proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 125 insertions, 0 deletions

diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
new file mode 100644
index 000000000000..4eb824ac2a3b
--- /dev/null
+++ b/sci-chemistry/nmrglue/Manifest
@@ -0,0 +1,2 @@
+DIST nmrglue-0.4-corrected.tar.gz 128298 SHA256 85c45750aef431f2c1326a9f4856eeac4da8aedbc94c6255de6e08e3ea35f316 SHA512 c2376ba8e8f993e6e4b536d67d4a780087ac8f811b2d5a846ff8b4785b02c0a4e86956c4205f90a17c5c0a2dc620d75fb7886fbad9cca314b548e3368137eda0 WHIRLPOOL eb8a2a5064b5fa5b60d16a70cf51667daa55f1584ed9d0ca3092af4672ed2c5cef56d135e82b35c107856d338fb0893248a1719b673a4e96c1edb2fb75243d08
+DIST nmrglue-0.5.tar.gz 142604 SHA256 a05c880bd0d5f0b388156409e18a5618742f829f2532d19970d05b11bfcc6103 SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 WHIRLPOOL 78f9d094a2ab1ebc01f452717fdc1cdeccc27951195c9dd6e97069a575722acf25442009b4ccede03ad728b0767fced4a2220a8072ccc1d604a9f62e9c45af4a
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..d1c1fa8f0564
--- /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>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </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-0.4.ebuild b/sci-chemistry/nmrglue/nmrglue-0.4.ebuild
new file mode 100644
index 000000000000..d39fd44820ce
--- /dev/null
+++ b/sci-chemistry/nmrglue/nmrglue-0.4.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="A module for working with NMR data in Python"
+HOMEPAGE="http://nmrglue.com/"
+SRC_URI="https://nmrglue.googlecode.com/files/${P}-corrected.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-python/ipython[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]"
+DEPEND=""
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..08dd91a5ab21
--- /dev/null
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+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/ipython[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${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
+}