From 47468c3efd4db6853274899070ab9a669287bb9c Mon Sep 17 00:00:00 2001 From: Tomoki Uda Date: Fri, 3 Jul 2026 21:36:09 +0900 Subject: [PATCH 1/2] chore: migrate dependency management from Poetry to uv - Move dev/docs tooling to PEP 735 [dependency-groups]; drop demo extras and all Poetry groups (demo lives in the ellphi-demo repo) - Replace poetry.lock with uv.lock; constrain numpy<2.5 in the dev lockfile until stubtest supports numpy's PEP 695 NDArray alias - Keep the poetry-core build backend so pip/uv installs still compile the C++ tangency backend; bump setuptools floor to >=78.1.1 (CVE-2025-47273, subsumes PR #126) and poetry-core to >=2.0 - Switch all four workflows to astral-sh/setup-uv with caching, uv sync/run/build; add a `uv lock --check` freshness step - Repurpose the demo-install job to smoke-test a plain sdist install - Bump codecov-action to v5 and make the upload non-blocking (#117) - Update README, CONTRIBUTING, AGENTS and docs to uv commands - Drop the ellphi.solver.MethodName stubtest allowlist entry, unused since mypy 1.20 Closes #121 Closes #117 Co-Authored-By: Claude Fable 5 --- .github/workflows/build-windows-wheels.yml | 9 +- .github/workflows/docs.yml | 15 +- .github/workflows/python-app.yml | 103 +- .github/workflows/release.yml | 34 +- AGENTS.md | 39 +- CONTRIBUTING.md | 23 +- README.md | 17 +- docs/eigen_backend_plan.md | 8 +- docs/hybrid_tuning.md | 2 +- poetry.lock | 5099 -------------------- pyproject.toml | 74 +- scripts/update_version.py | 2 +- src/ellphi/_tangency_cpp.py | 4 +- stubtest-allowlist.txt | 1 - uv.lock | 2536 ++++++++++ 15 files changed, 2690 insertions(+), 5276 deletions(-) delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/.github/workflows/build-windows-wheels.yml b/.github/workflows/build-windows-wheels.yml index abab1fb..a11b8fc 100644 --- a/.github/workflows/build-windows-wheels.yml +++ b/.github/workflows/build-windows-wheels.yml @@ -25,11 +25,14 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install Poetry - run: pip install --upgrade poetry + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + python-version: ${{ matrix.python-version }} - name: Build wheel - run: poetry build -f wheel + run: uv build --wheel - name: Verify wheel contains binary shell: pwsh diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f12f545..a967d1f 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,22 +16,19 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - - name: Install poetry - run: pipx install poetry - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: + enable-cache: true python-version: "3.10" - cache: "poetry" - name: Install dependencies - run: poetry install --with docs + run: uv sync --locked --group docs - name: Build docs - run: poetry run mkdocs build + run: uv run mkdocs build - name: Deploy to gh-pages if: github.event_name == 'push' && github.ref == 'refs/heads/main' - run: poetry run mkdocs gh-deploy --force + run: uv run mkdocs gh-deploy --force diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 0a88614..a58e5ef 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -25,41 +25,36 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - name: Install Eigen headers run: sudo apt-get update && sudo apt-get install -y libeigen3-dev - # -- Poetry ------------------------------------------------------ - - name: Install Poetry - run: pip install --upgrade poetry - - - name: Cache Poetry env - uses: actions/cache@v4 + # -- uv ---------------------------------------------------------- + - name: Install uv + uses: astral-sh/setup-uv@v6 with: - path: ~/.cache/pypoetry - key: ${{ runner.os }}-poetry-${{ hashFiles('pyproject.toml') }}-v2 + enable-cache: true + python-version: ${{ matrix.python-version }} - - name: Install project (dev extras) - run: poetry install --with dev # Install