From aa01bfb04e91361369abab0ea52723a9a8188079 Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Wed, 23 Apr 2014 15:05:28 -0400
Subject: [PATCH 1/6] a test for check_endian

---
 spectral_cube/tests/test_spectral_cube.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py
index 9c666235d..cf1899432 100644
--- a/spectral_cube/tests/test_spectral_cube.py
+++ b/spectral_cube/tests/test_spectral_cube.py
@@ -475,3 +475,25 @@ def test_ds9region():
     
     #region = 'circle(2,2,2)'
     #subcube = cube.subcube_from_ds9region(region)
+
+def test_endians():
+    """
+    Test that the endianness checking returns something in Native form
+    (this is only needed for non-numpy functions that worry about the
+    endianness of their data)
+    """
+    big = np.array([[[1],[2]]], dtype='>f4')
+    lil = np.array([[[1],[2]]], dtype='<f4')
+    mywcs = WCS(naxis=3)
+    mywcs.wcs.ctype[0] = 'RA'
+    mywcs.wcs.ctype[1] = 'DEC'
+    mywcs.wcs.ctype[2] = 'VELO'
+    
+    bigcube = SpectralCube(data=big, wcs=mywcs)
+    xbig = bigcube._get_filled_data(check_endian=True)
+
+    lilcube = SpectralCube(data=lil, wcs=mywcs)
+    xlil = lilcube._get_filled_data(check_endian=True)
+
+    assert xbig.dtype.byteorder == '='
+    assert xlil.dtype.byteorder == '='

From 11198da32e34b28f976ed49601dc1fa7d17a7d37 Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Wed, 23 Apr 2014 15:07:19 -0400
Subject: [PATCH 2/6] tests to make sure check_endian = off leaves data
 untouched

---
 spectral_cube/tests/test_spectral_cube.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py
index cf1899432..514d1e152 100644
--- a/spectral_cube/tests/test_spectral_cube.py
+++ b/spectral_cube/tests/test_spectral_cube.py
@@ -481,6 +481,11 @@ def test_endians():
     Test that the endianness checking returns something in Native form
     (this is only needed for non-numpy functions that worry about the
     endianness of their data)
+
+    WARNING: Because the endianness is machine-dependent, this may fail on
+    different architectures!  This is because numpy automatically converts
+    little-endian to native in the dtype parameter; I need a workaround for
+    this.
     """
     big = np.array([[[1],[2]]], dtype='>f4')
     lil = np.array([[[1],[2]]], dtype='<f4')
@@ -497,3 +502,9 @@ def test_endians():
 
     assert xbig.dtype.byteorder == '='
     assert xlil.dtype.byteorder == '='
+
+    xbig = bigcube._get_filled_data(check_endian=False)
+    xlil = lilcube._get_filled_data(check_endian=False)
+
+    assert xbig.dtype.byteorder == '>'
+    assert xlil.dtype.byteorder == '='

From 08899578e94282d7b76ad08c613ff877f61619a9 Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Tue, 26 Aug 2014 13:39:40 +0200
Subject: [PATCH 3/6] add bottleneck installation to travis

---
 .travis.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 08ddb7eab..1b7db9bcd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,6 +16,7 @@ env:
         - ASTROPY_VERSION=stable
         - CONDA_INSTALL='conda install -c astropy-ci-extras --yes'
         - PIP_INSTALL='pip install'
+        - BOTTLENECK=no
     matrix:
         - SETUP_CMD='egg_info'
 
@@ -34,7 +35,7 @@ matrix:
         # Try Astropy development version
         - python: 2.7
           env: ASTROPY_VERSION=development SETUP_CMD='test'
-        - python: 3.3
+        - python: 3.4
           env: ASTROPY_VERSION=development SETUP_CMD='test'
 
         # Try all python versions with the latest numpy
@@ -59,6 +60,12 @@ matrix:
         - python: 2.7
           env: NUMPY_VERSION=1.5 SETUP_CMD='test'
 
+        # Test with bottleneck
+        - python: 2.7
+          env: ASTROPY_VERSION=stable SETUP_CMD='test' bottleneck=yes NUMPY_VERSION=1.8
+        - python: 3.4
+          env: ASTROPY_VERSION=stable SETUP_CMD='test' bottleneck=yes NUMPY_VERSION=1.8
+
 before_install:
 
