testing/py-numpy: upgrade to 1.10.1

4 files changed, 237 insertions, 6 deletions

diff --git a/testing/py-numpy/APKBUILD b/testing/py-numpy/APKBUILD
index 360c8443ba..0bff22d5f5 100644
--- a/testing/py-numpy/APKBUILD
+++ b/testing/py-numpy/APKBUILD
@@ -1,8 +1,8 @@
-# Contributor: Francesco Colista <francesco.colista@gmail.com>
-# Maintainer: Francesco Colista <francesco.colista@gmail.com>
+# Contributor: Francesco Colista <fcolista@alpinelinux.org>
+# Maintainer: Francesco Colista <fcolista@alpinelinux.org>
 pkgname=py-numpy
 _pkgname=numpy
-pkgver=1.9.2
+pkgver=1.10.1
 pkgrel=0
 pkgdesc="Scientific tools for Python"
 url="http://numpy.scipy.org/"
@@ -14,6 +14,9 @@ makedepends="$depends_dev"
 install=""
 subpackages="$pkgname-dev $pkgname-doc"
 source="http://downloads.sourceforge.net/$_pkgname/$_pkgname-$pkgver.tar.gz
+	numpy-1.10.0-musl.patch
+	numpy-1.10.1-backport-1.patch
+	numpy-1.10.1-backport-2.patch
 	site.cfg"
 
 _builddir="$srcdir"/$_pkgname-$pkgver
@@ -43,9 +46,18 @@ package() {
 	install -m644 LICENSE.txt "$pkgdir"/usr/share/licenses/custom/$pkgname/LICENSE
 }
 
-md5sums="a1ed53432dbcd256398898d35bc8e645  numpy-1.9.2.tar.gz
+md5sums="3fed2b50906bc19018cec5fa26168aa5  numpy-1.10.1.tar.gz
+e00075bed14f650030a8704db7fda6ee  numpy-1.10.0-musl.patch
+aaa44b6c8af4abd24c286179c9b8e3c5  numpy-1.10.1-backport-1.patch
+89cac7e57396369d802c9e696b7bd801  numpy-1.10.1-backport-2.patch
 6f15bb8fe3d12faa8983a9e18bbea2a9  site.cfg"
-sha256sums="325e5f2b0b434ecb6e6882c7e1034cc6cdde3eeeea87dbc482575199a6aeef2a  numpy-1.9.2.tar.gz
+sha256sums="8b9f453f29ce96a14e625100d3dcf8926301d36c5f622623bf8820e748510858  numpy-1.10.1.tar.gz
+e4a84dab5561833299bb506acba2d1a5feea929af69bde56a10558612405f8ec  numpy-1.10.0-musl.patch
+386920fcba91099aedfe0c8105aa53f10f596f62d300684d802397769ba9b1e1  numpy-1.10.1-backport-1.patch
+ec6faad4e0105f3f291a43defed5c0f33ca669832589372a0b6ae92d9f5e4dd1  numpy-1.10.1-backport-2.patch
 8aa71c1aec2a9fdf6ab6167c92e86bdaf27f9a263b6b9849097ec7dcdf6d91a3  site.cfg"
-sha512sums="70470ebb9afef5dfd0c83ceb7a9d5f1b7a072b1a9b54b04f04f5ed50fbaedd5b4906bd500472268d478f94df9e749a88698b1ff30f2d80258e7f3fec040617d9  numpy-1.9.2.tar.gz
+sha512sums="ea717bac913a8e63bf93822bddbfe7701a3de00051bf3c7020f5e22756987becb5a2f96a6a52a36fc7c2b856815a782e450099688ce86b21fa94b0076b9ef376  numpy-1.10.1.tar.gz
+9f97a3f3e9890598444d78418cbc4aac75d06df8a10634bc94e8c346a70d3fb7efb45004cf0d5840646c7e72e2886234988ed01021b36ca87ed727470e44be75  numpy-1.10.0-musl.patch
+359076cdf1962744f1e0381d6e690422787307400db6ca51fb8f759f6af459666e9b4aad278bf4e89848fea5277204eab9459edb092fc2d9aa8dab14096eefe9  numpy-1.10.1-backport-1.patch
+8e1db75cd00209762b49f636549a4afccea1467f93b4ce94e02f3ada2f8be78a70fdfea51eb98a12690ef67b84734eb24d5a647def8022a4fddfc22cda4cb512  numpy-1.10.1-backport-2.patch
