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Update function name due to networkx version update #47

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Update function name due to networkx version update #47

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61fe441
Update function name due to networkx version update
Zhouuuuu5 Nov 15, 2023
5131675
Modified for Python 3.9+ and Cython 3.0+
Zhouuuuu5 Dec 5, 2023
471b75a
Update setup.py
Zhouuuuu5 Dec 5, 2023
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2 changes: 1 addition & 1 deletion fa2/forceatlas2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,7 @@ def forceatlas2_networkx_layout(self, G, pos=None, iterations=100, weight_attr=N
or (cynetworkx and isinstance(G, cynetworkx.classes.graph.Graph))
), "Not a networkx graph"
assert isinstance(pos, dict) or (pos is None), "pos must be specified as a dictionary, as in networkx"
M = networkx.to_scipy_sparse_matrix(G, dtype='f', format='lil', weight=weight_attr)
M = networkx.to_scipy_sparse_array(G, dtype='f', format='lil', weight=weight_attr)
if pos is None:
l = self.forceatlas2(M, pos=None, iterations=iterations)
else:
Expand Down
6 changes: 3 additions & 3 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
print(">>>> Cython is installed?")
try:
from Cython.Distutils import Extension
from Cython.Build import build_ext
from Cython.Build import build_ext, cythonize
USE_CYTHON = True
print('Yes\n')
except ImportError:
Expand All @@ -25,7 +25,7 @@
print(">>>> Are pre-generated C files available?")

if USE_CYTHON:
ext_modules = [Extension('fa2.fa2util', ['fa2/fa2util.py', 'fa2/fa2util.pxd'], cython_directives={'language_level' : 3})]
ext_modules = cythonize([Extension('fa2.fa2util', ['fa2/fa2util.py'], cython_directives={'language_level' : 3})])
cmdclass = {'build_ext': build_ext}
opts = {"ext_modules": ext_modules, "cmdclass": cmdclass}
elif path.isfile(path.join(here, 'fa2/fa2util.c')):
Expand Down Expand Up @@ -72,4 +72,4 @@
},
include_package_data=True,
**opts
)
)