From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/nmrglue/Manifest | 6 ++++ .../nmrglue/files/nmrglue-0.5-nohyper.patch | 33 +++++++++++++++++++++ sci-chemistry/nmrglue/metadata.xml | 29 ++++++++++++++++++ sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild | 34 ++++++++++++++++++++++ 4 files changed, 102 insertions(+) create mode 100644 sci-chemistry/nmrglue/Manifest create mode 100644 sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch create mode 100644 sci-chemistry/nmrglue/metadata.xml create mode 100644 sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild (limited to 'sci-chemistry/nmrglue') 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 +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 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + +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. + + + jjhelmus/nmrglue + + 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 +} -- cgit v1.2.3