 21ca8db304cbbf5949f07702f2a42bb5e5a0d641921e36649555a41b0e48f04e96f53760417823177ac27f6de24b2191e6e1d5f0eb393beafa29f7484e23284f  site.cfg"
diff --git a/testing/py-numpy/numpy-1.10.0-musl.patch b/testing/py-numpy/numpy-1.10.0-musl.patch
new file mode 100644
index 0000000000..36dec388f7
--- /dev/null
+++ b/testing/py-numpy/numpy-1.10.0-musl.patch
@@ -0,0 +1,19 @@
+--- a/numpy/core/src/private/npy_config.h.orig	2015-08-11 19:03:43.000000000 +0200
++++ b/numpy/core/src/private/npy_config.h	2015-10-08 08:20:25.489203036 +0200
+@@ -71,7 +71,7 @@
+ 
+ 
+ /* Disable broken gnu trig functions on linux */
+-#if defined(__linux__) && defined(__GNUC__)
++#if defined(__linux__) && defined(__GLIBC__)
+ 
+ #if defined(HAVE_FEATURES_H)
+ #include <features.h>
+@@ -96,6 +96,6 @@
+ #endif
+ #undef TRIG_OK
+ 
+-#endif /* defined(__linux__) && defined(__GNUC__) */
++#endif /* defined(__linux__) && defined(__GLIBC__) */
+ 
+ #endif
diff --git a/testing/py-numpy/numpy-1.10.1-backport-1.patch b/testing/py-numpy/numpy-1.10.1-backport-1.patch
new file mode 100644
index 0000000000..77a3c01037
--- /dev/null
+++ b/testing/py-numpy/numpy-1.10.1-backport-1.patch
@@ -0,0 +1,127 @@
+From 3a816a4db9b498eb64eb837fdcca0fa8ddbe063e Mon Sep 17 00:00:00 2001
+From: Allan Haldane <allan.haldane@gmail.com>
+Date: Sat, 17 Oct 2015 14:00:36 -0400
+Subject: [PATCH] BUG: recarrays viewed as subarrays don't convert to np.record
+ type
+
+Record array views were updated in #5943 to return np.record dtype
+where possible, but forgot about the case of sub-arrays.
+
+That's fixed here, so accessing subarray fields by attribute or index
+works sensibly, as well as viewing a record array as a subarray dtype,
+and printing subarrays.
+
+This also happens to fix #6459, since it affects the same lines.
+
+Fixes #6497 #6459
+---
+ numpy/core/records.py            | 30 +++++++++++++++++++-----------
+ numpy/core/tests/test_records.py | 23 +++++++++++++++++++++++
+ 2 files changed, 42 insertions(+), 11 deletions(-)
+
+diff --git a/numpy/core/records.py b/numpy/core/records.py
+index 4a99553..4ce3fe9 100644
+--- a/numpy/core/records.py
++++ b/numpy/core/records.py
+@@ -448,12 +448,14 @@ def __getattribute__(self, attr):
+ 
+         # At this point obj will always be a recarray, since (see
+         # PyArray_GetField) the type of obj is inherited. Next, if obj.dtype is
+-        # non-structured, convert it to an ndarray. If obj is structured leave
+-        # it as a recarray, but make sure to convert to the same dtype.type (eg
+-        # to preserve numpy.record type if present), since nested structured
+-        # fields do not inherit type.
++        # non-structured, convert it to an ndarray. Then if obj is structured
++        # with void type convert it to the same dtype.type (eg to preserve
++        # numpy.record type if present), since nested structured fields do not
++        # inherit type. Don't do this for non-void structures though.
