dev-python/astropy: Version bump

8 files changed, 303 insertions, 0 deletions

diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest
new file mode 100644
index 0000000..591f179
--- /dev/null
+++ b/dev-python/astropy/Manifest
@@ -0,0 +1 @@
+DIST astropy-1.1.1.tar.gz 8157305 SHA256 4d2e7a8bd5191a66d7e1a52beefb4a0b6f496a1e9e8212422613219cb514769f SHA512 bc3c370da32d5f0098dbfc2808dba9d4d4424d3dcfba4d7ffd84b39569387b79ad93086e10678c259237f9cfe1229725501d0dc4eba51c9d01a4cd8a72024fb4 WHIRLPOOL 5b40955f56e6f080ad93b224eabd345565ef9f5e7f5ccb00e2737bd714117bc9b35922a044fe4ccaddb9d30fa72e13dd560577392120bfbd0a9d10c8aaa5aa01
diff --git a/dev-python/astropy/astropy-1.1.1.ebuild b/dev-python/astropy/astropy-1.1.1.ebuild
new file mode 100644
index 0000000..cbe1283
--- /dev/null
+++ b/dev-python/astropy/astropy-1.1.1.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit distutils-r1
+
+DESCRIPTION="Core functionality for performing astrophysics with Python"
+HOMEPAGE="http://astropy.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+RDEPEND="
+	>=dev-libs/expat-2.1.0:0=
+	dev-python/configobj[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/ply[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	>=sci-astronomy/erfa-1.2:0=
+	>=sci-astronomy/wcslib-5:0=
+	>=sci-libs/cfitsio-3.360:0=
+	sys-libs/zlib:0="
+DEPEND="${RDEPEND}
+	>=dev-python/astropy-helpers-1.1[${PYTHON_USEDEP}]
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	virtual/pkgconfig
+	doc? (
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		media-gfx/graphviz
+	)
+	test? (
+		dev-libs/libxml2[${PYTHON_USEDEP}]
+		dev-python/pytest[${PYTHON_USEDEP}]
+		dev-python/h5py[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		sci-libs/scipy[${PYTHON_USEDEP}]
+	)"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-1.0.4-system-six.patch"
+	"${FILESDIR}/${PN}-1.0.4-system-configobj.patch"
+	"${FILESDIR}/${PN}-1.1.1-fix-wcs.patch"
+	"${FILESDIR}/${PN}-1.1.1-mark-kown-failures.patch"
+)
+
+python_prepare_all() {
+	export mydistutilsargs="--offline"
+	export ASTROPY_USE_SYSTEM_PYTEST=True
+	rm -r ${PN}_helpers || die
+	cp "${FILESDIR}"/astropy-ply.py astropy/extern/ply.py || die
+	rm -r cextern/{expat,erfa,cfitsio,wcslib} || die
+	sed -i -e '/auto_use/s/True/False/' setup.cfg || die
+	cat >> setup.cfg <<-EOF
+
+	[build]
+	use_system_libraries=1
+	EOF
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile_all() {
+	if use doc; then
+		python_export_best
+		VARTEXFONTS="${T}"/fonts \
+			MPLCONFIGDIR="${BUILD_DIR}" \
+			PYTHONPATH="${BUILD_DIR}"/lib \
+			esetup.py build_sphinx
+	fi
+}
+
+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/astropy/files/astropy-1.0.4-system-configobj.patch b/dev-python/astropy/files/astropy-1.0.4-system-configobj.patch
new file mode 100644
index 0000000..9578c0d
--- /dev/null
+++ b/dev-python/astropy/files/astropy-1.0.4-system-configobj.patch
@@ -0,0 +1,14 @@
+diff -ur astropy-0.4.1/astropy/config/configuration.py astropy-0.4.1.configobj/astropy/config/configuration.py
+--- astropy-0.4.1/astropy/config/configuration.py	2014-09-01 22:41:30.066853605 +0200
++++ astropy-0.4.1.configobj/astropy/config/configuration.py	2014-09-01 22:40:50.793528942 +0200
+@@ -23,7 +23,8 @@
+ import types
+ from warnings import warn
+ 
+-from ..extern.configobj import configobj, validate
++import configobj
++import validate
+ from ..utils.exceptions import AstropyWarning, AstropyDeprecationWarning
+ from ..utils import find_current_module
+ from ..utils.misc import InheritDocstrings
+
diff --git a/dev-python/astropy/files/astropy-1.0.4-system-six.patch b/dev-python/astropy/files/astropy-1.0.4-system-six.patch
new file mode 100644
index 0000000..8bfab98
--- /dev/null
+++ b/dev-python/astropy/files/astropy-1.0.4-system-six.patch
@@ -0,0 +1,12 @@
+diff -ur astropy-0.4.1/astropy/extern/six.py astropy-0.4.1.six/astropy/extern/six.py
+--- astropy-0.4.1/astropy/extern/six.py	2014-09-01 21:57:56.663393218 +0200
