Migrate from poetry to uv for env and package management#461
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📝 WalkthroughWalkthroughThis PR migrates the project's package management from Poetry to uv and switches versioning from poetry-dynamic-versioning to setuptools-scm. The build backend in pyproject.toml now uses setuptools with PEP 621 project metadata, dependencies are reorganized into standard sections, CI/CD workflows are updated to use uv instead of Poetry commands, and version resolution is simplified to use runtime metadata lookups. ChangesPoetry to uv and setuptools-scm Migration
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes Possibly related issues
Poem
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Actionable comments posted: 6
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In @.github/workflows/publish-docs.yml:
- Around line 20-23: The workflow currently references the third-party action as
"uses: astral-sh/setup-uv@v6", which is a floating tag; replace this with the
action pinned to a specific full commit SHA (e.g.,
"astral-sh/setup-uv@<full-commit-sha>") so the workflow is reproducible. Locate
the "uses: astral-sh/setup-uv@v6" entry in the publish-docs.yml file and update
it to the full commit SHA for the v6 release (obtain the SHA from the action's
GitHub repo tags or releases) and keep the existing "with:" inputs unchanged.
Ensure the updated line uses the exact 40-character commit SHA string.
In @.github/workflows/publish-pypi.yml:
- Around line 25-28: Replace the floating tag for the third-party action used in
the publish job: change the uses entry "astral-sh/setup-uv@v6" to the specific
commit SHA (e.g. "astral-sh/setup-uv@<full-commit-sha>") so the publish workflow
pins the exact action version; update the YAML in the publish job where the
action is referenced to use the full commit SHA instead of "v6".
In @.github/workflows/test.yml:
- Around line 36-41: The workflow misses the dev dependency group needed for
tests; update the steps that install and run tests (the "Install frozen
environment", "Run sphinx-docs build test", and "Run pytest" steps) to sync and
run with the dev group included (e.g., add --group dev to the uv sync command
and include --group dev or ensure uv run uses the synced env for the pytest and
sphinx-build steps) so pytest and test-only packages from
[dependency-groups].dev are available on a clean runner.
- Around line 30-33: The workflow uses a floating tag for the setup-uv action
("name: Setup uv" with "uses: astral-sh/setup-uv@v6"); replace the floating tag
with a specific commit SHA to pin the action for reproducible CI and
supply-chain safety. Update both occurrences of the step (the ones currently
using "astral-sh/setup-uv@v6") to use the corresponding commit SHA (e.g.,
"astral-sh/setup-uv@<full-commit-sha>") so the workflow references an immutable
revision.
In `@docs/source/contributing.md`:
- Line 165: Replace the incorrect sphinx-build invocation that uses "docs/source
doctest -W" (which treats "doctest" as the output dir) with an explicit builder
flag so doctest is run as the builder; update the command in the contributing
docs to use the builder option (e.g., "-b doctest" or "--builder doctest") with
the same source dir and warning flag so contributors run Sphinx doctest checks
correctly.
In `@pyproject.toml`:
- Around line 2-3: Update the build-system requirement to ensure SPDX parsing
for [project].license by raising the setuptools minimum in the pyproject.toml
build-system.requires entry (currently "setuptools>=64") to at least
"setuptools>=77.0.0" so the project-level license string (e.g., license =
"BSD-3-Clause") is parsed correctly; alternatively revert to the legacy license
table form if you cannot bump setuptools.
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Fix all unresolved CodeRabbit comments on this PR:
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ℹ️ Review info
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Configuration used: defaults
Review profile: CHILL
Plan: Pro
Run ID: 20bf56e9-c219-4bf7-8614-465c62239baf
⛔ Files ignored due to path filters (2)
poetry.lockis excluded by!**/*.lockuv.lockis excluded by!**/*.lock
📒 Files selected for processing (13)
.github/actions/setup-poetry/action.yml.github/dependabot.yml.github/workflows/publish-docs.yml.github/workflows/publish-pypi.yml.github/workflows/test.yml.gitignore.pre-commit-config.yamlcytotable/__init__.pycytotable/utils.pydocs/source/contributing.mdpyproject.tomlreadme.mdtests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py
💤 Files with no reviewable changes (2)
- .github/actions/setup-poetry/action.yml
- .pre-commit-config.yaml
gwaybio
approved these changes
Jun 5, 2026
| try: | ||
| # attempt to gather the development version from dunamai | ||
| # for scenarios where cytotable from source is used. | ||
| import dunamai |
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is this a dependency to remove from anywhere?
| numpy = [ | ||
| { version = "<=1.24.4", python = "<3.11" }, | ||
| { version = ">=1.26.0", python = ">=3.11" }, | ||
| keywords = [ "cellprofiler", "python", "single-cell-analysis", "way-lab" ] |
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Suggested change
| keywords = [ "cellprofiler", "python", "single-cell-analysis", "way-lab" ] | |
| keywords = [ "cellprofiler", "image-based-profiling", "python", "single-cell-analysis" ] |
Good to keep lab agnostic
| typing-extensions = "^4.14.0" | ||
| [dependency-groups] | ||
| dev = [ | ||
| "cytominer-database>=0.3.4,<0.4", |
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Description
This PR migrates from poetry to uv for environment and package management.
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