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dev-python/spectral-cube: initial import

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Package-Manager: portage-2.3.3
This commit is contained in:
Sébastien Fabbro
2016-12-09 18:28:49 +00:00
parent 179bf0795b
commit 452da31dd5
4 changed files with 211 additions and 0 deletions
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1
dev-python/spectral-cube/Manifest Normal file
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@@ -0,0 +1 @@
DIST spectral-cube-0.4.0.tar.gz 290453 SHA256 a08e60b314c0f6e44a3207725f962e4b9d4c9196232344f83828ca376d4c7877 SHA512 20970d1be0d836bd07ea96ee909300f28eaf2ab4ded7b4525eb68399d242b864fe93120a16ef2ef35eba5f547c0cbe90b07c27ef44ab1910dbbe97230fbab84e WHIRLPOOL 66c7d9b6d41c050dcd56048951a5a6a8c0306ae180a3042a7a066d4edd5f4ae654fad27ab325ca3e78d7a3e92d0167bc5057ca069e8db960aa23c4b18fcf78ab

139
dev-python/spectral-cube/files/spectral-cube-0.4.0-looseversion.patch Normal file
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@@ -0,0 +1,139 @@
From: Ole Streicher <olebole@debian.org>
Date: Tue, 12 Jul 2016 08:54:59 +0200
Subject: Use LooseVersion instead of StrictVersion.
StrictVersion fails on numpy RCs. LooseVersion is a compromise until something better is available.
---
spectral_cube/np_compat.py | 4 ++--
spectral_cube/spectral_cube.py | 4 ++--
spectral_cube/tests/test_masks.py | 4 ++--
spectral_cube/tests/test_moments.py | 4 ++--
spectral_cube/tests/test_spectral_cube.py | 10 +++++-----
5 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/spectral_cube/np_compat.py b/spectral_cube/np_compat.py
index e72b4d9..dd9080a 100644
--- a/spectral_cube/np_compat.py
+++ b/spectral_cube/np_compat.py
@@ -1,7 +1,7 @@
from __future__ import print_function, absolute_import, division
import numpy as np
-from distutils.version import StrictVersion
+from distutils.version import LooseVersion
def allbadtonan(function):
"""
@@ -11,7 +11,7 @@ def allbadtonan(function):
"""
def f(data, axis=None):
result = function(data, axis=axis)
- if StrictVersion(np.__version__) >= StrictVersion('1.9.0'):
+ if LooseVersion(np.__version__) >= LooseVersion('1.9.0'):
if axis is None:
if np.all(np.isnan(data)):
return np.nan
diff --git a/spectral_cube/spectral_cube.py b/spectral_cube/spectral_cube.py
index 231245d..fa61119 100644
--- a/spectral_cube/spectral_cube.py
+++ b/spectral_cube/spectral_cube.py
@@ -34,7 +34,7 @@ from .lower_dimensional_structures import (Projection, Slice, OneDSpectrum,
LowerDimensionalObject)
from .base_class import BaseNDClass, SpectralAxisMixinClass, DOPPLER_CONVENTIONS
-from distutils.version import StrictVersion
+from distutils.version import LooseVersion
__all__ = ['SpectralCube', 'VaryingResolutionSpectralCube']
@@ -2072,7 +2072,7 @@ class BaseSpectralCube(BaseNDClass, SpectralAxisMixinClass):
import yt
if ('dev' in yt.__version__ or
- StrictVersion(yt.__version__) >= StrictVersion('3.0')):
+ LooseVersion(yt.__version__) >= LooseVersion('3.0')):
from yt.frontends.fits.api import FITSDataset
from yt.units.unit_object import UnitParseError
diff --git a/spectral_cube/tests/test_masks.py b/spectral_cube/tests/test_masks.py
index 9116cb3..42a2125 100644
--- a/spectral_cube/tests/test_masks.py
+++ b/spectral_cube/tests/test_masks.py
@@ -14,7 +14,7 @@ from .. import (BooleanArrayMask, SpectralCube, LazyMask, LazyComparisonMask,
FunctionMask, CompositeMask)
from ..masks import is_broadcastable_and_smaller, dims_to_skip, view_of_subset
-from distutils.version import StrictVersion
+from distutils.version import LooseVersion
def test_spectral_cube_mask():
@@ -370,7 +370,7 @@ def test_flat_mask():
assert np.all(cube.sum(axis=0)[mask_array] == mcube.sum(axis=0)[mask_array])
assert np.all(np.isnan(mcube.sum(axis=0)[~mask_array]))
-@pytest.mark.skipif(StrictVersion(np.__version__) < StrictVersion('1.7'),
+@pytest.mark.skipif(LooseVersion(np.__version__) < LooseVersion('1.7'),
reason='Numpy <1.7 does not support multi-slice indexing.')
def test_flat_mask_spectral():
cube, data = cube_and_raw('adv.fits')
diff --git a/spectral_cube/tests/test_moments.py b/spectral_cube/tests/test_moments.py
index 9b118fd..82eff40 100644
--- a/spectral_cube/tests/test_moments.py
+++ b/spectral_cube/tests/test_moments.py
@@ -1,7 +1,7 @@
from __future__ import print_function, absolute_import, division
import warnings
-from distutils.version import StrictVersion
+from distutils.version import LooseVersion
import pytest
import numpy as np
@@ -78,7 +78,7 @@ axis_order = pytest.mark.parametrize(('axis', 'order'),
(1, 0), (1, 1), (1, 2),
(2, 0), (2, 1), (2, 2)))
-if StrictVersion(astropy.__version__[:3]) >= StrictVersion('1.0'):
+if LooseVersion(astropy.__version__[:3]) >= LooseVersion('1.0'):
# The relative error is slightly larger on astropy-dev
# There is no obvious reason for this.
rtol = 2e-7
diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py
index 025e6bd..4dce3bb 100644
--- a/spectral_cube/tests/test_spectral_cube.py
+++ b/spectral_cube/tests/test_spectral_cube.py
@@ -4,7 +4,7 @@ import operator
import itertools
import warnings
import mmap
-from distutils.version import StrictVersion, LooseVersion
+from distutils.version import LooseVersion, LooseVersion
# needed to test for warnings later
warnings.simplefilter('always', UserWarning)
@@ -468,12 +468,12 @@ class TestNumpyMethods(BaseTest):
scmed = self.c.apply_numpy_function(np.median, axis=0)
# this checks whether numpy <=1.9.3 has a bug?
# as far as I can tell, np==1.9.3 no longer has this bug/feature
- #if StrictVersion(np.__version__) <= StrictVersion('1.9.3'):
+ #if LooseVersion(np.__version__) <= LooseVersion('1.9.3'):
# # print statements added so we get more info in the travis builds
- # print("Numpy version is: {0}".format(StrictVersion(np.__version__)))
+ # print("Numpy version is: {0}".format(LooseVersion(np.__version__)))
# assert np.count_nonzero(np.isnan(scmed)) == 5
#else:
- # print("Numpy version is: {0}".format(StrictVersion(np.__version__)))
+ # print("Numpy version is: {0}".format(LooseVersion(np.__version__)))
assert np.count_nonzero(np.isnan(scmed)) == 6
scmed = self.c.apply_numpy_function(np.nanmedian, axis=0)
@@ -667,7 +667,7 @@ def test_read_write_rountrip(tmpdir):
assert cube.shape == cube.shape
assert_allclose(cube._data, cube2._data)
if (((hasattr(_wcs, '__version__')
- and StrictVersion(_wcs.__version__) < StrictVersion('5.9'))
+ and LooseVersion(_wcs.__version__) < LooseVersion('5.9'))
or not hasattr(_wcs, '__version__'))):
# see https://github.com/astropy/astropy/pull/3992 for reasons:
# we should upgrade this for 5.10 when the absolute accuracy is