     # Use utf8 encoding. Should be default, but this is insurance against
@@ -90,6 +97,9 @@ install:
     # YT
     - if [[ $SETUP_CMD != egg_info ]] && [[ $TRAVIS_PYTHON_VERSION == 2.7 ]] && [[ $NUMPY_VERSION == 1.8 ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION yt; fi
 
+    # Bottleneck
+    - if [[ $SETUP_CMD != egg_info ]] && [[ $BOTTLENECK == yes ]] && [[ $NUMPY_VERSION == 1.8 ]]; then $CONDA_INSTALL --channel https://conda.binstar.org/public bottleneck; fi
+
     # OPTIONAL DEPENDENCIES
     # Here you can add any dependencies your package may have. You can use
     # conda for packages available through conda, or pip for any other

From 65d1d02bdffee3507144f1615fd52d8c847bfa76 Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Tue, 26 Aug 2014 13:41:33 +0200
Subject: [PATCH 4/6] skip bottleneck tests if bottleneck not imported

---
 spectral_cube/tests/test_spectral_cube.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py
index 514d1e152..73eb58162 100644
--- a/spectral_cube/tests/test_spectral_cube.py
+++ b/spectral_cube/tests/test_spectral_cube.py
@@ -22,6 +22,12 @@
     yt_version = StrictVersion('0.0.0')
     ytOK = False
 
+try:
+    import bottleneck
+    bottleneckOK = True
+except ImportError:
+    bottleneckOK = False
+
 
 def cube_and_raw(filename):
     p = path(filename)
@@ -476,6 +482,7 @@ def test_ds9region():
     #region = 'circle(2,2,2)'
     #subcube = cube.subcube_from_ds9region(region)
 
+@pytest.mark.skipif(not bottleneckOK, reason='Bottleneck could not be imported')
 def test_endians():
     """
     Test that the endianness checking returns something in Native form

From 96e6457e1925adc02853f178c8b235fe9b5ea1fe Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Tue, 26 Aug 2014 13:44:11 +0200
Subject: [PATCH 5/6] change version of bottleneck to install

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1b7db9bcd..031287af6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -98,7 +98,8 @@ install:
     - if [[ $SETUP_CMD != egg_info ]] && [[ $TRAVIS_PYTHON_VERSION == 2.7 ]] && [[ $NUMPY_VERSION == 1.8 ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION yt; fi
 
     # Bottleneck
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $BOTTLENECK == yes ]] && [[ $NUMPY_VERSION == 1.8 ]]; then $CONDA_INSTALL --channel https://conda.binstar.org/public bottleneck; fi
+    # asmeurer currently (8/26/2014) supports numpy 1.8
+    - if [[ $SETUP_CMD != egg_info ]] && [[ $BOTTLENECK == yes ]] && [[ $NUMPY_VERSION == 1.8 ]]; then $CONDA_INSTALL --channel https://conda.binstar.org/asmeurer bottleneck; fi
 
     # OPTIONAL DEPENDENCIES
     # Here you can add any dependencies your package may have. You can use

From cd936b7348b87c25b86b50e654e06691215ab938 Mon Sep 17 00:00:00 2001
From: "Adam Ginsburg (keflavich)" <keflavich@gmail.com>
Date: Tue, 26 Aug 2014 13:47:22 +0200
Subject: [PATCH 6/6] fix a ridiculously silly bug in which the computed result
 wasn't returned

---
 spectral_cube/spectral_cube.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/spectral_cube/spectral_cube.py b/spectral_cube/spectral_cube.py
index 99a0818cb..10c5149f8 100644
--- a/spectral_cube/spectral_cube.py
+++ b/spectral_cube/spectral_cube.py
@@ -602,7 +602,9 @@ def median(self, axis=None, **kwargs):
                                                 projection=True,
                                                 check_endian=True, **kwargs)
         except ImportError:
-            return self.apply_function(np.median, axis=axis, **kwargs)
+            result = self.apply_function(np.median, axis=axis, **kwargs)
+
+        return result
 
     def percentile(self, q, axis=None, **kwargs):
         """