sem_cython12/README.md

# sem_cython12

OpenMP-parallel numerical kernel library for Python.  Pre-built
Linux and Windows binaries included; no compilation required at
install time.

## What is this for?

For an introduction to SEM (Similarity Energy Model) and how
`sem_cython12` fits in, see:

- [`docs/SEM_Overview.md`](./docs/SEM_Overview.md) — non-internal
  introduction to SEM, what it does, and how this library fits in.
- [`docs/SEM_Mathematical_Apparatus.md`](./docs/SEM_Mathematical_Apparatus.md)
  — capabilities-level description of the operators and engines
  exposed by the library.

## Contents

- `sem_cython12/sem_core12.cpython-3{10,11,12,13}-x86_64-linux-gnu.so` -
  compiled extensions (Linux, x86_64) for CPython 3.10 / 3.11 / 3.12 / 3.13.
- `sem_cython12/sem_core12.cp3{10,11,12,13}-win_amd64.pyd` -
  compiled extensions (Windows, AMD64) for CPython 3.10 / 3.11 / 3.12 / 3.13.
- `sem_cython12/wrapper.py` - Python API.
- `sem_cython12/__init__.py` - package entry.

Python's import system selects the correct binary for the running
interpreter automatically — install the whole package and the right
`.so` / `.pyd` is picked up by ABI tag.

## Compatibility

| Platform        | Architecture | Python                 | Runtime requirements        |
|-----------------|--------------|------------------------|-----------------------------|
| Linux           | x86_64       | CPython 3.10/3.11/3.12/3.13 | glibc >= 2.31, libgomp   |
| Windows 10/11   | AMD64        | CPython 3.10/3.11/3.12/3.13 | vcomp (ships with Windows) |
| macOS           | -            | -                      | not provided (contact sales@sevana.biz) |

Single Python dependency: `numpy >= 1.23` (see `requirements.txt`).

## How the binaries were built

- **Linux (`*.so`), cp312**: system gcc 13.3 on Ubuntu, OpenMP via
  `libgomp`, flags `-O3 -ffast-math -march=native -fopenmp`.
- **Linux (`*.so`), cp310 / cp311 / cp313**: conda-forge gcc inside
  isolated `python=3.10/3.11/3.13` envs (clean, system-Python-free
  build), same OpenMP and optimisation flags.
- **Windows (`*.pyd`), all four versions**: MSVC v14.50 (Visual Studio
  Build Tools 2026), OpenMP via `vcomp`, flags `/O2 /openmp`. Each
  built against the matching CPython interpreter installed via
  `winget`.

All eight binaries pass the same numerical smoke test
(`batch_max_similarity` over fixed-seed data) and produce identical
output to within float64 round-off.

## Install

```bash
git clone https://git.sevana.biz/vvs/sem_cython12.git
cd sem_cython12
pip install -r requirements.txt
# Make the package importable, either:
pip install -e .                      # if pyproject.toml/setup.py is added
# or just put the package on PYTHONPATH:
export PYTHONPATH=$PWD:$PYTHONPATH
```

## Quick start

```python
import numpy as np
from sem_cython12 import wrapper as cy

# Sanity check
assert cy.available(), "compiled extension did not load"
print("backend:", cy.backend())

# Thread count (defaults to ~50% of logical cores; set explicitly via
# either the SEM_NUM_THREADS env var or set_num_threads()):
cy.set_num_threads(8)
print("threads:", cy.get_num_threads())

# Example workload
rng = np.random.default_rng(0)
Q = rng.standard_normal((1000, 32))         # 1000 queries
M = rng.standard_normal((5000, 32))         # 5000 reference points

# For each query: max similarity to any reference, with kernel scale lam.
sim = cy.batch_max_similarity(Q, M, lam=1.0)
print(sim.shape, sim.dtype)                 # (1000,) float64
```

## API reference

All functions accept either Python lists or numpy arrays; inputs are
internally cast to contiguous `float64`.  Outputs are numpy arrays.

