dev-python/pyfits: add several patches from debian, also fixing #596240

Package-Manager: portage-2.3.2

4 files changed, 249 insertions, 5 deletions

diff --git a/dev-python/pyfits/files/01-system-cfitsio.patch b/dev-python/pyfits/files/01-system-cfitsio.patch
new file mode 100644
index 000000000000..f2ce935c7ea8
--- /dev/null
+++ b/dev-python/pyfits/files/01-system-cfitsio.patch
@@ -0,0 +1,176 @@
+From 70fe4dac3f68c3eed369d42e6a49e7865db8b250 Mon Sep 17 00:00:00 2001
+From: SVN-Git Migration <python-modules-team@lists.alioth.debian.org>
+Date: Thu, 8 Oct 2015 10:31:01 -0700
+Subject: 01-system-cfitsio.diff
+
+Patch-Name: 01-system-cfitsio.diff
+---
+ setup.cfg | 145 +++++++++++++++++++++++++++++++-------------------------------
+ 1 file changed, 73 insertions(+), 72 deletions(-)
+
+diff --git a/setup.cfg b/setup.cfg
+index 3a05c62..3a64f33 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -40,81 +40,81 @@ scripts =
+ 
+ [extension=pyfits.compression]
+ sources = 
+-	cextern/cfitsio/adler32.c
+-	cextern/cfitsio/buffers.c
+-	cextern/cfitsio/cfileio.c
+-	cextern/cfitsio/checksum.c
+-	cextern/cfitsio/crc32.c
+-	cextern/cfitsio/deflate.c
+-	cextern/cfitsio/drvrfile.c
+-	cextern/cfitsio/drvrgsiftp.c
+-	cextern/cfitsio/drvrmem.c
+-	cextern/cfitsio/drvrnet.c
+-	cextern/cfitsio/drvrsmem.c
+-	cextern/cfitsio/editcol.c
+-	cextern/cfitsio/edithdu.c
+-	cextern/cfitsio/eval_f.c
+-	cextern/cfitsio/eval_l.c
+-	cextern/cfitsio/eval_y.c
+-	cextern/cfitsio/fitscore.c
+-	cextern/cfitsio/fits_hcompress.c
+-	cextern/cfitsio/fits_hdecompress.c
+-	cextern/cfitsio/getcolb.c
+-	cextern/cfitsio/getcol.c
+-	cextern/cfitsio/getcold.c
+-	cextern/cfitsio/getcole.c
+-	cextern/cfitsio/getcoli.c
+-	cextern/cfitsio/getcolj.c
+-	cextern/cfitsio/getcolk.c
+-	cextern/cfitsio/getcoll.c
+-	cextern/cfitsio/getcolsb.c
+-	cextern/cfitsio/getcols.c
+-	cextern/cfitsio/getcolui.c
+-	cextern/cfitsio/getcoluj.c
+-	cextern/cfitsio/getcoluk.c
+-	cextern/cfitsio/getkey.c
+-	cextern/cfitsio/group.c
+-	cextern/cfitsio/grparser.c
+-	cextern/cfitsio/histo.c
+-	cextern/cfitsio/imcompress.c
+-	cextern/cfitsio/infback.c
+-	cextern/cfitsio/inffast.c
+-	cextern/cfitsio/inflate.c
+-	cextern/cfitsio/inftrees.c
+-	cextern/cfitsio/iraffits.c
+-	cextern/cfitsio/modkey.c
+-	cextern/cfitsio/pliocomp.c
+-	cextern/cfitsio/putcolb.c
+-	cextern/cfitsio/putcol.c
+-	cextern/cfitsio/putcold.c
+-	cextern/cfitsio/putcole.c
+-	cextern/cfitsio/putcoli.c
+-	cextern/cfitsio/putcolj.c
+-	cextern/cfitsio/putcolk.c
+-	cextern/cfitsio/putcoll.c
+-	cextern/cfitsio/putcolsb.c
+-	cextern/cfitsio/putcols.c
+-	cextern/cfitsio/putcolu.c
+-	cextern/cfitsio/putcolui.c
+-	cextern/cfitsio/putcoluj.c
+-	cextern/cfitsio/putcoluk.c
+-	cextern/cfitsio/putkey.c
+-	cextern/cfitsio/quantize.c
+-	cextern/cfitsio/region.c
+-	cextern/cfitsio/ricecomp.c
+-	cextern/cfitsio/scalnull.c
+-	cextern/cfitsio/swapproc.c
+-	cextern/cfitsio/trees.c
+-	cextern/cfitsio/uncompr.c
+-	cextern/cfitsio/wcssub.c
+-	cextern/cfitsio/wcsutil.c
+-	cextern/cfitsio/zcompress.c
+-	cextern/cfitsio/zuncompress.c
+-	cextern/cfitsio/zutil.c
++#	cextern/cfitsio/adler32.c
++#	cextern/cfitsio/buffers.c
++#	cextern/cfitsio/cfileio.c
