Accepting request 899444 from devel:languages:python:numeric
OBS-URL: https://build.opensuse.org/request/show/899444 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-sherpa?expand=0&rev=9
This commit is contained in:
Dominique Leuenberger
Git OBS Bridge
commit
b20946ac29
@ -1,3 +1,33 @@
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-------------------------------------------------------------------
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Fri Jun 11 09:52:54 UTC 2021 - Guillaume GARDET <guillaume.gardet@opensuse.org>
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- Update to 4.13.1:
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* documentation changes:
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- updates to documentation for TableModel, Notice2D, cache
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support for evaluating models, and low level optimization code
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- jupyter notebook uopdates
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* Infrastructure Changes:
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- the master branch has been migrated from master to main
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- updates to support numpy 1.20
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- updates to support astropy 4.2.1
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- updates to support matplotlib 3.4
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- test infrastructure clean up and updates
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* bug fixes:
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- fix an issue with cache evaluation on 1D models using
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integrated bins
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- fix for aarch64 build issue
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- fix to sherpa citation command
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- fix to honor clearwindow setting for plot_source
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- fix errors from save_data when the output file exists
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- fix build issues using gcc 7.3 with -Werror=format-security
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compilation flag
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- fix for reg_proj and reg_unc erroring out when the min or max
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arguments are tuples rather than lists
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- Drop upstreamed patches:
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* sherpa-fix-aarch64.patch
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* sherpa-numpy-1.20.patch
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* sherpa-mpl-3.4.patch
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-------------------------------------------------------------------
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-------------------------------------------------------------------
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Sat Apr 24 18:40:06 UTC 2021 - Ben Greiner <code@bnavigator.de>
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Sat Apr 24 18:40:06 UTC 2021 - Ben Greiner <code@bnavigator.de>
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@ -20,19 +20,13 @@
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%define skip_python2 1
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%define skip_python2 1
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%define skip_python36 1
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%define skip_python36 1
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Name: python-sherpa
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Name: python-sherpa
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Version: 4.13.0
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Version: 4.13.1
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Release: 0
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Release: 0
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Summary: Modeling and fitting package for scientific data analysis
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Summary: Modeling and fitting package for scientific data analysis
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License: GPL-3.0-only
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License: GPL-3.0-only
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URL: https://github.com/sherpa/sherpa/
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URL: https://github.com/sherpa/sherpa/
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Source: https://github.com/sherpa/sherpa/archive/%{version}.tar.gz#/sherpa-%{version}.tar.gz
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Source: https://github.com/sherpa/sherpa/archive/%{version}.tar.gz#/sherpa-%{version}.tar.gz
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Patch1: reproducible.patch
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Patch1: reproducible.patch
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# PATCH-FIX-UPSTREAM - https://github.com/sherpa/sherpa/issues/970
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Patch2: sherpa-fix-aarch64.patch
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# PATCH-FIX-UPSTREAM sherpa-numpy-1.20.patch badshah400@gmail.com - Fix test errors with numpy 1.20 [https://github.com/sherpa/sherpa/pull/1092]
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Patch3: sherpa-numpy-1.20.patch
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# PATCH-FIX-UPSTREAM sherpa-mpl-3.4.patch -- https://github.com/sherpa/sherpa/pull/1125
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Patch4: sherpa-mpl-3.4.patch
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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module numpy-devel}
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BuildRequires: %{python_module numpy-devel}
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BuildRequires: %{python_module setuptools}