core and development dependencies + - name: Check lockfile freshness + run: uv lock --check + + - name: Install project (dev group) + run: uv sync --locked # -- Lint / Format ---------------------------------------------- - name: flake8 - run: poetry run flake8 src tests scripts + run: uv run flake8 src tests scripts - name: black check - run: poetry run black --check src tests scripts + run: uv run black --check src tests scripts # -- Tests ------------------------------------------------------ - name: pytest with coverage - run: poetry run pytest --cov=src/ellphi --cov-report=xml + run: uv run pytest --cov=src/ellphi --cov-report=xml - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v4.0.1 + uses: codecov/codecov-action@v5 + continue-on-error: true with: token: ${{ secrets.CODECOV_TOKEN }} @@ -72,32 +67,23 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.11" - cache: "pip" - - name: Install Eigen headers run: sudo apt-get update && sudo apt-get install -y libeigen3-dev - - name: Install Poetry - run: pip install --upgrade poetry - - - name: Cache Poetry env - uses: actions/cache@v4 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: - path: ~/.cache/pypoetry - key: ${{ runner.os }}-poetry-${{ hashFiles('pyproject.toml') }}-v2 + enable-cache: true + python-version: "3.11" - - name: Install project (dev extras) - run: poetry install --with dev # Install core and development dependencies + - name: Install project (dev group) + run: uv sync --locked - name: mypy - run: poetry run mypy src + run: uv run mypy src - name: stubtest - run: MYPYPATH=src poetry run stubtest ellphi --allowlist stubtest-allowlist.txt + run: MYPYPATH=src uv run stubtest ellphi --allowlist stubtest-allowlist.txt package-test: runs-on: ubuntu-latest @@ -111,16 +97,17 @@ jobs: uses: actions/setup-python@v5 with: python-version: "3.11" - cache: "pip" - name: Install Eigen headers run: sudo apt-get update && sudo apt-get install -y libeigen3-dev - - name: Install Poetry - run: pip install --upgrade poetry + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true - name: Build package - run: poetry build + run: uv build - name: Check sdist content run: | @@ -142,14 +129,14 @@ jobs: # Create a fresh venv to test installation python -m venv test-env source test-env/bin/activate - + # Install the built wheel pip install dist/*.whl - + # Install test dependencies (pytest) # Note: runtime dependencies (numpy, etc.) are installed by pip automatically from the wheel metadata pip install pytest - + # Run tests against the installed package # We assume tests are in 'tests/' and we want to avoid importing from local 'src/' # So we move to a different directory or explicitely tell pytest where to look @@ -157,6 +144,9 @@ jobs: cd test_run pytest ../tests + # Demo dependencies now live in the separate ellphi-demo repository. + # This job (name kept for branch protection) now verifies that a plain + # `pip install` from the sdist compiles the C++ backend from source. demo-install: runs-on: ubuntu-latest steps: @@ -166,16 +156,21 @@ jobs: uses: actions/setup-python@v5 with: python-version: "3.11" - cache: "pip" - - - name: Install Poetry - run: pip install --upgrade poetry - - name: Cache Poetry env - uses: actions/cache@v4 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: - path: ~/.cache/pypoetry - key: ${{ runner.os }}-poetry-${{ hashFiles('pyproject.toml') }}-v2 + enable-cache: true - - name: Install project (demo extras) - run: poetry install --with demo # Ensure the demo dependency set resolves + - name: Build sdist + run: uv build --sdist + + - name: Install from sdist and smoke test + run: | + python -m venv test-env + source test-env/bin/activate + pip install dist/*.tar.gz + mkdir -p test_run + cd test_run + python -m ellphi --build-info + python -c "from ellphi.solver import