diff options
Diffstat (limited to 'dev-python/astroscrappy')
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> |