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BuildRequires: %{python_module setuptools}
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
|
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oid sha256:91b64be0ebc3429e68292d8025bb5dd25916ce645bef6159151678611319c99a
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size 12430999
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3
sherpa-4.13.1.tar.gz
Normal file
3
sherpa-4.13.1.tar.gz
Normal file
@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:2951d28c9012c90f9ba26ff0e989762843f574211f48f04c50f735bafa2dffed
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size 12637455
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@ -1,25 +0,0 @@
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diff -purN sherpa-4.12.1.orig/sherpa/utils/src/cephes/mconf.h sherpa-4.12.1/sherpa/utils/src/cephes/mconf.h
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--- sherpa-4.12.1.orig/sherpa/utils/src/cephes/mconf.h 2020-06-26 20:27:19.000000000 +0200
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+++ sherpa-4.12.1/sherpa/utils/src/cephes/mconf.h 2020-10-14 14:44:53.565068804 +0200
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@@ -173,6 +173,10 @@ typedef struct
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/* Define to support tiny denormal numbers, else undefine. */
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#define DENORMAL 1
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+/* https://github.com/sherpa/sherpa/issues/970 */
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+#define NOINFINITIES
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+#define NONANS
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+
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/* Define to ask for infinity support, else undefine. */
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#define INFINITIES 1
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#ifdef NOINFINITIES
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--- sherpa-4.12.1.orig/sherpa/tests/test_fit_unit.py 2020-06-26 20:27:19.000000000 +0200
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+++ sherpa-4.12.1/sherpa/tests/test_fit_unit.py 2020-10-14 15:08:34.798995079 +0200
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@@ -1867,7 +1867,7 @@ def test_fit_single(stat, usestat, usesy
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assert fit.method.name == 'levmar'
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fr = fit.fit()
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assert fr.succeeded
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- assert_almost_equal(fr.statval, finalstat)
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+ assert fr.statval == pytest.approx(finalstat, rel=7e-5)
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@pytest.mark.parametrize("stat,usestat,usesys,finalstat", [
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@ -1,150 +0,0 @@
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From 0187ded7223bbaded8022a28561182846b17ceb3 Mon Sep 17 00:00:00 2001
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From: Douglas Burke <dburke.gw@gmail.com>
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Date: Tue, 13 Apr 2021 16:29:45 -0400
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Subject: [PATCH 1/2] matlpotlib 3.4 has removed drawstyle from axes.errorbar
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The drawstyle argument has now been removed from some commands -
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this appears to just be the axes.errorbar function - in matplotlib
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version 3.4.
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---
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sherpa/plot/pylab_backend.py | 4 +---
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1 file changed, 1 insertion(+), 3 deletions(-)
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Index: sherpa-4.13.0/sherpa/plot/pylab_backend.py
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===================================================================
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--- sherpa-4.13.0.orig/sherpa/plot/pylab_backend.py
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+++ sherpa-4.13.0/sherpa/plot/pylab_backend.py
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@@ -1,6 +1,6 @@
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#
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-# Copyright (C) 2010, 2015, 2017, 2019, 2020
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-# Smithsonian Astrophysical Observatory
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+# Copyright (C) 2010, 2015, 2017, 2019, 2020, 2021
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+# Smithsonian Astrophysical Observatory
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#
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#
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# This program is free software; you can redistribute it and/or modify
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@@ -316,7 +316,6 @@ def histo(xlo, xhi, y, yerr=None, title=
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color=color,
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alpha=alpha,
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linestyle='',
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- drawstyle=drawstyle,
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marker=marker,
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markersize=markersize,
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markerfacecolor=markerfacecolor,
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@@ -446,7 +445,6 @@ def plot(x, y, yerr=None, xerr=None, tit
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objs = axes.errorbar(x, y, yerr, xerr,
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color=color,
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linestyle=linestyle,
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- drawstyle=drawstyle,
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marker=marker,
