lme-python 0.1.8__tar.gz → 0.1.11__tar.gz

lme_python-0.1.11/.JuliaFormatter.toml

@@ -0,0 +1,8 @@
+# JuliaFormatter defaults for comparison / parity scripts under comparisons/.
+indent = 4
+margin = 92
+always_for_in = true
+whitespace_typedefs = true
+whitespace_ops_in_indices = true
+remove_extra_newlines = true
+join_lines_based_on_source = true

{lme_python-0.1.8 → lme_python-0.1.11}/.github/workflows/audit.yml

@@ -1,24 +1,12 @@
 name: Security audit
 
+# Automatic runs: v* release tags only. Use workflow_dispatch for an on-demand audit.
+
 on:
-  schedule:
-    # Weekly: Mondays 12:00 UTC
-    - cron: "0 12 * * 1"
   workflow_dispatch:
   push:
-    branches: [master]
-    paths:
-      - "**/Cargo.toml"
-      - "**/Cargo.lock"
-      - "python/pyproject.toml"
-      - "python/requirements-ci.txt"
-  pull_request:
-    branches: [master]
-    paths:
-      - "**/Cargo.toml"
-      - "**/Cargo.lock"
-      - "python/pyproject.toml"
-      - "python/requirements-ci.txt"
+    tags:
+      - "v*"
 
 permissions:
   contents: read
@@ -49,25 +37,21 @@ jobs:
         run: cargo audit
 
   pip-audit:
-    name: pip-audit (python lockfile)
+    name: pip-audit (uv.lock)
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
 
-      - name: Set up Python
-        uses: actions/setup-python@v6
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v8.3.2
         with:
           python-version: "3.11"
-          cache: pip
-          cache-dependency-path: python/requirements-ci.txt
+          enable-cache: true
+          cache-dependency-glob: "python/uv.lock"
 
-      - name: Install locked CI dependencies
+      - name: pip-audit
         working-directory: python
         run: |
           set -euo pipefail
-          python -m pip install -U pip
-          python -m pip install -r requirements-ci.txt
-
-      - name: pip-audit
-        working-directory: python
-        run: python -m pip_audit
+          uv sync --extra dev --no-install-project
+          uv run pip-audit

{lme_python-0.1.8 → lme_python-0.1.11}/.github/workflows/benchmarks.yml

@@ -122,13 +122,24 @@ jobs:
       - name: Install R benchmark dependencies
         run: |
           mkdir -p "$R_LIBS_USER"
-          Rscript -e 'install.packages("lme4", repos="https://cloud.r-project.org", lib=Sys.getenv("R_LIBS_USER"))'
+          Rscript -e 'install.packages(c("lme4", "lmerTest", "car", "rlang", "styler"), repos="https://cloud.r-project.org", lib=Sys.getenv("R_LIBS_USER"))'
 
       - name: Install Julia benchmark dependencies
-        run: julia -e 'using Pkg; Pkg.add(["CSV", "DataFrames", "MixedModels"])'
+        run: julia -e 'using Pkg; Pkg.add(["CSV", "DataFrames", "JSON", "MixedModels", "GLM", "JuliaFormatter"])'
+
+      - name: Check comparison script formatting
+        run: python3 scripts/ci/lme_ci.py comparison-format-check --required
 
       - name: Build Rust examples
-        run: cargo build --release --examples
+        run: cargo build --release --locked --examples
+
+      - name: Run fair Rust vs Julia fit benchmark
+        run: |
+          python scripts/run_fair_rust_julia_benchmark.py \
+            --warmups "$BENCH_WARMUPS" \
+            --repeats "$BENCH_REPEATS" \
+            --output "benchmark-results/fair-rust-julia-${{ github.sha }}.json" \
+            --skip-rust-build
 
       - name: Run cross-language benchmark script
         id: cross_language_run
@@ -149,7 +160,9 @@ jobs:
         uses: actions/upload-artifact@v7
         with:
           name: cross-language-${{ github.sha }}
-          path: benchmark-results/cross-language-${{ github.sha }}.json
+          path: |
+            benchmark-results/cross-language-${{ github.sha }}.json
+            benchmark-results/fair-rust-julia-${{ github.sha }}.json
 
       - name: Attach cross-language artifact to GitHub Release
         if: always() && startsWith(github.ref, 'refs/tags/')
@@ -164,10 +177,17 @@ jobs:
             fi
           }
           gh release upload "${GITHUB_REF_NAME}" "benchmark-results/cross-language-${{ github.sha }}.json" --clobber
+          if [ -f "benchmark-results/fair-rust-julia-${{ github.sha }}.json" ]; then
+            gh release upload "${GITHUB_REF_NAME}" "benchmark-results/fair-rust-julia-${{ github.sha }}.json" --clobber
+          fi
 
