Accepting request 1133227 from devel:languages:python:numeric
- Update to 4.16.0: * enhancements: + the grouping commands like group_counts and group_snr now default to only grouping within the noticed range of channels, which is a change in behaviour + new plotting backend: Users can now choose between matplotlib and bokeh (experimental) support use of arbitrary python functions when linking model parameters + updates to fake_pha, save_all, allowing to write out RMF/ARF files + get_plot_prefs and get_contour_prefs call to simplify access to the plot and contour preferences + implementation of RMFPlot and DataIMGPlot classes and associated UI functions (plot_rmf, get_rmf_plot) + update support for XSPEC to include version 12.13.1, allow XSPEC table models which include the ESCALE parameter, and provide experimental support for writing out XSPEC table models. * changes to use the NumPy random generator API * bug fixes: + PHA source plot Y axis scaling (#1825) + fix model display for grouped data (#1779, #1784) + Change in the ordering of operations when grouping background PHA datasets. (#1881) - Drop patch numpy125.patch and numpy125-CI.patch: Included upstream. - Skip a misbehaving test. OBS-URL: https://build.opensuse.org/request/show/1133227 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-sherpa?expand=0&rev=18
This commit is contained in:
commit
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@ -1,96 +0,0 @@
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From 2aea86a2a596323e9c8e41275acbffa1e9a609a0 Mon Sep 17 00:00:00 2001
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From: Doug Burke <dburke@cfa.harvard.edu>
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Date: Mon, 17 Jul 2023 11:33:29 -0400
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Subject: [PATCH 1/2] Silence test warnings if pytest-doctestplus is not
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installed
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I originally tried adding the warnings to sherpa/conftest.py but
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this is happening in pytest itself, so I've taken advantage of
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the general filter-warnings capability to hide thse messages.
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Before this change, running pytest without pytest-doctestplus would
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result in messages like
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==================================================== warnings summary =====================================================
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../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
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/lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_norecursedirs
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self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
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../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
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/lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_plus
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self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
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../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
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/lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_plus_atol
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self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
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../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
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/lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_subpackage_requires
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self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
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../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
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/lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: text_file_format
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self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
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-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
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================================================= short test summary info =================================================
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---
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pytest.ini | 4 ++++
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1 file changed, 4 insertions(+)
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diff --git a/pytest.ini b/pytest.ini
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index fde2ab8e0c..e2c4c4847e 100644
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--- a/pytest.ini
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+++ b/pytest.ini
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@@ -2,6 +2,10 @@
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addopts = -rs --ignore=setup.py --ignore=test_requirements.txt
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norecursedirs = .git build dist tmp* .eggs
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text_file_format = rst
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+filterwarnings =
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+ # Since we can runpytest without loading pytest-doctestplus, hide
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+ # the warnings we get when this is done
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+ ignore::pytest.PytestConfigWarning
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doctest_plus = enabled
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doctest_plus_atol = 1e-4
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doctest_optionflags =
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From 14e43a098ecb9a5068d2886f6d4680b9cd878404 Mon Sep 17 00:00:00 2001
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From: Doug Burke <dburke@cfa.harvard.edu>
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Date: Mon, 17 Jul 2023 12:05:21 -0400
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Subject: [PATCH 2/2] Tests: hide NumPy 1.25 ndim > 0 warnings (crates)
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Although Sherpa has been updated to remove the deprecation
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warnnng from NumPy 1.25:
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Conversion of an array with ndim > 0 to a scalar is deprecated,
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and will error in future. Ensure you extract a single element
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from your array before performing this operation.
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(Deprecated NumPy 1.25.)
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it is still present in Crates (mid 2023), so hide the warning with
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the assumption we can revert this commit by mid December 2023.
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---
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sherpa/conftest.py | 5 +++++
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1 file changed, 5 insertions(+)
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diff --git a/sherpa/conftest.py b/sherpa/conftest.py
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index 97979b4e4b..339f252a51 100644
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--- a/sherpa/conftest.py
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+++ b/sherpa/conftest.py
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@@ -117,6 +117,11 @@ def pytest_collection_modifyitems(config, items):
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r'np.asscalar\(a\) is deprecated since NumPy v1.16, use a.item\(\) instead',
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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",
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+ # NumPy 1.25 warnings that are raised by (mid-2023) crates code.