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markersize=markersize,
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markerfacecolor=markerfacecolor,
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Index: sherpa-4.13.0/sherpa/astro/ui/tests/test_astro_ui_plot.py
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===================================================================
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--- sherpa-4.13.0.orig/sherpa/astro/ui/tests/test_astro_ui_plot.py
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+++ sherpa-4.13.0/sherpa/astro/ui/tests/test_astro_ui_plot.py
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@@ -1,5 +1,6 @@
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#
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-# Copyright (C) 2019, 2020 Smithsonian Astrophysical Observatory
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+# Copyright (C) 2019, 2020, 2021
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+# Smithsonian Astrophysical Observatory
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#
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#
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# This program is free software; you can redistribute it and/or modify
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@@ -1168,7 +1169,8 @@ def test_img_contour_function_kwarg(clea
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for i, ax in enumerate(axes, 1):
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- assert ax.get_geometry() == (2, 2, i)
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+ w = i - 1
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+ assert ax.get_subplotspec().get_geometry() == (2, 2, w, w)
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assert ax.get_xscale() == 'linear'
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assert ax.get_yscale() == 'linear'
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Index: sherpa-4.13.0/sherpa/ui/tests/test_ui_plot.py
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===================================================================
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--- sherpa-4.13.0.orig/sherpa/ui/tests/test_ui_plot.py
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+++ sherpa-4.13.0/sherpa/ui/tests/test_ui_plot.py
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@@ -1,5 +1,6 @@
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#
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-# Copyright (C) 2019, 2020 Smithsonian Astrophysical Observatory
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+# Copyright (C) 2019, 2020, 2021
|
|
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+# Smithsonian Astrophysical Observatory
|
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#
|
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#
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# This program is free software; you can redistribute it and/or modify
|
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@@ -1113,7 +1114,7 @@ def test_plot_single(session):
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ax = fig.axes[0]
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|
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- assert ax.get_geometry() == (1, 1, 1)
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+ assert ax.get_subplotspec().get_geometry() == (1, 1, 0, 0)
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assert ax.get_title() == ''
|
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assert ax.xaxis.get_label().get_text() == 'x'
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assert ax.yaxis.get_label().get_text() == 'y'
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@@ -1127,7 +1128,7 @@ def test_plot_single(session):
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ax = fig.axes[0]
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|
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- assert ax.get_geometry() == (1, 1, 1)
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+ assert ax.get_subplotspec().get_geometry() == (1, 1, 0, 0)
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assert ax.get_title() == 'Model'
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assert ax.xaxis.get_label().get_text() == 'x'
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assert ax.yaxis.get_label().get_text() == 'y'
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@@ -1179,7 +1180,8 @@ def test_plot_multiple(session):
|
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'Data / Model']),
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1):
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|
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- assert ax.get_geometry() == (2, 3, i)
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+ w = i - 1
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+ assert ax.get_subplotspec().get_geometry() == (2, 3, w, w)
|
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assert ax.get_title() == title
|
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assert ax.xaxis.get_label().get_text() == 'x'
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assert ax.yaxis.get_label().get_text() == ylabel
|
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@@ -1226,7 +1228,7 @@ def test_contour_single(session):
|
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ax = fig.axes[0]
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|
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- assert ax.get_geometry() == (1, 1, 1)
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+ assert ax.get_subplotspec().get_geometry() == (1, 1, 0, 0)
|
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assert ax.get_title() == ''
|
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assert ax.xaxis.get_label().get_text() == 'x0'
|
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assert ax.yaxis.get_label().get_text() == 'x1'
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@@ -1240,7 +1242,7 @@ def test_contour_single(session):
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ax = fig.axes[0]
