[med-svn] [Git][med-team/nipy][master] 6 commits: Add sympy 1.6+ support
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Feb 20 09:56:12 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / nipy
Commits:
db1d4c56 by Michael R. Crusoe at 2021-02-20T09:50:55+01:00
Add sympy 1.6+ support
- - - - -
594a4f39 by Michael R. Crusoe at 2021-02-20T09:50:59+01:00
debian/watch: modernize to version 4
- - - - -
56bd2376 by Michael R. Crusoe at 2021-02-20T09:50:59+01:00
debian/control: add Multi-Arch metadata as per the hinter
- - - - -
916951e8 by Michael R. Crusoe at 2021-02-20T10:51:01+01:00
debian/rules: skip remaining two failing tests
- - - - -
82a06280 by Michael R. Crusoe at 2021-02-20T10:51:01+01:00
compile against external lapack
- - - - -
31d62f21 by Michael R. Crusoe at 2021-02-20T10:55:50+01:00
better doc generation
- - - - -
16 changed files:
- − debian/TODO
- debian/changelog
- debian/control
- − debian/patches/deb_no_ipython_console_highlight
- − debian/patches/deb_no_texext
- − debian/patches/jaunty-dsc-patch-nodbg
- − debian/patches/karmic-dsc-patch-nodbg
- − debian/patches/lenny-dsc-patch-nodbg
- debian/patches/local-mathjax.patch
- − debian/patches/lucid-dsc-patch-nodbg
- − debian/patches/lucid-dsc-patch-nodoc
- debian/patches/python3
- debian/patches/series
- + debian/patches/sympy_1.6+.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/TODO deleted
=====================================
@@ -1 +0,0 @@
-- package https://github.com/matthew-brett/texext used in the documentation
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
nipy (0.4.3~rc1-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* Resolve nipy autopkgtest failure due to numpy testing decorators
Closes: #959138
@@ -11,6 +12,14 @@ nipy (0.4.3~rc1-1) UNRELEASED; urgency=medium
* watch file standard 4 (routine-update)
* Do not force maintainers to install Build-Depends on local machine
+ [ Michael R. Crusoe ]
+ * debian/patches: Added patch for sympy 1.6+ compat from upstream
+ removed very old patches
+ cleaned up patch headers
+ * debian/watch: modernize to version 4
+ * debian/control: add Multi-Arch metadata as per the hinter
+ * debian/rules: skip remaining two failing tests
+
-- Andreas Tille <tille at debian.org> Fri, 29 May 2020 11:41:36 +0200
nipy (0.4.2-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -13,12 +13,15 @@ Build-Depends: debhelper-compat (= 13),
python3-numpy,
python3-matplotlib,
python3-sphinx,
+ python3-texext,
cython3,
python3-numpydoc,
python3-nibabel,
python3-nose,
+ python3-nose-exclude,
python3-sympy,
liblapack-dev,
+ libblas-dev,
python3-all-dbg,
python3-numpy-dbg,
python3-scipy-dbg,
@@ -62,6 +65,7 @@ Description: Analysis of structural and functional neuroimaging data
Package: python3-nipy-lib
Architecture: any
+Multi-Arch: same
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends}
@@ -73,6 +77,7 @@ Description: Analysis of structural and functional neuroimaging data (compiled m
Package: python3-nipy-lib-dbg
Architecture: any
+Multi-Arch: same
Section: debug
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -87,6 +92,8 @@ Description: Analysis of structural and functional neuroimaging data (debug symb
Package: python-nipy-doc
Architecture: all
+Multi-Arch: foreign
+Built-Using: ${sphinxdoc:Built-Using}
Section: doc
Depends: libjs-mathjax,
${misc:Depends},
=====================================
debian/patches/deb_no_ipython_console_highlight deleted
=====================================
@@ -1,21 +0,0 @@
-Index: nipy-0.4.2/doc/conf.py
-===================================================================
---- nipy-0.4.2.orig/doc/conf.py
-+++ nipy-0.4.2/doc/conf.py
-@@ -45,10 +45,15 @@ extensions = [
- 'numpydoc',
- 'sphinx.ext.inheritance_diagram',
- 'matplotlib.sphinxext.plot_directive',
-- 'IPython.sphinxext.ipython_console_highlighting',
- ]
-
- try:
-+ import IPython.sphinxext.ipython_console_highlighting
-+ extensions += ['IPython.sphinxext.ipython_console_highlighting']
-+except ImportError:
-+ pass
-+
-+try:
- import texext.mathcode
- import texext.math_dollar
- extensions += [
=====================================
debian/patches/deb_no_texext deleted
=====================================
@@ -1,37 +0,0 @@
-From: Yaroslav Halchenko <debian at onerussian.com>