has_cpp_backend; assert has_cpp_backend(), 'C++ backend not available'" diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index ad8acff..d8378ce 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -42,16 +42,14 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: + enable-cache: true python-version: "3.12" - - name: Install Poetry - run: pip install --upgrade poetry - - name: Build sdist - run: poetry build -f sdist + run: uv build --sdist - name: Upload sdist uses: actions/upload-artifact@v4 @@ -71,19 +69,17 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install Eigen headers run: sudo apt-get update && sudo apt-get install -y libeigen3-dev - - name: Install Poetry - run: pip install --upgrade poetry + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + python-version: ${{ matrix.python-version }} - name: Build wheel - run: poetry build -f wheel + run: uv build --wheel - name: Upload wheel uses: actions/upload-artifact@v4 @@ -100,16 +96,14 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@v6 with: + enable-cache: true python-version: ${{ matrix.python-version }} - - name: Install Poetry - run: pip install --upgrade poetry - - name: Build wheel - run: poetry build -f wheel + run: uv build --wheel - name: Upload wheel uses: actions/upload-artifact@v4 diff --git a/AGENTS.md b/AGENTS.md index 8fcfc0f..1c885c6 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -10,30 +10,30 @@ This file provides instructions for AI agents working on this repository. Read i ### 1. One-Time Setup -Before you start working, set up your environment by running the following command. +Before you start working, set up your environment by running the following command. Dependencies are managed with [uv](https://docs.astral.sh/uv/). ```bash -poetry install +uv sync ``` -This command installs all Python dependencies and also compiles the C++ backend for the tangency solver. If the C++ code (`src/ellphi/_tangency_cpp_impl.cpp`) is modified, the backend will be automatically rebuilt the next time you run `poetry install`. +This command installs all Python dependencies (including the `dev` dependency group) and also compiles the C++ backend for the tangency solver. If the C++ code (`src/ellphi/_tangency_cpp_impl.cpp`) is modified, the backend will be automatically rebuilt the next time you run `uv sync`. Optional Eigen build (C++ linear algebra): - Install Eigen headers (Ubuntu: `apt-get install libeigen3-dev`, macOS: `brew install eigen`). -- Rebuild with `ELLPHI_USE_EIGEN=1` and `ELLPHI_EIGEN_INCLUDE` set to the Eigen include path. +- Rebuild with `ELLPHI_USE_EIGEN=1` and `ELLPHI_EIGEN_INCLUDE` set to the Eigen include path, forcing a reinstall of the project: `ELLPHI_USE_EIGEN=1 ELLPHI_EIGEN_INCLUDE=/usr/include/eigen3 uv sync --reinstall-package ellphi` - Linux default: `/usr/include/eigen3` - macOS default: `/opt/homebrew/include/eigen3` (Apple Silicon) or `/usr/local/include/eigen3` (Intel) -- Verify with `python -m ellphi --build-info` and check `cpp_linalg_kind`. +- Verify with `uv run python -m ellphi --build-info` and check `cpp_linalg_kind`. ### A Note on Managing Dependencies -If you need to add, remove, or update dependencies in `pyproject.toml`, you must also update the `poetry.lock` file to reflect these changes. After modifying `pyproject.toml`, run the following command: +If you need to add, remove, or update dependencies in `pyproject.toml`, you must also update the `uv.lock` file to reflect these changes. After modifying `pyproject.toml`, run the following command: ```bash -poetry lock +uv lock ``` -This ensures that the project's dependencies remain consistent and reproducible. After running the command, remember to commit both the `pyproject.toml` and `poetry.lock` files. +This ensures that the project's dependencies remain consistent and