION'" > ./"$PKG"/version.py - poetry version "$PKG_VERSION" - # replace all relative path dependencies with the current version: - sed -i 's/\(.*\) = .* path \= \"\.\..*/\1 = "'"$PKG_VERSION"'"/g' pyproject.toml - poetry publish --build + # Update version number in pyproject.toml + sed -i 's/version = "0.0.0"/version = "'"${PKG_VERSION}"'"/g' pyproject.toml + + # replace relative path dependencies (i.e. cluster-tools) with the current version: + sed -i 's/"cluster-tools"/"cluster-tools=='"${PKG_VERSION}"'"/g' pyproject.toml + + uv build + uv publish # Restore files mv pyproject.toml.bak pyproject.toml diff --git a/cluster_tools/Changelog.md b/cluster_tools/Changelog.md index 7900702c1..a80979750 100644 --- a/cluster_tools/Changelog.md +++ b/cluster_tools/Changelog.md @@ -14,6 +14,7 @@ For upgrade instructions, please check the respective *Breaking Changes* section ### Added ### Changed +- Replaced the Python package manager `poetry` with `uv`. [#1199](https://github.com/scalableminds/webknossos-libs/pull/1199) ### Fixed diff --git a/cluster_tools/README.md b/cluster_tools/README.md index 5d2f7f2b9..b1c48ef81 100644 --- a/cluster_tools/README.md +++ b/cluster_tools/README.md @@ -81,9 +81,9 @@ docker exec -it slurmctld bash docker exec -it c1 bash ``` -Make sure to install all extra dependencies, such as Kubernetes, with `poetry install --all-extras`. +Make sure to install all extra dependencies, such as Kubernetes, with `uv sync --all-extras`. -Tests can be executed with `cd tests && poetry run pytest -s tests.py` after entering the container. +Tests can be executed with `cd tests && uv run pytest -s tests.py` after entering the container. Linting can be run with `./lint.sh`. Code formatting (black) can be run with `./format.sh`. diff --git a/cluster_tools/cluster_tools/executors/dask.py b/cluster_tools/cluster_tools/executors/dask.py index 8c2da63fd..859530af0 100644 --- a/cluster_tools/cluster_tools/executors/dask.py +++ b/cluster_tools/cluster_tools/executors/dask.py @@ -118,7 +118,7 @@ def __init__( import distributed # noqa: F401 unused import except ModuleNotFoundError: logger.error( - 'The distributed Python package for Dask is not installed. cluster_tools does not install this dependency be default. Run `pip install cluster_tools[dask]` or `poetry install --extras "dask"` to install Dask support.' + 'The distributed Python package for Dask is not installed. cluster_tools does not install this dependency be default. Run `pip install cluster_tools[dask]` or `uv sync --extra "dask"` to install Dask support.' ) exit() diff --git a/cluster_tools/cluster_tools/schedulers/kube.py b/cluster_tools/cluster_tools/schedulers/kube.py index 99ef0abfb..e52be82bf 100644 --- a/cluster_tools/cluster_tools/schedulers/kube.py +++ b/cluster_tools/cluster_tools/schedulers/kube.py @@ -54,7 +54,7 @@ def __init__( import kubernetes # noqa: F401 unused import except ModuleNotFoundError: logger.error( - 'The Kubernetes Python package is not installed. cluster_tools does not install this dependency be default. Run `pip install cluster_tools[kubernetes]` or `poetry install --extras "kubernetes"` to install Kubernetes support.' + 'The Kubernetes Python package is not installed. cluster_tools does not install this dependency be default. Run `pip install cluster_tools[kubernetes]` or `uv sync --extra "kubernetes"` to install Kubernetes support.' ) exit() diff --git a/cluster_tools/dockered-slurm/docker-compose.yml b/cluster_tools/dockered-slurm/docker-compose.yml index cdbc9fcb7..b936f0926 100644 --- a/cluster_tools/dockered-slurm/docker-compose.yml +++ b/cluster_tools/dockered-slurm/docker-compose.yml @@ -15,7 +15,7 @@ services: - ..:/cluster_tools slurmdbd: - image: scalableminds/slurm-docker-cluster:master__5614367471 + image: scalableminds/slurm-docker-cluster:master__11274637426 command: ["slurmdbd"] container_name: slurmdbd hostname: slurmdbd @@ -31,7 +31,7 @@ services: - mysql slurmctld: - image: scalableminds/slurm-docker-cluster:master__5614367471 + image: scalableminds/slurm-docker-cluster:master__11274637426 command: ["slurmctld"] container_name: slurmctld environment: @@ -52,7 +52,7 @@ services: - "slurmdbd" c1: - image: scalableminds/slurm-docker-cluster:master__5614367471 + image: scalableminds/slurm-docker-cluster:master__11274637426 command: ["slurmd"] hostname: c1 container_name: c1 @@ -70,7 +70,7 @@ services: - "slurmctld" c2: - image: scalableminds/slurm-docker-cluster:master__5614367471 + image: scalableminds/slurm-docker-cluster:master__11274637426 command: ["slurmd"] hostname: c2 container_name: c2 diff --git a/cluster_tools/format.sh b/cluster_tools/format.sh index cd41104d5..02013f563 100755 --- a/cluster_tools/format.sh +++ b/cluster_tools/format.sh @@ -2,8 +2,8 @@ set -eEuo pipefail if [ $# -eq 1 ] && [ "$1" = "check" ]; then - poetry run ruff format --check . + uv run ruff format --check . else - poetry run ruff check --select I --fix . # format the imports - poetry run ruff format . + uv run ruff check --select I --fix . # format the imports + uv run ruff format . fi diff --git a/cluster_tools/lint.sh b/cluster_tools/lint.sh index d029d1abc..d9d719a60 100755 --- a/cluster_tools/lint.sh +++ b/cluster_tools/lint.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash set -eEuo pipefail -poetry run ruff check --fix . \ No newline at end of file +uv run ruff check --fix . \ No newline at end of file diff --git a/cluster_tools/poetry.lock b/cluster_tools/poetry.lock deleted file mode 100644 index 1b40ff3ca..000000000 --- a/cluster_tools/poetry.lock +++ /dev/null @@ -1,1074 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. - -[[package]] -name = "asttokens" -version = "2.4.1" -description = "Annotate AST trees with source code positions" -optional = false -python-versions = "*" -files = [ - {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, - {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, -] - -[package.dependencies] -six = ">=1.12.0" - -[package.extras] -astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] -test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] - -[[package]] -name = "cachetools" -version = "5.3.3" -description = "Extensible memoizing collections and decorators" -optional = true -python-versions = ">=3.7" -files = [ - {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"}, - {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"}, -] - -[[package]] -name = "certifi" -version = "2024.7.4" -description = "Python package for providing Mozilla's CA Bundle." -optional = true -python-versions = ">=3.6" -files = [ - {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, - {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, -] - -[[package]] -name = "charset-normalizer" -version = "3.3.2" -description = "The Real First Universal Charset Detector. 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+++ b/cluster_tools/pyproject.toml @@ -1,32 +1,37 @@ -[tool.poetry] +[project] name = "cluster_tools" version = "0.0.0" # filled by dunamai description = "Utility library for easily distributing code execution on clusters" -authors = ["scalable minds "] +authors = [{name= "scalable minds", email="hello@scalableminds.com"}] readme = "README.md" -license = "MIT" -repository = "https://github.com/scalableminds/webknossos-libs" - -[tool.poetry.extras] -kubernetes = ["kubernetes"] -dask = ["distributed"] -all = ["kubernetes", "distributed"] - -[tool.poetry.dependencies] -python = ">=3.9" -distributed = { version = "^2023.9.1", python = ">=3.9", optional = true } -kubernetes = {version = "^27.2.0", optional = true } -typing-extensions = "^4.4.0" - -[tool.poetry.group.dev.dependencies] -icecream = "^2.1.1" -mypy = "^1.0.0" -pytest = "^7.2.1" -ruff = "^0.5.0" +license = {text = "MIT"} +requires-python = ">=3.9" + +[project.urls] +Repository = "https://github.com/scalableminds/webknossos-libs" +Changelog = "https://github.com/scalableminds/webknossos-libs/blob/master/cluster_tools/Changelog.md" + + +[project.optional-dependencies] +kubernetes = ["distributed ~=2023.9.1"] +dask = ["kubernetes ~=27.2.0"] +all=["cluster_tools[kubernetes]", "cluster_tools[dask]"] + +[tool.uv] +dev-dependencies = [ + "typing-extensions ~=4.12.0", + "icecream ~=2.1.1", + "mypy ~=1.0.0", + "pytest ~=7.2.1", + "ruff ~=0.5.0", +] [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["setuptools>=70.0", "wheel; python_version>='3.12'"] +build-backend = "setuptools.build_meta" + +[tool.setuptools] +packages = ["cluster_tools"] [tool.ruff] # Exclude a variety of commonly ignored directories. @@ -56,8 +61,8 @@ exclude = [ line-length = 88 indent-width = 4 -# Assume Python 3.8 for automatic linting fixes -target-version = "py38" +# Assume Python 3.9 for automatic linting fixes +target-version = "py39" [tool.ruff.lint] # F = Pyflakes https://docs.astral.sh/ruff/rules/#pyflakes-f diff --git a/cluster_tools/test.sh b/cluster_tools/test.sh index 7e80dd4f3..8dd64ad35 100755 --- a/cluster_tools/test.sh +++ b/cluster_tools/test.sh @@ -1,4 +1,7 @@ #!/usr/bin/env bash set -eEuo pipefail -echo "test.sh is not available for cluster_tools yet" + cd tests + PYTEST_EXECUTORS=multiprocessing,sequential,test_pickling,debug_sequential uv run --frozen python -m pytest -sv test_all.py test_multiprocessing.py + + echo "Tests for the kubernetes, dask and SLURM executors are only run in the CI" diff --git a/cluster_tools/tests/Dockerfile b/cluster_tools/tests/Dockerfile index 36dc706d8..2c351c631 100644 --- a/cluster_tools/tests/Dockerfile +++ b/cluster_tools/tests/Dockerfile @@ -1,14 +1,13 @@ FROM python:3.11 +COPY --from=ghcr.io/astral-sh/uv:0.4.20 /uv /bin/uv + RUN mkdir /cluster_tools -COPY requirements.txt /cluster_tools -COPY poetry.lock /cluster_tools -COPY pyproject.toml /cluster_tools +COPY . /cluster_tools WORKDIR 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Via `--dis ## Development -Make sure to install all the required dependencies using Poetry: +Make sure to install all the required dependencies using [`uv`](https://docs.astral.sh/uv/): ```bash git clone git@github.com:scalableminds/webknossos-libs.git cd webknossos-libs -pip install -r requirements.txt cd webknossos -poetry install --all-extras +uv sync --all-extras ``` Please, format, lint, typecheck and unit test your code changes before merging them. diff --git a/docs/uv.lock b/docs/uv.lock new file mode 100644 index 000000000..f21cef642 --- /dev/null +++ b/docs/uv.lock @@ -0,0 +1,2232 @@ +version = 1 +requires-python = ">=3.9, <3.13" + +[[package]] +name = "aiohappyeyeballs" +version = "2.4.3" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/bc/69/2f6d5a019bd02e920a3417689a89887b39ad1e350b562f9955693d900c40/aiohappyeyeballs-2.4.3.tar.gz", hash = "sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586", 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deleted file mode 100644 index 864bf0489..000000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -dunamai==1.18.1 -poetry==1.8.2 diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md index 66e45e79f..07ff0680f 100644 --- a/webknossos/Changelog.md +++ b/webknossos/Changelog.md @@ -18,6 +18,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section - Added `add_mag_from_zarrarray` to `Layer` class, to add existing Zarr arrays as a mag of a layer. [#1151](https://github.com/scalableminds/webknossos-libs/pull/1151) ### Changed +- Replaced the Python package manager `poetry` with `uv`. [#1199](https://github.com/scalableminds/webknossos-libs/pull/1199) ### Fixed diff --git a/webknossos/Dockerfile b/webknossos/Dockerfile index 010e38918..026348670 100644 --- a/webknossos/Dockerfile +++ b/webknossos/Dockerfile @@ -1,21 +1,21 @@ -FROM python:3.10 +FROM python:3.12 -COPY requirements.txt / - -RUN pip install -r /requirements.txt +COPY --from=ghcr.io/astral-sh/uv:0.4.20 /uv /bin/uv RUN mkdir /webknossos COPY webknossos/webknossos /webknossos/webknossos -COPY webknossos/poetry.lock /webknossos/ +COPY webknossos/uv.lock /webknossos/ COPY webknossos/pyproject.toml /webknossos/ COPY webknossos/README.md /webknossos/ RUN mkdir /cluster_tools COPY cluster_tools/cluster_tools /cluster_tools/cluster_tools -COPY cluster_tools/poetry.lock /cluster_tools/ +COPY cluster_tools/uv.lock /cluster_tools/ COPY cluster_tools/pyproject.toml /cluster_tools/ COPY cluster_tools/README.md /cluster_tools/ WORKDIR /webknossos -RUN poetry config virtualenvs.create false && poetry install --all-extras +RUN uv export --all-extras --output-file requirements.txt && \ + uv pip sync --system requirements.txt && \ + uv cache clean \ No newline at end of file diff --git a/webknossos/README.md b/webknossos/README.md index a4ee9048e..d07f513e3 100644 --- a/webknossos/README.md +++ b/webknossos/README.md @@ -4,6 +4,7 @@ [![Build Status](https://img.shields.io/github/actions/workflow/status/scalableminds/webknossos-libs/.github/workflows/ci.yml?branch=master)](https://github.com/scalableminds/webknossos-libs/actions?query=workflow%3A%22CI%22) [![Documentation](https://img.shields.io/badge/docs-passing-brightgreen.svg)](https://docs.webknossos.org/webknossos-py) [![Code Style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) Python API for working with [WEBKNOSSOS](https://webknossos.org) datasets, annotations, and for WEBKNOSSOS server interaction. @@ -27,7 +28,7 @@ For the WEBKNOSSOS server, please refer to https://github.com/scalableminds/webk Please refer to [the documentation for further instructions](https://docs.webknossos.org/webknossos-py). ## Installation -The `webknossos` package requires at least Python 3.8. +The `webknossos` package requires at least Python 3.9. You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via pip: @@ -35,6 +36,8 @@ You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via p pip install webknossos ``` +To install `webknossos` with the depencies for all examples, support for CZI files, and BioFormats conversions, run: `pip install webknossos[all]`. + By default `webknossos` can only distribute any computations through multiprocessing or Slurm. For Kubernetes or Dask install these additional dependencies: ```bash @@ -44,13 +47,11 @@ pip install cluster_tools[dask] ## Examples See the [examples folder](examples) or the [the documentation](https://docs.webknossos.org/webknossos-py). -The dependencies for the examples are not installed by default. Use `poetry install --with examples` to install them. +The dependencies for the examples are not installed by default. Use `pip install webknossos[examples]` to install them. ## Contributions & Development Please see the [respective documentation page](https://docs.webknossos.org/webknossos-py/development.html). -The development dependencies not installed by default. Use `poetry install --with dev` to install them. - ## License [AGPLv3](https://www.gnu.org/licenses/agpl-3.0.html) Copyright [scalable minds](https://scalableminds.com) diff --git a/webknossos/format.sh b/webknossos/format.sh index cd41104d5..34d355e57 100755 --- a/webknossos/format.sh +++ b/webknossos/format.sh @@ -2,8 +2,8 @@ set -eEuo pipefail if [ $# -eq 1 ] && [ "$1" = "check" ]; then - poetry run ruff format --check . + uv run --frozen ruff format --check . else - poetry run ruff check --select I --fix . # format the imports - poetry run ruff format . + uv run --frozen ruff check --select I --fix . # format the imports + uv run --frozen ruff format . fi diff --git a/webknossos/lint.sh b/webknossos/lint.sh index d029d1abc..d1a2f576d 100755 --- a/webknossos/lint.sh +++ b/webknossos/lint.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash set -eEuo pipefail -poetry run ruff check --fix . \ No newline at end of file +uv run --frozen ruff check --fix . \ No newline at end of file diff --git a/webknossos/poetry.lock b/webknossos/poetry.lock deleted file mode 100644 index 884ccb991..000000000 --- a/webknossos/poetry.lock +++ /dev/null @@ -1,3522 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - 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"Typing :: Typed" + "Typing :: Typed", +] + +requires-python = ">=3.9,<3.13" + +dependencies = [ + "aiohttp ~=3.10.5", + "attrs >=22.0.0", + "boltons >=21.0.0", + "cattrs >=22.0.0", + "cluster-tools", + "fsspec ~=2024.6.0", + "httpx ~=0.27.0", + "loxun ~=2.0.0", + "natsort ~=8.4.0", + "networkx ~=3.2.1", + "numcodecs ~=0.12", + "numpy ~=2.0.0", + "pims ~=0.7.0", + "psutil ~=6.0.0", + "python-dateutil ~=2.8.0", + "python-dotenv ~=1.0.1", + "rich ~=13.8.0", + "scipy ~=1.13", + "typer ~=0.12.5", + "typing-extensions ~=4.0", + "universal-pathlib ~=0.2", + "wkw ==1.1.24", + "zarr ~=2.18.0", + "zarrita ==0.2.7", + "zipp ~=3.5.0", ] -include = ["webknossos/version.py"] # included explicitly since it's in .gitignore - -[tool.poetry.dependencies] -python = ">=3.9,<3.13" -aiohttp = "^3.8.1" -attrs = ">=22.0.0" -boltons = ">=21.0.0" -cattrs = ">=22.0.0" -cluster_tools = { path = "../cluster_tools/", develop = true } -fsspec = "^2024.6.0" -httpx = "^0.27.0" -loxun = "^2.0" -natsort = "^8.4.0" -networkx = "^3" -numcodecs = "^0.12" -numpy = "^2" -pims = "^0.7.0" -psutil = "^6" -python-dateutil = "^2.8.0" -python-dotenv = "^1" -rich = "^13" -scipy = "^1.9.0" -typer = "^0.12" -typing-extensions = "^4.0" -universal-pathlib = "^0.2" -wkw = "1.1.24" -zarr = "^2.18.0" -zarrita = "0.2.7" -zipp = "^3.5.0" - 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They can be opted into by apps. -imagecodecs = { version = ">=2021.11.20", optional = true } -JPype1 = { version = "^1.3.0", optional = true } -tifffile = { version = ">=2024.8.24", optional = true } -pylibCZIrw = { version = "4.1.1", source = "scm", optional = true} - -[tool.poetry.extras] -tifffile = ["tifffile"] -imagecodecs = ["imagecodecs"] -bioformats = ["JPype1"] -czi = ["pylibCZIrw"] -all = ["tifffile","imagecodecs","JPype1","pylibCZIrw"] - -[tool.poetry.group.dev] -optional = true - -[tool.poetry.group.dev.dependencies] -dask = { version = "^2023.9.1", python = ">=3.9", extras = ["distributed"] } -hypothesis = "^6.35.0" -icecream = "^2.1.1" -inducoapi = "^2.0.2" -jsonschema = "^4.6.0" -mypy = "^1.10.0" -pytest = "^8" -pytest-custom-exit-code = "^0.3.0" -pytest-recording = "^0.13.0" -pytest-split = "^0.9.0" -pytest-sugar = "^1" -pytest-timeout = "^2.3.0" -pytest-timestamper = "^0.0.10" -types-python-dateutil = "^2.9" -ruff = "^0.5" - -[tool.poetry.group.examples] -optional = true - -[tool.poetry.group.examples.dependencies] -# packages for examples: -fastremap = "^1.15.0" -pandas = "^2" -pooch = "^1.5.2" -s3fs = ">=2023.9.0" -tabulate = "^0.9" -scikit-learn = "^1.0.1" -scikit-image = "^0.24.0" - -[[tool.poetry.source]] -name = "PyPI" -priority = "primary" - -[[tool.poetry.source]] -name = "scm" -url = "https://pypi.scm.io/simple" -priority = "supplemental" + +[project.urls] +Homepage = "https://docs.webknossos.org/webknossos-py" +Repository = "https://github.com/scalableminds/webknossos-libs" +Documentation = "https://docs.webknossos.org" +Changelog = "https://github.com/scalableminds/webknossos-libs/blob/master/webknossos/Changelog.md" + +# A list of all of the optional dependencies. They can be opted into by other apps. +[project.optional-dependencies] +tifffile = ["tifffile >=2024.8.24"] +imagecodecs = ["imagecodecs >=2021.11.20"] +bioformats = ["JPype1 ~=1.5.0"] +czi = ["pylibCZIrw ==4.1.1"] +examples = [ + "fastremap ~=1.15.0", + "pandas ~=2.2.0", + "pooch ~=1.5.2", + "s3fs >=2023.9.0", + "tabulate >=0.9.0", + "scikit-learn ~=1.5.1", + "scikit-image ~=0.24.0" +] +all = [ + "webknossos[tifffile]", + "webknossos[imagecodecs]", + "webknossos[bioformats]", + "webknossos[czi]", + "webknossos[examples]", +] + +[tool.uv] +extra-index-url = ["https://pypi.scm.io/simple"] +dev-dependencies = [ + "dask[distributed] ~=2023.9.1; python_version >='3.9'", + "hypothesis ~=6.35.0", + "icecream ~=2.1.1", + "inducoapi ~=2.0.2", + "jsonschema ~=4.6.0", + "mypy ~=1.10.0", + "pytest ~=8.3.2", + "pytest-custom-exit-code ~=0.3.0", + "pytest-recording ~=0.13.0", + "vcrpy ~=6.0", + "pytest-split ~=0.9.0", + "pytest-sugar ~=1.0.0", + "pytest-timeout ~=2.3.0", + "pytest-timestamper ~=0.0.10", + "types-python-dateutil ~=2.9", + "ruff ~=0.6.0", +] + +[tool.uv.sources] +cluster-tools = { path = "../cluster_tools", editable = true } + +[project.scripts] +webknossos = "webknossos.cli.main:app" [tool.mypy] ignore_missing_imports = true @@ -140,15 +140,15 @@ exclude = [ "node_modules", "site-packages", "venv", - "webknossos/dataset/_utils/vendor" + "webknossos/dataset/_utils/vendor", ] # Same as Black. line-length = 88 indent-width = 4 -# Assume Python 3.8 for automatic linting fixes -target-version = "py38" +# Assume Python 3.9 for automatic linting fixes +target-version = "py39" [tool.ruff.lint] # F = Pyflakes https://docs.astral.sh/ruff/rules/#pyflakes-f @@ -181,9 +181,12 @@ line-ending = "auto" markers = ["with_vcr: Runs with VCR recording and optionally blocked network"] testpaths = ["tests"] -[tool.poetry.scripts] -webknossos = "webknossos.cli.main:app" - [build-system] -requires = ["poetry-core>=1.1"] -build-backend = "poetry.core.masonry.api" +requires = ["setuptools>=70.0", "wheel; python_version>='3.12'"] +build-backend = "setuptools.build_meta" + +[tool.setuptools] +packages = ["webknossos"] +# include = [ +# "webknossos/version.py", +# ] # included explicitly since it's in .gitignore diff --git a/webknossos/test.sh b/webknossos/test.sh index 63e2eaddf..c0012b451 100755 --- a/webknossos/test.sh +++ b/webknossos/test.sh @@ -10,7 +10,7 @@ export_vars # this will ensure that the current directory is added to sys.path # (which is standard python behavior). This is necessary so that the imports # refer to the checked out (and potentially modified) code. -PYTEST="poetry run python -m pytest --suppress-no-test-exit-code" +PYTEST="uv run --all-extras --frozen python -m pytest --suppress-no-test-exit-code" if [ $# -gt 0 ] && [ "$1" = "--refresh-snapshots" ]; then diff --git a/webknossos/tests/dataset/test_buffered_slice_utils.py b/webknossos/tests/dataset/test_buffered_slice_utils.py index 19c6f0707..a5a3be892 100644 --- a/webknossos/tests/dataset/test_buffered_slice_utils.py +++ b/webknossos/tests/dataset/test_buffered_slice_utils.py @@ -117,13 +117,16 @@ def test_buffered_slice_reader_along_different_axis(tmp_path: Path) -> None: mag_view = ds.add_layer("color", COLOR_CATEGORY, num_channels=3).add_mag(1) mag_view.write(test_cube, absolute_offset=offset) - with mag_view.get_buffered_slice_reader( - buffer_size=5, dimension=dim - ) as reader_a, mag_view.get_buffered_slice_reader( - absolute_bounding_box=BoundingBox(offset, cube_size_without_channel), - buffer_size=5, - dimension=dim, - ) as reader_b: + with ( + mag_view.get_buffered_slice_reader( + buffer_size=5, dimension=dim + ) as reader_a, + mag_view.get_buffered_slice_reader( + absolute_bounding_box=BoundingBox(offset, cube_size_without_channel), + buffer_size=5, + dimension=dim, + ) as reader_b, + ): i = 0 for slice_data_a, slice_data_b in zip(reader_a, reader_b): if dim == 0: diff --git a/webknossos/tests/test_cli.py b/webknossos/tests/test_cli.py index 8b184903d..afe18d2ff 100644 --- a/webknossos/tests/test_cli.py +++ b/webknossos/tests/test_cli.py @@ -93,9 +93,12 @@ def test_tiff_cubing_zarr_s3() -> None: assert (out_path / "tiff" / "1" / ".zarray").exists() assert (out_path / PROPERTIES_FILE_NAME).exists() - with (out_path / PROPERTIES_FILE_NAME).open("r") as file, ( - TESTDATA_DIR / "tiff" / "datasource-properties.zarr-fixture.json" - ).open("r") as fixture: + with ( + (out_path / PROPERTIES_FILE_NAME).open("r") as file, + (TESTDATA_DIR / "tiff" / "datasource-properties.zarr-fixture.json").open( + "r" + ) as fixture, + ): json_a = json.load(file) json_fixture = json.load(fixture) del json_a["id"] diff --git a/webknossos/typecheck.sh b/webknossos/typecheck.sh index 72e34ba18..7b60a836b 100755 --- a/webknossos/typecheck.sh +++ b/webknossos/typecheck.sh @@ -4,13 +4,13 @@ set -eEuo pipefail export MYPYPATH=./stubs echo "Typecheck webknossos..." -poetry run python -m mypy -p webknossos +uv run --frozen python -m mypy -p webknossos echo "Typecheck tests..." -poetry run python -m mypy -p tests +uv run --frozen python -m mypy -p tests echo "Typecheck examples..." -poetry run python -m mypy -p examples +uv run --frozen python -m mypy -p examples echo "Typecheck script_collection..." -poetry run python -m mypy -p script_collection +uv run --frozen python -m mypy -p script_collection diff --git a/webknossos/uv.lock b/webknossos/uv.lock new file mode 100644 index 000000000..97f0ec652 --- /dev/null +++ b/webknossos/uv.lock @@ -0,0 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a/webknossos/webknossos/annotation/annotation.py b/webknossos/webknossos/annotation/annotation.py index 43c8f5dbc..26f37bc16 100644 --- a/webknossos/webknossos/annotation/annotation.py +++ b/webknossos/webknossos/annotation/annotation.py @@ -106,9 +106,10 @@ def _extract_zip_folder(zip_file: ZipFile, out_path: Path, prefix: str) -> None: if zip_entry.filename.startswith(prefix) and not zip_entry.is_dir(): out_file_path = out_path / (zip_entry.filename[len(prefix) :]) out_file_path.parent.mkdir(parents=True, exist_ok=True) - with zip_file.open(zip_entry, "r") as zip_f, out_file_path.open( - "wb" - ) as out_f: + with ( + zip_file.open(zip_entry, "r") as zip_f, + out_file_path.open("wb") as out_f, + ): copyfileobj(zip_f, out_f) diff --git a/webknossos/webknossos/utils.py b/webknossos/webknossos/utils.py index c8e704c66..48d38a12e 100644 --- a/webknossos/webknossos/utils.py +++ b/webknossos/webknossos/utils.py @@ -340,9 +340,10 @@ def _append(path: Path, parts: Tuple[str, ...]) -> Path: if in_sub_path.is_dir(): _append(out_path, sub_path).mkdir(parents=True, exist_ok=True) else: - with _append(in_path, sub_path).open("rb") as in_file, _append( - out_path, sub_path - ).open("wb") as out_file: + with ( + _append(in_path, sub_path).open("rb") as in_file, + _append(out_path, sub_path).open("wb") as out_file, + ): copyfileobj(in_file, out_file)