++#	cextern/cfitsio/checksum.c
++#	cextern/cfitsio/crc32.c
++#	cextern/cfitsio/deflate.c
++#	cextern/cfitsio/drvrfile.c
++#	cextern/cfitsio/drvrgsiftp.c
++#	cextern/cfitsio/drvrmem.c
++#	cextern/cfitsio/drvrnet.c
++#	cextern/cfitsio/drvrsmem.c
++#	cextern/cfitsio/editcol.c
++#	cextern/cfitsio/edithdu.c
++#	cextern/cfitsio/eval_f.c
++#	cextern/cfitsio/eval_l.c
++#	cextern/cfitsio/eval_y.c
++#	cextern/cfitsio/fitscore.c
++#	cextern/cfitsio/fits_hcompress.c
++#	cextern/cfitsio/fits_hdecompress.c
++#	cextern/cfitsio/getcolb.c
++#	cextern/cfitsio/getcol.c
++#	cextern/cfitsio/getcold.c
++#	cextern/cfitsio/getcole.c
++#	cextern/cfitsio/getcoli.c
++#	cextern/cfitsio/getcolj.c
++#	cextern/cfitsio/getcolk.c
++#	cextern/cfitsio/getcoll.c
++#	cextern/cfitsio/getcolsb.c
++#	cextern/cfitsio/getcols.c
++#	cextern/cfitsio/getcolui.c
++#	cextern/cfitsio/getcoluj.c
++#	cextern/cfitsio/getcoluk.c
++#	cextern/cfitsio/getkey.c
++#	cextern/cfitsio/group.c
++#	cextern/cfitsio/grparser.c
++#	cextern/cfitsio/histo.c
++#	cextern/cfitsio/imcompress.c
++#	cextern/cfitsio/infback.c
++#	cextern/cfitsio/inffast.c
++#	cextern/cfitsio/inflate.c
++#	cextern/cfitsio/inftrees.c
++#	cextern/cfitsio/iraffits.c
++#	cextern/cfitsio/modkey.c
++#	cextern/cfitsio/pliocomp.c
++#	cextern/cfitsio/putcolb.c
++#	cextern/cfitsio/putcol.c
++#	cextern/cfitsio/putcold.c
++#	cextern/cfitsio/putcole.c
++#	cextern/cfitsio/putcoli.c
++#	cextern/cfitsio/putcolj.c
++#	cextern/cfitsio/putcolk.c
++#	cextern/cfitsio/putcoll.c
++#	cextern/cfitsio/putcolsb.c
++#	cextern/cfitsio/putcols.c
++#	cextern/cfitsio/putcolu.c
++#	cextern/cfitsio/putcolui.c
++#	cextern/cfitsio/putcoluj.c
++#	cextern/cfitsio/putcoluk.c
++#	cextern/cfitsio/putkey.c
++#	cextern/cfitsio/quantize.c
++#	cextern/cfitsio/region.c
++#	cextern/cfitsio/ricecomp.c
++#	cextern/cfitsio/scalnull.c
++#	cextern/cfitsio/swapproc.c
++#	cextern/cfitsio/trees.c
++#	cextern/cfitsio/uncompr.c
++#	cextern/cfitsio/wcssub.c
++#	cextern/cfitsio/wcsutil.c
++#	cextern/cfitsio/zcompress.c
++#	cextern/cfitsio/zuncompress.c
++#	cextern/cfitsio/zutil.c
+ 	src/compressionmodule.c
+ include_dirs = 
+ 	numpy
+-	cextern/cfitsio
++#	cextern/cfitsio
+ extra_compile_args = 
+ 	-Wno-declaration-after-statement
+ 	-Wno-unused-variable
+@@ -125,6 +125,7 @@ extra_compile_args =
+ 	-Wno-unused
+ 	-Wno-comments
+ 	-Wno-switch
++libraries = cfitsio
+ optional = True
+ fail_message = 
+ 	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/dev-python/pyfits/files/02-numpy-deprecation-warning.patch b/dev-python/pyfits/files/02-numpy-deprecation-warning.patch
new file mode 100644
index 000000000000..026e6b829d4d
--- /dev/null
+++ b/dev-python/pyfits/files/02-numpy-deprecation-warning.patch
@@ -0,0 +1,24 @@
+From 90cac05f8a5436a8dd3714ad29e2d81eb8b4d39b Mon Sep 17 00:00:00 2001
+From: Aurelien Jarno <aurelien@aurel32.net>
+Date: Tue, 2 Feb 2016 22:41:09 +0100
+Subject: Avoid DeprecationWarning from Numpy.
+
+Patch-Name: 02-numpy-deprecation-warning.diff
+---
+ pyfits/tests/test_division.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pyfits/tests/test_division.py b/pyfits/tests/test_division.py
+index da4df72..aa93264 100644
+--- a/pyfits/tests/test_division.py
