Update Toolchains (uv, ty, python, maturin, rust 2024) (#69)

* WIP: Fixed non-deterministic test error

* Updated tooling to use uv/ty instead of poetry/mypy

* Updated python/rust/maturin versions

* Added mac os to testing pipelines

* Properly enforced fixed with csv reading

* Minor tweaks for maintainability

* Minor version bump

* track npz files with git-lfs

* fix: add macos dynamic lookup linker flags for pyo3

docs/development.rst

@@ -14,7 +14,7 @@ Prerequisites
 
 -  Rust 1.70+ with Cargo
 -  Python 3.11+
--  Poetry
+-  uv
 -  Git
 
 Environment Setup
@@ -31,19 +31,19 @@ Environment Setup
 
    .. code:: bash
 
-      poetry install --with dev,docs
+      uv sync --group dev --group docs
 
 #. **Setup pre-commit hooks:**
 
    .. code:: bash
 
-      poetry run pre-commit install
+      uv run pre-commit install
 
 #. **Build the Rust extension:**
 
    .. code:: bash
 
-      poetry run maturin develop
+      uv run maturin develop
 
 ************************
  Code Style and Quality
@@ -55,7 +55,7 @@ Python Code
 ===========
 
 -  **Ruff**: For linting and formatting
--  **MyPy**: For type checking
+-  **ty**: For type checking
 -  **Pytest**: For testing
 
 Run quality checks:
@@ -63,14 +63,14 @@ Run quality checks:
 .. code:: bash
 
    # Format and lint Python code
-   poetry run ruff format .
-   poetry run ruff check .
+   uv run ruff format .
+   uv run ruff check .
 
    # Type checking
-   poetry run mypy .
+   uv run ty check
 
    # Run tests
-   poetry run pytest
+   uv run pytest
 
 Rust Code
 =========
@@ -105,10 +105,10 @@ Running Tests
 .. code:: bash
 
    # Run all tests
-   poetry run pytest
+   uv run pytest
 
    # Run with coverage
-   poetry run pytest --cov=read_aconity_layers
+   uv run pytest --cov=read_aconity_layers
 
    # Run Rust tests
    cargo test
@@ -144,14 +144,14 @@ Building Documentation
 .. code:: bash
 
    # Install documentation dependencies
-   poetry install --with docs
+   uv sync --group docs
 
    # Build documentation
    cd docs
    make html
 
    # Or build manually
-   poetry run sphinx-build -b html . _build/html
+   uv run sphinx-build -b html . _build/html
 
    # Serve locally (optional)
    make serve
@@ -199,9 +199,8 @@ The project uses pre-commit hooks that run automatically:
 
 -  Code formatting (Ruff, rustfmt)
 -  Linting (Ruff, Clippy)
--  Type checking (MyPy)
+-  Type checking (ty)
 -  Version bump validation
--  Poetry validation
 
 These checks must pass before commits are accepted.
 
@@ -253,7 +252,7 @@ Adding a New Function
 
 #. **Implement in Rust** (``src/rust_fn/mod.rs``)
 #. **Add Python binding** (``src/lib.rs``)
-#. **Update type stubs** (``read_layers.pyi``)
+#. **Update type stubs** (``read_aconity_layers.pyi``)
 #. **Add tests** for both Rust and Python
 #. **Update documentation**
 
@@ -262,8 +261,7 @@ Debugging Build Issues
 
 -  **Check Rust version**: Must be 1.70+
 -  **Verify PyO3 compatibility**: Should match Python version
--  **Clear build cache**: ``cargo clean`` and ``poetry env remove
-   --all``
+-  **Clear build cache**: ``cargo clean`` and ``rm -rf .venv``
 -  **Check dependencies**: Ensure all dev dependencies are installed
 
 Profiling Performance

docs/installation.rst

@@ -28,7 +28,7 @@ Prerequisites
 
 -  Rust 1.70 or higher
 -  Python 3.11 or higher
--  Poetry (for development)
+-  uv (for development)
 
 Build Steps
 ===========
@@ -44,19 +44,19 @@ Build Steps
 
    .. code:: bash
 
-      poetry install
+      uv sync
 
 #. Build the Rust extension:
 
    .. code:: bash
 
-      poetry run maturin develop
+      uv run maturin develop
 
 #. Run tests to verify installation:
 
    .. code:: bash
 
-      poetry run pytest
+      uv run pytest
 
 **************************
  Development Installation
@@ -66,12 +66,12 @@ For development work, you'll also want the development dependencies:
 
 .. code:: bash
 
-   poetry install --with dev,docs
+   uv sync --group dev --group docs
 
 This installs additional tools for:
 
 -  Code formatting (ruff)
--  Type checking (mypy)
+-  Type checking (ty)
 -  Testing (pytest)
 -  Documentation building (sphinx)
 

docs/justfile

@@ -1,7 +1,7 @@
 # Justfile for Sphinx documentation
 
 _sphinxopts := ""
-_sphinxbuild := "poetry run sphinx-build"
+_sphinxbuild := "uv run sphinx-build"
 _sourcedir := "."
 _builddir := "./_build"
 
@@ -23,7 +23,7 @@ ensure-rustdocgen:
 build-extension:
     @echo "Checking Rust toolchain..."
     @which cargo > /dev/null || (echo "Error: Rust/Cargo not found. Please install Rust toolchain." && exit 1)
-    cd .. && poetry run maturin develop
+    cd .. && uv run maturin develop
 
 # Clean build directory
 clean builddir=_builddir:
@@ -45,7 +45,7 @@ serve sphinxbuild=_sphinxbuild sourcedir=_sourcedir builddir=_builddir sphinxopt
 
 # Build documentation with live reload (requires sphinx-autobuild)
 livehtml sourcedir=_sourcedir builddir=_builddir sphinxopts=_sphinxopts: ensure-rustdocgen build-extension
-    poetry run sphinx-autobuild "{{sourcedir}}" "{{builddir}}/html" {{sphinxopts}}
+    uv run sphinx-autobuild "{{sourcedir}}" "{{builddir}}/html" {{sphinxopts}}
 
 # Check for broken links
 linkcheck sphinxbuild=_sphinxbuild sourcedir=_sourcedir builddir=_builddir sphinxopts=_sphinxopts: