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authorFrancesco Colista <fcolista@alpinelinux.org>2015-11-21 11:40:30 +0000
committerFrancesco Colista <fcolista@alpinelinux.org>2015-11-21 11:40:30 +0000
commitf13db13c08d419f70dc3c40c5ecbb87ed34297b1 (patch)
tree0cd62466ed5f8f27716b64fbd57c975ddf1125ee /testing
parent61e5b070fafa0743614b8f9c9f88bc5cd9e1fe2b (diff)
downloadaports-f13db13c08d419f70dc3c40c5ecbb87ed34297b1.tar.bz2
aports-f13db13c08d419f70dc3c40c5ecbb87ed34297b1.tar.xz
testing/py-numpy: upgrade to 1.10.1
Diffstat (limited to 'testing')
-rw-r--r--testing/py-numpy/APKBUILD24
-rw-r--r--testing/py-numpy/numpy-1.10.0-musl.patch19
-rw-r--r--testing/py-numpy/numpy-1.10.1-backport-1.patch127
-rw-r--r--testing/py-numpy/numpy-1.10.1-backport-2.patch73
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)