       - name: Fail if cross-language benchmarks failed
         if: steps.cross_language_run.outputs.status != '0'
         run: |
+          json="benchmark-results/cross-language-${{ github.sha }}.json"
+          if [ -f "$json" ]; then
+            python3 scripts/ci/lme_ci.py benchmark-failures "$json" >&2 || true
+          fi
           echo "Cross-language benchmark script failed with exit code ${{ steps.cross_language_run.outputs.status }}." >&2
           exit 1
 

{lme_python-0.1.8 → lme_python-0.1.11}/.github/workflows/ci.yml

@@ -1,16 +1,13 @@
 name: CI
 
+# Automatic runs: v* release tags only. Use workflow_dispatch for an intentional
+# pre-release check on any branch (Actions → CI → Run workflow).
+
 on:
   push:
-    branches: [master]
-    paths-ignore:
-      - "**/*.md"
-      - "LICENSE"
-  pull_request:
-    branches: [master]
-    paths-ignore:
-      - "**/*.md"
-      - "LICENSE"
+    tags:
+      - "v*"
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -77,35 +74,25 @@ jobs:
         if: matrix.os == 'macos-latest'
         run: echo "OPENBLAS_TARGET=ARMV8" >> "$GITHUB_ENV"
 
-      - name: Build
-        run: cargo build --verbose --locked
-
       - name: Run tests
         run: cargo test --verbose --locked
 
-      - name: Set up Python
-        uses: actions/setup-python@v6
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v8.3.2
         with:
           python-version: "3.11"
-          cache: pip
-          cache-dependency-path: python/requirements-ci.txt
+          enable-cache: true
+          cache-dependency-glob: "python/uv.lock"
 
       - name: Python bindings (maturin develop, pytest, wheel install, pytest)
         working-directory: python
         shell: bash
         run: |
           set -euo pipefail
-          python -m venv .venv
-          if [ -f .venv/Scripts/python.exe ]; then
-            VPY=.venv/Scripts/python.exe
-          else
-            VPY=.venv/bin/python
-          fi
-          "$VPY" -m pip install -U pip
-          "$VPY" -m pip install -r requirements-ci.txt
-          "$VPY" -m maturin develop --release
-          "$VPY" -m pytest tests/ -v
-          "$VPY" -m maturin build --release -o dist
+          uv sync --extra dev --no-install-project
+          uv run maturin develop --release
+          uv run pytest tests/ -v
+          uv run maturin build --release -o dist
           shopt -s nullglob
           wheels=(dist/lme_python-*.whl)
           if [ ${#wheels[@]} -eq 0 ]; then
@@ -113,8 +100,8 @@ jobs:
             ls -la dist 2>/dev/null || true
             exit 1
           fi
-          "$VPY" -m pip install --force-reinstall "${wheels[0]}"
-          "$VPY" -m pytest tests/ -v
+          uv run pip install --force-reinstall "${wheels[0]}"
+          uv run pytest tests/ -v
 
   rust-all-targets:
     name: Rust check (all targets)
@@ -205,28 +192,22 @@ jobs:
             target
           key: ubuntu-cargo-${{ hashFiles('**/Cargo.lock') }}
           restore-keys: ubuntu-cargo-
-      - name: Set up Python
-        uses: actions/setup-python@v6
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v8.3.2
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: python/requirements-ci.txt
+          enable-cache: true
+          cache-dependency-glob: "python/uv.lock"
+
       - name: Python bindings (maturin develop, pytest, wheel install, pytest)
         working-directory: python
         shell: bash
         run: |
           set -euo pipefail
-          python -m venv .venv
-          if [ -f .venv/Scripts/python.exe ]; then
-            VPY=.venv/Scripts/python.exe
-          else
-            VPY=.venv/bin/python
-          fi
-          "$VPY" -m pip install -U pip
-          "$VPY" -m pip install -r requirements-ci.txt
-          "$VPY" -m maturin develop --release
-          "$VPY" -m pytest tests/ -v
-          "$VPY" -m maturin build --release -o dist
+          uv sync --extra dev --no-install-project
+          uv run maturin develop --release
+          uv run pytest tests/ -v
+          uv run maturin build --release -o dist
           shopt -s nullglob
           wheels=(dist/lme_python-*.whl)
           if [ ${#wheels[@]} -eq 0 ]; then
@@ -234,8 +215,8 @@ jobs:
             ls -la dist 2>/dev/null || true
             exit 1
           fi
-          "$VPY" -m pip install --force-reinstall "${wheels[0]}"
-          "$VPY" -m pytest tests/ -v
+          uv run pip install --force-reinstall "${wheels[0]}"
+          uv run pytest tests/ -v
 
