diff --git a/.github/workflows/dependabot.yml b/.github/workflows/dependabot.yml index d55c0f4..f7c7c1f 100644 --- a/.github/workflows/dependabot.yml +++ b/.github/workflows/dependabot.yml @@ -28,14 +28,10 @@ jobs: uses: actions/setup-python@v6 with: python-version: "3.11" - - name: Setup for poetry - run: | - python -m pip install poetry - poetry self add "poetry-dynamic-versioning[plugin]" - - name: Install environment - run: poetry install --no-interaction --no-ansi - # run pre-commit - - uses: pre-commit/action@v3.0.1 + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 + # run pre-commmit checks using prek for faster execution + - uses: j178/prek-action@v1 id: pre_commit continue-on-error: true - name: Check for changes diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml index 37cc53c..5e2cc4c 100644 --- a/.github/workflows/publish-docs.yml +++ b/.github/workflows/publish-docs.yml @@ -23,20 +23,14 @@ jobs: - uses: actions/setup-python@v6 with: python-version: "3.11" - - name: Setup for poetry - run: | - python -m pip install poetry poetry-dynamic-versioning - - name: Simulate version tag for cosmicqc install compatibility - run: | - poetry version 99.0.0 - - name: poetry deps - run: poetry install + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 - name: Build documentation run: | mkdir pages touch pages/.nojekyll cd docs - poetry run sphinx-build src build + uv run --frozen --with docs sphinx-build src build # remove any doctrees dirs which aren't needed for publishing find ./build -type d -name '.doctrees' -exec rm -rf {} + cp -r build/* ../pages/ @@ -45,6 +39,3 @@ jobs: with: branch: pages folder: pages - - name: Reset version to 0.0.0 - run: | - poetry version 0.0.0 diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 75f5591..a0a4842 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -23,12 +23,9 @@ jobs: uses: actions/setup-python@v6 with: python-version: "3.11" - - name: Setup for poetry - run: | - python -m pip install poetry poetry-dynamic-versioning - - name: Install environment - run: poetry install --without dev --no-interaction --no-ansi - - name: poetry build distribution content - run: poetry build + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 + - name: uv build distribution content + run: uv build - name: Publish package distributions to PyPI uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index c2a0d64..eb6587c 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -21,14 +21,8 @@ jobs: uses: actions/setup-python@v6 with: python-version: "3.11" - - name: Setup for poetry - run: | - python -m pip install poetry - - name: Simulate version tag for cosmicqc install compatibility - run: | - poetry version 99.0.0 - - name: Install environment - run: poetry install --with dev --no-interaction --no-ansi + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 # run pre-commit - uses: pre-commit/action@v3.0.1 id: pre_commit @@ -50,24 +44,15 @@ jobs: uses: actions/setup-python@v6 with: python-version: ${{ matrix.python_version }} - - name: Setup for poetry - run: | - python -m pip install poetry - - name: Simulate version tag for cosmicqc install compatibility - run: | - poetry version 99.0.0 - - name: Install environment - run: poetry install --with dev --no-interaction --no-ansi + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 - name: Run pytest (non-3.13) if: ${{ matrix.python_version != '3.13' }} # run all tests - run: poetry run pytest -o addopts= + run: uv run --frozen pytest -o addopts= - name: Run pytest (py 3.13) if: ${{ matrix.python_version == '3.13' }} # run all tests except integration tests with cosmicqc run: | - poetry run pytest -o addopts= \ + uv run --frozen pytest -o addopts= \ --ignore=tests/test_project_integration.py - - name: Reset version to 0.0.0 - run: | - poetry version 0.0.0 diff --git a/.gitignore b/.gitignore index 770b919..9340386 100644 --- a/.gitignore +++ b/.gitignore @@ -145,3 +145,6 @@ cython_debug/ # jupyter notebook build files from myst-nb docs/jupyter_execute + +# version placeholder is updated during builds +_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c093517..65bc07c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,12 +14,8 @@ repos: )$ - id: check-yaml - id: detect-private-key -- repo: https://github.com/python-poetry/poetry - rev: "2.3.2" - hooks: - - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.12.1" + rev: "v2.16.1" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell @@ -66,14 +62,13 @@ repos: rev: v0.6.0 hooks: - id: pre-commit-update - args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert", - "--keep", "pyproject-fmt"] + args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert"] - repo: local hooks: - id: code-cov-gen name: Generate code coverage language: system - entry: poetry run coverage run -m pytest -o addopts= + entry: uv run --frozen coverage run -m pytest -o addopts= pass_filenames: false always_run: true - repo: https://github.com/Weird-Sheep-Labs/coverage-pre-commit diff --git a/README.md b/README.md index f60c2bd..dff1373 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Build Status](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/cytomining/CytoDataFrame/actions/workflows/run-tests.yml?query=branch%3Amain) ![Coverage Status](https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/media/coverage-badge.svg) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) -[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/) +[![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) [![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.14797074.svg)](https://doi.org/10.5281/zenodo.14797074) ![](https://raw.githubusercontent.com/cytomining/coSMicQC/refs/heads/main/docs/presentations/2024-09-18-SBI2-Conference/images/cosmicqc-example-cytodataframe.png) diff --git a/docs/presentations/2025-sbi2/readme.md b/docs/presentations/2025-sbi2/readme.md index d699210..3512f7e 100644 --- a/docs/presentations/2025-sbi2/readme.md +++ b/docs/presentations/2025-sbi2/readme.md @@ -15,10 +15,10 @@ See the following examples for more information: ```bash # preview the poster during development -poetry run poe poster-preview +uv run poe poster-preview # build the poster PDF from source -poetry run poe poster-render +uv run poe poster-render ``` ## References diff --git a/docs/src/contributing.md b/docs/src/contributing.md index f1ad45e..fc68898 100644 --- a/docs/src/contributing.md +++ b/docs/src/contributing.md @@ -15,7 +15,7 @@ Please open a [new security advisory notice](https://github.com/cytomining/CytoD ## Development -This project leverages development environments managed by Python [Poetry](https://python-poetry.org/). +This project leverages development environments managed by [uv](https://docs.astral.sh/uv/). We leverage interactions with the Docker through Python to achieve reproducible results through containers. We use [pytest](https://docs.pytest.org/) for testing and [GitHub actions](https://docs.github.com/en/actions) for automated tests. @@ -24,8 +24,8 @@ We use [pytest](https://docs.pytest.org/) for testing and [GitHub actions](https Perform the following steps to setup a Python development environment. 1. [Install Python](https://www.python.org/downloads/) (we recommend using [`pyenv`](https://github.com/pyenv/pyenv) or similar) -1. [Install Poetry](https://python-poetry.org/docs/#installation) -1. [Install Poetry Environment](https://python-poetry.org/docs/basic-usage/#installing-dependencies): `poetry install` +1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/) +1. Install project dependencies: `uv sync --all-groups` ### Linting @@ -44,13 +44,13 @@ These automated tests generally must pass in order to merge work into this repos ### Testing Work added to this project is automatically tested using [pytest](https://docs.pytest.org/) via [GitHub Actions](https://docs.github.com/en/actions). -Pytest is installed through the Poetry environment for this project. +Pytest is installed through the uv-managed environment for this project. We recommend testing your work before opening pull requests with proposed changes. You can run pytest on your work using the following example: ```sh -% poetry run pytest +% uv run pytest ``` Pytest output includes a terminal coverage summary to help track current @@ -89,13 +89,12 @@ We will check for accuracy, style, code coverage, and scope. ## Versioning -We use [`poetry-dynamic-versioning`](https://github.com/mtkennerly/poetry-dynamic-versioning) to help version this software through [`PEP 440`](https://peps.python.org/pep-0440/) standards. +We use [`setuptools-scm`](https://setuptools-scm.readthedocs.io/) to help version this software through [`PEP 440`](https://peps.python.org/pep-0440/) standards. Configuration for versioning is found within the `pyproject.toml` file. All builds for packages include dynamic version data to help label distinct versions of the software. -`poetry-dynamic-versioning` uses `git` tags to help distinguish version data. -We also use the `__init__.py` file as a place to persist the version data for occaissions where the `git` history is unavailable or unwanted. +`setuptools-scm` uses `git` tags to help distinguish version data. +We also use `src/cytodataframe/_version.py` as a place