++++ astropy-0.4.1.six/astropy/extern/six.py	2014-09-01 21:59:02.940933294 +0200
+@@ -13,7 +13,7 @@
+ # Update this to prevent Astropy from using its bundled copy of six
+ # (but only if some other version of at least _SIX_MIN_VERSION can
+ # be provided)
+-_SIX_SEARCH_PATH = ['astropy.extern.bundled.six', 'six']
++_SIX_SEARCH_PATH = ['six', 'astropy.extern.bundled.six']
+ 
+ 
+ def _find_module(name, path=None):
diff --git a/dev-python/astropy/files/astropy-1.1.1-fix-wcs.patch b/dev-python/astropy/files/astropy-1.1.1-fix-wcs.patch
new file mode 100644
index 0000000..efb1273
--- /dev/null
+++ b/dev-python/astropy/files/astropy-1.1.1-fix-wcs.patch
@@ -0,0 +1,15 @@
+Author: Kacper Kowalik <xarthisius.kk@gmail.com>
+Description: Copy keys to a list, since orignal map is modified
+Url: https://github.com/astropy/astropy/issues/4477
+Bug:  https://github.com/astropy/astropy/issues/4460
+--- a/astropy/wcs/wcs.py
++++ b/astropy/wcs/wcs.py
+@@ -988,7 +988,7 @@
+         """
+         # Never pass SIP coefficients to wcslib
+         # CTYPE must be passed with -SIP to wcslib
+-        for key in (m.group() for m in map(SIP_KW.match, header.keys())
++        for key in (m.group() for m in map(SIP_KW.match, list(header))
+                     if m is not None):
+             del header[key]
+ 
diff --git a/dev-python/astropy/files/astropy-1.1.1-mark-kown-failures.patch b/dev-python/astropy/files/astropy-1.1.1-mark-kown-failures.patch
new file mode 100644
index 0000000..2e2c82a
--- /dev/null
+++ b/dev-python/astropy/files/astropy-1.1.1-mark-kown-failures.patch
@@ -0,0 +1,99 @@
+Author: Ole Streicher <olebole@debian.org>
+Description: Mark all known test failures as xfail.
+ These failures have been discussed with upstream.
+--- a/astropy/io/fits/tests/test_connect.py
++++ b/astropy/io/fits/tests/test_connect.py
+@@ -136,6 +136,8 @@
+         # while reading is to check whether col.null is present. For float columns, col.null
+         # is not initialized
+ 
++# see https://github.com/astropy/astropy/issues/3415
++    @pytest.mark.xfail()
+     def test_read_from_fileobj(self, tmpdir):
+         filename = str(tmpdir.join('test_read_from_fileobj.fits'))
+         hdu = BinTableHDU(self.data)
+@@ -172,6 +174,8 @@
+     def setup_method(self, method):
+         warnings.filterwarnings('always')
+ 
++# see https://github.com/astropy/astropy/issues/3415
++    @pytest.mark.xfail()
+     def test_read(self, tmpdir):
+         filename = str(tmpdir.join('test_read.fits'))
+         self.hdus.writeto(filename)
+@@ -189,6 +193,8 @@
+             Table.read(filename, hdu=0)
+         assert exc.value.args[0] == 'No table found in hdu=0'
+ 
++# see https://github.com/astropy/astropy/issues/3415
++    @pytest.mark.xfail()
+     @pytest.mark.parametrize('hdu', [1, 'first'])
+     def test_read_with_hdu_1(self, tmpdir, hdu):
+         filename = str(tmpdir.join('test_read_with_hdu_1.fits'))
+--- a/astropy/wcs/wcs.py
++++ b/astropy/wcs/wcs.py
+@@ -84,6 +84,8 @@
+ if six.PY3 or platform.system() == 'Windows':
+     __doctest_skip__ = ['WCS.all_world2pix']
+ 
++# see https://github.com/astropy/astropy/issues/3380
++__doctest_skip__ = ['WCS.all_world2pix']
+ 
+ if _wcs is not None:
+     WCSBase = _wcs._Wcs
+--- a/astropy/tests/tests/test_socketblocker.py
++++ b/astropy/tests/tests/test_socketblocker.py
+@@ -66,8 +66,8 @@
+ def _square(x):
+     return x ** 2
+ 
+-
+-@pytest.mark.skipif('not PY3_4 or sys.platform == "win32" or sys.platform.startswith("gnu0")')
++# see https://github.com/astropy/astropy/issues/4193
++@pytest.mark.skipif(True, reason="Blocks on Debian CI test")
+ def test_multiprocessing_forkserver():
+     """
+     Test that using multiprocessing with forkserver works.  Perhaps
+--- a/astropy/coordinates/tests/test_api_ape5.py
++++ b/astropy/coordinates/tests/test_api_ape5.py
+@@ -319,7 +319,8 @@
+     # coordinate object, and one that returns a cartesian matrix but does *not*
+     # require `newobj` or `fk5frame` - this allows optimization of the transform.