   docs:
     name: Build docs

lme_python-0.1.11/.github/workflows/crate-publish-dry-run.yml

@@ -0,0 +1,43 @@
+name: Publish Rust crate
+
+# Publishes to crates.io only on v* tag pushes. Manual dispatch validates with
+# cargo publish --dry-run (no registry token required).
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: publish-crate-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  publish:
+    name: cargo publish
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: dtolnay/rust-toolchain@stable
+
+      - name: Validate crate package (dry run)
+        if: github.event_name == 'workflow_dispatch'
+        run: cargo publish --dry-run --locked
+
+      - name: Publish root crate
+        if: startsWith(github.ref, 'refs/tags/')
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
+        run: |
+          VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
+          if cargo search lme-rs --limit 1 2>/dev/null | grep -q "= \"$VERSION\""; then
+            echo "lme-rs $VERSION already on crates.io; skipping publish."
+            exit 0
+          fi
+          test -n "$CARGO_REGISTRY_TOKEN" || { echo "CARGO_REGISTRY_TOKEN repository secret is required to publish a new version" >&2; exit 1; }
+          cargo publish --locked

{lme_python-0.1.8 → lme_python-0.1.11}/.github/workflows/python-release.yml

@@ -1,16 +1,10 @@
 name: Build and Publish Python Wheels
 
-# Trigger on pushes to the master branch or when a release tag (v*) is pushed
+# Trigger automatically only for release tags; use workflow_dispatch for manual builds.
 on:
   push:
-    branches:
-      - master
     tags:
-      - 'v*'
-  pull_request:
-    paths:
-      - 'python/**'
-      - 'src/**'
+      - "v*"
   workflow_dispatch:
 
 permissions:
@@ -27,6 +21,9 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Validate legal notices
+        run: python scripts/ci/check_legal_compliance.py
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -43,6 +40,11 @@ jobs:
         env:
           CFLAGS: "-std=gnu99"
           CFLAGS_aarch64_unknown_linux_gnu: "-std=gnu99"
+      - name: Add third-party notices to wheels
+        run: |
+          for wheel in dist/*.whl; do
+            python scripts/ci/package_wheel_notices.py "$wheel"
+          done
       - name: Upload wheels
         uses: actions/upload-artifact@v7
         with:
@@ -60,12 +62,17 @@ jobs:
         with:
           python-version: '3.10'
           architecture: ${{ matrix.target }}
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Validate legal notices
+        run: python scripts/ci/check_legal_compliance.py
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
           args: --release --out dist --manifest-path python/Cargo.toml
           sccache: 'true'
+      - name: Add third-party notices to wheels
+        run: Get-ChildItem dist/*.whl | ForEach-Object { python scripts/ci/package_wheel_notices.py $_.FullName }
       - name: Upload wheels
         uses: actions/upload-artifact@v7
         with:
@@ -82,6 +89,9 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Validate legal notices
+        run: python scripts/ci/check_legal_compliance.py
       - name: Set OpenBLAS target (Apple Silicon wheel)
         if: matrix.target == 'aarch64'
         run: echo "OPENBLAS_TARGET=ARMV8" >> "$GITHUB_ENV"
@@ -91,6 +101,11 @@ jobs:
           target: ${{ matrix.target }}
           args: --release --out dist --manifest-path python/Cargo.toml
           sccache: 'true'
+      - name: Add third-party notices to wheels
+        run: |
+          for wheel in dist/*.whl; do
+            python scripts/ci/package_wheel_notices.py "$wheel"
+          done
       - name: Upload wheels
         uses: actions/upload-artifact@v7
         with:
@@ -101,6 +116,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Validate legal notices
+        run: python scripts/ci/check_legal_compliance.py
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:
@@ -123,12 +141,25 @@ jobs:
       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
       contents: write  # needed to create GitHub Release
     steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
       - uses: actions/download-artifact@v7
         with:
           path: dist
           pattern: wheels-*
           merge-multiple: true
 
+      - name: Normalize and verify wheel licenses
+        run: |
+          set -euo pipefail
+          for wheel in dist/*.whl; do
+            python scripts/ci/package_wheel_notices.py "$wheel"
+          done
+
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
 

