CostaLab · jsnagai · Aug 20, 2026 · Aug 20, 2026 · Aug 20, 2026
diff --git a/dist/scaccordion-0.2.1.6-py2.py3-none-any.whl b/dist/scaccordion-0.2.1.6-py2.py3-none-any.whl
diff --git a/dist/scaccordion-0.2.1.6-py3-none-any.whl b/dist/scaccordion-0.2.1.6-py3-none-any.whl
diff --git a/dist/scaccordion-0.2.1.6.tar.gz b/dist/scaccordion-0.2.1.6.tar.gz
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,14 @@
 myst-parser
 nbsphinx
-sphinx_rtd_theme
-sphinx
+sphinxcontrib-bibtex
+sphinx
+plotly
+sphinx-rtd-size
+gprofiler-official
+sankeyflow
+nbformat
+anndata
+scanpy
+sphinx-design
+sphinx-book-theme
+pygments
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -15,6 +15,9 @@
 version = '0.1.8.8'
 
 extensions = [
+    'sphinx_design',
+    "sphinx.ext.napoleon",
+    'sphinxcontrib.bibtex',
     'sphinx.ext.duration',
     'sphinx.ext.doctest',
     'sphinx.ext.autodoc',
@@ -29,10 +32,54 @@
     'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
 }
 intersphinx_disabled_domains = ['std']
-
 templates_path = ['_templates']
 
-html_theme = 'sphinx_rtd_theme'
+# -- HTML output options
+html_theme = 'sphinx_book_theme'
+html_logo = "_static/logo.png"
+# Specific parameters passed directly to the 'sphinx_book_theme'.
+html_theme_options = {
+    "repository_url": "https://github.com/CostaLab/pyCrossTalkeR",
+    "use_repository_button": True,
+    "use_download_button": True,
+    "use_fullscreen_button": True,
+    "collapse_navbar": True,
+    "show_toc_level": 4,
+    "show_navbar_depth": 2,
+    "logo": {
+        "text": "<b>pyCrossTalkeR</b>",
+    }
+}
+
+
+sphinx_rtd_size_width = "85%"
+
+
+# -- It hides the input/output prompt numbers (In [1]: / Out [1]:).
+nbsphinx_prolog = """
+.. raw:: html
+
+    <style>
+        div.nbinput.container div.prompt,
+        div.nboutput.container div.prompt,
+        span.prompt {
+            display: none !important;
+            min-width: 0 !important;
+            padding: 0 !important;
+        }
+    </style>
+"""
 
 # -- Options for EPUB output
-epub_show_urls = 'footnote'
+epub_show_urls = 'footnote'    
+
+# -- Static files configuration
+html_js_files = [
+    "require.min.js",
+    "custom.js",
+]
+
+html_static_path = ["_static"]
+html_css_files = [
+    "custom.css",
+]
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,34 +1,31 @@
 [tool.poetry]
 name = "scaccordion"
-version = "0.2.1.5"
+version = "0.2.1.6"
 description = ""
 authors = ["James Nagai <james.nagai@gmail.com>"]
 readme = "README.md"
+
 include = [
     { path = "data/"},
 ]
 
-
 [tool.poetry.dependencies]
-python = "^3.11"
-setuptools = "82.0.1"
-Cython = "^3.2.0"
-scikit-learn = "^1.5.2"
-matplotlib = "^3.9.1"
+python = ">=3.11.14"
+scikit-learn = ">1.5.2"
+matplotlib = ">3.9.1"
 seaborn = "^0.13.2"
-pot = "^0.9.4"
-rpy2 = "^3.5.10"
-pydiffmap = "^0.2.0.1"
-networkx = "^3.3"
-tqdm = "^4.66.5"
-tables = "^3.9.1"
-skimpy = "^0.0.14"
-phate = "^1.0.11"
-conorm = "^1.2.0"
-scipy = "^1.6.0"
-numpy="^2.0.0"
-genieclust="^1.3.0"
-kmedoids = "^0.5.3.1"
+pot = ">0.9.4"
+rpy2 = ">3.5.10"
+pydiffmap = ">=0.2.0.1"
+networkx = ">3.3"
+tqdm = ">4.66.5"
+tables = ">3.9.1"
+skimpy = ">0.0.14"
+phate = ">=2.0.0"
+scipy = ">1.6.0"
+numpy=">1.24"
+genieclust=">1.1.5"
+kmedoids = ">0.5.3.1"
 
