Accepting request 1109765 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/1109765
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-sherpa?expand=0&rev=17

numpy125-CI.patch

@@ -0,0 +1,96 @@
+From 2aea86a2a596323e9c8e41275acbffa1e9a609a0 Mon Sep 17 00:00:00 2001
+From: Doug Burke <dburke@cfa.harvard.edu>
+Date: Mon, 17 Jul 2023 11:33:29 -0400
+Subject: [PATCH 1/2] Silence test warnings if pytest-doctestplus is not
+ installed
+
+I originally tried adding the warnings to sherpa/conftest.py but
+this is happening in pytest itself, so I've taken advantage of
+the general filter-warnings capability to hide thse messages.
+
+Before this change, running pytest without pytest-doctestplus would
+result in messages like
+
+==================================================== warnings summary =====================================================
+../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
+  /lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_norecursedirs
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
+  /lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_plus
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
+  /lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_plus_atol
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
+  /lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: doctest_subpackage_requires
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+../../../lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373
+  /lagado2.real/local/anaconda/envs/sherpa-main/lib/python3.11/site-packages/_pytest/config/__init__.py:1373: PytestConfigWarning: Unknown config option: text_file_format
+
+    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+================================================= short test summary info =================================================
+---
+ pytest.ini | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/pytest.ini b/pytest.ini
+index fde2ab8e0c..e2c4c4847e 100644
+--- a/pytest.ini
++++ b/pytest.ini
+@@ -2,6 +2,10 @@
+ addopts = -rs --ignore=setup.py --ignore=test_requirements.txt
+ norecursedirs = .git build dist tmp* .eggs
+ text_file_format = rst
++filterwarnings =
++    # Since we can runpytest without loading pytest-doctestplus, hide
++    # the warnings we get when this is done
++    ignore::pytest.PytestConfigWarning
+ doctest_plus = enabled
+ doctest_plus_atol = 1e-4
+ doctest_optionflags =
+
+From 14e43a098ecb9a5068d2886f6d4680b9cd878404 Mon Sep 17 00:00:00 2001
+From: Doug Burke <dburke@cfa.harvard.edu>
+Date: Mon, 17 Jul 2023 12:05:21 -0400
+Subject: [PATCH 2/2] Tests: hide NumPy 1.25 ndim > 0 warnings (crates)
+
+Although Sherpa has been updated to remove the deprecation
+warnnng from NumPy 1.25:
+
+  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.)
+
+it is still present in Crates (mid 2023), so hide the warning with
+the assumption we can revert this commit by mid December 2023.
+---
+ sherpa/conftest.py | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/sherpa/conftest.py b/sherpa/conftest.py
+index 97979b4e4b..339f252a51 100644
+--- a/sherpa/conftest.py
++++ b/sherpa/conftest.py
+@@ -117,6 +117,11 @@ def pytest_collection_modifyitems(config, items):
+             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",
+ 
++            # NumPy 1.25 warnings that are raised by (mid-2023) crates code.
++            # Hopefully this can be removed by December 2023.
++            #
++            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. \(Deprecated NumPy 1.25.\)",
++
+         ],
+     UserWarning:
+         [

