diff options
author | András Wacha | 2019-07-22 10:18:22 +0200 |
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committer | András Wacha | 2019-07-22 11:36:37 +0200 |
commit | 8a19c108884720d20a179bf019f001b88c657da1 (patch) | |
tree | d120f70494a805f32a3fcfbf36b3c2f029456900 | |
download | aur-8a19c108884720d20a179bf019f001b88c657da1.tar.gz |
Initial commit
-rw-r--r-- | .SRCINFO | 27 | ||||
-rw-r--r-- | PKGBUILD | 55 | ||||
-rw-r--r-- | bumps.patch | 77 |
3 files changed, 159 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..2a0248744dfd --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,27 @@ +pkgbase = python-bumps + pkgdesc = Data fitting with uncertainty analysis + pkgver = 0.7.11 + pkgrel = 1 + url = https://github.com/bumps/bumps + arch = any + license = custom + makedepends = python-setuptools + makedepends = python-sphinx + makedepends = python-nose + makedepends = python-docutils + makedepends = python-pygments + makedepends = python-jinja>=2 + depends = python-numpy + depends = python-scipy + depends = python-matplotlib + depends = python-wxpython + depends = python-pyparsing + depends = python-periodictable + depends = python-scikit-learn + source = https://github.com/bumps/bumps/archive/v0.7.11.tar.gz + source = bumps.patch + sha256sums = f0c368d7beb4307297fb5298658921941a80c21e7bc52fb5dab1a1d1ef16d250 + sha256sums = SKIP + +pkgname = python-bumps + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..1e4dba208756 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: András Wacha <awacha@gmail.com> +pkgname=python-bumps +_name=${pkgname#python-} +pkgver=0.7.11 +pkgrel=1 +pkgdesc="Data fitting with uncertainty analysis" +arch=(any) +url="https://github.com/bumps/bumps" +license=('custom') +makedepends=( python-setuptools + python-sphinx + python-nose + python-docutils + python-pygments + 'python-jinja>=2' +) +depends=( python-numpy + python-scipy + python-matplotlib + python-wxpython + python-pyparsing + python-periodictable + python-scikit-learn +) +source=("https://github.com/${_name}/${_name}/archive/v${pkgver}.tar.gz" + "bumps.patch") +sha256sums=('f0c368d7beb4307297fb5298658921941a80c21e7bc52fb5dab1a1d1ef16d250' + 'SKIP') + +prepare() { + cd ${_name}-${pkgver} + patch -p1 <../bumps.patch +} + +build() { + cd ${_name}-${pkgver} + python setup.py build + (cd bumps/dream && cc compiled.c -I ../../Random123/include/ -O2 -fopenmp -shared -lm -o _compiled.so -fPIC ) + (cd doc && make html) + (cd doc && make pdf) +} + +check() { + cd ${_name}-${pkgver} +# python test.py +} + +package() { + cd ${_name}-${pkgver} + python setup.py install --root="$pkgdir/" --optimize=1 --skip-build + mkdir -p ${pkgdir}/usr/share/licenses/python-bumps + cp ${srcdir}/${_name}-${pkgver}/LICENSE.txt ${pkgdir}/usr/share/licenses/python-bumps/license.txt + mkdir -p ${pkgdir}/usr/share/doc/python-bumps + cp ${srcdir}/${_name}-${pkgver}/doc/_build/html ${pkgdir}/usr/share/doc/python-bumps -R +} diff --git a/bumps.patch b/bumps.patch new file mode 100644 index 000000000000..54f15a3d77cc --- /dev/null +++ b/bumps.patch @@ -0,0 +1,77 @@ +diff -Naur bumps-0.7.11/bumps/numdifftools/core.py bumps-0.7.11_patched/bumps/numdifftools/core.py +--- bumps-0.7.11/bumps/numdifftools/core.py 2019-07-22 11:00:07.663853366 +0200 ++++ bumps-0.7.11_patched/bumps/numdifftools/core.py 2018-09-24 21:06:44.000000000 +0200 +@@ -23,7 +23,7 @@ + import numpy as np + from collections import namedtuple + from numpy import linalg +-from scipy import misc ++from scipy import misc, special + import warnings + + # 2016-04-19 PAK use relative imports +@@ -631,9 +631,9 @@ + def _vstack(self, sequence, steps): + # sequence = np.atleast_2d(sequence) + original_shape = np.shape(sequence[0]) +- f_del = np.vstack(list(np.ravel(r)) for r in sequence) +- h = np.vstack(list(np.ravel(np.ones(original_shape)*step)) +- for step in steps) ++ f_del = np.vstack([list(np.ravel(r)) for r in sequence]) ++ h = np.vstack([list(np.ravel(np.ones(original_shape)*step)) ++ for step in steps]) + if f_del.size != h.size: + raise ValueError('fun did not return data of correct size ' + + '(it must be vectorized)') +@@ -683,6 +683,7 @@ + >>> np.allclose(fd(1), 2.71828183) + True + ++ >>> fd = nd.Derivative(np.exp) + >>> d2 = fd([1, 2]) + >>> np.allclose(d2, [ 2.71828183, 7.3890561 ]) + True +@@ -781,7 +780,7 @@ + inv_sr = 1.0 / step_ratio + offset = [1, 1, 2, 2, 4, 1, 3][parity] + c0 = [1.0, 1.0, 1.0, 2.0, 24.0, 1.0, 6.0][parity] +- c = c0/misc.factorial(np.arange(offset, step * nterms + offset, step)) ++ c = c0/special.factorial(np.arange(offset, step * nterms + offset, step)) + [i, j] = np.ogrid[0:nterms, 0:nterms] + return np.atleast_2d(c[j] * inv_sr ** (i * (step * j + offset))) + +diff -Naur bumps-0.7.11/doc/conf.py bumps-0.7.11_patched/doc/conf.py +--- bumps-0.7.11/doc/conf.py 2019-07-22 11:01:21.761248474 +0200 ++++ bumps-0.7.11_patched/doc/conf.py 2018-09-24 21:06:44.000000000 +0200 +@@ -51,8 +51,8 @@ + #'sphinx.ext.jsmath', + 'sphinx.ext.mathjax', + #'only_directives', ++ 'matplotlib.sphinxext.mathmpl', ++ #'matplotlib.sphinxext.only_directives', +- #'matplotlib.sphinxext.mathmpl', +- 'matplotlib.sphinxext.only_directives', + 'matplotlib.sphinxext.plot_directive', + #'inheritance_diagram', + 'dollarmath', +diff -Naur bumps-0.7.11/doc/Makefile bumps-0.7.11_patched/doc/Makefile +--- bumps-0.7.11/doc/Makefile 2019-07-22 11:00:58.871022945 +0200 ++++ bumps-0.7.11_patched/doc/Makefile 2018-09-24 21:06:44.000000000 +0200 +@@ -4,7 +4,7 @@ + # You can set these variables from the command line. + PYTHON ?= python + SPHINXOPTS = ++SPHINXBUILD = sphinx-build +-SPHINXBUILD = $(PYTHON) -m sphinx.__init__ + #sphinx-build + PAPER = + BUILDDIR = _build +@@ -12,7 +12,7 @@ + # Internal variables. + PAPEROPT_a4 = -D latex_paper_size=a4 + PAPEROPT_letter = -D latex_paper_size=letter ++ALLSPHINXOPTS = -a $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + + .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp \ + devhelp epub latex pdf text man changes linkcheck doctest |