reinit the tree, so we can have metadata

4 files changed, 102 insertions, 0 deletions

diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
new file mode 100644
index 000000000000..fdbace82d4de
--- /dev/null
+++ b/sci-chemistry/nmrglue/Manifest
@@ -0,0 +1,6 @@
+AUX nmrglue-0.5-nohyper.patch 1408 SHA256 96ad150a0d6f01a135c20a30c022fa80fef9c56a02122467e19fb91819294a0c SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd WHIRLPOOL f373fc8912b073aa8012bcf612691a7b45514e613fbe7f448a3d9cf70aec42a2cceaed705c1d1e65a81a2ae692c18dce2b8f297a0baf07a3a6febd0f285b1032
+DIST nmrglue-0.5.tar.gz 142604 SHA256 a05c880bd0d5f0b388156409e18a5618742f829f2532d19970d05b11bfcc6103 SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 WHIRLPOOL 78f9d094a2ab1ebc01f452717fdc1cdeccc27951195c9dd6e97069a575722acf25442009b4ccede03ad728b0767fced4a2220a8072ccc1d604a9f62e9c45af4a
+EBUILD nmrglue-0.5-r1.ebuild 731 SHA256 8f832d11ad367640d71ab63e939ead804a9520dbb468061d5637df94c586fe09 SHA512 22d3bae493423dc2e3fa3a3c5a5e9a110f68ada07b0a9d30176c350f4705d0e5a96697c3a4864241ee8b9c428313b8f47fee70850fcfabfac3a971c0346ca51f WHIRLPOOL 6075e70b8dad7083e3503966cc3a17f06a7ba15459c54a236ae6b98e98bcaa8688085acd8f256b1ddf2eebbae0483d06b22becdfa92d48a10d6c5113f83ad660
+MISC ChangeLog 3013 SHA256 0b9b8c10a0cb9043bb7c2a2972adba6faa8308e0215dd89651e9c473ffcc784e SHA512 a43ad6398854e7d9c35b6523ed46a7f7ed18d1c5b51f46c97dc044f5048d9a5841eb919dcc18b13a6fcabd717a9513fcd3f6abb7291988f053bb7ac8cbb8fcd1 WHIRLPOOL 033b185e10956e706b1159ecfde8f39e696ee98d5b611d98f67f2910a62995f65380b4b732418acfb81124da35ddddaab575eff997cdf8804dced22bf7856a9f
+MISC ChangeLog-2015 689 SHA256 26d93992a39ef4db578883a615b7fbce1285e1e8fddc5cf04a4173563c18f131 SHA512 70d1328005577e4eb76ddec29f84ace2bdcafe8e9219ebd203be0e2aa15ee4f77d7de2d688000edf83c6fb20325ec79ad6c99a2b55c70fc15cc91086844ad054 WHIRLPOOL 12d264ee1a48880d27f85ea5ece5c2c52768785bcebc3c31b5f25dad3c1e147ead8d2934ab3c97ee7e95393cde8381195dc0dc22cd25bc65aa50d638459ab9fd
+MISC metadata.xml 1338 SHA256 0714c426b85786c120b47cfbc8b40f2d678dc144447a01c899dd5482203d3e3e SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c WHIRLPOOL a5b90cf56e472f26409d11452ebc17d0a53c63e1074ed359a6da47950d58340c5649cfe1f94b319e947fc2adc9bed8b25fc27717ed412d0a121e8669c464904e
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
index 000000000000..103f5b154d0b
--- /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/metadata.xml b/sci-chemistry/nmrglue/metadata.xml
new file mode 100644
index 000000000000..55fa34fcbc44
--- /dev/null
+++ b/sci-chemistry/nmrglue/metadata.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <longdescription>
+Nmrglue has the ability to read, write and convert between a number of NMR file 
+formats including Agilent/Varian, Bruker, NMRPipe, Sparky, SIMPSON, Rowland NMR 
+Toolkit files. The files, which are represented in Python as dictionaries of 
+spectral parameters and NumPy ndarray objects, can be easily examined, modified 
+and processed as desired.
+
+Nmrglue provides a number of functions for processing NMR data such as 
+apodization, spectral shifting, Fourier and other transformations, baseline 
+smoothing and flattening, and linear prediction modeling and extrapolation. 
+In addition new processing schemes can be implemented easily using the nmrglue 
+provided functions and the multitude of numerical routines provided by the NumPy
+and SciPy packages.
+
+When used in conjunction with the matplotlib (or other) python plotting library 
+nmrglue can be used to create publication quality figures of NMR spectrum or 
+examine data interactively.
+</longdescription>
+  <upstream>
+    <remote-id type="github">jjhelmus/nmrglue</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
new file mode 100644
index 000000000000..9f1cae764afb
--- /dev/null
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="A module for working with NMR data in Python"
+HOMEPAGE="http://nmrglue.com/"
+SRC_URI="https://github.com/jjhelmus/nmrglue/releases/download/v${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]"
+DEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/nose[${PYTHON_USEDEP}]
+	)
+"
+
+PATCHES=( "${FILESDIR}"/${P}-nohyper.patch )
+
+python_test() {
+	nosetests --verbosity=3 || die
+}