From f66617c5702b29e144404c42267aae9342370215 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 25 Apr 2020 17:47:37 -0700 Subject: [PATCH 01/20] FIX import of decorators for newer versions of numpy --- nipy/algorithms/clustering/tests/test_vmm.py | 6 +++++- nipy/algorithms/diagnostics/tests/test_screen.py | 8 +++++++- nipy/testing/__init__.py | 7 +++++++ nipy/tests/test_scripts.py | 8 +++++++- 4 files changed, 26 insertions(+), 3 deletions(-) diff --git a/nipy/algorithms/clustering/tests/test_vmm.py b/nipy/algorithms/clustering/tests/test_vmm.py index 1223808f5b..8c80d2a780 100644 --- a/nipy/algorithms/clustering/tests/test_vmm.py +++ b/nipy/algorithms/clustering/tests/test_vmm.py @@ -13,7 +13,11 @@ select_vmm_cv) from nose.tools import assert_true, assert_equal -from numpy.testing import decorators +try: + from numpy.testing import decorators +except ImportError: + from numpy.testing import dec + decorators = dec from nibabel.optpkg import optional_package diff --git a/nipy/algorithms/diagnostics/tests/test_screen.py b/nipy/algorithms/diagnostics/tests/test_screen.py index f9e43682c5..89b9cf252a 100644 --- a/nipy/algorithms/diagnostics/tests/test_screen.py +++ b/nipy/algorithms/diagnostics/tests/test_screen.py @@ -23,7 +23,13 @@ from nose.tools import (assert_true, assert_false, assert_equal, assert_raises) from numpy.testing import (assert_array_equal, assert_array_almost_equal, - assert_almost_equal, decorators) + assert_almost_equal) + +try: + from numpy.testing import decorators +except ImportError: + from numpy.testing import dec + decorators = dec from nipy.testing import funcfile from nipy.testing.decorators import needs_mpl_agg diff --git a/nipy/testing/__init__.py b/nipy/testing/__init__.py index c044b6acb4..96bb82d517 100644 --- a/nipy/testing/__init__.py +++ b/nipy/testing/__init__.py @@ -36,6 +36,13 @@ anatfile = os.path.join(basedir, 'anatomical.nii.gz') from numpy.testing import * +# Re import decorators/dec depending on numpy's version +try: + from numpy.testing import decorators +except ImportError: + from numpy.testing import dec + decorators = dec + # Overwrites numpy.testing.Tester from .nosetester import NipyNoseTester as Tester test = Tester().test diff --git a/nipy/tests/test_scripts.py b/nipy/tests/test_scripts.py index cd96d870b1..cea7beccb0 100644 --- a/nipy/tests/test_scripts.py +++ b/nipy/tests/test_scripts.py @@ -19,7 +19,13 @@ from nose.tools import assert_true, assert_false, assert_equal, assert_raises from ..testing import funcfile -from numpy.testing import decorators, assert_almost_equal +from numpy.testing import assert_almost_equal + +try: + from numpy.testing import decorators +except ImportError: + from numpy.testing import dec + decorators = dec from nipy.testing.decorators import make_label_dec From dbb05bb6d1e8a3be465b67b8884b7f2eba1eaef9 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 25 Apr 2020 17:57:46 -0700 Subject: [PATCH 02/20] FIX couple of missing numpy.testing --- nipy/externals/transforms3d/tests/test_quaternions.py | 2 +- nipy/testing/decorators.py | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/nipy/externals/transforms3d/tests/test_quaternions.py b/nipy/externals/transforms3d/tests/test_quaternions.py index 9d5cd554d9..465651f984 100644 --- a/nipy/externals/transforms3d/tests/test_quaternions.py +++ b/nipy/externals/transforms3d/tests/test_quaternions.py @@ -8,7 +8,7 @@ # Recent (1.2) versions of numpy have this decorator try: from numpy.testing.decorators import slow -except ImportError: +except (ImportError, ModuleNotFoundError): def slow(t): t.slow = True return t diff --git a/nipy/testing/decorators.py b/nipy/testing/decorators.py index 5d8be8b4ec..e7c7012a6d 100644 --- a/nipy/testing/decorators.py +++ b/nipy/testing/decorators.py @@ -8,7 +8,10 @@ from __future__ import print_function from __future__ import absolute_import -from numpy.testing.decorators import * +try: + from numpy.testing.decorators import * +except ModuleNotFoundError: + from numpy.testing._private.decorators import * from nipy.utils import templates, example_data, DataError From a7d502b7d53477d6764314bbe10a105521bbfa6d Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 25 Apr 2020 19:04:20 -0700 Subject: [PATCH 03/20] FIX doctest for nosetester and sympy's implemented functions --- nipy/fixes/numpy/testing/nosetester.py | 2 +- nipy/modalities/fmri/tests/test_aliases.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nipy/fixes/numpy/testing/nosetester.py b/nipy/fixes/numpy/testing/nosetester.py index 4be245dbe2..355ab0d50b 100644 --- a/nipy/fixes/numpy/testing/nosetester.py +++ b/nipy/fixes/numpy/testing/nosetester.py @@ -21,7 +21,7 @@ def get_package_name(filepath): Examples -------- - >>> np.testing.nosetester.get_package_name('nonsense') + >>> get_package_name('nonsense') 'numpy' """ diff --git a/nipy/modalities/fmri/tests/test_aliases.py b/nipy/modalities/fmri/tests/test_aliases.py index 9e59323431..38b35cdf40 100644 --- a/nipy/modalities/fmri/tests/test_aliases.py +++ b/nipy/modalities/fmri/tests/test_aliases.py @@ -44,7 +44,7 @@ def test_implemented_function(): func = sympy.Function('myfunc') assert_false(hasattr(func, '_imp_')) f = implemented_function(func, lambda x: 2*x) - assert_true(hasattr(func, '_imp_')) + assert_true(hasattr(f, '_imp_')) def test_lambdify(): From 063ee60a7b251899a0c506eb486ce20534af41d8 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 25 Apr 2020 19:17:11 -0700 Subject: [PATCH 04/20] FIX also fix scipy's misc/special deprecation --- nipy/algorithms/statistics/rft.py | 5 ++++- nipy/algorithms/statistics/tests/test_rft.py | 5 ++++- nipy/labs/group/permutation_test.py | 7 +++++-- 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/nipy/algorithms/statistics/rft.py b/nipy/algorithms/statistics/rft.py index 286b38a8d5..b214ea780f 100644 --- a/nipy/algorithms/statistics/rft.py +++ b/nipy/algorithms/statistics/rft.py @@ -20,7 +20,10 @@ from numpy.linalg import pinv from scipy import stats -from scipy.misc import factorial +try: + from scipy.misc import factorial +except ImportError: + from scipy.special import factorial from scipy.special import gamma, gammaln, beta, hermitenorm # Legacy repr printing from numpy. diff --git a/nipy/algorithms/statistics/tests/test_rft.py b/nipy/algorithms/statistics/tests/test_rft.py index d2fa197042..2d432d34c9 100644 --- a/nipy/algorithms/statistics/tests/test_rft.py +++ b/nipy/algorithms/statistics/tests/test_rft.py @@ -6,7 +6,10 @@ from scipy.special import gammaln, hermitenorm import scipy.stats -from scipy.misc import factorial +try: + from scipy.misc import factorial +except ImportError: + from scipy.special import factorial from .. import rft diff --git a/nipy/labs/group/permutation_test.py b/nipy/labs/group/permutation_test.py index 2449259400..9035de90f0 100644 --- a/nipy/labs/group/permutation_test.py +++ b/nipy/labs/group/permutation_test.py @@ -6,7 +6,10 @@ # Third-party imports import numpy as np -import scipy.misc as sm +try: + from scipy.misc import comb +except ImportError: + from scipy.special import comb import warnings # Our own imports @@ -374,7 +377,7 @@ def calibrate(self, nperms=DEF_NPERMS, clusters=None, elif self.nsamples == 2: n1,p = self.data1.shape[self.axis], self.data1.shape[1-self.axis] n2 = self.data2.shape[self.axis] - max_nperms = sm.comb(n1+n2,n1,exact=1) + max_nperms = comb(n1+n2,n1,exact=1) data = np.concatenate((self.data1,self.data2), self.axis) if self.vardata1 is not None: vardata = np.concatenate((self.vardata1,self.vardata2), self.axis) From 3949e64f9bc4f95666ba1fc1cf090b25cbfd8c8e Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sun, 26 Apr 2020 09:47:25 -0700 Subject: [PATCH 05/20] FIX replace ModuleNotFoundError with ImportError for py <= 3.5 --- nipy/externals/transforms3d/tests/test_quaternions.py | 2 +- nipy/testing/decorators.