ShobiStassen / PARC

MIT License
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`run_umap_hnsw` doesn't work #25

Closed ahill187 closed 4 months ago

ahill187 commented 7 months ago

Version Information

Python 3.10
MacOSx

Error

When calling run_umap_hnsw in the example in the README, I get the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
     16 graph = Parc1.knngraph_full()
---> 17 X_umap = Parc1.run_umap_hnsw(X, graph)
     18 plt.scatter(X_umap[:, 0], X_umap[:, 1], c=Parc1.labels)
     19 plt.show()

File python3.10/site-packages/parc/_parc.py:595, in PARC.run_umap_hnsw(self, X_input, graph, n_components, alpha, negative_sample_rate, gamma, spread, min_dist, init_pos, random_state)
    593 print('a,b, spread, dist', a, b, spread, min_dist)
    594 t0 = time.time()
--> 595 X_umap = simplicial_set_embedding(data=X_input, graph=graph, n_components=n_components, initial_alpha=alpha,
    596                                   a=a, b=b, n_epochs=0, metric_kwds={}, gamma=gamma,
    597                                   negative_sample_rate=negative_sample_rate, init=init_pos,
    598                                   random_state=np.random.RandomState(random_state), metric='euclidean',
    599                                   verbose=1)
    600 return X_umap

TypeError: simplicial_set_embedding() missing 3 required positional arguments: 'densmap', 'densmap_kwds', and 'output_dens'