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

numpy125-CI.patch

@@ -1,96 +0,0 @@
-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

@@ -1,89 +0,0 @@
-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 +1,31 @@
+-------------------------------------------------------------------
+Fri Dec 15 03:54:30 UTC 2023 - Steve Kowalik <steven.kowalik@suse.com>
+
+- 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.
+
 -------------------------------------------------------------------
 Thu Sep  7 12:24:59 UTC 2023 - Markéta Machová <mmachova@suse.com>
 

python-sherpa.spec

@@ -17,17 +17,13 @@
 
 
 Name:           python-sherpa
-Version:        4.15.1
+Version:        4.16.0
 Release:        0
 Summary:        Modeling and fitting package for scientific data analysis
 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}
@@ -105,6 +101,7 @@ donttest="test_save"
 donttest+=" or (test_regproj and sherpa.plot.dummy_backend)"
 donttest+=" or (test_fit_single and Chi2XspecVar)"
 %endif
+donttest+=" or test_Griewank"
 %pytest_arch %{?jobs:-n %jobs} --pyargs sherpa -k "not ($donttest)"
 
 %post
@@ -121,7 +118,7 @@ donttest+=" or (test_fit_single and Chi2XspecVar)"
 %python_alternative %{_bindir}/sherpa_test
 %python_alternative %{_bindir}/sherpa_smoke
 %{python_sitearch}/sherpa
-%{python_sitearch}/sherpa-%{version}*-info
+%{python_sitearch}/sherpa-%{version}.dist-info
 %{python_sitearch}/stk.so
 %{python_sitearch}/group.so
 

sherpa-4.15.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:3b3c4b7ce8a03a2cf2c5f3d1f288a6f332885ca04c50b1a829d4a244281f3112
-size 13362922

sherpa-4.16.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:95e665d87048a26e203785e6efbb9f44cf75cb6ea0c9ee853e3796b5a0c9444f
+size 13686939

sherpa-test-data-4.15.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a6b6335bd6ad84ff28a7fdc32b5cc45952c7aded193bc55154f4e208736c4126
-size 134765085

sherpa-test-data-4.16.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:27d356af9d819ca0a5df9cca2ff8f29444629a33a9d5d347ed790a8d4596b7f5
+size 137774612