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