Your message dated Mon, 29 May 2017 18:52:38 +0100
with message-id <[email protected]>
and subject line Re: Bug#863522: unblock: python-numpy/1:1.12.1-3
has caused the Debian Bug report #863522,
regarding unblock: python-numpy/1:1.12.1-3
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863522: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=863522
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--- Begin Message ---
Package: release.debian.org
Severity: normal
User: [email protected]
Usertags: unblock
Please unblock package python-numpy
This upload fixes a bug when using numpy.abs() on numpy.nan on some
architectures; the bug is minor, but a user noticed nonetheless, the patch comes
directly from upstream and it's just a one-liner with extensive tests.
Source debdiff is attached
unblock python-numpy/1:1.12.1-3
-- System Information:
Debian Release: stretch/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64
(x86_64)
Foreign Architectures: i386
Kernel: Linux 4.2.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru python-numpy-1.12.1/debian/changelog
python-numpy-1.12.1/debian/changelog
--- python-numpy-1.12.1/debian/changelog 2017-04-05 06:26:43.000000000
-0400
+++ python-numpy-1.12.1/debian/changelog 2017-05-27 19:44:59.000000000
-0400
@@ -1,3 +1,10 @@
+python-numpy (1:1.12.1-3) unstable; urgency=medium
+
+ * debian/patches/0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
+ - fix RuntimeWarning on numpy.abs(numpy.nan) on some archs; Closes: #863192
+
+ -- Sandro Tosi <[email protected]> Sat, 27 May 2017 19:44:59 -0400
+
python-numpy (1:1.12.1-2) unstable; urgency=medium
* Team upload
diff -Nru python-numpy-1.12.1/debian/.git-dpm
python-numpy-1.12.1/debian/.git-dpm
--- python-numpy-1.12.1/debian/.git-dpm 2017-04-04 12:49:56.000000000 -0400
+++ python-numpy-1.12.1/debian/.git-dpm 2017-05-27 19:44:59.000000000 -0400
@@ -1,6 +1,6 @@
# see git-dpm(1) from git-dpm package
-4b26915f32eec3afa476d678bc7831ab7b1899c1
-4b26915f32eec3afa476d678bc7831ab7b1899c1
+285b463e037cd9aeaf37ccc90ccf3349cc84b88a
+285b463e037cd9aeaf37ccc90ccf3349cc84b88a
db9ad0d21c51a5a4983387c232c00bd6f844e406
db9ad0d21c51a5a4983387c232c00bd6f844e406
python-numpy_1.12.1.orig.tar.gz
diff -Nru
python-numpy-1.12.1/debian/patches/0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
python-numpy-1.12.1/debian/patches/0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
---
python-numpy-1.12.1/debian/patches/0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
1969-12-31 19:00:00.000000000 -0500
+++
python-numpy-1.12.1/debian/patches/0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
2017-05-27 19:44:59.000000000 -0400
@@ -0,0 +1,89 @@
+From 285b463e037cd9aeaf37ccc90ccf3349cc84b88a Mon Sep 17 00:00:00 2001
+From: James Cowgill <[email protected]>
+Date: Tue, 7 Mar 2017 11:39:01 +0000
+Subject: BUG: Don't signal FP exceptions in np.absolute
+
+Fixes #8686
+
+This PR centers around this piece of code in
`numpy/core/src/umath/loops.c.src`:
+```c
+UNARY_LOOP {
+ const @type@ in1 = *(@type@ *)ip1;
+ const @type@ tmp = in1 > 0 ? in1 : -in1;
+ /* add 0 to clear -0.0 */
+ *((@type@ *)op1) = tmp + 0;
+}
+```
+
+If in1 is `NaN`, the C99 standard requires that the comparison `in1 > 0`
+signals `FE_INVALID`, but the usual semantics for the absolute function are
+that no FP exceptions should be generated (eg compare to C `fabs` and Python
+`abs`). This was probably never noticed due to a bug in GCC x86 where all
+floating point comparisons do not signal exceptions, however Clang on x86 and
+GCC on other architectures (including ARM and MIPS) do signal an FP exception
+here.