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nipy/externals/transforms3d/tests/test_quaternions.py b/nipy/externals/transforms3d/tests/test_quaternions.py index 465651f984..9d5cd554d9 100644 --- a/nipy/externals/transforms3d/tests/test_quaternions.py +++ b/nipy/externals/transforms3d/tests/test_quaternions.py @@ -8,7 +8,7 @@ # Recent (1.2) versions of numpy have this decorator try: from numpy.testing.decorators import slow -except (ImportError, ModuleNotFoundError): +except ImportError: def slow(t): t.slow = True return t diff --git a/nipy/testing/decorators.py b/nipy/testing/decorators.py index e7c7012a6d..d3b1ef07bd 100644 --- a/nipy/testing/decorators.py +++ b/nipy/testing/decorators.py @@ -10,7 +10,7 @@ try: from numpy.testing.decorators import * -except ModuleNotFoundError: +except ImportError: from numpy.testing._private.decorators import * from nipy.utils import templates, example_data, DataError From 02124d772d6f5ea16430bb33268eebbc8391faa4 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sun, 26 Apr 2020 10:09:52 -0700 Subject: [PATCH 06/20] FIX travis check if exist before installing --- .travis.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0b7fd22d78..10e5e967c9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -94,7 +94,9 @@ before_install: - if [ -n "$PRE_DEPENDS" ]; then pip install $EXTRA_PIP_FLAGS $PRE_DEPENDS; fi - - pip install $EXTRA_PIP_FLAGS $DEPENDS + - if [ -n "$DEPENDS" ]; then + pip install $EXTRA_PIP_FLAGS $DEPENDS; + fi - if [ "${COVERAGE}" == "1" ]; then pip install coverage; pip install coveralls codecov; From ea1dd6804cd1bf25e3a9a0365208c4caed0f7328 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Mon, 27 Apr 2020 09:34:50 -0700 Subject: [PATCH 07/20] FIX require sphinx <3.0 for docs --- doc-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc-requirements.txt b/doc-requirements.txt index 8040e1fcd0..8bf2f27751 100644 --- a/doc-requirements.txt +++ b/doc-requirements.txt @@ -1,7 +1,7 @@ # Requirements for building docs # Check these dependencies against doc/conf.py -r dev-requirements.txt -sphinx>=1.0 +sphinx>=1.0,<3.0 numpydoc matplotlib texext From d5aece6e206cf10a909c6678671c4d2978f2dd16 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 22 May 2020 14:24:28 -0700 Subject: [PATCH 08/20] FIX use sympy.Dummy instead of sympy.symbol.Dummy --- nipy/algorithms/statistics/formula/formulae.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipy/algorithms/statistics/formula/formulae.py b/nipy/algorithms/statistics/formula/formulae.py index e1cfdba5bf..ed2e5896fe 100644 --- a/nipy/algorithms/statistics/formula/formulae.py +++ b/nipy/algorithms/statistics/formula/formulae.py @@ -267,10 +267,10 @@ def __mul__(self, other): return sympy.Symbol.__mul__(self, other) -class Beta(sympy.symbol.Dummy): +class Beta(sympy.Dummy): ''' A symbol tied to a Term `term` ''' def __new__(cls, name, term): - new = sympy.symbol.Dummy.__new__(cls, name) + new = sympy.Dummy.__new__(cls, name) new._term = term return new From 5e4120229fd6c88100fe6f6a9e4f0eed94b3e7b9 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 11:07:05 -0700 Subject: [PATCH 09/20] MNT remove obsolete python 3.5, add 3.7, 3.8 --- .travis.