scFates 1.2.3__tar.gz → 1.2.4__tar.gz

{scfates-1.2.3/scFates.egg-info → scfates-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scFates
-Version: 1.2.3
+Version: 1.2.4
 Summary: scanpy compatible python suite for fast tree inference and advanced pseudotime downstream analysis
 Author: Louis Faure
 Project-URL: Repository, https://github.com/LouisFaure/scFates
@@ -26,7 +26,7 @@ Requires-Dist: typing_extensions
 Requires-Dist: scikit-learn
 Requires-Dist: scikit-misc
 Requires-Dist: simpleppt>=1.1.3
-Requires-Dist: elpigraph-python==0.3.2
+Requires-Dist: elpigraph-python>=0.3.4
 Requires-Dist: networkx>3.0
 Requires-Dist: igraph>=0.9.6
 Requires-Dist: adjustText>=0.7.3

{scfates-1.2.3 → scfates-1.2.4}/pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "scikit-learn",
     "scikit-misc",
     "simpleppt>=1.1.3",
-    "elpigraph-python==0.3.2",
+    "elpigraph-python>=0.3.4",
     "networkx>3.0",
     "igraph>=0.9.6",
     "adjustText>=0.7.3",

{scfates-1.2.3 → scfates-1.2.4}/scFates/tools/graph_fitting.py

@@ -23,132 +23,6 @@ from .. import settings
 from .utils import get_X
 
 
-def _patch_elpigraph_grammar():
-    """Monkey-patch elpigraph's AddNode2Node to fix numpy 2.x scalar assignment.
-
-    In elpigraph 0.3.2, ``ineighbour`` is a 1-element array but is used as a
-    scalar index, causing ``ValueError: setting an array element with a sequence``
-    on numpy ≥ 2.0 (Linux x86 build) because:
-      - ``Mus[ineighbour]`` returns shape ``(1,)`` assigned to a scalar slot
-      - ``NodePositions[ineighbour,]`` returns shape ``(1, ndims)`` instead of ``(ndims,)``
-    """
-    try:
-        import elpigraph.src.grammar_operations as _go
-    except ImportError:
-        return
-
-    _orig = _go.AddNode2Node
-
-    def _patched_AddNode2Node(
-        X,
-        NodePositions,
-        ElasticMatrix,
-        partition,
-        AdjustVect,
-        FixNodesAtPoints,
-        Max_K=float("inf"),
-        MaxNumberOfGraphCandidates=float("inf"),
-        PointWeights=None,
-    ):
-        import numpy as _np
-
-        nNodes = NodePositions.shape[0]
-        Mus = ElasticMatrix.diagonal()
-        Lambda = ElasticMatrix.copy()
-        _np.fill_diagonal(Lambda, 0)
-        indL = Lambda > 0
-        Connectivities = indL.sum(axis=0)
-
-        if PointWeights is not None:
-            assoc = _np.bincount(
-                partition[partition > -1].ravel(),
-                weights=PointWeights[partition > -1].ravel(),
-                minlength=nNodes,
-            )
-        else:
-            assoc = _np.bincount(
-                partition[partition > -1].ravel(), minlength=nNodes
-            )
-
-        npProt = _np.vstack(
-            (NodePositions, _np.zeros((1, NodePositions.shape[1])))
-        )
-        emProt = _np.vstack(
-            (
-                _np.hstack((Lambda, _np.zeros((nNodes, 1)))),
-                _np.zeros((1, nNodes + 1)),
-            )
-        )
-        niProt = _np.arange(nNodes + 1, dtype=int)
-        MuProt = _np.zeros(nNodes + 1)
-        MuProt[:-1] = Mus
-
-        if not _np.isinf(Max_K):
-            Degree = _np.sum(ElasticMatrix > 0, axis=1)
-            Degree[Degree > 1] = Degree[Degree > 1] - 1
-            if _np.sum(Degree <= Max_K) > 1:
-                idx_nodes = _np.where(Degree <= Max_K)[0]
-            else:
-                raise ValueError(
-                    "AddNode2Node impossible with the current parameters!"
-                )
-        else:
-            idx_nodes = _np.array(range(nNodes))
-
-        if MaxNumberOfGraphCandidates < len(idx_nodes) and _np.isinf(Max_K):
-            idx_nodes = _np.argsort(assoc)[::-1][:MaxNumberOfGraphCandidates]
-        elif MaxNumberOfGraphCandidates < len(idx_nodes) and not (
-            _np.isinf(Max_K)
-        ):
-            nGraphs = [
-                i
-                for i in _np.argsort(assoc)[::-1]
-                if i in idx_nodes
-            ]
-            idx_nodes = _np.array(nGraphs)[:MaxNumberOfGraphCandidates]
-
-        if FixNodesAtPoints != []:
-            idx_nodes = idx_nodes[
-                ~_np.isin(idx_nodes, _np.arange(len(FixNodesAtPoints)))
-            ]
-
-        NodePositionsArray = [npProt.copy() for i in range(len(idx_nodes))]
-        ElasticMatrices = [emProt.copy() for i in range(len(idx_nodes))]
-        NodeIndicesArray = _np.repeat(
-            niProt[:, _np.newaxis], len(idx_nodes), axis=1
-        )
-        AdjustVectArray = [AdjustVect + [False] for i in range(len(idx_nodes))]
-
-        for j, i in enumerate(idx_nodes):
-            MuProt[-1] = 0
-            meanL = Lambda[i, indL[i,]].mean(axis=0)
-            ElasticMatrices[j][nNodes, i] = ElasticMatrices[j][i, nNodes] = meanL
-
-            if Connectivities[i] == 1:
-                ineighbour = _np.nonzero(indL[i,])[0][0]  # scalar, not array
-                NewNodePosition = (
-                    2 * NodePositions[i,] - NodePositions[ineighbour,]
-                )
-                MuProt[i] = Mus[ineighbour]  # scalar assignment
-            else:
-                if assoc[i] == 0:
-                    NewNodePosition = NodePositions[indL[:, i]].mean(axis=0)
-                else:
-                    NewNodePosition = X[(partition == i).ravel()].mean(axis=0)
-
-            NodePositionsArray[j][nNodes, :] = NewNodePosition
-            _np.fill_diagonal(ElasticMatrices[j], MuProt)
-
-        return (
-            NodePositionsArray,
-            ElasticMatrices,
-            AdjustVectArray,
-            NodeIndicesArray,
-        )
-
-    _go.AddNode2Node = _patched_AddNode2Node
-
-
 def curve(
     adata: AnnData,
     Nodes: int = None,
@@ -592,8 +466,6 @@ def tree_epg(
 