+ 
+-
++# Temporary mark until scipy/numpy is fully on 3.5
++@pytest.mark.xfail()
+ def test_highlevel_api():
+     J2001 = time.Time('J2001', scale='utc')
+ 
+--- a/astropy/visualization/tests/test_histogram.py
++++ b/astropy/visualization/tests/test_histogram.py
+@@ -50,6 +50,8 @@
+     assert patches2[0].axes is ax[1]
+ 
+ 
++# see https://github.com/astropy/astropy/issues/4329
++@pytest.mark.xfail()
+ @pytest.mark.skipif('not HAS_PLT')
+ def test_hist_autobin(rseed=0):
+     rng = np.random.RandomState(rseed)
+--- a/astropy/table/tests/test_info.py
++++ b/astropy/table/tests/test_info.py
+@@ -6,6 +6,7 @@
+ import warnings
+ import numpy as np
+ 
++from ...tests.helper import pytest
+ from ...extern import six
+ from ... import units as u
+ from ... import time
+@@ -225,7 +226,8 @@
+         t.info(out=out)
+         assert out.getvalue().splitlines() == exp
+ 
+-
++# see https://github.com/astropy/astropy/issues/4336
++@pytest.mark.xfail()
+ def test_ignore_warnings():
+     t = table.Table([[np.nan, np.nan]])
+     with warnings.catch_warnings(record=True) as warns:
diff --git a/dev-python/astropy/files/astropy-ply.py b/dev-python/astropy/files/astropy-ply.py
new file mode 100644
index 0000000..19eb104
--- /dev/null
+++ b/dev-python/astropy/files/astropy-ply.py
@@ -0,0 +1,58 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+"""
+Handle loading ply package from system or from the bundled copy
+"""
+
+import imp
+from distutils.version import StrictVersion
+
+
+def _find_module(name, path=None):
+    """
+    Alternative to `imp.find_module` that can also search in subpackages.
+    """
+
+    parts = name.split('.')
+
+    for part in parts:
+        if path is not None:
+            path = [path]
+
+        fh, path, descr = imp.find_module(part, path)
+
+    return fh, path, descr
+
+_PLY_MIN_VERSION = StrictVersion('3.4')
+
+# Update this to prevent Astropy from using its bundled copy of ply
+# (but only if some other version of at least _PLY_MIN_VERSION can
+# be provided)
+_PLY_SEARCH_PATH = ['ply']
+
+
+for mod_name in _PLY_SEARCH_PATH:
+    try:
+        mod_info = _find_module(mod_name)
+        #mod_lex_info = _find_module(mod_name + '.lex')
+    except ImportError:
+        continue
+
+    mod = imp.load_module(__name__, *mod_info)
+    #mod_lex = imp.load_module(__name__ + '.lex', *mod_lex_info)
+
+    try:
+    #    if StrictVersion(mod_lex.__version__) >= _PLY_MIN_VERSION:
+    #        break
+        break
+    except (AttributeError, ValueError):
+        # Attribute error if the ply module isn't what it should be and doesn't
+        # have a .__version__; ValueError if the version string exists but is
+        # somehow bogus/unparseable
+        continue
+else:
+    raise ImportError(
+        "Astropy requires the 'ply' module of minimum version {0}; "
+        "normally this is bundled with the astropy package so if you get "
+        "this warning consult the packager of your Astropy "
+        "distribution.".format(_PLY_MIN_VERSION))
diff --git a/dev-python/astropy/metadata.xml b/dev-python/astropy/metadata.xml
new file mode 100644
index 0000000..85615ff
--- /dev/null
+++ b/dev-python/astropy/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">
+  Astropy is a community-driven package intended to contain much of
+  the core functionality and some common tools needed for performing
+  astronomy and astrophysics with Python.
+</longdescription>
+  <upstream>
+    <remote-id type="pypi">astropy</remote-id>
+  </upstream>
+</pkgmetadata>