{lme_python-0.1.8 → lme_python-0.1.11}/.github/workflows/repo-metadata.yml

@@ -1,12 +1,12 @@
 name: Sync Repository Metadata
 
+# Automatic runs: v* release tags only. Use workflow_dispatch to sync the About
+# box from Cargo.toml without tagging.
+
 on:
   push:
-    branches: [master]
-    paths:
-      - Cargo.toml
-      - scripts/sync_github_repo_metadata.py
-      - .github/workflows/repo-metadata.yml
+    tags:
+      - "v*"
   workflow_dispatch:
 
 permissions:

{lme_python-0.1.8 → lme_python-0.1.11}/.gitignore

@@ -10,6 +10,7 @@ flamegraph.svg
 artifacts/
 benchmark-results/
 benchmark-site/
+.r-lib/
 site/
 
 # Python bindings

{lme_python-0.1.8 → lme_python-0.1.11}/AGENTS.md

@@ -38,7 +38,7 @@ flowchart TD
 | [`scripts/ci/lme_ci.py`](lme_ci.py) | One cross-platform implementation (stdlib Python 3.10+) |
 | [`lefthook.yml`](../lefthook.yml) | Declarative hooks, **parallel** pre-commit, `stage_fixed` auto-staging |
 | [`mise.toml`](../mise.toml) | Pins Rust, Python 3.11, uv, lefthook, task — reproducible dev env |
-| [`uv`](https://docs.astral.sh/uv/) | Fast venv creation (`uv venv --python 3.11`), no repo-root `.venv` backup dance |
+| [`uv`](https://docs.astral.sh/uv/) | Locked Python env (`uv sync` + `uv.lock`); Ruff via `uv tool run` |
 | **Ruff** | `python/tests` + `python/examples` on `task lint`; staged auto-fix on commit |
 | **pre-push hook** | Automatic `preflight` (lint + `cargo check --all-targets` + `cargo audit` + repo metadata dry-run) |
 
@@ -65,8 +65,11 @@ task hooks:install
 |---|---|---|
 | `**/*.rs` | `fmt` then `clippy` | `stage_fixed: true` re-stages rustfmt fixes |
 | `python/**/*.py` | `ruff-staged --fix` | Ruff check + format; auto-stages fixes |
+| `comparisons/**/*.R`, `tests/*.R` | `r-format-staged --fix` | **styler** when Rscript + styler are installed; skips otherwise |
+| `comparisons/**/*.jl` | `julia-format-staged --fix` | **JuliaFormatter** when julia + JuliaFormatter are installed; skips otherwise |
 | `Cargo.toml`, `Cargo.lock`, `python/Cargo.toml`, `python/Cargo.lock` | `cargo check --all-targets` | Catches link/BLAS issues on your platform when manifests change |
 | `Cargo.toml`, `scripts/sync_github_repo_metadata.py` | `repo-metadata` dry-run (+ token verify if `REPO_ADMIN_TOKEN` set) | Validates About-box payload before GHA metadata sync |
+| `comparisons/**`, benchmark script/workflow | `benchmarks-smoke` | Rust sleepstudy example timing (release build) |
 
 Runs **in parallel** where safe (Ruff vs Rust fmt). Clippy waits on fmt (`priority`); manifest `check` runs after clippy (`priority` 3).
 
@@ -81,7 +84,8 @@ Runs **`preflight`** in parallel with itself as one command:
 1. `lint` — Rust fmt/clippy + Ruff
 2. `cargo check --workspace --all-targets --locked` — compile graph including tests/examples
 3. `cargo audit` — root crate + `python/` (same as GHA audit job, without `pip-audit`)
-4. `repo-metadata` — dry-run from `Cargo.toml`; **`--verify-token`** when `REPO_ADMIN_TOKEN` is in the environment
+4. `legal` — fixture provenance plus third-party license metadata and bundled notices
+5. `repo-metadata` — dry-run from `Cargo.toml`; **`--verify-token`** when `REPO_ADMIN_TOKEN` is in the environment
 
 Install `cargo-audit` once: `cargo install cargo-audit` (pinned in GHA as 0.22.1).
 
@@ -96,18 +100,26 @@ If GHA reports `401 Bad credentials` on **Sync Repository Metadata**, rotate the
 
 Bypass: `git push --no-verify`.
 