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|
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- assert ax.get_geometry() == (1, 1, 1)
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+ assert ax.get_subplotspec().get_geometry() == (1, 1, 0, 0)
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assert ax.get_title() == 'Model'
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assert ax.xaxis.get_label().get_text() == 'x0'
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assert ax.yaxis.get_label().get_text() == 'x1'
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@@ -1287,7 +1289,8 @@ def test_contour_multiple(session):
|
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'Ratio of Data to Model']),
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1):
|
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|
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- assert ax.get_geometry() == (2, 3, i)
|
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+ w = i - 1
|
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+ assert ax.get_subplotspec().get_geometry() == (2, 3, w, w)
|
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assert ax.get_title() == title
|
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assert ax.xaxis.get_label().get_text() == 'x0'
|
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assert ax.yaxis.get_label().get_text() == 'x1'
|
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@@ -1343,7 +1346,8 @@ def test_contour_xxx(plotfunc, title, pc
|
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['', 'Residuals']),
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1):
|
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|
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- assert ax.get_geometry() == (2, 1, i)
|
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+ w = i - 1
|
|
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+ assert ax.get_subplotspec().get_geometry() == (2, 1, w, w)
|
|
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assert ax.get_title() == title
|
|
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assert ax.xaxis.get_label().get_text() == 'x0'
|
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assert ax.yaxis.get_label().get_text() == 'x1'
|
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@@ -1352,7 +1356,7 @@ def test_contour_xxx(plotfunc, title, pc
|
|
||||||
assert len(fig.axes) == 1
|
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|
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ax = fig.axes[0]
|
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- assert ax.get_geometry() == (1, 1, 1)
|
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+ assert ax.get_subplotspec().get_geometry() == (1, 1, 0, 0)
|
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assert ax.get_title() == title
|
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assert ax.xaxis.get_label().get_text() == 'x0'
|
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assert ax.yaxis.get_label().get_text() == 'x1'
|
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@ -1,200 +0,0 @@
|
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From 1ca81268c560b712677f91c98c5481ef473bfa0e Mon Sep 17 00:00:00 2001
|
|
||||||
From: Douglas Burke <dburke.gw@gmail.com>
|
|
||||||
Date: Sun, 31 Jan 2021 19:03:24 -0500
|
|
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Subject: [PATCH 1/3] Whitelist np.bool/int/float warning from NumPy 1.20 in
|
|
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tests
|
|
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|
|
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As well as white-listing the warnings I've had to tweak one set
|
|
||||||
of tests which was explicitly checking the warning messages
|
|
||||||
(and so needed to ignore the known warnings).
|
|
||||||
---
|
|
||||||
.../astro/tests/test_astro_data_swift_unit.py | 21 ++++++----
|
|
||||||
sherpa/conftest.py | 38 +++++++++++++++----
|
|
||||||
2 files changed, 43 insertions(+), 16 deletions(-)
|
|
||||||
|
|
||||||
Index: sherpa-4.13.0/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
||||||
===================================================================
|
|
||||||
--- sherpa-4.13.0.orig/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
||||||
+++ sherpa-4.13.0/sherpa/astro/tests/test_astro_data_swift_unit.py
|
|
||||||
@@ -172,7 +172,12 @@ def test_read_pha_fails_rmf(make_data_pa
|
|
||||||
assert emsg in str(excinfo.value)
|
|
||||||
|
|
||||||
|
|
||||||
-def validate_replacement_warning(ws, rtype, label):
|
|
||||||
+def validate_replacement_warning(ws, rtype, label, is_known_warning):
|
|
||||||
+ """Check that there is one expected warning."""
|
|
||||||
+
|
|
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+ # Filter out the "allowed" warnings.
|
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||||||
+ #
|
|
||||||
+ ws = [w for w in ws if not is_known_warning(w)]
|
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|
|
||||||
assert len(ws) == 1
|
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w = ws[0]
|
|
||||||
@@ -185,7 +190,7 @@ def validate_replacement_warning(ws, rty
|
|
||||||
|
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@requires_data
|
|
||||||
@requires_fits
|
|
||||||
-def test_read_arf(make_data_path):
|
|
||||||
+def test_read_arf(make_data_path, is_known_warning):
|
|
||||||
"""Can we read in a Swift ARF."""
|
|
||||||
|
|
||||||
infile = make_data_path(ARFFILE)
|
|
||||||
@@ -194,7 +199,7 @@ def test_read_arf(make_data_path):
|
|
||||||
warnings.simplefilter("always")
|
|
||||||
arf = io.read_arf(infile)
|
|
||||||
|
|
||||||
- validate_replacement_warning(ws, 'ARF', infile)
|
|
||||||
+ validate_replacement_warning(ws, 'ARF', infile, is_known_warning)
|
|
||||||
|
|
||||||
assert isinstance(arf, DataARF)
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|
|
||||||
@@ -262,7 +267,7 @@ def test_read_arf_fails_rmf(make_data_pa
|
|
||||||
|
|
||||||
@requires_data
|
|
||||||
@requires_fits
|
|
||||||
-def test_read_rmf(make_data_path):
|
|
||||||
+def test_read_rmf(make_data_path, is_known_warning):
|
|
||||||
"""Can we read in a Swift RMF."""