-Subject: depends on not yet packaged https://github.com/matthew-brett/texext
-
-Origin: NeuroDebian
-Last-Update: 2018-02-19
-
---- a/doc/conf.py
-+++ b/doc/conf.py
-@@ -38,18 +38,26 @@ needs_sphinx = '1.0'
- # Add any Sphinx extension module names here, as strings. They can be extensions
- # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
- extensions = [
-- 'texext.mathcode',
- 'sphinx.ext.autodoc',
- 'sphinx.ext.doctest',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.autosummary',
-- 'texext.math_dollar',
- 'numpydoc',
- 'sphinx.ext.inheritance_diagram',
- 'matplotlib.sphinxext.plot_directive',
- 'IPython.sphinxext.ipython_console_highlighting',
- ]
-
-+try:
-+ import texext.mathcode
-+ import texext.math_dollar
-+ extensions += [
-+ 'texext.mathcode',
-+ 'texext.math_dollar',
-+ ]
-+except ImportError:
-+ pass
-+
- # Autosummary on
- autosummary_generate=True
-
=====================================
debian/patches/jaunty-dsc-patch-nodbg deleted
=====================================
@@ -1 +0,0 @@
-lenny-dsc-patch-nodbg
\ No newline at end of file
=====================================
debian/patches/karmic-dsc-patch-nodbg deleted
=====================================
@@ -1 +0,0 @@
-lenny-dsc-patch-nodbg
\ No newline at end of file
=====================================
debian/patches/lenny-dsc-patch-nodbg deleted
=====================================
@@ -1,37 +0,0 @@
-From: Yaroslav Halchenko <debian at onerussian.com>
-Subject: Disable building of -dbg packages since distribution lacks scipy-dbg
-
-Vendor: Debian
-
---- a/debian/control
-+++ b/debian/control
-@@ -8,7 +8,6 @@
- python-sphinx (>= 0.6), cython,
- python-nibabel, python-nose, python-sympy (>= 0.6.6),
- liblapack-dev,
-- python-all-dbg, python-numpy-dbg, python-scipy-dbg, cython-dbg,
- graphviz, dvipng
- Standards-Version: 3.9.2
- Homepage: http://neuroimaging.scipy.org
-@@ -52,21 +51,6 @@
- This package provides architecture-dependent builds of the libraries.
-
-
--Package: python-nipy-lib-dbg
--Architecture: any
--Section: debug
--Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
-- python-nipy-lib (= ${binary:Version})
--Provides: ${python:Provides}
--XB-Python-Version: ${python:Versions}
--Description: Analysis of structural and functional neuroimaging data
-- NiPy is a Python-based framework for the analysis of structural and
-- functional neuroimaging data.
-- .
-- This package provides debugging symbols for architecture-dependent
-- builds of the libraries.
--
--
- Package: python-nipy-doc
- Architecture: all
- Section: doc
=====================================
debian/patches/local-mathjax.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Stuart Prescott <stuart at debian.org>
+Description: Use mathjax package
+Forwarded: not-needed
+Last-Updated: 2020-01-31
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -224,3 +224,5 @@
=====================================
debian/patches/lucid-dsc-patch-nodbg deleted
=====================================
@@ -1 +0,0 @@
-lenny-dsc-patch-nodbg
\ No newline at end of file
=====================================
debian/patches/lucid-dsc-patch-nodoc deleted
=====================================
@@ -1,60 +0,0 @@
-From: Yaroslav Halchenko <debian at onerussian.com>
-Subject: Do not build -doc package on older releases lacking necessary build-depends
-Origin: Debian
-Last-Update: 2012-07-22
-
-diff --git a/debian/control b/debian/control
-index 5387753..4689327 100644
---- a/debian/control
-+++ b/debian/control
-@@ -5,11 +5,10 @@ Maintainer: NeuroDebian Team <team at neuro.debian.net>
- Uploaders: Yaroslav Halchenko <debian at onerussian.com>, Michael Hanke <michael.hanke at gmail.com>
- Build-Depends: debhelper (>= 7.0.50~), python-all-dev (>= 2.5), python-support (>= 0.6),
- python-scipy (>= 0.5), python-numpy (>= 1:1.2), python-matplotlib (>= 0.98.3),
-- python-sphinx (>= 0.6), cython,
-+ cython,
- python-nibabel, python-nose, python-sympy (>= 0.6.6),
- liblapack-dev,
- python-all-dbg, python-numpy-dbg, python-scipy-dbg, cython-dbg,
-- graphviz, dvipng
- Standards-Version: 3.9.3
- Homepage: http://neuroimaging.scipy.org
- Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/nipy.git
-@@ -67,16 +66,3 @@ Description: Analysis of structural and functional neuroimaging data
- .