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+ # Hopefully this can be removed by December 2023.
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+ #
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+ r"Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. \(Deprecated NumPy 1.25.\)",
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+
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],
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UserWarning:
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[
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@ -1,89 +0,0 @@
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From 740fcd0da87d3aefa41aa3962cc8f1ddb7ab3cab Mon Sep 17 00:00:00 2001
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From: Doug Burke <dburke@cfa.harvard.edu>
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Date: Tue, 20 Jun 2023 15:31:55 -0400
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Subject: [PATCH] NumPy 1.25 support
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NumPy 1.25 deprecates converting a ndarray that is not a 0d value,
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so for our cases this is
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int(value)
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info("message %g", value)
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where value is a ndarray of length 1. The simple fix is to explictly
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access the first element - so
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answer = int(value[0])
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info("message %g", value[0])
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although for the int case (in the PSF convolution instrument code) I
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have not looked through to determine if value is always guaranteed to
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be a ndarray, so it is more like
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if np.isscalar(value):
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newval = value
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else:
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newval = value[0]
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answer = int(newval)
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---
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sherpa/fit.py | 13 +++++++++----
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sherpa/instrument.py | 12 ++++++++++--
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2 files changed, 19 insertions(+), 6 deletions(-)
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Index: sherpa-4.15.1/sherpa/fit.py
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===================================================================
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--- sherpa-4.15.1.orig/sherpa/fit.py
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+++ sherpa-4.15.1/sherpa/fit.py
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@@ -1258,8 +1258,13 @@ class Fit(NoNewAttributesAfterInit):
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def get_par_name(ii):
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return self.model.pars[self.thaw_indices[ii]].fullname
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- # Call from a parameter estimation method, to report
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- # that limits for a given parameter have been found
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+ # Call from a parameter estimation method, to report that
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+ # limits for a given parameter have been found At present (mid
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+ # 2023) it looks like lower/upper are both single-element
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+ # ndarrays, hence the need to convert to a scalar by accessing
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+ # the first element (otherwise there's a deprecation warning
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+ # from NumPy 1.25).
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+ #
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def report_progress(i, lower, upper):
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if i < 0:
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pass
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@@ -1268,11 +1273,11 @@ class Fit(NoNewAttributesAfterInit):
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if isnan(lower) or isinf(lower):
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info("%s \tlower bound: -----" % name)
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else:
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- info("%s \tlower bound: %g" % (name, lower))
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+ info("%s \tlower bound: %g" % (name, lower[0]))
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if isnan(upper) or isinf(upper):
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info("%s \tupper bound: -----" % name)
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else:
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- info("%s \tupper bound: %g" % (name, upper))
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+ info("%s \tupper bound: %g" % (name, upper[0]))
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# If starting fit statistic is chi-squared or C-stat,
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# can calculate reduced fit statistic -- if it is
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Index: sherpa-4.15.1/sherpa/instrument.py
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===================================================================
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--- sherpa-4.15.1.orig/sherpa/instrument.py
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+++ sherpa-4.15.1/sherpa/instrument.py
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@@ -357,9 +357,17 @@ class PSFKernel(Kernel):
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# and Python 3.8 - causes a TypeError with the message
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# "only integer scalar arrays can be converted to a scalar index"
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# to be thrown here if sent directly to set_origin. So
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- # we convert to a Python integer type.
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+ # we convert to a Python integer type. In NumPy 1.25 it became
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+ # a deprecation error to call int on an array with ndim > 0.
