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Accepting request 1228824 from devel:languages:python:numeric

Browse Source 
- Update to 4.17.0
  * This release of Sherpa includes various enhancements,
    documentation updates, bug fixes, and infrastructure changes.
  ## enhancements:
  * add calc_model and calc_source functions to return an evaluated
    model/source array
  * added wstat to plot_pvalue for the likelihood ratio test
  * changed XSpec interface to use FunctionUtility C++ API instead
    of XSFortran API
  * improved support for PHA data starting at channel 0 and
    handling of STAT_ERR and SYS_ERR PHA columns which are set to 0
  * improved guess for complex models
  * improved filtering handling
  * several updates to enhance plotting capabilities and layout
  ## documentation changes:
  * added paper citations to front page of Sherpa Read the Docs
    documentation
  * cleaned up various typos and URL references
  * added examples such as use of set_x/y_label
  ## infrastructure and testing:
  * improved test coverage
  * many updates to CI
  * drop support for Python 3.9 and numpy <1.24
  * initial/experimental support for Python 3.12
  ## bug fixes:
  * fixed an issue with plotting 1D data with asymmetric errs after
    filter
  * include the default identifier in save_all output if it has
    been changed
- Drop numpy2.patch
- Add sherpa-pr2188-np2docstrings.patch gh#sherpa/sherpa#2188
- Add sherpa-suse-libdir.patch

OBS-URL: https://build.opensuse.org/request/show/1228824
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-sherpa?expand=0&rev=23
This commit is contained in:
Ana Guerrero 2024-12-08 10:37:24 +00:00 committed by Git OBS Bridge
commit 45f8ea50e6
9 changed files with 384 additions and 339 deletions
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297
numpy2.patch
View File

@ -1,297 +0,0 @@
From 72028ffe7ce2566a8f1e88c2c06d79cf5f0be9c1 Mon Sep 17 00:00:00 2001
From: Douglas Burke <dburke.gw@gmail.com>
Date: Thu, 27 Jun 2024 12:42:52 -0400
Subject: [PATCH 1/7] root: internal code cleanup
The root-finding code is not documented well. This adds a small
wrapper routine to avoid some replicated code, but could we
just add this to transformed_quad_coef() instead - which is
not explicitly marked as an external routine?
Several comments have been added for potential future work.
---
sherpa/utils/__init__.py | 38 ++++++++++++++++++++++-----------
sherpa/utils/tests/test_root.py | 5 +++++
2 files changed, 30 insertions(+), 13 deletions(-)
Index: sherpa-4.16.1/sherpa/utils/__init__.py
===================================================================
--- sherpa-4.16.1.orig/sherpa/utils/__init__.py
+++ sherpa-4.16.1/sherpa/utils/__init__.py
@@ -1480,7 +1480,7 @@ def create_expr_integrated(lovals, hival
delim : str, optional
The separator for a range.
eps : number, optional
- The tolerance for comparing two numbers with sao_fcmp.
+ This value is unused.
Raises
------
@@ -3389,6 +3389,7 @@ def bisection(fcn, xa, xb, fa=None, fb=N
return [[None, None], [[xa, fa], [xb, fb]], nfev[0]]
+# Is this used at all?
def quad_coef(x, f):
"""
p( x ) = f( xc ) + A ( x - xc ) + B ( x - xc ) ( x - xb )
@@ -3461,6 +3462,11 @@ def transformed_quad_coef(x, f):
xa, xb, xc = x[0], x[1], x[2]
fa, fb, fc = f[0], f[1], f[2]
+ # What happens if xb_xa or xc_xa are 0? That is, either
+ # xa == xb
+ # xc == xa
+ # Is the assumption that this just never happen?
+ #
xc_xb = xc - xb
fc_fb = fc - fb
A = fc_fb / xc_xb
@@ -3472,6 +3478,21 @@ def transformed_quad_coef(x, f):
return [B, C]
+def _get_discriminant(xa, xb, xc, fa, fb, fc):
+ """Wrap up code to transformed_quad_coef.
+
+ This is common code that could be added to transformed_quad_coef
+ but is left out at the moment, to make it easier to look back
+ at code changes. There is no description of the parameters as
+ the existing code has none.
