Fill functions in src/geom_nmf and tests

README.md

@@ -99,6 +99,11 @@ To activate the virtual environment:
 ```sh
 poetry shell
 ```
+or 
+
+```sh
+poetry env activate
+```
 
 Your prompt will change to indicate you're inside the environment. To exit when you're done:
 

src/geom_nmf/__init__.py

@@ -1,7 +1,35 @@
-from importlib.metadata import version
+"""
+geom_nmf
+========
+Geometric NMF: geometric non-negative matrix factorization via maximum-volume simplex fitting.
+
+Public API
+----------
+GeomNMF                      Main pipeline.
+nfindr                       N-FINDR endmember extraction (standalone).
+log_simplex_volume           Log-volume of a simplex spanned by K points.
+compute_Phi                  Source attribution matrix from source means and H.
+estimate_weights             Recover W from Y and H.
+permute_to_reference         Permute estimated H, W, Phi to best match a reference ordering.
+barplot_Phi                  Grouped bar plot of Phi (% attribution per source and feature).
+"""
 
-from ._base import GeomNMF
-from . import _viz as viz
+from importlib.metadata import version
+from .core import GeomNMF, GeomNMFResult
+from .nfindr import nfindr
+from .endmembers import log_simplex_volume
+from .weights import compute_Phi, estimate_weights
+from .utils import permute_to_reference
+from .plot import barplot_Phi
 
 __version__ = version("geom-nmf")
-__all__ = ["GeomNMF", "viz"]
+__all__ = [
+    "GeomNMF",
+    "GeomNMFResult",
+    "nfindr",
+    "log_simplex_volume",
+    "compute_Phi",
+    "estimate_weights",
+    "permute_to_reference",
+    "barplot_Phi"
+]