+
+Fix by clearing the floating point exceptions after the loop has
+finished. The alternative of rewriting the loop to use `npy_fabs`
+instead would also work but has performance issues because that function
+is not inlined. The `test_abs_neg_blocked` is adjusted not to ignore
+`FE_INVALID` errors because now both absolute and negate should never
+produce an FP exceptions.
+---
+ numpy/core/src/umath/loops.c.src | 1 +
+ numpy/core/tests/test_umath.py | 30 ++++++++++++++----------------
+ 2 files changed, 15 insertions(+), 16 deletions(-)
+
+diff --git a/numpy/core/src/umath/loops.c.src
b/numpy/core/src/umath/loops.c.src
+index 3c11908..7e683ab 100644
+--- a/numpy/core/src/umath/loops.c.src
++++ b/numpy/core/src/umath/loops.c.src
+@@ -1840,6 +1840,7 @@ NPY_NO_EXPORT void
+ *((@type@ *)op1) = tmp + 0;
+ }
+ }
++ npy_clear_floatstatus();
+ }
+
+ NPY_NO_EXPORT void
+diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py
+index 6fea832..fad75cd 100644
+--- a/numpy/core/tests/test_umath.py
++++ b/numpy/core/tests/test_umath.py
+@@ -1226,22 +1226,20 @@ class TestAbsoluteNegative(TestCase):
+ np.negative(inp, out=out)
+ assert_equal(out, tgt, err_msg=msg)
+
+- # will throw invalid flag depending on compiler optimizations
+- with np.errstate(invalid='ignore'):
+- for v in [np.nan, -np.inf, np.inf]:
+- for i in range(inp.size):
+- d = np.arange(inp.size, dtype=dt)
+- inp[:] = -d
+- inp[i] = v
+- d[i] = -v if v == -np.inf else v
+- assert_array_equal(np.abs(inp), d, err_msg=msg)
+- np.abs(inp, out=out)
+- assert_array_equal(out, d, err_msg=msg)
+-
+- assert_array_equal(-inp, -1*inp, err_msg=msg)
+- d = -1 * inp
+- np.negative(inp, out=out)
+- assert_array_equal(out, d, err_msg=msg)
++ for v in [np.nan, -np.inf, np.inf]:
++ for i in range(inp.size):
++ d = np.arange(inp.size, dtype=dt)
++ inp[:] = -d
++ inp[i] = v
++ d[i] = -v if v == -np.inf else v
++ assert_array_equal(np.abs(inp), d, err_msg=msg)
++ np.abs(inp, out=out)
++ assert_array_equal(out, d, err_msg=msg)
++
++ assert_array_equal(-inp, -1*inp, err_msg=msg)
++ d = -1 * inp
++ np.negative(inp, out=out)
++ assert_array_equal(out, d, err_msg=msg)
+
+ def test_lower_align(self):
+ # check data that is not aligned to element size
diff -Nru python-numpy-1.12.1/debian/patches/series
python-numpy-1.12.1/debian/patches/series
--- python-numpy-1.12.1/debian/patches/series 2017-04-04 12:49:56.000000000
-0400
+++ python-numpy-1.12.1/debian/patches/series 2017-05-27 19:44:59.000000000
-0400
@@ -4,3 +4,4 @@
adapt_swig_docs_to_debian.patch
0005-Dont-fail-if-we-cant-import-mingw32.patch
0006-disable-asserts-on-ppc-with-broken-malloc-only-longd.patch
+0007-BUG-Don-t-signal-FP-exceptions-in-np.absolute.patch
--- End Message ---
--- Begin Message ---
On Sat, May 27, 2017 at 10:23:24PM -0400, Sandro Tosi wrote:
> This upload fixes a bug when using numpy.abs() on numpy.nan on some
> architectures; the bug is minor, but a user noticed nonetheless, the patch
> comes
> directly from upstream and it's just a one-liner with extensive tests.
Unblocked (the usual caveats, no precedent, etc, etc)
--
Jonathan Wiltshire [email protected]
Debian Developer http://people.debian.org/~jmw
4096R: 0xD3524C51 / 0A55 B7C5 1223 3942 86EC 74C3 5394 479D D352 4C51
--- End Message ---