++++ b/pyfits/tests/test_division.py
+@@ -18,7 +18,8 @@ class TestDivisionFunctions(PyfitsTestCase):
+         a1 = np.rec.array(
+             s,
+             dtype=np.dtype([('c1', '>i4'), ('c2', '|S3'),
+-                         ('c3', '>f4'), ('c4', '|i1')]))
++                         ('c3', '>f4'), ('c4', '|i1')]),
++            shape=len(s) // 12)
+ 
+     def test_card_with_continue(self):
+         h = fits.PrimaryHDU()
diff --git a/dev-python/pyfits/files/03-fix-for-cfitsio-3380.patch b/dev-python/pyfits/files/03-fix-for-cfitsio-3380.patch
new file mode 100644
index 000000000000..d0fac84d1e22
--- /dev/null
+++ b/dev-python/pyfits/files/03-fix-for-cfitsio-3380.patch
@@ -0,0 +1,43 @@
+Author: Ole Streicher <olebole@debian.org>
+Description: Update image tests for cfitsio 3.380
+ Make TFORMx check more flexible. The maximal column length in cfitsio
+ changed between version 3370 and 3380. This patch checks their syntax,
+ without a specific length.
+ .
+ HCOMPRESSed images are allowed to deviate from the original by about
+ 1/quantize_level of the RMS in each tile. This patch changes the absolute
+ identity test
+Bug: https://github.com/astropy/astropy/issues/4646
+Bug: https://github.com/astropy/astropy/issues/4647
+Bug-Debian: https://bugs.debian.org/816595
+--- a/pyfits/tests/test_image.py
++++ b/pyfits/tests/test_image.py
+@@ -2,6 +2,7 @@
+ 
+ import math
+ import os
++import re
+ import time
+ import warnings
+ 
+@@ -1014,7 +1015,7 @@
+         hdu.writeto(self.temp('test.fits'))
+ 
+         with fits.open(self.temp('test.fits')) as hdul:
+-            assert (hdul['SCI'].data == cube).all()
++            assert np.abs(hdul['SCI'].data - cube).max() < 1./15.
+ 
+     def test_subtractive_dither_seed(self):
+         """
+@@ -1269,8 +1270,8 @@
+ 
+         with fits.open(self.temp('test.fits'),
+                        disable_image_compression=True) as h:
+-            assert h[1].header['TFORM1'] == '1PB(30)'
+-            assert h[1].header['TFORM2'] == '1PB(359)'
++            assert re.match(r'^1PB\(\d+\)$', h[1].header['TFORM1'])
++            assert re.match(r'^1PB\(\d+\)$', h[1].header['TFORM2'])
+ 
+     def test_compression_update_header(self):
+         """Regression test for
+
diff --git a/dev-python/pyfits/pyfits-3.4.ebuild b/dev-python/pyfits/pyfits-3.4-r1.ebuild
index dd6036d52f28..a62069c9b4f8 100644
--- a/dev-python/pyfits/pyfits-3.4.ebuild
+++ b/dev-python/pyfits/pyfits-3.4-r1.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 python3_{4,5} )
 
@@ -32,12 +32,13 @@ DEPEND="${RDEPEND}
 		 )
 	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
 
-PATCHES=( "${FILESDIR}"/${PN}-3.2.1-unbundle-cfitsio.patch )
+PATCHES=( "${FILESDIR}"/01-system-cfitsio.patch
+		  "${FILESDIR}"/02-numpy-deprecation-warning.patch
+		  "${FILESDIR}"/03-fix-for-cfitsio-3380.patch )
 
 python_prepare_all() {
-	sed -i \
-		-e "s/\(hook_package_dir = \)lib/\1$(get_libdir)/g" \
-		"${S}"/setup.cfg || die
+	sed -e "s/\(hook_package_dir = \)lib/\1$(get_libdir)/g" \
+		-i "${S}"/setup.cfg || die
 
 	# https://github.com/spacetelescope/PyFITS/issues/95
 	sed -e "s/except UserWarning, w/except UserWarning as w/" \