reproducible. After running the command, remember to commit both the `pyproject.toml` and `uv.lock` files. CI verifies lockfile freshness with `uv lock --check`, so a stale `uv.lock` will fail the build. ### 2. Run Test and Lint @@ -41,18 +41,21 @@ In this repository, all CI tests must pass before PRs are merged. Therefore, bef ```bash # Format and verify formatting -poetry run black src tests scripts -poetry run black --check src tests scripts +uv run black src tests scripts +uv run black --check src tests scripts # Lint and static analysis -poetry run flake8 src tests scripts -poetry run mypy src tests +uv run flake8 src tests scripts +uv run mypy src tests # Type Stub Validation -MYPYPATH=src poetry run stubtest ellphi --allowlist stubtest-allowlist.txt +MYPYPATH=src uv run stubtest ellphi --allowlist stubtest-allowlist.txt # Tests -poetry run pytest +uv run pytest + +# Lockfile freshness (if pyproject.toml changed) +uv lock --check ``` If CI introduces new tools, immediately add them to this checklist. @@ -64,7 +67,7 @@ If CI introduces new tools, immediately add them to this checklist. **Command:** ```bash -MYPYPATH=src poetry run stubtest ellphi --allowlist stubtest-allowlist.txt +MYPYPATH=src uv run stubtest ellphi --allowlist stubtest-allowlist.txt ``` **Purpose:** @@ -84,9 +87,8 @@ When `stubtest` reports a failure, it means there is a mismatch between the impl This section documents the reasons for each entry in the `stubtest-allowlist.txt` file. * `ellphi._solver_python.MethodName` -* `ellphi.solver.MethodName` -**Reason:** These entries are necessary because the `MethodName` type alias is defined as a `typing.Literal` in the implementation, but it is simplified to `str` in the corresponding stub files (`.pyi`). This simplification is intentional to avoid duplicating the literal values in the stub, which would make it harder to maintain. +**Reason:** This entry is necessary because the `MethodName` type alias is defined as a `typing.Literal` in the implementation, but it is simplified to `str` in the corresponding stub file (`.pyi`). This simplification is intentional to avoid duplicating the literal values in the stub, which would make it harder to maintain. (An equivalent entry for the `ellphi.solver` re-export was needed with older mypy versions but is reported as unused since mypy 1.20.) #### Managing the Allowlist @@ -113,7 +115,8 @@ do **not** require the full Python CI checklist (black/flake8/mypy/pytest). Instead, run: ```bash -poetry run mkdocs build +uv sync --group docs +uv run mkdocs build ``` and confirm it exits without errors before committing. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6430c42..d56ef76 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -30,7 +30,7 @@ We only bump versions at two moments: Use the version sync script so that metadata and runtime version stay aligned: ```bash -poetry run python scripts/update_version.py 0.1.2.dev0 +uv run python scripts/update_version.py 0.1.2.dev0 ``` ## Release Notes @@ -57,9 +57,9 @@ Right before the release, replace it with a dated heading such as: from the release branch. 5. On that version-bump branch: - finalize `RELEASE_NOTES.md` - - run `poetry run python scripts/update_version.py 0.1.2` + - run `uv run python scripts/update_version.py 0.1.2` - run all required local checks - - run `poetry run mkdocs build` + - run `uv run mkdocs build` 6. Open a PR from the version-bump branch back into the release branch and merge it after CI passes. 