From 9e873a9ae66a6b00d025c320504e3a48414341bb Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph.weston@cea.fr>
Date: Fri, 7 Aug 2015 19:58:04 +0200
Subject: [PATCH] fix sparse matrix creation for Python 3 + memoryviews
Under Python 3, `scipy.sparse.coo_matrix` fails when passed memoryviews.
We coerce the memoryviews to numpy arrays before passing them to the
`coo_matrix`. Even though this is kind of a hack it shouldn't be very
inefficient as no data is actually copied. See
https://github.com/scipy/scipy/issues/5123 for details.
---
kwant/_system.pyx | 22 ++++++++++++++++++----
1 file changed, 18 insertions(+), 4 deletions(-)
diff --git a/kwant/_system.pyx b/kwant/_system.pyx
index 396b9175..beebd946 100644
--- a/kwant/_system.pyx
+++ b/kwant/_system.pyx
@@ -85,8 +85,15 @@ def make_sparse(ham, args, CGraph gr, diag,
rows_cols[1, k] = j + from_off[n_fs]
k += 1
- return sp.coo_matrix((data[:k], rows_cols[:, :k]),
- shape=(to_off[-1], from_off[-1]))
+ # hack around a bug in Scipy + Python 3 + memoryviews
+ # see https://github.com/scipy/scipy/issues/5123 for details
+ np_data = np.asarray(data)
+ np_rows_cols = np.asarray(rows_cols)
+ np_to_off = np.asarray(to_off)
+ np_from_off = np.asarray(from_off)
+
+ return sp.coo_matrix((np_data[:k], np_rows_cols[:, :k]),
+ shape=(np_to_off[-1], np_from_off[-1]))
@cython.boundscheck(False)
@@ -148,8 +155,15 @@ def make_sparse_full(ham, args, CGraph gr, diag,
rows_cols[0, k + 1] = rows_cols[1, k] = j + from_off[fs]
k += 2
- return sp.coo_matrix((data[:k], rows_cols[:, :k]),
- shape=(to_off[-1], from_off[-1]))
+ # hack around a bug in Scipy + Python 3 + memoryviews
+ # see https://github.com/scipy/scipy/issues/5123 for details
+ np_data = np.asarray(data)
+ np_rows_cols = np.asarray(rows_cols)
+ np_to_off = np.asarray(to_off)
+ np_from_off = np.asarray(from_off)
+
+ return sp.coo_matrix((np_data[:k], np_rows_cols[:, :k]),
+ shape=(np_to_off[-1], np_from_off[-1]))
@cython.boundscheck(False)
--
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