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index 0b7fd22d78..fc58517342 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,9 +22,9 @@ env: - INSTALL_TYPE="pip" python: - - 3.4 - - 3.5 - 3.6 + - 3.7 + - 3.8 matrix: include: @@ -38,7 +38,7 @@ matrix: - PRE_DEPENDS="numpy==1.6.0" - DEPENDS="scipy==0.9.0 sympy==0.7.0 nibabel==1.2.0" # Test compiling against external lapack - - python: 3.4 + - python: 3.6 env: - NIPY_EXTERNAL_LAPACK=1 addons: @@ -59,17 +59,17 @@ matrix: - INSTALL_TYPE=requirements - DEPENDS= # test 3.5 against pre-release builds of everything - - python: 3.5 + - python: 3.6 env: - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS" # test python setup.py install - - python: 3.5 + - python: 3.6 env: - INSTALL_TYPE=setup - - python: 3.5 + - python: 3.6 env: - INSTALL_TYPE="pip_e" - - python: 3.5 + - python: 3.6 env: - DOC_BUILD=1 addons: From 5c6d00ed78a0a70aedb45e146c74c937148d3fe8 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 11:28:54 -0700 Subject: [PATCH 10/20] FIX sympy version --- .travis.yml | 3 ++- requirements.txt | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 8b48bf927a..c6d8f66db9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -133,7 +133,8 @@ script: pip install -r doc-requirements.txt # Work round bug in Sympy atoms docstring as of 1.1.0 # https://github.com/sympy/sympy/pull/12900 - pip install git+https://github.com/sympy/sympy.git + # pip install git+https://github.com/sympy/sympy.git + pip install "sympy<1.6" make html-stamp pdf-stamp else # Change into an innocuous directory and find tests from installation diff --git a/requirements.txt b/requirements.txt index 61e7e7284c..e2219b040e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ # See nipy/info.py for requirement definitions numpy>=1.6.0 scipy>=0.9.0 -sympy>=0.7.0 +sympy>=0.7.0,<1.6 nibabel>=1.2.0 From a49a734d85cb328be57385c8bb5cc1690f79eb78 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 11:40:37 -0700 Subject: [PATCH 11/20] FIX sympy requirement --- .travis.yml | 2 +- nipy/info.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index c6d8f66db9..e20fcc7ba5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,7 +14,7 @@ cache: env: global: - - DEPENDS="numpy scipy sympy matplotlib nibabel" + - DEPENDS="numpy scipy sympy<1.6 matplotlib nibabel" - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com" - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS" diff --git a/nipy/info.py b/nipy/info.py index e93c00d09e..9c7dfe9d6b 100644 --- a/nipy/info.py +++ b/nipy/info.py @@ -170,7 +170,7 @@ MICRO = _version_micro ISRELEASE = _version_extra == '' VERSION = __version__ -REQUIRES = ["numpy", "scipy", "sympy", "nibabel"] +REQUIRES = ["numpy", "scipy", "sympy<1.6", "nibabel"] STATUS = 'beta' # Versions and locations of optional data packages From 31d93e51f077347229b1b091394bcb411cfcc2ba Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 11:46:19 -0700 Subject: [PATCH 12/20] Try this way for sympy requirements --- nipy/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipy/info.py b/nipy/info.py index 9c7dfe9d6b..78363858c1 100644 --- a/nipy/info.py +++ b/nipy/info.py @@ -170,7 +170,7 @@ MICRO = _version_micro ISRELEASE = _version_extra == '' VERSION = __version__ -REQUIRES = ["numpy", "scipy", "sympy<1.6", "nibabel"] +REQUIRES = ["numpy", "scipy", "sympy(<1.6)", "nibabel"] STATUS = 'beta' # Versions and locations of optional data packages From d771f777364a28d1705c863d58b16405daf160e1 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 11:54:53 -0700 Subject: [PATCH 13/20] FIX remove deprecated kwarg for matplotlib.use --- nipy/labs/viz_tools/test/test_activation_maps.py | 8 ++++---- nipy/labs/viz_tools/test/test_cm.py | 6 +++--- nipy/labs/viz_tools/test/test_slicers.py | 4 ++-- nipy/testing/decorators.py | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/nipy/labs/viz_tools/test/test_activation_maps.py b/nipy/labs/viz_tools/test/test_activation_maps.py index 069cc7b007..915a5e0394 100644 --- a/nipy/labs/viz_tools/test/test_activation_maps.py +++ b/nipy/labs/viz_tools/test/test_activation_maps.py @@ -10,7 +10,7 @@ try: import matplotlib as mp # Make