chore: migrate dependency management from Poetry to uv

[t-uda]

Summary

Migrates dependency management from Poetry to uv, per issue #121.

• pyproject.toml
  • Removed the demo optional-dependencies extra and all [tool.poetry.group.*] groups; demo handling now lives in the separate ellphi-demo repository.
  • Dev and docs tooling moved to PEP 735 [dependency-groups] (dev installed by uv sync by default, docs via --group docs). Runtime deps stay in PEP 621 [project.dependencies]; matplotlib remains a mandatory runtime dependency.
  • Build backend kept as poetry-core: [tool.poetry.build].script = "scripts/build_tangency_cpp.py" is what makes any PEP 517 install (pip, uv) compile the C++ tangency backend, so [tool.poetry] / [tool.poetry.build] and the poetry-core backend are retained (floor bumped to poetry-core>=2.0 since the metadata is PEP 621). Verified empirically: uv sync and a plain sdist install both build _tangency_cpp_impl.so.
  • setuptools>=78.1.1 in [build-system] and the dev group (CVE-2025-47273) — this subsumes PR Bump setuptools minimum version to 78.1.1 #126, which can be closed once this merges.
  • [tool.uv] constraint-dependencies = ["numpy<2.5"]: numpy 2.5 exposes NDArray as a PEP 695 type alias that stubtest cannot verify on Python ≥ 3.12 (ellphi.FloatArray is inconsistent, runtime is not a type). This constrains only the dev lockfile; the published package keeps numpy>=1.26. Follow-up when stubtest/numpy catch up.
• Lockfile: poetry.lock deleted; uv.lock committed. CI now verifies freshness with uv lock --check (lesson from poetry.lock: demo-only transitive dependencies incorrectly listed in main group #124), and installs use uv sync --locked.
• Workflows (all four): astral-sh/setup-uv@v6 with caching, uv sync / uv run / uv build. Job ids and check names (test (3.10..3.12), typecheck, package-test, demo-install, docs, build-windows (...), build-sdist, build-linux) are preserved for branch protection.
  • demo-install: the demo dependency set no longer exists, so the job (name kept) is repurposed to build the sdist with uv build --sdist and smoke-test a plain pip install from it, verifying the C++ backend compiles from source — a path no other job covered (package-test installs the wheel).
  • Fixes CI: Codecov upload step can fail even when tests pass #117 in python-app.yml: codecov/codecov-action bumped v4.0.1 → v5 and the upload step is now continue-on-error: true, so a Codecov outage cannot fail CI.
• Docs: README, CONTRIBUTING, AGENTS (checklist rewritten to uv run ...), docs/hybrid_tuning.md, docs/eigen_backend_plan.md, plus scripts/update_version.py usage text and the rebuild hint in src/ellphi/_tangency_cpp.py error message.
• stubtest allowlist: ellphi.solver.MethodName removed — mypy 1.20 (now locked) reports it as an unused allowlist entry, which stubtest treats as an error. ellphi._solver_python.MethodName is still required. AGENTS.md justification section updated accordingly.

Closes #121
Closes #117

Verification (local, macOS arm64, uv 0.11.8)

All commands run on this branch; every one passed:

Command	Status
uv sync (builds C++ backend)	pass
uv run python -m ellphi --build-info → cpp_backend_available=True	pass
uv run black src tests scripts	pass (47 files unchanged)
uv run black --check src tests scripts	pass
uv run flake8 src tests scripts	pass
uv run mypy src tests	pass (33 files)
MYPYPATH=src uv run stubtest ellphi --allowlist stubtest-allowlist.txt	pass (on both Python 3.11 and 3.12)
uv run pytest	pass (243 passed)
uv run mkdocs build	pass (one pre-existing griffe warning)
uv lock --check	pass
uv build (sdist + wheel; sdist contains .cpp, no binaries; wheel contains .so, .pyi, py.typed)	pass

Poetry itself is not installed on this machine; per the migration's premise, no Poetry backwards compatibility was verified or intended.

Deviations / reviewer notes

• Caret constraints were translated to explicit ranges (e.g. flake8>=7.3.0,<8); exact pins (mkdocstrings==0.25.0, mkdocs-autorefs==1.3.1) kept as-is.
• The numpy<2.5 dev-lock constraint and the removed ellphi.solver.MethodName allowlist entry are consequences of the fresh resolution (numpy 2.5, mypy 1.20) — flagging them explicitly since they go slightly beyond a pure tooling swap.
• The wheel built by uv build carries the same interpreter-specific tag scheme (cp312-cp312-<platform>) poetry-core produced before, so the per-Python matrix in release.yml is unchanged.

🤖 Generated with Claude Code

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Codecov Report

✅ All modified and coverable lines are covered by tests.

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[Copilot]

Pull request overview

Migrates the project’s development/dependency management workflow from Poetry to uv, updating CI and contributor docs accordingly while keeping poetry-core as the PEP 517 build backend to preserve the C++ extension build behavior.

Changes:

• Move dev/docs dependencies to PEP 735 [dependency-groups] and add uv-specific configuration in pyproject.toml.
• Update GitHub Actions workflows to use astral-sh/setup-uv@v6, uv sync, uv run, and uv build, including lockfile freshness checks.
• Refresh docs/tooling guidance (README/CONTRIBUTING/AGENTS) and adjust stubtest allowlist entries.

Reviewed changes

Copilot reviewed 13 out of 15 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
stubtest-allowlist.txt	Removes an unused stubtest allowlist entry.
src/ellphi/_tangency_cpp.py	Updates rebuild guidance text for the C++ backend version mismatch error.
scripts/update_version.py	Updates usage instructions from Poetry to uv.
README.md	Removes demo extra install instructions and points to the external demo repo; updates source-build guidance to uv.
pyproject.toml	Replaces Poetry dependency groups with PEP 735 dependency-groups and adds [tool.uv] constraints; bumps build requirements.
docs/hybrid_tuning.md	Updates example command to use uv run.
docs/eigen_backend_plan.md	Updates Eigen rebuild instructions to use uv.
CONTRIBUTING.md	Updates contributor workflow commands from Poetry to uv (including docs group install).
AGENTS.md	Rewrites the local-check checklist and dependency instructions to use uv + uv.lock.
.github/workflows/release.yml	Switches release builds from Poetry to uv build.
.github/workflows/python-app.yml	Updates CI jobs to use uv for sync/run/build; adds uv lock --check; repurposes demo-install to sdist install smoke test.
.github/workflows/docs.yml	Switches docs build/deploy from Poetry to uv (docs dependency group).
.github/workflows/build-windows-wheels.yml	Switches wheel build from Poetry to uv build --wheel.

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[t-uda]

LGTM!