 [build-system]
 requires = ["poetry-core"]

diff --git a/scaccordion/__pycache__/__init__.cpython-310.pyc b/scaccordion/__pycache__/__init__.cpython-310.pyc
diff --git a/scaccordion/__pycache__/__init__.cpython-312.pyc b/scaccordion/__pycache__/__init__.cpython-312.pyc
diff --git a/scaccordion/plots/__pycache__/__init__.cpython-312.pyc b/scaccordion/plots/__pycache__/__init__.cpython-312.pyc
diff --git a/scaccordion/plots/__pycache__/accplots.cpython-312.pyc b/scaccordion/plots/__pycache__/accplots.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/Accordion.cpython-310.pyc b/scaccordion/tools/__pycache__/Accordion.cpython-310.pyc
diff --git a/scaccordion/tools/__pycache__/Accordion.cpython-312.pyc b/scaccordion/tools/__pycache__/Accordion.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/GOT.cpython-312.pyc b/scaccordion/tools/__pycache__/GOT.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/GWOT.cpython-312.pyc b/scaccordion/tools/__pycache__/GWOT.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/KBarycenters.cpython-312.pyc b/scaccordion/tools/__pycache__/KBarycenters.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/__init__.cpython-310.pyc b/scaccordion/tools/__pycache__/__init__.cpython-310.pyc
diff --git a/scaccordion/tools/__pycache__/__init__.cpython-312.pyc b/scaccordion/tools/__pycache__/__init__.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/datasets.cpython-312.pyc b/scaccordion/tools/__pycache__/datasets.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/distances.cpython-312.pyc b/scaccordion/tools/__pycache__/distances.cpython-312.pyc
diff --git a/scaccordion/tools/__pycache__/utils.cpython-310.pyc b/scaccordion/tools/__pycache__/utils.cpython-310.pyc
diff --git a/scaccordion/tools/__pycache__/utils.cpython-312.pyc b/scaccordion/tools/__pycache__/utils.cpython-312.pyc
diff --git a/scaccordion/tools/distances.py b/scaccordion/tools/distances.py
@@ -32,7 +32,8 @@ def getGRD(G,weight='weight',normalize=False, degnorm=False, axis=1):
         If this is a string, then edge weights will be accessed via the
         edge attribute with this key (that is, the weight of the edge
         joining `u` to `v` will be ``G.edges[u, v][weight]``). If no
-        such edge attribute exists, the weight of the edge is assumed to
+        such edge attributeactl.distances.getCTD(tmp + Aall)
+ exists, the weight of the edge is assumed to
         be one.
         If this is a function, the weight of an edge is the value
         returned by the function. The function must accept exactly three

diff --git a/tests/__pycache__/__init__.cpython-310.pyc b/tests/__pycache__/__init__.cpython-310.pyc
diff --git a/tests/__pycache__/__init__.cpython-312.pyc b/tests/__pycache__/__init__.cpython-312.pyc
diff --git a/tests/__pycache__/test_GOT.cpython-310-pytest-8.3.3.pyc b/tests/__pycache__/test_GOT.cpython-310-pytest-8.3.3.pyc
diff --git a/tests/__pycache__/test_GOT.cpython-312-pytest-9.1.1.pyc b/tests/__pycache__/test_GOT.cpython-312-pytest-9.1.1.pyc
diff --git a/tests/__pycache__/test_GWOT.cpython-310-pytest-8.3.3.pyc b/tests/__pycache__/test_GWOT.cpython-310-pytest-8.3.3.pyc
diff --git a/tests/__pycache__/test_GWOT.cpython-312-pytest-9.1.1.pyc b/tests/__pycache__/test_GWOT.cpython-312-pytest-9.1.1.pyc
diff --git a/tests/__pycache__/test_datasets.cpython-310-pytest-8.3.3.pyc b/tests/__pycache__/test_datasets.cpython-310-pytest-8.3.3.pyc
diff --git a/tests/__pycache__/test_datasets.cpython-312-pytest-9.1.1.pyc b/tests/__pycache__/test_datasets.cpython-312-pytest-9.1.1.pyc
diff --git a/tutorials/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/tutorials/.ipynb_checkpoints/Untitled-checkpoint.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tutorials/Untitled.ipynb b/tutorials/Untitled.ipynb
@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}