really sure that we don't try to open an Xserver connection. - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') except ImportError: @@ -28,7 +28,7 @@ def test_demo_plot_map(): # This is only a smoke test - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') demo_plot_map() @@ -38,7 +38,7 @@ def test_demo_plot_map(): def test_plot_anat(): # This is only a smoke test - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') data = np.zeros((20, 20, 20)) @@ -85,7 +85,7 @@ def test_plot_map_empty(): # Test that things don't crash when we give a map with nothing above # threshold # This is only a smoke test - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') data = np.zeros((20, 20, 20)) diff --git a/nipy/labs/viz_tools/test/test_cm.py b/nipy/labs/viz_tools/test/test_cm.py index 9c4c434990..203df3e795 100644 --- a/nipy/labs/viz_tools/test/test_cm.py +++ b/nipy/labs/viz_tools/test/test_cm.py @@ -8,7 +8,7 @@ try: import matplotlib as mp # Make really sure that we don't try to open an Xserver connection. - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') except ImportError: @@ -19,14 +19,14 @@ def test_dim_cmap(): # This is only a smoke test - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl dim_cmap(pl.cm.jet) def test_replace_inside(): # This is only a smoke test - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') replace_inside(pl.cm.jet, pl.cm.hsv, .2, .8) diff --git a/nipy/labs/viz_tools/test/test_slicers.py b/nipy/labs/viz_tools/test/test_slicers.py index 80df02dddd..33bcffc3b0 100644 --- a/nipy/labs/viz_tools/test/test_slicers.py +++ b/nipy/labs/viz_tools/test/test_slicers.py @@ -7,7 +7,7 @@ try: import matplotlib as mp # Make really sure that we don't try to open an Xserver connection. - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') except ImportError: @@ -25,7 +25,7 @@ def test_demo_ortho_slicer(): # conditioned on presence of MNI templated if not find_mni_template(): raise nose.SkipTest("MNI Template is absent for the smoke test") - mp.use('svg', warn=False) + mp.use('svg') import pylab as pl pl.switch_backend('svg') demo_ortho_slicer() diff --git a/nipy/testing/decorators.py b/nipy/testing/decorators.py index d3b1ef07bd..addb357079 100644 --- a/nipy/testing/decorators.py +++ b/nipy/testing/decorators.py @@ -127,7 +127,7 @@ def needs_mpl_agg(func): import matplotlib.pyplot as plt from nose.tools import make_decorator def agg_func(*args, **kwargs): - matplotlib.use('agg', warn=False) + matplotlib.use('agg') plt.switch_backend('agg') return func(*args, **kwargs) return make_decorator(func)(agg_func) From bd588bbaba9ae3a2670ba9b2317bf3afd8f70981 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 12:13:32 -0700 Subject: [PATCH 14/20] FIX sympy issue for docstrings --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index e20fcc7ba5..06055a51fb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -134,7 +134,7 @@ script: # Work round bug in Sympy atoms docstring as of 1.1.0 # https://github.com/sympy/sympy/pull/12900 # pip install git+https://github.com/sympy/sympy.git - pip install "sympy<1.6" + pip install "sympy<1.1.0" make html-stamp pdf-stamp else # Change into an innocuous directory and find tests from installation From d1d9420b94d6bda7a9704267830e3dda8e71d7eb Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 13:07:45 -0700 Subject: [PATCH 15/20] FIX try an even older sympy for docs --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 06055a51fb..ce298ac50d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -134,7 +134,7 @@ script: # Work round bug in Sympy atoms docstring as of 1.1.0 # https://github.com/sympy/sympy/pull/12900 # pip install git+https://github.com/sympy/sympy.git - pip install "sympy<1.1.0" + pip install "sympy<1.0" make html-stamp pdf-stamp else # Change into