7. Open a PR from the release branch into `main` and merge it. @@ -103,7 +103,7 @@ See the comments at the top of `release.yml` for one-time setup steps. Mirror CI locally. Run the exact commands listed in `AGENTS.md` and `.github/workflows/python-app.yml`, in the same order when relevant. For docs and release-note changes, also mirror `.github/workflows/docs.yml` by running -`poetry run mkdocs build`. Do not skip steps. If something cannot run, stop +`uv run mkdocs build` (after `uv sync --group docs`). Do not skip steps. If something cannot run, stop and document the blocker. ## Optional Eigen Build (C++ linear algebra) @@ -116,7 +116,7 @@ If you want to test the Eigen build locally: 2. Rebuild the extension with: ```bash -ELLPHI_USE_EIGEN=1 ELLPHI_EIGEN_INCLUDE=/usr/include/eigen3 poetry install +ELLPHI_USE_EIGEN=1 ELLPHI_EIGEN_INCLUDE=/usr/include/eigen3 uv sync --reinstall-package ellphi ``` On macOS, use `/opt/homebrew/include/eigen3` (Apple Silicon) or @@ -125,7 +125,7 @@ On macOS, use `/opt/homebrew/include/eigen3` (Apple Silicon) or Verify via: ```bash -python -m ellphi --build-info +uv run python -m ellphi --build-info ``` ## Docs CI and Deployment @@ -134,21 +134,24 @@ python -m ellphi --build-info to `ellphi-*`, and via `workflow_dispatch`. - It deploys to `gh-pages` only on pushes to `main`. - `.github/workflows/python-app.yml` contains a `demo-install` job that checks - the demo dependency set; it is not the docs deployment workflow. + a plain install from the sdist; it is not the docs deployment workflow. ## Documentation ### Building and previewing ```bash +# Install the docs dependency group once +uv sync --group docs + # One-off build -poetry run mkdocs build +uv run mkdocs build # Live-reload server (http://127.0.0.1:8000) -poetry run mkdocs serve +uv run mkdocs serve ``` -Run `poetry run mkdocs build` before committing any docs change and confirm +Run `uv run mkdocs build` before committing any docs change and confirm the build completes without errors. ### English style diff --git a/README.md b/README.md index dddcdf7..d5f28bb 100644 --- a/README.md +++ b/README.md @@ -22,15 +22,12 @@ Install from PyPI: pip install ellphi ``` -To install with demo dependencies for notebooks and examples: - -```bash -pip install ellphi[demo] -``` +Demo notebooks and their dependencies live in the separate +[ellphi-demo](https://github.com/t-uda/ellphi-demo) repository. ## Optional Eigen build (from source) -If you build from source (for example, with `poetry install`), you can enable +If you build from source (for example, with `uv sync`), you can enable the C++ linear algebra implementation based on Eigen. Install Eigen headers: @@ -41,7 +38,7 @@ Install Eigen headers: Then build with: ```bash -ELLPHI_USE_EIGEN=1 ELLPHI_EIGEN_INCLUDE=/usr/include/eigen3 poetry install +ELLPHI_USE_EIGEN=1 ELLPHI_EIGEN_INCLUDE=/usr/include/eigen3 uv sync --reinstall-package ellphi ``` On macOS, use `/opt/homebrew/include/eigen3` (Apple Silicon) or @@ -137,9 +134,9 @@ To get started with development, clone the repository and set up your environmen git clone https://github.com/t-uda/ellphi.git cd ellphi -# Install dependencies, including development tools -poetry install --with dev +# Install dependencies, including development tools (requires uv) +uv sync # Run the tests to make sure everything is set up correctly -poetry run pytest +uv run pytest ``` diff --git a/docs/eigen_backend_plan.md b/docs/eigen_backend_plan.md index 9590164..84b1959 100644 --- a/docs/eigen_backend_plan.md +++ b/docs/eigen_backend_plan.md @@ -21,7 +21,7 @@ Notes: ## Build without Eigen If Eigen headers are not available, build without enabling it: 1) Do not set `ELLPHI_USE_EIGEN`. -2) Run `poetry install` to build the C++ extension with the internal solver. +2) Run `uv sync` to build the C++ extension with the internal solver. 3) If `ELLPHI_USE_EIGEN=1` is set without headers, the build fails with a clear error asking for `ELLPHI_EIGEN_INCLUDE`. @@ -32,7 +32,7 @@ If Eigen headers are not available, build without enabling it: 2) If Eigen is not in a standard include location, set: - `ELLPHI_EIGEN_INCLUDE="/path/to/eigen3"` 3) Rebuild the extension: - - `poetry install` + - `uv sync --reinstall-package ellphi` - If needed, delete `src/ellphi/_tangency_cpp_impl*.so` before reinstalling. 