-**macOS Apple Silicon BLAS** (`openblas-static` vs MKL) is only exercised on `macos-latest` in GHA — Windows/Linux preflights cannot catch that matrix cell. After changing `Cargo.toml` BLAS target tables or release workflows, run `task ci` or wait for the macOS CI job.
+**macOS Apple Silicon BLAS** (`openblas-static` vs MKL) is only exercised on `macos-latest` in GHA — Windows/Linux preflights cannot catch that matrix cell. GHA now runs automatically only for `v*` tags (plus manual dispatch), so after changing `Cargo.toml` BLAS target tables or release workflows, run `task ci` locally or manually dispatch the CI workflow before tagging.
+
+**Cross-language benchmarks** (R + Julia, tag-only [`.github/workflows/benchmarks.yml`](.github/workflows/benchmarks.yml)): pre-commit runs `benchmarks-smoke` when `comparisons/**` changes (Rust `sleepstudy` example only). Full matrix needs R (`lme4`, `lmerTest`, `car`, `rlang`, `styler`) and Julia (`JuliaFormatter`) — run it through the tag/manual GHA workflow or `task benchmarks:preflight` with R installed. Comparison script formatting is checked in that GHA job; locally use `task lint:comparisons` (skips when tools are missing) or `task lint:comparisons:required` when R/Julia formatters are installed.
 
 ## 3. Before finishing work (manual)
 
+If you changed **LMM fit throughput** ([`src/math.rs`](src/math.rs) intercept path, [`src/optimizer.rs`](src/optimizer.rs) θ search), read **[OPTIMIZATION.md](OPTIMIZATION.md)** and re-run the fair harness cases listed there.
+
 ### Quick path
 
 ```powershell
 task lint
+task test:fast   # unit tests only (~seconds after compile)
 task preflight   # same as pre-push hook (without pip-audit)
 task audit       # full security audit incl. pip-audit
+task legal       # provenance and third-party license records
 ```
 
+Full integration tests: `task test` or `cargo test --locked` (uses `[profile.test] opt-level = 2` in [`Cargo.toml`](Cargo.toml)).
+
 Runs Rust (`fmt --check` + clippy) and Python Ruff on `python/tests` and `python/examples`.
 
 If you changed **Python bindings**:
@@ -150,7 +162,7 @@ python scripts/ci/lme_ci.py ci
 python scripts/ci/lme_ci.py ci --reuse-venv --skip-wheel-reinstall
 ```
 
-**CI-only:** multi-OS matrix, Python 3.10/3.12/3.13, production-load gates, `cargo audit` / `pip-audit`.
+**GHA-only:** multi-OS matrix, Python 3.10/3.12/3.13, production-load gates, and `pip-audit`. These workflows are release-oriented: automatic runs are limited to `v*` tags, with manual dispatch available for pre-release checks.
 
 ## `lme_ci.py` commands
 
@@ -160,9 +172,19 @@ python scripts/ci/lme_ci.py ci --reuse-venv --skip-wheel-reinstall
 | `lint` | Rust + Python static checks |
 | `preflight` | Pre-push: lint + check + cargo audit + repo metadata |
 | `audit` | cargo audit + pip-audit (GHA mirror) |
+| `legal` | Third-party notices, fixture provenance, and Rust license metadata |
 | `repo-metadata` | Dry-run GitHub About sync; verify token if `REPO_ADMIN_TOKEN` set |
+| `benchmarks-smoke` | Release examples + one Rust cross-language benchmark |
+| `benchmarks-preflight` | `benchmarks-smoke` + optional `sleepstudy.R` when R/lme4 present |
+| `benchmarks-fair-rust-julia` | Fair fit-only Rust vs MixedModels.jl timing (tier-A cases; see [BENCHMARK_COVERAGE.md](../BENCHMARK_COVERAGE.md); skip if Julia/packages missing) |
+| `perf-breakdown` | Rust `LME_PERF_DIAG` vs Julia `optsum.feval`; reports `prepare` / `fit_prepared` / cold `lmer` |
 | `rust-lint` | `fmt --check` + clippy |
 | `ruff-lint` | Ruff on `python/tests` + `python/examples` |
+| `comparison-format-check` | Optional styler/JuliaFormatter check on `comparisons/` (+ `tests/*.R`); use `--required` in GHA |
+| `r-format-staged --fix` | Staged R comparison/golden-parity scripts |
+| `julia-format-staged --fix` | Staged Julia comparison scripts |
+| `build-test` | `cargo test` (full suite) |
+| `test-fast` | `cargo test --lib` only (quick unit tests) |
 | `rust-all` | Rust slice without Python bindings tests |
 | `python` | Maturin + pytest (+ wheel pass) |
 | `ruff-staged --fix` | Staged Python lint/format |