numpy125.patch

@@ -0,0 +1,89 @@
+From 740fcd0da87d3aefa41aa3962cc8f1ddb7ab3cab Mon Sep 17 00:00:00 2001
+From: Doug Burke <dburke@cfa.harvard.edu>
+Date: Tue, 20 Jun 2023 15:31:55 -0400
+Subject: [PATCH] NumPy 1.25 support
+
+NumPy 1.25 deprecates converting a ndarray that is not a 0d value,
+so for our cases this is
+
+    int(value)
+    info("message %g", value)
+
+where value is a ndarray of length 1. The simple fix is to explictly
+access the first element - so
+
+    answer = int(value[0])
+    info("message %g", value[0])
+
+although for the int case (in the PSF convolution instrument code) I
+have not looked through to determine if value is always guaranteed to
+be a ndarray, so it is more like
+
+    if np.isscalar(value):
+        newval = value
+    else:
+        newval = value[0]
+    answer = int(newval)
+---
+ sherpa/fit.py        | 13 +++++++++----
+ sherpa/instrument.py | 12 ++++++++++--
+ 2 files changed, 19 insertions(+), 6 deletions(-)
+
+Index: sherpa-4.15.1/sherpa/fit.py
+===================================================================
+--- sherpa-4.15.1.orig/sherpa/fit.py
++++ sherpa-4.15.1/sherpa/fit.py
+@@ -1258,8 +1258,13 @@ class Fit(NoNewAttributesAfterInit):
+         def get_par_name(ii):
+             return self.model.pars[self.thaw_indices[ii]].fullname
+ 
+-        # Call from a parameter estimation method, to report
+-        # that limits for a given parameter have been found
++        # Call from a parameter estimation method, to report that
++        # limits for a given parameter have been found At present (mid
++        # 2023) it looks like lower/upper are both single-element
++        # ndarrays, hence the need to convert to a scalar by accessing
++        # the first element (otherwise there's a deprecation warning
++        # from NumPy 1.25).
++        #
+         def report_progress(i, lower, upper):
+             if i < 0:
+                 pass
+@@ -1268,11 +1273,11 @@ class Fit(NoNewAttributesAfterInit):
+                 if isnan(lower) or isinf(lower):
+                     info("%s \tlower bound: -----" % name)
+                 else:
+-                    info("%s \tlower bound: %g" % (name, lower))
++                    info("%s \tlower bound: %g" % (name, lower[0]))
+                 if isnan(upper) or isinf(upper):
+                     info("%s \tupper bound: -----" % name)
+                 else:
+-                    info("%s \tupper bound: %g" % (name, upper))
++                    info("%s \tupper bound: %g" % (name, upper[0]))
+ 
+         # If starting fit statistic is chi-squared or C-stat,
+         # can calculate reduced fit statistic -- if it is
+Index: sherpa-4.15.1/sherpa/instrument.py
+===================================================================
+--- sherpa-4.15.1.orig/sherpa/instrument.py
++++ sherpa-4.15.1/sherpa/instrument.py
+@@ -357,9 +357,17 @@ class PSFKernel(Kernel):
+             # and Python 3.8 - causes a TypeError with the message
+             # "only integer scalar arrays can be converted to a scalar index"
+             # to be thrown here if sent directly to set_origin. So
+-            # we convert to a Python integer type.
++            # we convert to a Python integer type. In NumPy 1.25 it became
++            # a deprecation error to call int on an array with ndim > 0.
+             #
+-            origin = set_origin(kshape, int(brightPixel))
++            # assume there is only one element in brightPixel if not
++            # a scalar
++            #
++            if not numpy.isscalar(brightPixel):
++                loc = brightPixel[0]
++            else:
++                loc = brightPixel
++            origin = set_origin(kshape, int(loc))
+ 
+         if self.origin is None:
+             self.origin = origin

python-sherpa.changes

@@ -1,3 +1,8 @@
+-------------------------------------------------------------------
+Thu Sep  7 12:24:59 UTC 2023 - Markéta Machová <mmachova@suse.com>
+
+- Add upstream patches numpy125.patch and numpy125-CI.patch
+
 -------------------------------------------------------------------
 Mon May 29 13:52:34 UTC 2023 - Dirk Müller <dmueller@suse.com>
 

python-sherpa.spec

@@ -24,6 +24,10 @@ License:        GPL-3.0-only
 URL:            https://github.com/sherpa/sherpa/
 Source0:        https://github.com/sherpa/sherpa/archive/%{version}.tar.gz#/sherpa-%{version}.tar.gz
 Source1:        https://github.com/sherpa/sherpa-test-data/archive/refs/tags/%{version}.tar.gz#/sherpa-test-data-%{version}.tar.gz
+# PATCH-FIX-UPSTREAM https://github.com/sherpa/sherpa/pull/1807 NumPy 1.25 support
+Patch:          numpy125.patch
+# PATCH-FIX-UPSTREAM https://github.com/sherpa/sherpa/pull/1819 CI: hide NumPy 1.25 array ndim>0 deprecation warnings
+Patch:          numpy125-CI.patch
 BuildRequires:  %{python_module devel >= 3.8}
 BuildRequires:  %{python_module numpy-devel >= 1.19}
 BuildRequires:  %{python_module pip}
@@ -54,7 +58,7 @@ user to construct models from definitions and fit those models to
 data, using a variety of statistics and optimization methods.
 
 %prep
-%setup -q -n sherpa-%{version} -a1
+%autosetup -p1 -n sherpa-%{version} -a1
 # uncomment system libs https://sherpa.readthedocs.io/en/latest/install.html#fftw
 sed -i "s|#fftw=local|fftw=local|" setup.cfg
 sed -i "s|#fftw-include[-_]dirs.*$|fftw-include-dirs=%{_includedir}|" setup.cfg