+
+ """
+
+ [B, C] = transformed_quad_coef([xa, xb, xc], [fa, fb, fc])
+ discriminant = max(C * C - 4.0 * fc * B, 0.0)
+ return B, C, discriminant
+
+
def demuller(fcn, xa, xb, xc, fa=None, fb=None, fc=None, args=(),
maxfev=32, tol=1.0e-6):
"""A root-finding algorithm using Muller's method.
@@ -3578,10 +3599,7 @@ def demuller(fcn, xa, xb, xc, fa=None, f
while nfev[0] < maxfev:
- [B, C] = transformed_quad_coef([xa, xb, xc], [fa, fb, fc])
-
- discriminant = max(C * C - 4.0 * fc * B, 0.0)
-
+ B, C, discriminant = _get_discriminant(xa, xb, xc, fa, fb, fc)
if is_nan(B) or is_nan(C) or \
0.0 == C + mysgn(C) * np.sqrt(discriminant):
return [[None, None], [[None, None], [None, None]], nfev[0]]
@@ -3685,11 +3703,7 @@ def new_muller(fcn, xa, xb, fa=None, fb=
if abs(fc) <= tol:
return [[xc, fc], [[xa, fa], [xb, fb]], nfev[0]]
- tran = transformed_quad_coef([xa, xb, xc], [fa, fb, fc])
- B = tran[0]
- C = tran[1]
-
- discriminant = max(C * C - 4.0 * fc * B, 0.0)
+ B, C, discriminant = _get_discriminant(xa, xb, xc, fa, fb, fc)
xd = xc - 2.0 * fc / (C + mysgn(C) * np.sqrt(discriminant))
@@ -3827,11 +3841,9 @@ def apache_muller(fcn, xa, xb, fa=None,
oldx = 1.0e128
while nfev[0] < maxfev:
- tran = transformed_quad_coef([xa, xb, xc], [fa, fb, fc])
- B = tran[0]
- C = tran[1]
- discriminant = max(C * C - 4.0 * fc * B, 0.0)
- den = mysgn(C) * np.sqrt(discriminant)
+
+ B, C, discriminant = _get_discriminant(xa, xb, xc, fa, fb, fc)
+ den = np.sign(C) * np.sqrt(discriminant)
xplus = xc - 2.0 * fc / (C + den)
if C != den:
xminus = xc - 2.0 * fc / (C - den)
@@ -4008,9 +4020,13 @@ def zeroin(fcn, xa, xb, fa=None, fb=None
warning('%s: %s fa * fb < 0 is not met', __name__, fcn.__name__)
return [[None, None], [[None, None], [None, None]], nfev[0]]
+ # With NumPy 2.0 the casting rules changed, leading to some
+ # behavioural changes in this code. The simplest fix was to
+ # make sure DBL_EPSILON did not remain a np.float32 value.
+ #
xc = xa
fc = fa
- DBL_EPSILON = np.finfo(np.float32).eps
+ DBL_EPSILON = float(np.finfo(np.float32).eps)
while nfev[0] < maxfev:
prev_step = xb - xa
Index: sherpa-4.16.1/sherpa/utils/tests/test_root.py
===================================================================
--- sherpa-4.16.1.orig/sherpa/utils/tests/test_root.py
+++ sherpa-4.16.1/sherpa/utils/tests/test_root.py
@@ -1,5 +1,6 @@
#
-# Copyright (C) 2007, 2016, 2018, 2020, 2021 Smithsonian Astrophysical Observatory
+# Copyright (C) 2007, 2016, 2018, 2020, 2021, 2024
+# Smithsonian Astrophysical Observatory
#
#
# This program is free software; you can redistribute it and/or modify
@@ -27,7 +28,7 @@ from sherpa.utils import demuller, bisec
zeroin
-def sqr(x, *args):
+def sqr(x):
return x * x
@@ -177,9 +178,7 @@ def prob34(x, *args):
return 1.0 / x - numpy.sin(x) + 1.0
-def prob35(x, *args):
- return (x*x - 2.0) * x - 5.0
-
+# prob35 was the same as prob16
def prob36(x, *args):
return 1.0 / x - 1.0
@@ -288,7 +287,6 @@ def demuller2(fcn, xa, xb, fa=None, fb=N
(prob32, 0.1, 0.9),
(prob33, 2.8, 3.1),
(prob34, -1.3, -0.5),
- (prob35, 2.0, 3.0),
(prob36, 0.5, 1.5),
(prob37, 0.5, 5.0),
(prob38, 1.0, 4.0),
Index: sherpa-4.16.1/sherpa/estmethods/__init__.py
===================================================================
--- sherpa-4.16.1.orig/sherpa/estmethods/__init__.py
+++ sherpa-4.16.1/sherpa/estmethods/__init__.py
@@ -380,6 +380,11 @@ def covariance(pars, parmins, parmaxes,
eflag = est_success
ubound = diag[num]
lbound = -diag[num]
+
+ # What happens when lbound or ubound is NaN? This is
+ # presumably why the code is written as it is below (e.g. a
+ # pass if the values can be added to pars[num]).