+         if obj.dtype.fields:
+-            return obj.view(dtype=(self.dtype.type, obj.dtype.fields))
++            if issubclass(obj.dtype.type, nt.void):
++                return obj.view(dtype=(self.dtype.type, obj.dtype))
++            return obj
+         else:
+             return obj.view(ndarray)
+ 
+@@ -463,8 +465,9 @@ def __getattribute__(self, attr):
+     # Thus, you can't create attributes on-the-fly that are field names.
+     def __setattr__(self, attr, val):
+ 
+-        # Automatically convert (void) dtypes to records.
+-        if attr == 'dtype' and issubclass(val.type, nt.void):
++        # Automatically convert (void) structured types to records
++        # (but not non-void structures, subarrays, or non-structured voids)
++        if attr == 'dtype' and issubclass(val.type, nt.void) and val.fields:
+             val = sb.dtype((record, val))
+ 
+         newattr = attr not in self.__dict__
+@@ -499,7 +502,9 @@ def __getitem__(self, indx):
+         # we might also be returning a single element
+         if isinstance(obj, ndarray):
+             if obj.dtype.fields:
+-                return obj.view(dtype=(self.dtype.type, obj.dtype.fields))
++                if issubclass(obj.dtype.type, nt.void):
++                    return obj.view(dtype=(self.dtype.type, obj.dtype))
++                return obj
+             else:
+                 return obj.view(type=ndarray)
+         else:
+@@ -519,11 +524,14 @@ def __repr__(self):
+             # If this is a full record array (has numpy.record dtype),
+             # or if it has a scalar (non-void) dtype with no records,
+             # represent it using the rec.array function. Since rec.array
+-            # converts dtype to a numpy.record for us, use only dtype.descr,
+-            # not repr(dtype).
++            # converts dtype to a numpy.record for us, convert back
++            # to non-record before printing
++            plain_dtype = self.dtype
++            if plain_dtype.type is record:
++                plain_dtype = sb.dtype((nt.void, plain_dtype))
+             lf = '\n'+' '*len("rec.array(")
+             return ('rec.array(%s, %sdtype=%s)' %
+-                          (lst, lf, repr(self.dtype.descr)))
++                          (lst, lf, plain_dtype))
+         else:
+             # otherwise represent it using np.array plus a view
+             # This should only happen if the user is playing
+diff --git a/numpy/core/tests/test_records.py b/numpy/core/tests/test_records.py
+index 7a18f29..290bc4f 100644
+--- a/numpy/core/tests/test_records.py
++++ b/numpy/core/tests/test_records.py
+@@ -121,6 +121,23 @@ def test_recarray_views(self):
+         assert_equal(type(rv), np.recarray)
+         assert_equal(rv.dtype.type, np.record)
+ 
++        # check that accessing nested structures keep record type, but
++        # not for subarrays, non-void structures, non-structured voids
++        test_dtype = [('a', 'f4,f4'), ('b', 'V8'), ('c', ('f4',2)),
++                      ('d', ('i8', 'i4,i4'))]
++        r = np.rec.array([((1,1), b'11111111', [1,1], 1),
++                          ((1,1), b'11111111', [1,1], 1)], dtype=test_dtype)
++        assert_equal(r.a.dtype.type, np.record)
++        assert_equal(r.b.dtype.type, np.void)
++        assert_equal(r.c.dtype.type, np.float32)
++        assert_equal(r.d.dtype.type, np.int64)
++        # check the same, but for views
++        r = np.rec.array(np.ones(4, dtype='i4,i4'))
++        assert_equal(r.view('f4,f4').dtype.type, np.record)
++        assert_equal(r.view(('i4',2)).dtype.type, np.int32)
++        assert_equal(r.view('V8').dtype.type, np.void)
++        assert_equal(r.view(('i8', 'i4,i4')).dtype.type, np.int64)
++
+         #check that we can undo the view