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#
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- origin = set_origin(kshape, int(brightPixel))
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+ # assume there is only one element in brightPixel if not
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+ # a scalar
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+ #
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+ if not numpy.isscalar(brightPixel):
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+ loc = brightPixel[0]
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+ else:
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+ loc = brightPixel
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+ origin = set_origin(kshape, int(loc))
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if self.origin is None:
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self.origin = origin
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@ -1,3 +1,31 @@
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-------------------------------------------------------------------
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Fri Dec 15 03:54:30 UTC 2023 - Steve Kowalik <steven.kowalik@suse.com>
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- Update to 4.16.0:
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* enhancements:
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+ the grouping commands like group_counts and group_snr now default to
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only grouping within the noticed range of channels, which is a change
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in behaviour
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+ new plotting backend: Users can now choose between matplotlib and
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bokeh (experimental) support use of arbitrary python functions when
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linking model parameters
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+ updates to fake_pha, save_all, allowing to write out RMF/ARF files
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+ get_plot_prefs and get_contour_prefs call to simplify access to the
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plot and contour preferences
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+ implementation of RMFPlot and DataIMGPlot classes and associated UI
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functions (plot_rmf, get_rmf_plot)
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+ update support for XSPEC to include version 12.13.1, allow XSPEC
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table models which include the ESCALE parameter, and provide
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experimental support for writing out XSPEC table models.
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* changes to use the NumPy random generator API
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* bug fixes:
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+ PHA source plot Y axis scaling (#1825)
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+ fix model display for grouped data (#1779, #1784)
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+ Change in the ordering of operations when grouping background PHA
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datasets. (#1881)
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- Drop patch numpy125.patch and numpy125-CI.patch: Included upstream.
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- Skip a misbehaving test.
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-------------------------------------------------------------------
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Thu Sep 7 12:24:59 UTC 2023 - Markéta Machová <mmachova@suse.com>
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@ -17,17 +17,13 @@
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Name: python-sherpa
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Version: 4.15.1
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Version: 4.16.0
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Release: 0
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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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URL: https://github.com/sherpa/sherpa/
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Source0: https://github.com/sherpa/sherpa/archive/%{version}.tar.gz#/sherpa-%{version}.tar.gz
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Source1: https://github.com/sherpa/sherpa-test-data/archive/refs/tags/%{version}.tar.gz#/sherpa-test-data-%{version}.tar.gz
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# PATCH-FIX-UPSTREAM https://github.com/sherpa/sherpa/pull/1807 NumPy 1.25 support
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Patch: numpy125.patch
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# PATCH-FIX-UPSTREAM https://github.com/sherpa/sherpa/pull/1819 CI: hide NumPy 1.25 array ndim>0 deprecation warnings
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Patch: numpy125-CI.patch
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BuildRequires: %{python_module devel >= 3.8}
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BuildRequires: %{python_module numpy-devel >= 1.19}
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BuildRequires: %{python_module pip}
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@ -105,6 +101,7 @@ donttest="test_save"
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donttest+=" or (test_regproj and sherpa.plot.dummy_backend)"
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donttest+=" or (test_fit_single and Chi2XspecVar)"
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%endif
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donttest+=" or test_Griewank"
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%pytest_arch %{?jobs:-n %jobs} --pyargs sherpa -k "not ($donttest)"
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%post
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@ -121,7 +118,7 @@ donttest+=" or (test_fit_single and Chi2XspecVar)"
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%python_alternative %{_bindir}/sherpa_test
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%python_alternative %{_bindir}/sherpa_smoke
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%{python_sitearch}/sherpa
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%{python_sitearch}/sherpa-%{version}*-info
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%{python_sitearch}/sherpa-%{version}.dist-info
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%{python_sitearch}/stk.so
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%{python_sitearch}/group.so
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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 sha256:3b3c4b7ce8a03a2cf2c5f3d1f288a6f332885ca04c50b1a829d4a244281f3112
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size 13362922
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3
sherpa-4.16.0.tar.gz
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3
sherpa-4.16.0.tar.gz
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version https://git-lfs.github.com/spec/v1
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oid sha256:95e665d87048a26e203785e6efbb9f44cf75cb6ea0c9ee853e3796b5a0c9444f
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size 13686939
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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:a6b6335bd6ad84ff28a7fdc32b5cc45952c7aded193bc55154f4e208736c4126
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size 134765085
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3
sherpa-test-data-4.16.0.tar.gz
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3
sherpa-test-data-4.16.0.tar.gz
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@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:27d356af9d819ca0a5df9cca2ff8f29444629a33a9d5d347ed790a8d4596b7f5
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size 137774612
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