|
|
||||||
|
|
||||||
infile = make_data_path(RMFFILE)
|
|
||||||
@@ -271,7 +276,7 @@ def test_read_rmf(make_data_path):
|
|
||||||
warnings.simplefilter("always")
|
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||||||
rmf = io.read_rmf(infile)
|
|
||||||
|
|
||||||
- validate_replacement_warning(ws, 'RMF', infile)
|
|
||||||
+ validate_replacement_warning(ws, 'RMF', infile, is_known_warning)
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|
||||||
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|
||||||
assert isinstance(rmf, DataRMF)
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|
||||||
|
|
||||||
@@ -362,7 +367,7 @@ def test_read_rmf_fails_arf(make_data_pa
|
|
||||||
|
|
||||||
@requires_data
|
|
||||||
@requires_fits
|
|
||||||
-def test_can_use_swift_data(make_data_path):
|
|
||||||
+def test_can_use_swift_data(make_data_path, is_known_warning):
|
|
||||||
"""A basic check that we can read in and use the Swift data.
|
|
||||||
|
|
||||||
Unlike the previous tests, that directly access the io module,
|
|
||||||
@@ -383,14 +388,14 @@ def test_can_use_swift_data(make_data_pa
|
|
||||||
warnings.simplefilter("always")
|
|
||||||
ui.load_rmf(rmffile)
|
|
||||||
|
|
||||||
- validate_replacement_warning(ws, 'RMF', rmffile)
|
|
||||||
+ validate_replacement_warning(ws, 'RMF', rmffile, is_known_warning)
|
|
||||||
|
|
||||||
arffile = make_data_path(ARFFILE)
|
|
||||||
with warnings.catch_warnings(record=True) as ws:
|
|
||||||
warnings.simplefilter("always")
|
|
||||||
ui.load_arf(arffile)
|
|
||||||
|
|
||||||
- validate_replacement_warning(ws, 'ARF', arffile)
|
|
||||||
+ validate_replacement_warning(ws, 'ARF', arffile, is_known_warning)
|
|
||||||
|
|
||||||
assert ui.get_analysis() == 'energy'
|
|
||||||
|
|
||||||
Index: sherpa-4.13.0/sherpa/conftest.py
|
|
||||||
===================================================================
|
|
||||||
--- sherpa-4.13.0.orig/sherpa/conftest.py
|
|
||||||
+++ sherpa-4.13.0/sherpa/conftest.py
|
|
||||||
@@ -116,7 +116,12 @@ known_warnings = {
|
|
||||||
# Matplotlib version 2 warnings (from HTML notebook represention)
|
|
||||||
#
|
|
||||||
r'np.asscalar\(a\) is deprecated since NumPy v1.16, use a.item\(\) instead',
|
|
||||||
- r"Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working"
|
|
||||||
+ r"Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working",
|
|
||||||
+
|
|
||||||
+ # numpy 1.20 bool/float issue
|
|
||||||
+ r'`np.bool` is a deprecated alias for the builtin `bool`. .*',
|
|
||||||
+ r'`np.int` is a deprecated alias for the builtin `int`. .*',
|
|
||||||
+ r'`np.float` is a deprecated alias for the builtin `float`. .*',
|
|
||||||
],
|
|
||||||
UserWarning:
|
|
||||||
[
|
|
||||||
@@ -140,18 +145,11 @@ known_warnings = {
|
|
||||||
# See https://github.com/ContinuumIO/anaconda-issues/issues/6678
|
|
||||||
r"numpy.dtype size changed, may indicate binary " +
|
|
||||||
r"incompatibility. Expected 96, got 88",
|
|
||||||
- # I am getting the following from astropy with at least python 2.7 during the conda tests
|
|
||||||
- r"numpy.ufunc size changed, may indicate binary ",
|
|
||||||
+ # See https://github.com/numpy/numpy/pull/432
|
|
||||||
+ r"numpy.ufunc size changed",
|
|
||||||
+ # numpy 1.20 shows this in some tests
|
|
||||||
+ r"numpy.ndarray size changed, may indicate binary "
|
|
||||||
],
|
|
||||||
- VisibleDeprecationWarning:
|
|
||||||
- [],
|
|
||||||
-}
|
|
||||||
-
|
|
||||||
-# Since Sherpa now requires Python 3.5 at a minumum, the following
|
|
||||||
-# are always added, but kept as a separate dict and then merged
|
|
||||||
-# to make it clearer where they came from.
