lme-python 0.1.1__tar.gz

lme_python-0.1.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  test:
+    name: Test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install OpenBLAS (macOS)
+        if: matrix.os == 'macos-latest'
+        run: brew install openblas
+
+      - name: Install OpenBLAS (Ubuntu)
+        if: matrix.os == 'ubuntu-latest'
+        run: sudo apt-get update && sudo apt-get install -y libopenblas-dev
+
+      - name: Cache cargo registry & build
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: ${{ runner.os }}-cargo-
+
+      - name: Build
+        run: cargo build --verbose
+
+      - name: Run tests
+        run: cargo test --verbose
+
+      - name: Check formatting
+        if: matrix.os == 'ubuntu-latest'
+        run: cargo fmt --check
+
+      - name: Run clippy
+        if: matrix.os == 'ubuntu-latest'
+        run: cargo clippy -- -D warnings
+
+  docs:
+    name: Build docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Build documentation
+        run: cargo doc --no-deps --verbose

lme_python-0.1.1/.github/workflows/python-release.yml

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+name: Build and Publish Python Wheels
+
+# Trigger on pushes to the master branch or when a release tag (v*) is pushed
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+    paths:
+      - 'python/**'
+      - 'src/**'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --manifest-path python/Cargo.toml -i python3.10
+          sccache: 'true'
+          manylinux: auto
+          before-script-linux: |
+            if command -v apt-get >/dev/null 2>&1; then
+              apt-get update && apt-get install -y pkg-config libssl-dev
+            elif command -v yum >/dev/null 2>&1; then
+              yum install -y pkgconfig openssl-devel
+            fi
+        env:
+          CFLAGS: "-std=gnu99"
+          CFLAGS_aarch64_unknown_linux_gnu: "-std=gnu99"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          architecture: ${{ matrix.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --manifest-path python/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.target }}
+          path: dist
+
+  macos:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install OpenBLAS
+        run: brew install openblas
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --manifest-path python/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path python/Cargo.toml
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  publish:
+    name: Publish to PyPI
+    needs: [linux, windows, macos, sdist]
+    runs-on: ubuntu-latest
+    # Only publish to PyPI on tag pushes (e.g., git tag v0.1.0 && git push origin v0.1.0)
+    if: "startsWith(github.ref, 'refs/tags/')"
+    environment: pypi
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: write  # needed to create GitHub Release
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          pattern: wheels-*
+          merge-multiple: true
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - name: Upload to GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: dist/*

lme_python-0.1.1/.gitignore

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+/target
+reference/
+rlib/
+julia-portable/
+julia-portable.zip
+flamegraph.svg
+
+# Python bindings
+python/target/
+python/.venv/
+__pycache__/
+*.whl
+.pytest_cache/
+*.log

lme_python-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2026-03-08
+
+### Added
+
+- **Core LMM** — `lmer()` with REML and ML estimation, matching R's `lme4` to 4 decimal places
+- **GLMM** — `glmer()` with Poisson, Binomial, Gaussian, and Gamma families via Laplace approximation
+- **Predictions** — `predict()`, `predict_conditional()`, `predict_response()`, `predict_conditional_response()` with `allow_new_levels` support
+- **Inference** — Satterthwaite and Kenward-Roger degrees of freedom, robust sandwich standard errors
+- **Model comparison** — `anova()` for likelihood ratio tests between nested models
+- **Diagnostics** — `confint()` for Wald confidence intervals, `simulate()` for parametric bootstrap
+- **Formula parser** — Wilkinson notation with nested (`a/b`), crossed (`a + b`), and correlated slope+intercept (`x | group`) random effects
+- **Sparse matrix architecture** — Compressed sparse column format with sparse Cholesky for large datasets
+- **Python bindings** — `lme_python` package via PyO3/maturin with `lmer()`, `glmer()`, `predict()`
+- **Documentation** — `GUIDE.md`, `PYTHON_GUIDE.md`, and cross-language `COMPARISONS.md`