4) Quick sanity check: ```bash @@ -52,8 +52,8 @@ If Eigen headers are not available, build without enabling it: Notes: - Host: Ubuntu aarch64 (local dev machine) - Eigen: 3.4.0 (`libeigen3-dev`) -- Build: deleted `_tangency_cpp_impl.so` then rebuilt for each mode via `poetry install` -- Run: `OMP_NUM_THREADS=1 poetry run python scripts/benchmark_dim_scale.py` +- Build: deleted `_tangency_cpp_impl.so` then rebuilt for each mode via `uv sync --reinstall-package ellphi` +- Run: `OMP_NUM_THREADS=1 uv run python scripts/benchmark_dim_scale.py` - joblib emitted a permissions warning and ran in serial mode CPP results (avg_time_ms): diff --git a/docs/hybrid_tuning.md b/docs/hybrid_tuning.md index c5ce6ce..11d8dea 100644 --- a/docs/hybrid_tuning.md +++ b/docs/hybrid_tuning.md @@ -20,7 +20,7 @@ set. All numbers below come from running: ```bash -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim 30 --dims 2 3 4 5 --extreme-fraction 0.45 \ --output docs/hybrid_tuning_summary.json ``` diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 2fb69e3..0000000 --- a/poetry.lock +++ /dev/null @@ -1,5099 +0,0 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. - -[[package]] -name = "anyio" -version = "4.12.0" -description = "High-level concurrency and networking framework on top of asyncio or Trio" -optional = false -python-versions = ">=3.9" -groups = ["main", "demo"] -files = [ - {file = "anyio-4.12.0-py3-none-any.whl", hash = "sha256:dad2376a628f98eeca4881fc56cd06affd18f659b17a747d3ff0307ced94b1bb"}, - {file = "anyio-4.12.0.tar.gz", hash = "sha256:73c693b567b0c55130c104d0b43a9baf3aa6a31fc6110116509f27bf75e21ec0"}, -] - -[package.dependencies] -exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} -idna = ">=2.8" -typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} - 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"jupyterlab>=4.1", - "ipykernel>=6.28", - "nbformat>=5.10", - "plotly>=5.22", - "pandas>=2.2.0", - "homcloud>=4.8.0", - "tqdm>=4.67.1", - "seaborn>=0.13", +# Development dependencies (PEP 735, managed by uv). +# `uv sync` installs the `dev` group by default; use `--group docs` for docs. +[dependency-groups] +dev = [ + "setuptools>=78.1.1", + "flake8>=7.3.0,<8", + "black[jupyter]>=25.1.0,<26", + "mypy>=1.8,<2", + "scipy-stubs>=1.16.0.2,<2; python_version >= '3.11'", + "pytest>=8.4.1,<9", + "packaging>=25.0,<26", + "pytest-cov>=7.0.0,<8", ] +docs = [ + "mkdocs>=1.6.0,<2", + "mkdocs-material>=9.5.0,<10", + "mkdocstrings[python]==0.25.0", + "mkdocs-autorefs==1.3.1", +] + +[tool.uv] +# numpy 2.5 exposes NDArray as a PEP 695 type alias, which stubtest cannot +# verify on Python >= 3.12 (`ellphi.FloatArray is inconsistent, runtime is +# not a type`). Constrain the development lockfile until stubtest/numpy +# catch up; the published package keeps `numpy>=1.26`. +constraint-dependencies = ["numpy<2.5"] +# The `[tool.poetry]` sections below are kept because the build backend is +# poetry-core: `[tool.poetry.build].script` compiles the C++ tangency backend +# during any PEP 517 build (pip, uv, ...). Dependency management itself is +# handled by uv (see `[dependency-groups]` and uv.lock). [tool.poetry] packages = [{ include = "ellphi", from = "src" }] package-mode = true @@ -72,38 +90,6 @@ include = [ [tool.poetry.build] script = "scripts/build_tangency_cpp.py" -[tool.poetry.group.dev.dependencies] -setuptools = ">=65" -flake8 = "^7.3.0" -black = { version = "^25.1.0", extras = ["jupyter"] } -mypy = "^1.8" -scipy-stubs = { version = "^1.16.0.2", python = ">=3.11" } -pytest = "^8.4.1" -packaging = "^25.0" -pytest-cov = "^7.0.0" - -[tool.poetry.group.demo] -optional = true - -[tool.poetry.group.demo.dependencies] -jupyterlab = ">=4.1" -ipykernel = ">=6.28" -nbformat = ">=5.10" -plotly = ">=5.22" -pandas = "^2.2.0" -homcloud = "^4.8.0" -tqdm = "^4.67.1" -seaborn = "^0.13" - -[tool.poetry.group.docs] -optional = true - -[tool.poetry.group.docs.dependencies] -mkdocs = "^1.6.0" -mkdocs-material = "^9.5.0" -mkdocstrings = {extras = ["python"], version = "0.25.0"} -mkdocs-autorefs = "1.3.1" - [tool.mypy] mypy_path = "src" @@ -111,5 +97,5 @@ mypy_path = "src" allowlist = "stubtest-allowlist.txt" [build-system] -requires = ["poetry-core>=1.9.0", "setuptools>=65"] +requires = ["poetry-core>=2.0", "setuptools>=78.1.1"] build-backend = "poetry.core.masonry.api" diff --git a/scripts/update_version.py b/scripts/update_version.py index b33f338..d675573 100755 --- a/scripts/update_version.py +++ b/scripts/update_version.py @@ -2,7 +2,7 @@ """Synchronize project version in packaging metadata and the runtime module. Usage: - poetry run python scripts/update_version.py 1.2.3 + uv run python scripts/update_version.py 1.2.3 The script validates the provided version against PEP 440, normalizes it to the canonical form, and writes the value to both `pyproject.toml` and diff --git a/src/ellphi/_tangency_cpp.py b/src/ellphi/_tangency_cpp.py index 740c3ed..bc27bda 100644 --- a/src/ellphi/_tangency_cpp.py +++ b/src/ellphi/_tangency_cpp.py @@ -66,8 +66,8 @@ def _validate_library_version(lib: ctypes.CDLL) -> None: "C++ backend version mismatch: " f"library reports '{actual}' but ellphi expects '{expected}'. 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now covers both uv and pip (`pip install --force-reinstall .`) and uses the correct scripts/build_tangency_cpp.py path - .github/workflows/python-app.yml: fix "explicitely" typo - README.md: clarify that maintained demo notebooks live in ellphi-demo while in-repo notebooks/ examples remain but their extra dependencies are no longer declared by this package Co-Authored-By: Claude Fable 5 --- .github/workflows/python-app.yml | 2 +- README.md | 7 +++++-- docs/eigen_backend_plan.md | 3 ++- scripts/hybrid_tuning.sh | 18 +++++++++--------- src/ellphi/_tangency_cpp.py | 8 +++++--- 5 files changed, 22 insertions(+), 16 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index a58e5ef..2a8e07f 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -139,7 +139,7 @@ jobs: # Run tests against the installed package # We assume tests are in 'tests/' and we want to avoid importing from local 'src/' - # So we move to a different directory or explicitely tell pytest where to look + # So we move to a different directory or explicitly tell pytest where to look mkdir -p test_run cd test_run pytest ../tests diff --git a/README.md b/README.md index d5f28bb..2a9452d 100644 --- a/README.md +++ b/README.md @@ -22,8 +22,11 @@ Install from PyPI: pip install ellphi ``` -Demo notebooks and their dependencies live in the separate -[ellphi-demo](https://github.com/t-uda/ellphi-demo) repository. +Maintained demo notebooks and their dependencies live in the separate +[ellphi-demo](https://github.com/t-uda/ellphi-demo) repository. The +`notebooks/` directory in this repository still contains example notebooks, +but their extra dependencies (Jupyter, plotly, homcloud, ...) are no longer +declared by this package; install them separately to run the notebooks. ## Optional Eigen build (from source) diff --git a/docs/eigen_backend_plan.md b/docs/eigen_backend_plan.md index 84b1959..85554d4 100644 --- a/docs/eigen_backend_plan.md +++ b/docs/eigen_backend_plan.md @@ -32,7 +32,8 @@ If Eigen headers are not available, build without enabling it: 2) If Eigen is not in a standard include location, set: - `ELLPHI_EIGEN_INCLUDE="/path/to/eigen3"` 3) Rebuild the extension: - - `uv sync --reinstall-package ellphi` + - `ELLPHI_USE_EIGEN=1 uv sync --reinstall-package ellphi` + (prepend `ELLPHI_EIGEN_INCLUDE=/path/to/eigen3` if set in step 2) - If needed, delete `src/ellphi/_tangency_cpp_impl*.so` before reinstalling. 4) Quick sanity check: ```bash diff --git a/scripts/hybrid_tuning.sh b/scripts/hybrid_tuning.sh index 0b5555f..40f72e0 100755 --- a/scripts/hybrid_tuning.sh +++ b/scripts/hybrid_tuning.sh @@ -12,7 +12,7 @@ METHODS="brentq brenth algsig+newton newton" # 1) Normal Low-Dim (2D, 3D) - The "Happy Path" # Expect hybrid_8x3 to shine here. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 2 3 \ --extreme-fraction 0.0 \ --methods $METHODS \ @@ -26,7 +26,7 @@ poetry run python scripts/hybrid_tuning.py \ # 2) Extreme Low-Dim (2D, 3D) - Stress Test # Compare hybrid_8x3 failure rate vs hybrid_28x3/brent. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 2 3 \ --extreme-fraction 1.0 \ --hybrid-combos "$HYBRID_COMBOS" \ @@ -38,7 +38,7 @@ poetry run python scripts/hybrid_tuning.py \ # 3) Normal High-Dim (10D, 20D) - Scaling Check # Check if hybrid_8x3 scales to high dims in benign geometry. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 10 20 \ --extreme-fraction 0.0 \ --hybrid-combos "$HYBRID_COMBOS" \ @@ -50,7 +50,7 @@ poetry run python scripts/hybrid_tuning.py \ # 4) Extreme High-Dim (10D, 20D) - The "Worst Case" # Expect hybrid_8x3 to fail. Evaluate hybrid_28x3 vs brent. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 10 20 \ --extreme-fraction 1.0 \ --hybrid-combos "$HYBRID_COMBOS" \ @@ -62,7 +62,7 @@ poetry run python scripts/hybrid_tuning.py \ # 5) Multi-Dim (20D to 50D) - Seeking the "Strategy Shift" # Check if hybrid still works for much higher dimention. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SMALL_SAMPLES --dims `seq 20 3 50` \ --extreme-fraction 0.0 \ --methods $METHODS \ @@ -75,7 +75,7 @@ poetry run python scripts/hybrid_tuning.py \ # 2) Extreme Low-Dim (2D, 3D) - Stress Test # Compare hybrid_8x3 failure rate vs hybrid_28x3/brent. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 2 3 \ --extreme-fraction 1.0 \ --methods $METHODS \ @@ -89,7 +89,7 @@ poetry run python scripts/hybrid_tuning.py \ # 3) Normal High-Dim (10D, 20D) - Scaling Check # Check if hybrid_8x3 scales to high dims in benign geometry. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 10 20 \ --extreme-fraction 0.0 \ --methods $METHODS \ @@ -103,7 +103,7 @@ poetry run python scripts/hybrid_tuning.py \ # 4) Extreme High-Dim (10D, 20D) - The "Worst Case" # Expect hybrid_8x3 to fail. Evaluate hybrid_28x3 vs brent. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SAMPLES --dims 10 20 \ --extreme-fraction 1.0 \ --methods $METHODS \ @@ -116,7 +116,7 @@ poetry run python scripts/hybrid_tuning.py \ # 5) Multi-Dim (20D to 50D) - Seeking the "Strategy Shift" # Check if hybrid still works for much higher dimention. -poetry run python scripts/hybrid_tuning.py \ +uv run python scripts/hybrid_tuning.py \ --samples-per-dim $SMALL_SAMPLES --dims `seq 20 3 50` \ --extreme-fraction 0.0 \ --methods $METHODS \ diff --git a/src/ellphi/_tangency_cpp.py b/src/ellphi/_tangency_cpp.py index bc27bda..9049573 100644 --- a/src/ellphi/_tangency_cpp.py +++ b/src/ellphi/_tangency_cpp.py @@ -65,9 +65,11 @@ def _validate_library_version(lib: ctypes.CDLL) -> None: raise RuntimeError( "C++ backend version mismatch: " f"library reports '{actual}' but ellphi expects '{expected}'. " - "Rebuild the extension yourself (e.g., run 'python " - "build_tangency_cpp.py' or 'uv sync --reinstall-package " - "ellphi'); it is not rebuilt automatically during import." + "Rebuild the extension yourself: in a development checkout " + "run 'uv sync --reinstall-package ellphi' or " + "'python scripts/build_tangency_cpp.py'; with pip, run " + "'pip install --force-reinstall .' from the source tree. " + "It is not rebuilt automatically during import." )