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Replace deprecated numpy tostring/fromstring with tobytes/frombuffer #379

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Replace deprecated numpy tostring/fromstring with tobytes/frombuffer #379

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2ec408a
Replace deprecated numpy tostring/fromstring with tobytes/frombuffer
marouenbg Mar 24, 2026
31d4ec2
Fix pandas 4.x compatibility in cobra test and condor
marouenbg Mar 24, 2026
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5 changes: 3 additions & 2 deletions netZooPy/condor/condor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,13 +305,14 @@ def matrices(self, c,resolution):
# Computes weighted biadjacency matrix.
A = np.matrix(np.zeros((p, q)))
for edge in self.net.iterrows():
A[gn[edge[1][1]], rg[edge[1][0]]] = edge[1][2]
row = edge[1]
A[gn[row.iloc[1]], rg[row.iloc[0]]] = row.iloc[2]

# Computes node degrees for the nodesets.
ki = A.sum(1)
dj = A.sum(0)
# Computes sum of edges and bimodularity matrix.
m = float(sum(ki))
m = float(ki.sum())
B = A - resolution*((ki @ dj) / m)

# d = self.index_dict
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12 changes: 6 additions & 6 deletions netZooPy/lioness/lioness.py
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Expand Up @@ -412,16 +412,16 @@ def __lioness_loop(self, i):
return(np.array([0]))
else:
if self.computing == "gpu" and i == 0:
self.total_lioness_network = np.fromstring(
np.transpose(lioness_network).tostring(), dtype=lioness_network.dtype
self.total_lioness_network = np.frombuffer(
np.transpose(lioness_network).tobytes(), dtype=lioness_network.dtype
)[:,np.newaxis]

elif self.computing == "gpu" and i != 0:
self.total_lioness_network = np.column_stack(
(
self.total_lioness_network,
np.fromstring(
np.transpose(lioness_network).tostring(),
np.frombuffer(
np.transpose(lioness_network).tobytes(),
dtype=lioness_network.dtype,
),
)
Expand Down Expand Up @@ -467,9 +467,9 @@ def __par_lioness_loop(self, i, output, online_coexpression=None):

# TODO: why this? Should we remove it?
# if i == 0:
# self.total_lioness_network = np.fromstring(np.transpose(lioness_network).tostring(),dtype=lioness_network.dtype)
# self.total_lioness_network = np.frombuffer(np.transpose(lioness_network).tobytes(),dtype=lioness_network.dtype)
# else:
# self.total_lioness_network=np.column_stack((self.total_lioness_network ,np.fromstring(np.transpose(lioness_network).tostring(),dtype=lioness_network.dtype)))
# self.total_lioness_network=np.column_stack((self.total_lioness_network ,np.frombuffer(np.transpose(lioness_network).tobytes(),dtype=lioness_network.dtype)))
if self.ignore_final:
return(np.array([0]))
else:
Expand Down
5 changes: 3 additions & 2 deletions tests/test_cobra.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,8 @@ def test_cobra():
pd.testing.assert_frame_equal(G, G_gt, rtol=1e-10, check_exact=False)

q = psi.shape[0]
X_mean = np.mean(X.to_numpy(), axis=0)
for i in range(q):
C = Q.to_numpy().dot(np.mean(X, axis=0)[i] * np.diag(psi.to_numpy()[i, :])).dot(Q.to_numpy().T)
C_gt = Q_gt.to_numpy().dot(np.mean(X, axis=0)[i] * np.diag(psi_gt.to_numpy()[i, :])).dot(Q_gt.to_numpy().T)
C = Q.to_numpy().dot(X_mean[i] * np.diag(psi.to_numpy()[i, :])).dot(Q.to_numpy().T)
C_gt = Q_gt.to_numpy().dot(X_mean[i] * np.diag(psi_gt.to_numpy()[i, :])).dot(Q_gt.to_numpy().T)
pd.testing.assert_frame_equal(pd.DataFrame(C), pd.DataFrame(C_gt), rtol=1e-10, check_exact=False)
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