an innocuous directory and find tests from installation From df6112029c851081c99496a542ca8ca2471ef81a Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 13:10:46 -0700 Subject: [PATCH 16/20] FIX actually need a more recent version of sympy for docs --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index ce298ac50d..5e919fdefe 100644 --- a/.travis.yml +++ b/.travis.yml @@ -134,7 +134,7 @@ script: # Work round bug in Sympy atoms docstring as of 1.1.0 # https://github.com/sympy/sympy/pull/12900 # pip install git+https://github.com/sympy/sympy.git - pip install "sympy<1.0" + pip install "sympy<1.2" make html-stamp pdf-stamp else # Change into an innocuous directory and find tests from installation From 678292eae2335059370e2490866ba70b57765626 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 13:32:13 -0700 Subject: [PATCH 17/20] FIX check if reverting back to dev version works --- .travis.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 5e919fdefe..ea3283d298 100644 --- a/.travis.yml +++ b/.travis.yml @@ -133,8 +133,7 @@ script: pip install -r doc-requirements.txt # Work round bug in Sympy atoms docstring as of 1.1.0 # https://github.com/sympy/sympy/pull/12900 - # pip install git+https://github.com/sympy/sympy.git - pip install "sympy<1.2" + pip install git+https://github.com/sympy/sympy.git make html-stamp pdf-stamp else # Change into an innocuous directory and find tests from installation From e9036802af2404aa6f09bd5113117faecc2daf91 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 9 Oct 2020 13:50:49 -0700 Subject: [PATCH 18/20] Try using older version of numpydoc --- doc-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc-requirements.txt b/doc-requirements.txt index 8bf2f27751..840467cefc 100644 --- a/doc-requirements.txt +++ b/doc-requirements.txt @@ -2,7 +2,7 @@ # Check these dependencies against doc/conf.py -r dev-requirements.txt sphinx>=1.0,<3.0 -numpydoc +numpydoc<=1.0 matplotlib texext ipython From a8ac795268ce350aae405f08c1705b11c2323b02 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 10 Oct 2020 11:56:06 -0700 Subject: [PATCH 19/20] CI change python versions on appveyor too --- .appveyor.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.appveyor.yml b/.appveyor.yml index cf72da45c4..15cb7438c3 100644 --- a/.appveyor.yml +++ b/.appveyor.yml @@ -10,12 +10,12 @@ environment: - PYTHON: C:\Python27-x64 # Doctest fail from the long Ls, as in (1L, 2L) != (1, 2) EXTRA_FLAGS: "--without-doctest" - - PYTHON: C:\Python34 - - PYTHON: C:\Python34-x64 - - PYTHON: C:\Python35 - - PYTHON: C:\Python35-x64 - PYTHON: C:\Python36 - PYTHON: C:\Python36-x64 + - PYTHON: C:\Python37 + - PYTHON: C:\Python37-x64 + - PYTHON: C:\Python38 + - PYTHON: C:\Python38-x64 install: # Prepend newly installed Python to the PATH of this build (this cannot be @@ -29,7 +29,7 @@ install: - echo "C:\Program Files\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 > "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\bin\amd64/vcvars64.bat" # Install the dependencies of the project. - - pip install numpy Cython nose nibabel sympy scipy + - pip install numpy Cython nose nibabel "sympy<1.6" scipy # Pin wheel to 0.26 to avoid Windows ABI tag for built wheel - pip install wheel==0.26 # install From 982215efa53c135da3d376dec01d4ab6641a17cd Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 10 Oct 2020 12:14:51 -0700 Subject: [PATCH 20/20] CI try to pin numpydoc to an older version --- doc-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc-requirements.txt b/doc-requirements.txt index 840467cefc..2bc87948d8 100644 --- a/doc-requirements.txt +++ b/doc-requirements.txt @@ -2,7 +2,7 @@ # Check these dependencies against doc/conf.py -r dev-requirements.txt sphinx>=1.0,<3.0 -numpydoc<=1.0 +numpydoc==0.8.0 matplotlib texext ipython