to persist version data for occasions where the `git` history is unavailable or unwanted. -The following command is used to add `poetry-dynamic-versioning` to Poetry for use with this project: `poetry self add "poetry-dynamic-versioning[plugin]"`. Versioning for the project is intended to align with GitHub Releases which provide `git` tag capabilities. ### Releases @@ -109,7 +108,7 @@ Several manual and automated steps are involved with publishing CytoDataFrame re See below for an overview of how this works. Notes about [semantic version](https://en.wikipedia.org/wiki/Software_versioning#Semantic_versioning) (semver) specifications: -CytoDataFrame version specifications are controlled through [`poetry-dynamic-versioning`](https://github.com/mtkennerly/poetry-dynamic-versioning) which leverages [`dunamai`](https://github.com/mtkennerly/dunamai) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and commits. +CytoDataFrame version specifications are controlled through [`setuptools-scm`](https://setuptools-scm.readthedocs.io/) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and commits. CytoDataFrame release git tags are automatically applied through [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) and related inferred changes from [`release-drafter`](https://github.com/release-drafter/release-drafter). 1. Open a pull request and use a repository label for `release-` to label the pull request for visibility with [`release-drafter`](https://github.com/release-drafter/release-drafter) (for example, see [CytoDataFrame#24](https://github.com/cytomining/CytoDataFrame/pull/24) as a reference of a semver patch update). @@ -130,9 +129,9 @@ See below for some examples of how to build documentation locally. ```shell # build single-version sphinx documentation # (useful for troubleshooting potential issues) -poetry run sphinx-build docs/src docs/build +uv run sphinx-build docs/src docs/build # build multi-version sphinx documentation # (used in production) -poetry run sphinx-multiversion docs/src docs/build +uv run sphinx-multiversion docs/src docs/build ``` diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 4d0dfa2..0000000 --- a/poetry.lock +++ /dev/null @@ -1,7054 +0,0 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. - -[[package]] -name = "accessible-pygments" -version = "0.0.5" -description = "A collection of accessible pygments styles" -optional = false -python-versions = ">=3.9" -groups = ["docs"] -files = [ - 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-python = ">=3.11,<3.14" -# used for data management -pandas = [ - { version = "<2.2.2", python = "<3.9" }, - { version = "^2.2.2", python = ">=3.9" }, -] -# used for data ingest and export -pyarrow = ">=16" -# used for environment detection -ipython = ">=8.12.3,<10.0.0" -# used for image processing -scikit-image = [ - { version = "^0.19.3", python = "<3.9" }, - { version = ">0.19.3", python = ">=3.9" }, +license = "BSD-3-Clause" +authors = [ { name = "Way Science Community" } ] +requires-python = ">=3.11,<3.14" +classifiers = [ + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", ] -# dependency of scikit-image -pywavelets = [ - { version = "^1.4.1", python = "<3.9" }, - { version = ">1.4.1", python = ">=3.9" }, +dynamic = [ "version" ] +dependencies = [ + "imagecodecs>=2024.9.22,<2027", + "imageio>=2.37,<3", + "ipython>=8.12.3,<10", + "ipyvolume>=0.6.3,<0.7", + "ipywidgets>=8.1.7,<9", + "matplotlib>=3.9.3,<4", + "nest-asyncio>=1.6,<2", + "ome-arrow>=0.0.3,<0.0.7", + "opencv-python>=4.10.0.84,<5", + "pandas<2.2.2; python_full_version<'3.9'", + "pandas>=2.2.2,<3; python_full_version>='3.9'", + "pyarrow>=16", + "pyvista>=0.46.4", + "pywavelets>=1.4.1,<2; python_full_version<'3.9'", + "pywavelets>1.4.1; python_full_version>='3.9'", + "scikit-image>=0.19.3,<0.20; python_full_version<'3.9'", + "scikit-image>0.19.3; python_full_version>='3.9'", + "trame>=3.12", + "trame-vtk>=2.10", + "trame-vuetify>=3.1", ] -# used for image modifications in cytodataframe -opencv-python = "^4.10.0.84" -imagecodecs = ">=2024.9.22,<2027.0.0" -matplotlib = "^3.9.3" -ipywidgets = "^8.1.7" -imageio = "^2.37.0" -ome-arrow = ">=0.0.3,<0.0.7" -pyvista = ">=0.46.4" -trame = ">=3.12" -trame-vtk = ">=2.10" -trame-vuetify = ">=3.1" -ipyvolume = "^0.6.3" -nest-asyncio = "^1.6.0" - -[tool.poetry.group.dev.dependencies] -# provides testing capabilities for project -pytest = ">=8.3.3,<10.0.0" -# used for test data generation -sqlalchemy = ">=1.3.6,<3" -# added to generate test coverage reports -coverage = "^7.6.0" -jupyterlab = "^4.3.0" -jupytext = "^1.16.4" -# jupyterlab/httpx requires a modern httpcore; avoid