Migrate from poetry to uv

.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

.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

.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

.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

.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

.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

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)

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

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-<semver release type>` 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
 ```