lme-python 0.1.7__tar.gz → 0.1.9__tar.gz

lme_python-0.1.9/.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-0.1.7 → lme_python-0.1.9}/.github/workflows/audit.yml

@@ -1,24 +1,10 @@
 name: Security 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 +35,21 @@ 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@v6
         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-0.1.7 → lme_python-0.1.9}/.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-0.1.7 → lme_python-0.1.9}/.github/workflows/ci.yml

@@ -2,15 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [master]
-    paths-ignore:
-      - "**/*.md"
-      - "LICENSE"
-  pull_request:
-    branches: [master]
-    paths-ignore:
-      - "**/*.md"
-      - "LICENSE"
+    tags:
+      - "v*"
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -23,6 +17,28 @@ env:
   CARGO_TERM_COLOR: always
 
 jobs:
+  rust-lint:
+    name: Rust fmt & clippy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Install OpenBLAS
+        run: sudo apt-get update && sudo apt-get install -y libopenblas-dev
+      - name: Cache cargo registry & build
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            target
+          key: ubuntu-lint-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: ubuntu-lint-
+      - name: rustfmt --check
+        run: python3 scripts/ci/lme_ci.py fmt-check
+      - name: clippy
+        run: python3 scripts/ci/lme_ci.py clippy
+
   test:
     name: Test (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
@@ -37,10 +53,6 @@ jobs:
       - 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
@@ -55,35 +67,29 @@ jobs:
           key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
           restore-keys: ${{ runner.os }}-cargo-
 
-      - name: Build
-        run: cargo build --verbose --locked
+      - name: Set OpenBLAS target (macOS)
+        if: matrix.os == 'macos-latest'
+        run: echo "OPENBLAS_TARGET=ARMV8" >> "$GITHUB_ENV"
 
       - 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@v6
         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 [ ${#wheels[@]} -eq 0 ]; then
@@ -91,8 +97,8 @@ jobs:
             ls -la dist 2>/dev/null || true
             exit 1
           fi
-          "$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)
@@ -183,28 +189,22 @@ 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@v6
         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 [ ${#wheels[@]} -eq 0 ]; then
@@ -212,8 +212,8 @@ jobs:
             ls -la dist 2>/dev/null || true
             exit 1
           fi
-          "$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-0.1.7 → lme_python-0.1.9}/.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:
@@ -82,8 +76,9 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
-      - name: Install OpenBLAS
-        run: brew install openblas
+      - name: Set OpenBLAS target (Apple Silicon wheel)
+        if: matrix.target == 'aarch64'
+        run: echo "OPENBLAS_TARGET=ARMV8" >> "$GITHUB_ENV"
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:

{lme_python-0.1.7 → lme_python-0.1.9}/.github/workflows/repo-metadata.yml

@@ -2,11 +2,8 @@ name: Sync Repository Metadata
 
 on:
   push:
-    branches: [master]
-    paths:
-      - Cargo.toml
-      - scripts/sync_github_repo_metadata.py
-      - .github/workflows/repo-metadata.yml
+    tags:
+      - "v*"
   workflow_dispatch:
 
 permissions:
@@ -24,10 +21,20 @@ jobs:
         run: |
           if [ -z "$REPO_ADMIN_TOKEN" ]; then
             echo "REPO_ADMIN_TOKEN is not set."
-            echo "Create a fine-grained PAT or GitHub App token with repository Administration: write."
+            echo "Create a fine-grained PAT with repository Administration: Read and write."
+            echo "Add it under Settings → Secrets and variables → Actions → REPO_ADMIN_TOKEN."
             exit 1
           fi
 
+      - name: Dry-run metadata payload
+        run: python scripts/sync_github_repo_metadata.py --dry-run
+
+      - name: Verify admin token is valid
+        env:
+          REPO_ADMIN_TOKEN: ${{ secrets.REPO_ADMIN_TOKEN }}
+          GITHUB_REPOSITORY: ${{ github.repository }}
+        run: python scripts/sync_github_repo_metadata.py --verify-token
+
       - name: Sync repository metadata
         env:
           REPO_ADMIN_TOKEN: ${{ secrets.REPO_ADMIN_TOKEN }}