19
dev-python/spectral-cube/metadata.xml Normal file
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@@ -0,0 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-astronomy@gentoo.org</email>
<name>Gentoo Astronomy Project</name>
</maintainer>
<longdescription lang="en">
The spectral-cube astronomy python module provides an easy way to
read, manipulate, analyze, and write data cubes with two
positional dimensions and one spectral dimension, optionally with
Stokes parameters. It aims to be a versatile data container for
building custom analysis routines.
</longdescription>
<upstream>
<remote-id type="pypi">spectral-cube</remote-id>
<remote-id type="github">astropy/spectral-cube</remote-id>
</upstream>
</pkgmetadata>

52
dev-python/spectral-cube/spectral-cube-0.4.0.ebuild Normal file
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@@ -0,0 +1,52 @@
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
PYTHON_COMPAT=( python{2_7,3_4,3_5} )
inherit distutils-r1
DESCRIPTION="Manipulate astronomical data cubes with Python"
HOMEPAGE="https://spectral-cube.readthedocs.org/"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
LICENSE="BSD"
SLOT="0"
IUSE="doc test"
RDEPEND="dev-python/astropy[${PYTHON_USEDEP}]"
DEPEND="${RDEPEND}
dev-python/astropy-helpers[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]
doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
PATCHES=( "${FILESDIR}"/${P}-looseversion.patch )
python_prepare_all() {
sed -i -e '/auto_use/s/True/False/' setup.cfg || die
distutils-r1_python_prepare_all
}
python_compile_all() {
if use doc; then
python_setup
PYTHONPATH="${BUILD_DIR}"/lib \
esetup.py build_sphinx --no-intersphinx
fi
}
python_test() {
pushd spectral_cube/tests/data > /dev/null
"${PYTHON}" make_test_cubes.py
popd > /dev/null
esetup.py test
}
python_install_all() {
use doc && local HTML_DOCS=( docs/_build/html/ )
distutils-r1_python_install_all
}