Backport fix for agilent data conversion

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/nmrglue/ChangeLog b/sci-chemistry/nmrglue/ChangeLog
index f09722ee8f4ae0545189466aca1d39ea19947994..ec1161cd75cfedd3c710f73031de600ba5c0da8c 100644 (file)
--- a/sci-chemistry/nmrglue/ChangeLog
+++ b/sci-chemistry/nmrglue/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/nmrglue
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/ChangeLog,v 1.2 2015/02/20 08:54:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/ChangeLog,v 1.3 2015/03/04 08:17:14 jlec Exp $
+
+*nmrglue-0.5-r1 (04 Mar 2015)
+
+  04 Mar 2015; Justin Lecher <jlec@gentoo.org> +files/nmrglue-0.5-nohyper.patch,
+  +nmrglue-0.5-r1.ebuild, -nmrglue-0.5.ebuild:
+  Backport fix for agilent data conversion
 
 *nmrglue-0.5 (20 Feb 2015)
 

diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
index 6830f6a753162f9391667b96d316ad75611eb0ef..21cc53ca6483215d6f1a1ee23ad12d5416bbb325 100644 (file)
--- a/sci-chemistry/nmrglue/Manifest
+++ b/sci-chemistry/nmrglue/Manifest
@@ -1,28 +1,29 @@
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 DIST nmrglue-0.4-corrected.tar.gz 128298 SHA256 85c45750aef431f2c1326a9f4856eeac4da8aedbc94c6255de6e08e3ea35f316 SHA512 c2376ba8e8f993e6e4b536d67d4a780087ac8f811b2d5a846ff8b4785b02c0a4e86956c4205f90a17c5c0a2dc620d75fb7886fbad9cca314b548e3368137eda0 WHIRLPOOL eb8a2a5064b5fa5b60d16a70cf51667daa55f1584ed9d0ca3092af4672ed2c5cef56d135e82b35c107856d338fb0893248a1719b673a4e96c1edb2fb75243d08
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diff --git a/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch
new file mode 100644 (file)
index 0000000..103f5b1
--- /dev/null
+++ b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch
@@ -0,0 +1,33 @@
+From ba1eee9e71623110511545c058afe2a92e139aa5 Mon Sep 17 00:00:00 2001
+From: Jonathan Helmus <jjhelmus@gmail.com>
+Date: Tue, 3 Mar 2015 19:47:05 -0600
+Subject: [PATCH] pipe_proc.py tp function correctly sets FDSIZE.
+
+Fixes issue #27
+---
+ nmrglue/process/pipe_proc.py | 7 +++++--
+ 1 file changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/nmrglue/process/pipe_proc.py b/nmrglue/process/pipe_proc.py
+index 79b6303..8c1271c 100644
+--- a/nmrglue/process/pipe_proc.py
++++ b/nmrglue/process/pipe_proc.py
+@@ -1527,13 +1527,16 @@ def tp(dic, data, hyper=False, nohyper=False, auto=False, nohdr=False):
+         data = np.array(p.tp_hyper(data), dtype="complex64")
+     else:
+         data = p.tp(data)
+-        if dic[fn2 + "QUADFLAG"] != 1 and nohyper is not True:
++        if dic[fn2 + "QUADFLAG"] != 1 and nohyper is False:
+             # unpack complex as needed
+             data = np.array(p.c2ri(data), dtype="complex64")
+ 
+     # update the dimentionality and order
+     dic["FDSLICECOUNT"] = data.shape[0]
+-    if data.dtype == 'float32':
++    if (data.dtype == 'float32') and (nohyper is True):
++        # when nohyper is True and the new last dimension was complex
++        # prior to transposing then FDSIZE is set as if the dimension was
++        # converted to complex data, that is half the actual size.
+         dic["FDSIZE"] = data.shape[1] / 2
+     else:
+         dic["FDSIZE"] = data.shape[1]

diff --git a/sci-chemistry/nmrglue/nmrglue-0.5.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
similarity index 88%
rename from sci-chemistry/nmrglue/nmrglue-0.5.ebuild
rename to sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
index 256c2ac94ad774e34fc69a2ad4973067d23aa14a..f408354620a7432541562f43731b1f36691a6c34 100644 (file)
--- a/sci-chemistry/nmrglue/nmrglue-0.5.ebuild
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/nmrglue-0.5.ebuild,v 1.1 2015/02/20 08:54:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild,v 1.1 2015/03/04 08:17:14 jlec Exp $
 
 EAPI=5
 
@@ -29,6 +29,8 @@ DEPEND="
        )
 "
 
+PATCHES=( "${FILESDIR}"/${P}-nohyper.patch )
+
 python_test() {
        nosetests --verbosity=3 || die
 }