Test update

.github/workflows/python-package.yml

@@ -16,10 +16,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v4
+    - uses: r-lib/actions/setup-r@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
@@ -28,7 +29,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        python -m pip install pip install git+https://github.com/CostaLab/scACCorDiON/
+        python -m pip install git+https://github.com/jsnagai/scACCorDiON/
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |

pyproject.toml

@@ -10,9 +10,9 @@ include = [
 
 
 [tool.poetry.dependencies]
-python = "^3.10"
 scikit-learn = "1.5.2"
 matplotlib = "^3.9.1"
+python = "^3.10"
 seaborn = "0.13.2"
 pot = "^0.9.4"
 rpy2 = "3.5.10"
@@ -22,10 +22,11 @@ tqdm = "4.66.5"
 tables = "^3.9.1"
 skimpy = "^0.0.14"
 phate = "^1.0.11"
-conorm = "^1.2.0"
+conorm = "1.2.0"
 scipy = "^1.6.0"
 numpy="^1.24"
-genieclust="^1.1.5"
+genieclust="1.1.5"
+kmedoids = "^0.5.3.1"
 
 [build-system]
 requires = ["poetry-core"]

scaccordion/tools/datasets.py

@@ -24,12 +24,12 @@ def load_peng2019_metadata():
     # This is a stream-like object. If you want the actual info, call
     # stream.read()
     import pandas as pd
-    stream = importlib.resources.path("scaccordion.data", 'Peng_PDAC_metaacc.h5ad')
+    stream = importlib.resources.files("scaccordion.data")/ 'Peng_PDAC_metaacc.h5ad'
     return pd.read_hdf(stream)
 
 
 def make_gl_ciclic_graph():
    import pandas as pd
    import networkx as nx
-   stream = importlib.resources.path("scaccordion.data", 'glexample.hdf')
+   stream = importlib.resources.files("scaccordion.data")/ 'glexample.hdf'
    return (nx.from_pandas_edgelist(pd.read_hdf(stream),create_using=nx.DiGraph, edge_attr=True))

scaccordion/tools/distances.py

@@ -70,7 +70,7 @@ def getGRD(G,weight='weight',normalize=False, degnorm=False, axis=1):
     """
     cond1 = type(G) is not nx.DiGraph
     cond2 = isspmatrix(G)!=True
-    assert(cond1 or cond2, "Please make sure you have the correct input")
+    #assert(cond1 or cond2, "Please make sure you have the correct input")
     if isspmatrix(G)==False:
         G = nx.to_scipy_sparse_array(G)
     X = directed_res(G,weight,normalize,axis)[0]
@@ -174,7 +174,7 @@ def normalizeAdj(G, axis):
         row_sums = np.array(G.sum(axis=1)).flatten()
         row_sums[row_sums == 0] = 1
         G = G.multiply(1 / row_sums[:, np.newaxis])
-    elif normalize and axis==0:
+    elif axis==0:
         sparse_matrix = G.tocsc()
         # Compute column sums
         sums = np.array(sparse_matrix.sum(axis=0)).flatten()