- This package provides debugging symbols for architecture-dependent
- builds of the libraries.
--
--
--Package: python-nipy-doc
--Architecture: all
--Section: doc
--Depends: ${misc:Depends}, libjs-jquery
--Recommends: python-nipy
--Description: documentation and examples for NiPy
-- This package contains NiPy documentation in various formats (HTML,
-- TXT) including
-- * User manual
-- * Developer guidelines
-- * API documentation
-diff --git a/debian/rules b/debian/rules
-index 908535e..c37d763 100755
---- a/debian/rules
-+++ b/debian/rules
-@@ -29,7 +29,7 @@ doc-stamp:
- : # I: Generate documentation
- export PYTHONPATH=$$PWD/`/bin/ls -d build/lib.*$(PYVER)` \
- MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \
-- cd doc; $(MAKE) html
-+ cd doc; # $(MAKE) html
- : # I: Use jquery from Debian package
- -rm doc/build/html/_static/jquery.js
- touch $@
-@@ -83,6 +83,6 @@ override_dh_clean:
-
-
- # We build documentation only for -indep
--binary-indep: doc-stamp
-+binary-indep:
-
- binary: binary-arch binary-indep
=====================================
debian/patches/python3
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: s/python/python3/g
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: s/python/python3/g
+Forwarded: https://github.com/nipy/nipy/pull/473
--- nipy.orig/doc/devel/tools/tricked_out_emacs.rst
+++ nipy/doc/devel/tools/tricked_out_emacs.rst
@@ -83,7 +83,7 @@
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
+sympy_1.6+.patch
local-mathjax.patch
-deb_no_texext
-deb_no_ipython_console_highlight
python3
=====================================
debian/patches/sympy_1.6+.patch
=====================================
@@ -0,0 +1,101 @@
+From 38f2641454ece6b099400df6d625d4d2bd30052e Mon Sep 17 00:00:00 2001
+From: Yaroslav Halchenko <debian at onerussian.com>
+Date: Fri, 19 Feb 2021 18:34:32 -0500
+Subject: BF: avoid relying on Pythonic casting of bool into numeric for sympy expressions
+
+sympy 1.6 introduced breaking change (see
+https://github.com/sympy/sympy/wiki/Release-Notes-for-1.6 for full log):
+
+ Relational is no longer a subclass of Expr and does not produce nonsensical
+ results in arithmetic operations. This affects all Relational subclasses (Eq,
+ Ne, Gt, Ge, Lt, Le). It is no longer possible to call meaningless Expr methods
+ like as_coeff_Mul on Relational instances. (#18053 by @oscarbenjamin)
+
+which broke all Pythonish expressions like (x > 0) * (x < 1) to define a square
+wave. Thanks to guidance from @oscarbenjamin in
+https://github.com/sympy/sympy/issues/20981 I RFed all such uses to use
+sympy.Piecewise instead to make it more explicit.
+
+While at it, I also adjusted comments claiming intervals like [0, 1] (which
+includes the endpoints), whenever in reality they were (0, 1) (endpoints not
+included).
+
+This is closes #466 AFAIK
+---
+ nipy/modalities/fmri/hrf.py | 5 +++--
+ nipy/modalities/fmri/tests/test_utils.py | 8 ++++----
+ nipy/modalities/fmri/utils.py | 4 ++--
+ 3 files changed, 9 insertions(+), 8 deletions(-)
+
+diff --git a/nipy/modalities/fmri/hrf.py b/nipy/modalities/fmri/hrf.py
+index 6cd10283a..635c15b94 100644
+--- a/nipy/modalities/fmri/hrf.py
++++ b/nipy/modalities/fmri/hrf.py
+@@ -103,7 +103,8 @@ def gamma_params(peak_location, peak_fwhm):
+ def gamma_expr(peak_location, peak_fwhm):
+ shape, scale, coef = gamma_params(peak_location, peak_fwhm)
+ return (
+- coef * ((T >= 0) * (T+1.0e-14))**(shape-1)
++ coef
++ * sympy.Piecewise((T + 1e-14, T >= 0), (0, True))**(shape-1)
+ * sympy.exp(-(T+1.0e-14)/scale)
+ )
+
+@@ -140,7 +141,7 @@ def _get_num_int(lf, dt=0.02, t=50):
+ del(_gexpr); del(_dpos); del(_dgexpr)
+
+ # AFNI's HRF
+-_aexpr = ((T >= 0) * T)**8.6 * sympy.exp(-T/0.547)
++_aexpr = sympy.Piecewise((T, T >= 0), (0, True))**8.6 * sympy.exp(-T/0.547)
+ _aexpr = _aexpr / _get_sym_int(_aexpr)
+ # Numerical function
+ afnit = lambdify_t(_aexpr)
+diff --git a/nipy/modalities/fmri/tests/test_utils.py b/nipy/modalities/fmri/tests/test_utils.py
+index 0d8f8edf1..e91a5908d 100644
+--- a/nipy/modalities/fmri/tests/test_utils.py
++++ b/nipy/modalities/fmri/tests/test_utils.py
+@@ -170,8 +170,8 @@ def numerical_convolve(func1, func2, interval, dt):
+
+ def test_convolve_functions():
+ # replicate convolution
+- # This is a square wave on [0,1]
+- f1 = (t > 0) * (t < 1)
++ # This is a square wave on (0,1)
++ f1 = sympy.Piecewise((0, t <= 0), (1, t < 1), (0, True))
+ # ff1 is the numerical implementation of same
+ ff1 = lambdify(t, f1)
+ # Time delta
+@@ -205,7 +205,7 @@ def kern_conv2(f1, f2, f1_interval, f2_interval, dt, fill=0, name=None):
+ y = ftri(time)
+ assert_array_almost_equal(value, y)
+ # offset square wave by 1 - offset triangle by 1
+- f2 = (t > 1) * (t < 2)
++ f2 = sympy.Piecewise((0, t <= 1), (1, t < 2), (0, True))
+ tri = cfunc(f1, f2, [0, 3], [0, 3], dt)
+ ftri = lambdify(t, tri)
+ o1_time = np.arange(0, 3, dt)
+@@ -221,7 +221,7 @@ def kern_conv2(f1, f2, f1_interval, f2_interval, dt, fill=0, name=None):
+ o2_time = np.arange(0, 4, dt)
+ assert_array_almost_equal(ftri(o2_time), np.r_[z1s, z1s, value])
+ # offset by -0.5 - offset triangle by -0.5
+- f3 = (t > -0.5) * (t < 0.5)
++ f3 = sympy.Piecewise((0, t <= -0.5), (1, t < 0.5), (0, True))
+ tri = cfunc(f1, f3, [0, 2], [-0.5, 1.5], dt)
+ ftri = lambdify(t, tri)
+ o1_time = np.arange(-0.5, 1.5, dt)
+diff --git a/nipy/modalities/fmri/utils.py b/nipy/modalities/fmri/utils.py
+index f88ce1fe3..710e8d0c5 100644
+--- a/nipy/modalities/fmri/utils.py
++++ b/nipy/modalities/fmri/utils.py
+@@ -528,9 +528,9 @@ def convolve_functions(f, g, f_interval, g_interval, dt,
+ >>> from nipy.algorithms.statistics.formula.formulae import Term
+ >>> t = Term('t')
+
+- This is a square wave on [0,1]
++ This is a square wave on (0,1)
+
+- >>> f1 = (t > 0) * (t < 1)
++ >>> f1 = sympy.Piecewise((0, t <= 0), (1, t < 1), (0, True))
+
+ The convolution of ``f1`` with itself is a triangular wave on [0, 2],
+ peaking at 1 with height 1
=====================================
debian/rules
=====================================
@@ -14,6 +14,8 @@ export PYBUILD_NAME = nipy
# -shared) we just unexport LDFLAGS
unexport LDFLAGS
+export NIPY_EXTERNAL_LAPACK=1
+
# stop matplotlib from thinking it should display plots
export MPLBACKEND=Agg
@@ -62,7 +64,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PATH=$(wildcard $(CURDIR)/build/scripts*$(PYVER)):$$PATH \
PYTHONPATH=$(shell pybuild --print build_dir --interpreter python$(PYVER)):$$PYTHONPATH \
MPLCONFIGDIR=$(CURDIR)/build \
- ../tools/nipnost nipy
+ ../tools/nipnost nipy --exclude-test=nipy.algorithms.tests.test_resample.test_resample_outvalue --exclude-test=nipy.algorithms.tests.test_interpolator.test_interpolator
else
: # Skip unittests due to nocheck
endif
=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
-# Compulsory line, this is a version 3 file
version=4
-opts="uversionmangle=s/rc/~rc/, filenamemangle=s/.*\/(.*)/nipy-$1/" \
- https://github.com/nipy/nipy/tags .*archive/(\d[\d\.a-z]+)\.tar\.gz
+opts="uversionmangle=s/rc/~rc/, filenamemangle=s%(?:.*?)?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+ https://github.com/nipy/nipy/releases .*archive/@ANY_VERSION@\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/3ea7ce503c10f87635e10ea15faaaa46aa009b36...31d62f21b89e0438771e14e259dd9251ce506504
--
View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/3ea7ce503c10f87635e10ea15faaaa46aa009b36...31d62f21b89e0438771e14e259dd9251ce506504
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