[sagemath] 02/04: Add upstream patches for numpy 1.13
Ximin Luo
infinity0 at debian.org
Fri Nov 10 18:55:52 UTC 2017
This is an automated email from the git hooks/post-receive script.
infinity0 pushed a commit to annotated tag debian/8.0-10
in repository sagemath.
commit 4c078e8b29e9c17b4fb4d0ea10b7826e28a353f8
Author: Ximin Luo <infinity0 at debian.org>
Date: Thu Oct 19 23:02:56 2017 +0200
Add upstream patches for numpy 1.13
---
debian/changelog | 1 +
debian/patches/series | 1 +
debian/patches/u0-version-numpy-1.13.patch | 112 +++++++++++++++++++++++++++++
3 files changed, 114 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index b39eb15..e79be2f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ sagemath (8.0-10) UNRELEASED; urgency=medium
* New patches:
- u0-version-arb-2.11.1.patch
+ - u0-version-numpy-1.13.patch
-- Ximin Luo <infinity0 at debian.org> Fri, 10 Nov 2017 18:39:02 +0100
diff --git a/debian/patches/series b/debian/patches/series
index 16a83ae..f7bdc19 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,6 +3,7 @@
u0-version-cython-0.26.patch #23360
u0-version-scipy-0.19.1.patch #23594
u0-version-sphinx-1.6.patch #23023
+u0-version-numpy-1.13.patch #24063
u0-version-arb-2.11.1.patch
# Patches that have open upstream tickets
diff --git a/debian/patches/u0-version-numpy-1.13.patch b/debian/patches/u0-version-numpy-1.13.patch
new file mode 100644
index 0000000..6a0eabd
--- /dev/null
+++ b/debian/patches/u0-version-numpy-1.13.patch
@@ -0,0 +1,112 @@
+From 3a5b70d9bc38575e2d77ab8a4f73d7f53b31d1bc Mon Sep 17 00:00:00 2001
+From: Jeroen Demeyer <jdemeyer at cage.ugent.be>
+Date: Wed, 18 Oct 2017 14:49:22 +0200
+Subject: Don't use NumPy functions on Sage Elements
+
+---
+ src/sage/matrix/matrix_double_dense.pyx | 14 +++++++-------
+ 1 file changed, 7 insertions(+), 7 deletions(-)
+
+From bfb8061c316a0fc30ebd1730073f0cacf5d77539 Mon Sep 17 00:00:00 2001
+From: Jeroen Demeyer <jdemeyer at cage.ugent.be>
+Date: Wed, 18 Oct 2017 15:22:20 +0200
+Subject: Silence warnings from old matplotlib + new numpy
+
+---
+ src/sage/all.py | 18 +++++++++++-------
+ 1 file changed, 11 insertions(+), 7 deletions(-)
+
+--- a/sage/src/sage/matrix/matrix_double_dense.pyx
++++ b/sage/src/sage/matrix/matrix_double_dense.pyx
+@@ -2567,7 +2567,7 @@
+ unitary = T._is_lower_triangular(tol)
+ if unitary:
+ for 0 <= i < self._nrows:
+- if numpy.absolute(numpy.absolute(T.get_unsafe(i,i)) - 1) > tol:
++ if abs(abs(T.get_unsafe(i,i)) - 1) > tol:
+ unitary = False
+ break
+ elif algorithm == 'naive':
+@@ -2576,11 +2576,11 @@
+ for i from 0 <= i < self._nrows:
+ # off-diagonal, since P is Hermitian
+ for j from 0 <= j < i:
+- if numpy.absolute(P.get_unsafe(i,j)) > tol:
++ if abs(P.get_unsafe(i,j)) > tol:
+ unitary = False
+ break
+ # at diagonal
+- if numpy.absolute(P.get_unsafe(i,i)-1) > tol:
++ if abs(P.get_unsafe(i,i) - 1) > tol:
+ unitary = False
+ if not unitary:
+ break
+@@ -2619,7 +2619,7 @@
+ cdef Py_ssize_t i, j
+ for i in range(self._nrows):
+ for j in range(i+1, self._ncols):
+- if numpy.absolute(self.get_unsafe(i,j)) > tol:
++ if abs(self.get_unsafe(i,j)) > tol:
+ return False
+ return True
+
+@@ -2777,14 +2777,14 @@
+ hermitian = T._is_lower_triangular(tol)
+ if hermitian:
+ for i in range(T._nrows):
+- if numpy.absolute(numpy.imag(T.get_unsafe(i,i))) > tol:
++ if abs(T.get_unsafe(i,i).imag()) > tol:
+ hermitian = False
+ break
+ elif algorithm == 'naive':
+ hermitian = True
+ for i in range(self._nrows):
+ for j in range(i+1):
+- if numpy.absolute(self.get_unsafe(i,j) - self.get_unsafe(j,i).conjugate()) > tol:
++ if abs(self.get_unsafe(i,j) - self.get_unsafe(j,i).conjugate()) > tol:
+ hermitian = False
+ break
+ if not hermitian:
+@@ -2976,7 +2976,7 @@
+ # two products are Hermitian, need only check lower triangle
+ for i in range(self._nrows):
+ for j in range(i+1):
+- if numpy.absolute(left.get_unsafe(i,j) - right.get_unsafe(i,j)) > tol:
++ if abs(left.get_unsafe(i,j) - right.get_unsafe(i,j)) > tol:
+ normal = False
+ break
+ if not normal:
+--- a/sage/src/sage/all.py
++++ b/sage/src/sage/all.py
+@@ -310,20 +310,24 @@
+ O.close()
+
+
+-# Set a new random number seed as the very last thing
+-# (so that printing initial_seed() and using that seed
+-# in set_random_seed() will result in the same sequence you got at
+-# Sage startup).
+-set_random_seed()
+-
+ import warnings
+ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
+ # Ignore all deprecations from IPython etc.
+ warnings.filterwarnings('ignore',
+ module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
+-# but not those that have OUR deprecation warnings
++# Ignore warnings due to matplotlib-1.5 together with numpy-1.13
++warnings.filterwarnings('ignore', module='matplotlib[.]contour|numpy[.]ma[.]core')
++# However, be sure to keep OUR deprecation warnings
+ warnings.filterwarnings('default',
+ '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.')
+
++
++# Set a new random number seed as the very last thing
++# (so that printing initial_seed() and using that seed
++# in set_random_seed() will result in the same sequence you got at
++# Sage startup).
++set_random_seed()
++
++
+ # From now on it is ok to resolve lazy imports
+ sage.misc.lazy_import.finish_startup()
--
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