### Configuration

| Function | Purpose |
|---|---|
| `available() -> bool` | True iff the compiled extension loaded |
| `backend() -> str` | `'cython12'` or `'python-fallback'` |
| `get_num_threads() -> int` | Active OpenMP worker count |
| `set_num_threads(n: int)` | Set OpenMP worker count (n >= 1) |

### Distance / similarity

| Function | Inputs | Output |
|---|---|---|
| `batch_max_similarity(X_query, X_members, lam)` | `(Q, D)`, `(M, D)`, `lam > 0` | `(Q,)` - per-query similarity score in `[0, 1]` against the closest member |
| `concept_support_matrix(X_query, member_mats, lam)` | `(Q, D)`, list of `(M_k, D)`, `lam > 0` | `(Q, K)` - one similarity column per member set |
| `pairwise_distances(X)` | `(N, D)` | `(N, N)` - symmetric distance matrix between rows |
| `nn_distances(X)` | `(N, D)` | `(N,)` - min positive distance per row; `inf` if none |

### Best-tradeoff filtering

| Function | Inputs | Output |
|---|---|---|
| `pareto_core_mask(S)` | `(N, k)` | `(N,)` byte mask: rows that survive the multi-objective best-tradeoff filter |
| `one_sided_mask(S)` | `(N, k)` | `(N, k)` byte mask: rows contributing meaningfully on a single column only |
| `non_redundant_witnesses(S)` | `(N, k)` | int32 array of row indices contributing meaningfully across multiple columns |

### Vector reduction

| Function | Inputs | Output |
|---|---|---|
| `extend_frontier_kernel(cur_centers, cur_radii, new_emb, cur_arity)` | `(F, D)`, `(F,)`, `(A, D)`, `int` | `(flat_centers (F*A, D), flat_radii (F*A,))` |

See the wrapper docstrings for exact semantics of each function.

## Demos

Three runnable demos live in [`demos/`](./demos/):

1. [`01_iris_boundary.py`](./demos/01_iris_boundary.py) — rediscovers
   the famous Iris versicolor/virginica boundary specimens with no
   training, using only `concept_support_matrix` and `pairwise_distances`.
2. [`02_anomaly_detection.py`](./demos/02_anomaly_detection.py) —
   parameter-free anomaly detection that matches IsolationForest's
   AUC=1.0 on a synthetic benchmark, using only `batch_max_similarity`.
3. [`03_multicriteria_selection.py`](./demos/03_multicriteria_selection.py)
   — recovers 5/5 hidden balanced candidates that naive sum-of-scores
   ranking misses, using `pareto_core_mask` and `non_redundant_witnesses`.

A standalone copy of the demos repository is also published at
https://git.sevana.biz/vvs/sem_cython12-demos.

## Performance notes

Threads are configured globally per process; calling
`set_num_threads(n)` updates the OpenMP team size for all subsequent
calls.  The default uses approximately 50% of the host's logical
cores so other processes are not starved on shared machines.

For workloads dominated by `pairwise_distances` and
`pareto_core_mask`, near-linear scaling up to ~8 threads is typical
on commodity x86 hardware.  `batch_max_similarity` is BLAS-friendly
and benefits most from larger `M` (reference set) at fixed `D`.

## Memory / threading model

- All arrays are processed in shared memory; no inter-process
  serialisation.
- Each routine releases the GIL during its inner loops, so calling
  it concurrently from Python threads is safe.
- The compiled extension links against the system OpenMP runtime
  (`libgomp`); avoid mixing with conda's `intel-openmp` in the same
  process if possible.

## Privacy / telemetry

`sem_cython12` performs **no network I/O**, opens no sockets, and
writes no files outside the calling process's working directory.
There is no telemetry, no usage reporting, and no licence-server
check-in.  All computation is in-process on local arrays.

## Diagnostics

`backend()` returns `'python-fallback'` only when the `.so` failed
to import (wrong architecture, glibc too old, missing libgomp).  In
that state, every numerical function raises `RuntimeError`; check
`available()` before each batch to fail loudly rather than silently
fall back.

## Licence

The Software is licensed under the terms contained in the [LICENSE](./LICENSE)
file in this repository.

In short:
- **Research and non-commercial use**: granted free of charge under
  the conditions in section 2 of the LICENSE.
- **Commercial use**: requires a separate written commercial
  licence from the Licensor.  Contact `sales@sevana.biz`.
- **No warranty**: the Software is provided strictly "AS IS",
  without warranty of any kind.  The Licensor's total aggregate
  liability is limited to zero.

Please read the LICENSE file in full before using the Software.

## Support

Open an issue at https://git.sevana.biz/vvs/sem_cython12.