|
|
||||||
-#
|
|
||||||
-python3_warnings = {
|
|
||||||
ResourceWarning:
|
|
||||||
[
|
|
||||||
r"unclosed file .*king_kernel.txt.* closefd=True>",
|
|
||||||
@@ -166,17 +164,9 @@ python3_warnings = {
|
|
||||||
r"unclosed file .*/dev/null.* closefd=True>",
|
|
||||||
r"unclosed file .*table.txt.* closefd=True>",
|
|
||||||
],
|
|
||||||
- RuntimeWarning:
|
|
||||||
- [r"invalid value encountered in sqrt",
|
|
||||||
- # See https://github.com/ContinuumIO/anaconda-issues/issues/6678
|
|
||||||
- r"numpy.dtype size changed, may indicate binary " +
|
|
||||||
- r"incompatibility. Expected 96, got 88",
|
|
||||||
- # See https://github.com/numpy/numpy/pull/432
|
|
||||||
- r"numpy.ufunc size changed"
|
|
||||||
- ],
|
|
||||||
+ VisibleDeprecationWarning:
|
|
||||||
+ [],
|
|
||||||
}
|
|
||||||
-known_warnings.update(python3_warnings)
|
|
||||||
-
|
|
||||||
|
|
||||||
if have_astropy:
|
|
||||||
astropy_warnings = {
|
|
||||||
@@ -230,13 +220,8 @@ def capture_all_warnings(request, recwar
|
|
||||||
pytestconfig injected service for accessing the configuration data
|
|
||||||
|
|
||||||
"""
|
|
||||||
- def known(warning):
|
|
||||||
- message = warning.message
|
|
||||||
- for known_warning in known_warnings[type(message)]:
|
|
||||||
- pattern = re.compile(known_warning)
|
|
||||||
- if pattern.match(str(message)):
|
|
||||||
- return True
|
|
||||||
- return False
|
|
||||||
+
|
|
||||||
+ known = check_known_warning
|
|
||||||
|
|
||||||
def fin():
|
|
||||||
warnings = [w for w in recwarn.list
|
|
||||||
@@ -263,6 +248,28 @@ def capture_all_warnings(request, recwar
|
|
||||||
request.addfinalizer(fin)
|
|
||||||
|
|
||||||
|
|
||||||
+def check_known_warning(warning):
|
|
||||||
+ """Return True if this is an "allowed" warning."""
|
|
||||||
+
|
|
||||||
+ message = warning.message
|
|
||||||
+ for known_warning in known_warnings[type(message)]:
|
|
||||||
+ pattern = re.compile(known_warning)
|
|
||||||
+ if pattern.match(str(message)):
|
|
||||||
+ return True
|
|
||||||
+
|
|
||||||
+ return False
|
|
||||||
+
|
|
||||||
+
|
|
||||||
+@pytest.fixture
|
|
||||||
+def is_known_warning():
|
|
||||||
+ """Returns a function that returns True if this is an "allowed" warning.
|
|
||||||
+
|
|
||||||
+ It is not expected that this will see much use.
|
|
||||||
+ """
|
|
||||||
+
|
|
||||||
+ return check_known_warning
|
|
||||||
+
|
|
||||||
+
|
|
||||||
def pytest_configure(config):
|
|
||||||
"""
|
|
||||||
This configuration hook overrides the default mechanism for test data self-discovery, if the --test-data command line
|
|
||||||
Loading…
Reference in New Issue
Block a user