Metadata-Version: 2.2
Name: press
Version: 0.9.0
Summary: Perturbation-Resampled Enrichment with Semantic Smoothing
Author-Email: Phi Bya <phi@wayne.edu>
License: Copyright (c) 2026 Tin Nguyen Lab, Wayne State University.
         All rights reserved.
         
         This software is distributed in compiled form only. No licence to the source
         code is granted. Permission to use, copy, or redistribute the compiled
         binaries is not granted by this notice and must be obtained from the
         copyright holder.
         
         PLACEHOLDER: these terms are a conservative default and have not been
         reviewed. Replace this file with the intended licence before any wider
         distribution.
         
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: C++
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: Other/Proprietary License
Project-URL: Homepage, https://github.com/tinnlab/PRESS
Requires-Python: >=3.9
Requires-Dist: numpy>=1.21
Description-Content-Type: text/markdown

# press

Python bindings for **PRESS** — Perturbation-Resampled Enrichment with Semantic
Smoothing.

Gene-set analysis that ranks sets with a competitive, frequency-weighted rank
statistic, smooths that ranking over a semantic k-nearest-neighbour graph of the
sets themselves, and reports significance from a self-calibrated
variance-component test.

The compiled core is shared with the R package, so results agree across
languages by construction.

## Install

```bash
pip install press --index-url https://tinnlab.github.io/pypi/simple/
```

Binary wheels only — there is no source distribution.

## Use

```python
import numpy as np, press

result = press.run(
    exprs=expr,                  # genes x samples, float64
    gene_names=genes,            # len == n_genes
    group=labels,                # len == n_samples, exactly 2 distinct values
    set_names=list(sets),
    set_genes=list(sets.values()),
)
order = np.argsort(result["p_value_raw"])   # best-ranked sets first
```

`exprs` is accepted in either C or Fortran order without a copy.

## Licence

See [LICENSE](LICENSE). Compiled binaries only; the source is not distributed.
