dev-python/astroscrappy: initial import

Package-Manager: portage-2.2.27

7 files changed, 245 insertions, 0 deletions

diff --git a/dev-python/astroscrappy/Manifest b/dev-python/astroscrappy/Manifest
new file mode 100644
index 000000000000..bf4e65b949d3
--- /dev/null
+++ b/dev-python/astroscrappy/Manifest
@@ -0,0 +1 @@
+DIST astroscrappy-1.0.3.tar.gz 422209 SHA256 843af0ec1fb7439a886f05690a52d96342c3bd505dfdef42e922a66b67a89776 SHA512 2e96e8e62f81c770802a3c7699ca4455c640bb000aa4bffc22149745eed4e7e33cc4b297649020a601ff7fb242c0545cf9391c19ee2687adab26ac494d37dbb2 WHIRLPOOL 8ee318233639617608a4c4aea0a75227317f3ca695430c49882a1396178eb3655bd80169291de2631c752c81d41016dcda85653eb1caa372cfd7c0d49080fd67
diff --git a/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild b/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild
new file mode 100644
index 000000000000..97478225956b
--- /dev/null
+++ b/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild
@@ -0,0 +1,58 @@
+# 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 toolchain-funcs flag-o-matic
+
+DESCRIPTION="Optimized cosmic ray annihilation astropy python module"
+HOMEPAGE="https://github.com/astropy/astroscrappy"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc openmp test"
+
+RDEPEND="
+	dev-python/astropy[${PYTHON_USEDEP}]
+	dev-python/astropy-helpers[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]"
+
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+PATCHES=(
+	"${FILESDIR}/${P}-dont-install-binary.patch"
+	"${FILESDIR}/${P}-endian-fix-tests.patch"
+	"${FILESDIR}/${P}-numpy-fix-tests.patch"
+	"${FILESDIR}/${P}-respect-user-flag.patch"
+)
+
+DOCS=( CHANGES.rst )
+
+python_prepare_all() {
+	sed -i -e '/auto_use/s/True/False/' setup.cfg || die
+	use openmp && tc-has-openmp && append-flags -fopenmp
+	distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+	use doc && esetup.py build_sphinx
+}
+
+python_test() {
+	esetup.py test
+}
+
+python_install_all() {
+	use doc && local HTML_DOCS=( docs/_build/html/. )
+	distutils-r1_python_install_all
+}
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch
new file mode 100644
index 000000000000..4c69f00cc88d
--- /dev/null
+++ b/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch
@@ -0,0 +1,14 @@
+Author: Ole Streicher <olebole@debian.org>
+Description: Don't install example/template binary
+--- a/setup.py
++++ b/setup.py
+@@ -80,9 +80,6 @@
+ 
+ # Define entry points for command-line scripts
+ entry_points = {}
+-entry_points['console_scripts'] = [
+-    'astropy-package-template-example = packagename.example_mod:main',
+-]
+ 
+ # Include all .c files, recursively, including those generated by
+ # Cython, since we can not do this in MANIFEST.in with a "dynamic"
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch
new file mode 100644
index 000000000000..7a2bbb6299c6
--- /dev/null
+++ b/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch
@@ -0,0 +1,100 @@
+From 5b5ce99c63d03e60b6027f09f72231db11a87bf2 Mon Sep 17 00:00:00 2001
+From: Curtis McCully <cmccully@lcogt.net>
+Date: Thu, 3 Dec 2015 12:02:38 -0800
+Subject: [PATCH] Made tests not endian specific.
+--- a/astroscrappy/tests/test_utils.py
++++ b/astroscrappy/tests/test_utils.py
+@@ -56,7 +56,7 @@
+ 
+ 
+ def test_medfilt5():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed5 = ndimage.filters.median_filter(a, size=(5, 5), mode='nearest')
+     npmed5[:2, :] = a[:2, :]
+     npmed5[-2:, :] = a[-2:, :]
+@@ -68,7 +68,7 @@
+ 
+ 
+ def test_medfilt7():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed7 = ndimage.filters.median_filter(a, size=(7, 7), mode='nearest')
+     npmed7[:3, :] = a[:3, :]
+     npmed7[-3:, :] = a[-3:, :]
+@@ -80,7 +80,7 @@
+ 
+ 
+ def test_sepmedfilt3():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed3 = ndimage.filters.median_filter(a, size=(1, 3), mode='nearest')
+     npmed3[:, :1] = a[:, :1]
+     npmed3[:, -1:] = a[:, -1:]
+@@ -95,7 +95,7 @@
+ 
+ 
+ def test_sepmedfilt5():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed5 = ndimage.filters.median_filter(a, size=(1, 5), mode='nearest')
+     npmed5[:, :2] = a[:, :2]
+     npmed5[:, -2:] = a[:, -2:]
+@@ -110,7 +110,7 @@
+ 
+ 
+ def test_sepmedfilt7():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed7 = ndimage.filters.median_filter(a, size=(1, 7), mode='nearest')
+     npmed7[:, :3] = a[:, :3]
+     npmed7[:, -3:] = a[:, -3:]
+@@ -125,7 +125,7 @@
+ 
+ 
+ def test_sepmedfilt9():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npmed9 = ndimage.filters.median_filter(a, size=(1, 9), mode='nearest')
+     npmed9[:, :4] = a[:, :4]
+     npmed9[:, -4:] = a[:, -4:]
+@@ -174,7 +174,7 @@
+ 
+ 
+ def test_subsample():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     npsubsamp = np.zeros((a.shape[0] * 2, a.shape[1] * 2), dtype=np.float32)
+     for i in range(a.shape[0]):
+         for j in range(a.shape[1]):
+@@ -189,8 +189,8 @@
+ 
+ def test_rebin():
+     a = np.ascontiguousarray(np.random.random((2002, 2002)), dtype=np.float32)
+-    a = a.astype('<f4')
+-    nprebin = np.zeros((1001, 1001), dtype=np.float32).astype('<f4')
++    a = a.astype('f4')
++    nprebin = np.zeros((1001, 1001), dtype=np.float32).astype('f4')
+     for i in range(1001):
+         for j in range(1001):
+             nprebin[i, j] = (a[2 * i, 2 * j] + a[2 * i + 1, 2 * j] +
+@@ -202,7 +202,7 @@
+ 
+ 
+ def test_laplaceconvolve():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
+     k = np.array([[0.0, -1.0, 0.0], [-1.0, 4.0, -1.0], [0.0, -1.0, 0.0]])
+     k = k.astype('<f4')
+     npconv = ndimage.filters.convolve(a, k, mode='constant', cval=0.0)
+@@ -211,8 +211,8 @@
+ 
+ 
+ def test_convolve():
+-    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
+-    k = np.ascontiguousarray(np.random.random((5, 5))).astype('<f4')
++    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
++    k = np.ascontiguousarray(np.random.random((5, 5))).astype('f4')
+     npconv = ndimage.filters.convolve(a, k, mode='constant', cval=0.0)
+     cconv = convolve(a, k)
+     assert_allclose(cconv, npconv, rtol=0, atol=1e-5)
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch
new file mode 100644
index 000000000000..d7a1c93a5740
--- /dev/null
+++ b/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch
@@ -0,0 +1,21 @@
+Author: Ole Streicher <olebole@debian.org>
+Description: Cast the numpy arrays in the test to the same data type
+Bug: https://ci.debian.net/data/packages/unstable/amd64/a/astroscrappy/20160112_151253.autopkgtest.log.gz
+--- a/astroscrappy/tests/test_astroscrappy.py
++++ b/astroscrappy/tests/test_astroscrappy.py
+@@ -36,7 +36,7 @@
+     imdata += gaussian(imdata.shape, x, y, brightness, 3.5)
+ 
+ # Add the poisson noise
+-imdata = np.random.poisson(imdata)
++imdata = np.float32(np.random.poisson(imdata))
+ 
+ # Add readnoise
+ imdata += np.random.normal(0.0, 10.0, size=(1001, 1001))
+@@ -60,4 +60,4 @@
+     # contrast that we can turn our detection threshold up.
+     mask, _clean = detect_cosmics(imdata, readnoise=10., gain=1.0,
+                                   sigclip=6, sigfrac=1.0)
+-    assert (mask == expected_crmask).sum() == (1001 * 1001)
+\ No newline at end of file
++    assert (mask == expected_crmask).sum() == (1001 * 1001)
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch
new file mode 100644
index 000000000000..fb7bca64ce7f
--- /dev/null
+++ b/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch
@@ -0,0 +1,35 @@
+--- astroscrappy/astroscrappy/utils/setup_package.py.orig	2016-03-09 22:50:34.304043122 +0000
++++ astroscrappy/astroscrappy/utils/setup_package.py	2016-03-09 22:54:53.560783823 +0000
+@@ -43,30 +43,11 @@
+                     sources=med_sources,
+                     include_dirs=include_dirs,
+                     libraries=libraries,
+-                    language="c",
+-                    extra_compile_args=['-g', '-O3', '-funroll-loops',
+-                                        '-ffast-math'])
++                    language="c")
+     ext_im = Extension(name=str("astroscrappy.utils.image_utils"),
+                     sources=im_sources,
+                     include_dirs=include_dirs,
+                     libraries=libraries,
+-                    language="c",
+-                    extra_compile_args=['-g', '-O3', '-funroll-loops',
+-                                        '-ffast-math'])
+-
+-    has_openmp, outputs = check_openmp()
+-    if has_openmp:
+-        ext_med.extra_compile_args.append('-fopenmp')
+-        ext_im.extra_compile_args.append('-fopenmp')
+-        ext_med.extra_link_args = ['-g', '-fopenmp']
+-        ext_im.extra_link_args = ['-g', '-fopenmp']
+-    else:
+-        log.warn('OpenMP was not found. '
+-                 'astroscrappy will be compiled without OpenMP. '
+-                 '(Use the "-v" option of setup.py for more details.)')
+-        log.debug(('(Start of OpenMP info)\n'
+-                   'compiler stdout:\n{0}\n'
+-                   'compiler stderr:\n{1}\n'
+-                   '(End of OpenMP info)').format(*outputs))
++                    language="c")
+ 
+     return [ext_med, ext_im]
diff --git a/dev-python/astroscrappy/metadata.xml b/dev-python/astroscrappy/metadata.xml
new file mode 100644
index 000000000000..4b2263cd8f74
--- /dev/null
+++ b/dev-python/astroscrappy/metadata.xml
@@ -0,0 +1,16 @@
+<?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">
+    ccdproc is a AstroPy-affliated package for the basic reduction of
+    CCD images. It provides a framework for accounting for error propagation
+    and bad pixel tracking through the reduction steps.
+  </longdescription>
+  <upstream>
+    <remote-id type="pypi">ccdproc</remote-id>
+  </upstream>
+</pkgmetadata>