resolver selecting 0.13.x -httpcore = ">=0.18,<1.1" -black = ">=24.10,<27.0" -isort = ">=5.13.2,<8.0.0" -jupyterlab-code-formatter = "^3.0.2" -duckdb = "^1.1.3" -# version specifications below used to help surpass 3.13-based installations -cosmicqc = { version = ">=1.0.1", markers = "python_version < '3.13' and python_version >= '3.10'" } -poethepoet = ">=0.37,<0.42" - -[tool.poetry.group.docs.dependencies] -# used for rendering docs into docsite -sphinx = ">=7,<10" -# used for rendering markdown through sphinx -myst-parser = ">=3,<6" -# used for rendering notebooks through myst parser -myst-nb = "^1.1.2" -# used for extension sphinx-multiversion and to fix git-based challenges with default branch handling -sphinx-multiversion = { git = "https://github.com/J-RN/sphinx-multiversion", rev = "a77f0c862dace3a62c18fc866da60ef7dde3873d" } -# used for gathering version data for docsite -dunamai = "^1.22.0" -# used for theming the docsite -pydata-sphinx-theme = "^0.16.0" - -[tool.poetry.requires-plugins] -poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] } -[tool.poetry-dynamic-versioning] -enable = true -style = "pep440" -vcs = "git" -substitution.files = [ "src/cytodataframe/__init__.py" ] +[dependency-groups] +dev = [ + "black>=24.10,<27", + "cosmicqc>=1.0.1; python_version<'3.13' and python_version>='3.10'", + "coverage>=7.6,<8", + "duckdb>=1.1.3,<2", + "httpcore>=0.18,<0.19", + "isort>=5.13.2,<8", + "jupyterlab>=4.3,<5", + "jupyterlab-code-formatter>=3.0.2,<4", + "jupytext>=1.16.4,<2", + "poethepoet>=0.37,<0.42", + "pytest>=8.3.3,<10", + "pytest-cov>=5,<8", + "sqlalchemy>=1.3.6,<3", +] +docs = [ + "dunamai>=1.22,<2", + "myst-nb>=1.1.2,<2", + "myst-parser>=3,<6", + "pydata-sphinx-theme>=0.16,<0.17", + "sphinx>=9,<9.1", + "sphinx-multiversion", +] -# defines various development tasks +[tool.setuptools] +package-dir = { "" = "src" } +packages.find.where = [ "src" ] [tool.setuptools_scm] root = "." +version_scheme = "no-guess-dev" +local_scheme = "no-local-version" +version_file = "src/cytodataframe/_version.py" + +[tool.uv] +default-groups = [ + "dev", + "docs", +] +sources.sphinx-multiversion = { git = "https://github.com/J-RN/sphinx-multiversion", rev = "a77f0c862dace3a62c18fc866da60ef7dde3873d" } [tool.ruff] -target-version = "py38" +target-version = "py311" line-length = 88 fix = true lint.select = [ @@ -137,8 +125,8 @@ ini_options.addopts = "--cov=src/cytodataframe --cov-report=term-missing:skip-co # settings to avoid errors with cv2 and coverage # see here for more: https://github.com/nedbat/coveragepy/issues/1653 run.omit = [ - "config.py", "config-3.py", + "config.py", ] [tool.jupytext] diff --git a/src/cytodataframe/__init__.py b/src/cytodataframe/__init__.py index 81154a8..f1dc227 100644 --- a/src/cytodataframe/__init__.py +++ b/src/cytodataframe/__init__.py @@ -4,6 +4,5 @@ from .frame import CytoDataFrame -# note: version placeholder is updated during build -# by poetry-dynamic-versioning. +# note: version placeholder is updated during builds __version__ = "0.0.0" diff --git a/tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py b/tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py index 12d46eb..72b3fd9 100644 --- a/tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py +++ b/tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py @@ -4,7 +4,7 @@ This file may be processed using the following command from the root of the project repository: -`poetry run python tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py` +`uv run python tests/data/cytotable/NF1_cellpainting_data/gather_and_create_data.py` """ import pathlib diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_image_data.py b/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_image_data.py index a63eec1..ee6fde2 100644 --- a/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_image_data.py +++ b/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_image_data.py @@ -4,7 +4,7 @@ This file may be processed using the following command from the root of the project repository: -`poetry run python tests/data/cytotable/NF1_cellpainting_data_shrunken/create.py` +`uv run python tests/data/cytotable/NF1_cellpainting_data_shrunken/create_image_data.py` """ import pathlib diff --git a/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_mask_data.py b/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_mask_data.py index d360508..2dc9087 100644 --- a/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_mask_data.py +++ b/tests/data/cytotable/NF1_cellpainting_data_shrunken/create_mask_data.py @@ -6,7 +6,7 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