+         arrs = [np.ones(4, dtype='f4,i4'), np.ones(4, dtype='f8')]
+         for arr in arrs:
+@@ -135,6 +152,12 @@ def test_recarray_repr(self):
+         a = np.array(np.ones(4, dtype='f8'))
+         assert_(repr(np.rec.array(a)).startswith('rec.array'))
+ 
++        # check that the 'np.record' part of the dtype isn't shown
++        a = np.rec.array(np.ones(3, dtype='i4,i4'))
++        assert_equal(repr(a).find('numpy.record'), -1)
++        a = np.rec.array(np.ones(3, dtype='i4'))
++        assert_(repr(a).find('dtype=int32') != -1)
++
+     def test_recarray_from_names(self):
+         ra = np.rec.array([
+             (1, 'abc', 3.7000002861022949, 0),
diff --git a/testing/py-numpy/numpy-1.10.1-backport-2.patch b/testing/py-numpy/numpy-1.10.1-backport-2.patch
new file mode 100644
index 0000000000..9c33704f8e
--- /dev/null
+++ b/testing/py-numpy/numpy-1.10.1-backport-2.patch
@@ -0,0 +1,73 @@
+From 0d25dc4175e00cdaf9545e8b1b1a5b879cf67248 Mon Sep 17 00:00:00 2001
+From: Ethan Kruse <eakruse@uw.edu>
+Date: Mon, 19 Oct 2015 13:29:01 -0700
+Subject: [PATCH 1/2] Potential fix for #6462
+
+---
+ numpy/lib/function_base.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py
+index 555d083..fef69df 100644
+--- a/numpy/lib/function_base.py
++++ b/numpy/lib/function_base.py
+@@ -3339,7 +3339,7 @@ def _median(a, axis=None, out=None, overwrite_input=False):
+         indexer[axis] = slice(index-1, index+1)
+ 
+     # Check if the array contains any nan's
+-    if np.issubdtype(a.dtype, np.inexact):
++    if np.issubdtype(a.dtype, np.inexact) and sz > 0:
+         # warn and return nans like mean would
+         rout = mean(part[indexer], axis=axis, out=out)
+         part = np.rollaxis(part, axis, part.ndim)
+
+From 59d859fb2160950ac93267d7461ad952145c8724 Mon Sep 17 00:00:00 2001
+From: Ethan Kruse <eakruse@uw.edu>
+Date: Tue, 20 Oct 2015 11:40:49 -0700
+Subject: [PATCH 2/2] Added tests for median of empty arrays
+
+---
+ numpy/lib/tests/test_function_base.py | 30 ++++++++++++++++++++++++++++++
+ 1 file changed, 30 insertions(+)
+
+diff --git a/numpy/lib/tests/test_function_base.py b/numpy/lib/tests/test_function_base.py
+index 4516c92..aa41c1f 100644
+--- a/numpy/lib/tests/test_function_base.py
++++ b/numpy/lib/tests/test_function_base.py
+@@ -2597,6 +2597,36 @@ def test_nan_behavior(self):
+             assert_equal(np.median(a, (0, 2)), b)
+             assert_equal(len(w), 1)
+ 
++    def test_empty(self):
++        # empty arrays
++        a = np.array([], dtype=float)
++        with warnings.catch_warnings(record=True) as w:
++            warnings.filterwarnings('always', '', RuntimeWarning)
++            assert_equal(np.median(a), np.nan)
++            assert_(w[0].category is RuntimeWarning)
++
++        # multiple dimensions
++        a = np.array([], dtype=float, ndmin=3)
++        # no axis
++        with warnings.catch_warnings(record=True) as w:
++            warnings.filterwarnings('always', '', RuntimeWarning)
++            assert_equal(np.median(a), np.nan)
++            assert_(w[0].category is RuntimeWarning)
++
++        # axis 0 and 1
++        b = np.array([], dtype=float, ndmin=2)
++        with warnings.catch_warnings(record=True) as w:
++            warnings.filterwarnings('always', '', RuntimeWarning)
++            assert_equal(np.median(a, axis=0), b)
++            assert_equal(np.median(a, axis=1), b)
++
++        # axis 2
++        b = np.array(np.nan, dtype=float, ndmin=2)
++        with warnings.catch_warnings(record=True) as w:
++            warnings.filterwarnings('always', '', RuntimeWarning)
++            assert_equal(np.median(a, axis=2), b)
++            assert_(w[0].category is RuntimeWarning)
++
+     def test_object(self):
+         o = np.arange(7.)
+         assert_(type(np.median(o.astype(object))), float)