     import elpigraph
 
-    _patch_elpigraph_grammar()
-
     logg.hint(
         "parameters used \n"
         "    "
@@ -656,8 +528,6 @@ def curve_epg(
 ):
     import elpigraph
 
-    _patch_elpigraph_grammar()
-
     X, use_rep = get_data(adata, use_rep, ndims_rep)
     X = X.values
 
@@ -723,8 +593,6 @@ def circle_epg(
 ):
     import elpigraph
 
-    _patch_elpigraph_grammar()
-
     X, use_rep = get_data(adata, use_rep, ndims_rep)
     X = X.values
 

{scfates-1.2.3 → scfates-1.2.4/scFates.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scFates
-Version: 1.2.3
+Version: 1.2.4
 Summary: scanpy compatible python suite for fast tree inference and advanced pseudotime downstream analysis
 Author: Louis Faure
 Project-URL: Repository, https://github.com/LouisFaure/scFates
@@ -26,7 +26,7 @@ Requires-Dist: typing_extensions
 Requires-Dist: scikit-learn
 Requires-Dist: scikit-misc
 Requires-Dist: simpleppt>=1.1.3
-Requires-Dist: elpigraph-python==0.3.2
+Requires-Dist: elpigraph-python>=0.3.4
 Requires-Dist: networkx>3.0
 Requires-Dist: igraph>=0.9.6
 Requires-Dist: adjustText>=0.7.3

{scfates-1.2.3 → scfates-1.2.4}/scFates.egg-info/requires.txt

@@ -17,7 +17,7 @@ typing_extensions
 scikit-learn
 scikit-misc
 simpleppt>=1.1.3
-elpigraph-python==0.3.2
+elpigraph-python>=0.3.4
 networkx>3.0
 igraph>=0.9.6
 adjustText>=0.7.3