From 92f0098adfab4dd29265899ac3b6c182df70b5c4 Mon Sep 17 00:00:00 2001 From: vbhardwaj Date: Sun, 5 May 2024 19:58:14 +0200 Subject: [PATCH] cleanup --- pyproject.toml | 3 +-- requirements.txt | 1 - sincei/TopicModels.py | 1 - sincei/_deprecated.py | 2 +- 4 files changed, 2 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 86c8fbc..6608c4e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ authors = [ {name = "Vivek Bhardwaj"}, ] maintainers = [ - {name = "Vivek Bhardwaj", email = "vivbhr@gmail.com"}, + {name = "Vivek Bhardwaj", email = "v.bhardwaj@uu.nl"}, ] classifiers = [ "Intended Audience :: Science/Research", @@ -33,7 +33,6 @@ dependencies = [ "deeptools", "leidenalg", "networkx", - "community", "python-igraph", # for debug logging (referenced from the issue template) "session-info", diff --git a/requirements.txt b/requirements.txt index 8cbf05c..a3a7ddf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,5 +6,4 @@ deeptools gensim leidenalg networkx -community python-igraph diff --git a/sincei/TopicModels.py b/sincei/TopicModels.py index 27f3f5a..b7a6907 100644 --- a/sincei/TopicModels.py +++ b/sincei/TopicModels.py @@ -9,7 +9,6 @@ from sklearn.metrics import pairwise_distances import leidenalg as la -# import community import umap from scanpy._utils import get_igraph_from_adjacency from scanpy.neighbors import ( diff --git a/sincei/_deprecated.py b/sincei/_deprecated.py index fbbfc37..05cebfc 100644 --- a/sincei/_deprecated.py +++ b/sincei/_deprecated.py @@ -134,7 +134,7 @@ def cluster_LSA( G : igraph object Graph object. """ - + import community # cluster on cel-topic dist _distances = pairwise_distances(cell_topic.iloc[:, 1:], metric=distance_metric) knn_indices, knn_distances = _get_indices_distances_from_dense_matrix(_distances, nk)