{lme_python-0.1.7 → lme_python-0.1.9}/.gitignore

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

lme_python-0.1.9/AGENTS.md

@@ -0,0 +1,192 @@
+# Agent and contributor pre-flights
+
+This repo uses **four tiers** of checks (one more than a typical Task + bash-hook setup). Pick the tier that matches how much you changed.
+
+## Architecture (vs duplicated shell scripts)
+
+```mermaid
+flowchart TD
+  subgraph entry [Entry points]
+    task[Taskfile.yml]
+    lh[Lefthook]
+    gha[GitHub Actions]
+    legacy[scripts/local_ci.*]
+  end
+
+  subgraph core [Single implementation]
+    lme["scripts/ci/lme_ci.py"]
+  end
+
+  subgraph tools [Pinned tooling via mise.toml]
+    mise[mise install]
+    uv[uv — Python venv + Ruff]
+    lk[lefthook — git hooks]
+  end
+
+  task --> lme
+  lh --> lme
+  gha --> lme
+  legacy --> lme
+  mise --> uv
+  mise --> lk
+```
+
+**Why this is better than parallel `.ps1` / `.sh` trees:**
+
+| Piece | Role |
+|---|---|
+| [`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/) | 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) |
+
+[`Taskfile.yml`](../Taskfile.yml) is a thin alias layer; it does not duplicate logic.
+
+## 0. One-time setup
+
+```powershell
+mise install          # rust, python 3.11, uv, lefthook, task
+task setup            # mise install + lefthook install
+```
+
+Or install tools manually, then:
+
+```powershell
+task hooks:install
+```
+
+## 1. On `git commit` (Lefthook — parallel, staged-only)
+
+[`lefthook.yml`](../lefthook.yml) runs only when matching files are staged:
+
+| Staged | Command | Notes |
+|---|---|---|
+| `**/*.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).
+
+**Not** on commit: full `cargo test`, maturin/pytest, `pip-audit`.
+
+Bypass once: `git commit --no-verify`.
+
+## 2. On `git push` (Lefthook pre-push)
+
+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
+
+Install `cargo-audit` once: `cargo install cargo-audit` (pinned in GHA as 0.22.1).
+
+To catch **expired metadata tokens** before push (optional):
+
+```powershell
+$env:REPO_ADMIN_TOKEN = "<fine-grained PAT with Administration: Read and write>"
+task repo-metadata
+```
+
+If GHA reports `401 Bad credentials` on **Sync Repository Metadata**, rotate the secret: **Settings → Secrets and variables → Actions → `REPO_ADMIN_TOKEN`**.
+
+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. 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
+```
+
+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**:
+
+```powershell
+task python
+```
+
+### Rust-only
+
+```powershell
+task rust
+```
+
+### Python-only
+
+```powershell
+task lint:python
+task python
+```
+
+Direct runner (no Task):
+
+```powershell
+python scripts/ci/lme_ci.py lint
+python scripts/ci/lme_ci.py python --reuse-venv
+```
+
+## 4. Before PR / large refactors
+
+```powershell
+task          # full core CI mirror
+task ci:fast  # reuse python/.venv, skip wheel-reinstall pytest
+```
+
+Equivalent:
+
+```powershell
+python scripts/ci/lme_ci.py ci
+python scripts/ci/lme_ci.py ci --reuse-venv --skip-wheel-reinstall
+```
+
+**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
+
+| Command | Purpose |
+|---|---|
+| `ci` | Full core CI |
+| `lint` | Rust + Python static checks |
+| `preflight` | Pre-push: lint + check + cargo audit + repo metadata |
+| `audit` | cargo audit + pip-audit (GHA mirror) |
+| `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 |
+| `hooks-install` | `lefthook install` |
+
+Run `python scripts/ci/lme_ci.py --help` for the full list.
+
+See also [`CONTRIBUTING.md`](../CONTRIBUTING.md).