+ #
if pars[num] + ubound < parhardmaxes[num]:
pass
else:
@@ -1093,6 +1098,7 @@ def confidence(pars, parmins, parmaxes,
print_status(myblog.blogger.info, verbose, status_prefix[dirn],
delta_zero, lock)
+ # This should really set the error flag appropriately.
error_flags.append(est_success)
#
Index: sherpa-4.16.1/sherpa/fit.py
===================================================================
--- sherpa-4.16.1.orig/sherpa/fit.py
+++ sherpa-4.16.1/sherpa/fit.py
@@ -277,7 +277,7 @@ class FitResults(NoNewAttributesAfterIni
self.succeeded = results[0]
self.parnames = tuple(p.fullname for p in fit.model.get_thawed_pars())
- self.parvals = tuple(results[1])
+ self.parvals = tuple(float(r) for r in results[1])
self.istatval = init_stat
self.statval = results[2]
self.dstatval = np.abs(results[2] - init_stat)
@@ -439,25 +439,28 @@ class ErrorEstResults(NoNewAttributesAft
self.sigma = fit.estmethod.sigma
self.percent = erf(self.sigma / sqrt(2.0)) * 100.0
self.parnames = tuple(p.fullname for p in parlist if not p.frozen)
- self.parvals = tuple(p.val for p in parlist if not p.frozen)
+ self.parvals = tuple(float(p.val) for p in parlist if not p.frozen)
self.parmins = ()
self.parmaxes = ()
- self.nfits = 0
for i in range(len(parlist)):
if (results[2][i] == est_hardmin or
- results[2][i] == est_hardminmax):
+ results[2][i] == est_hardminmax or
+ results[0][i] is None # It looks like confidence does not set the flag
+ ):
self.parmins = self.parmins + (None,)
warning("hard minimum hit for parameter %s", self.parnames[i])
else:
- self.parmins = self.parmins + (results[0][i],)
+ self.parmins = self.parmins + (float(results[0][i]),)
if (results[2][i] == est_hardmax or
- results[2][i] == est_hardminmax):
+ results[2][i] == est_hardminmax or
+ results[1][i] is None # It looks like confidence does not set the flag
+ ):
self.parmaxes = self.parmaxes + (None,)
warning("hard maximum hit for parameter %s", self.parnames[i])
else:
- self.parmaxes = self.parmaxes + (results[1][i],)
+ self.parmaxes = self.parmaxes + (float(results[1][i]),)
self.nfits = results[3]
self.extra_output = results[4]
Index: sherpa-4.16.1/sherpa/astro/tests/test_astro.py
===================================================================
--- sherpa-4.16.1.orig/sherpa/astro/tests/test_astro.py
+++ sherpa-4.16.1/sherpa/astro/tests/test_astro.py
@@ -206,7 +206,7 @@ def test_sourceandbg(parallel, run_threa
assert fit_results.numpoints == 1330
assert fit_results.dof == 1325
- assert covarerr[0] == approx(0.012097, rel=1e-3)
+ assert covarerr[0] == approx(0.012097, rel=1.05e-3)
assert covarerr[1] == approx(0, rel=1e-3)
assert covarerr[2] == approx(0.000280678, rel=1e-3)
assert covarerr[3] == approx(0.00990783, rel=1e-3)
Index: sherpa-4.16.1/docs/developer/index.rst
===================================================================
--- sherpa-4.16.1.orig/docs/developer/index.rst
+++ sherpa-4.16.1/docs/developer/index.rst
@@ -100,6 +100,17 @@ files and shows exactly which lines were
Run doctests locally
--------------------
+
+.. note::
+ The documentation tests are known to fail if NumPy 2.0 is installed
+ because the representation of NumPy types such as ``np.float64``
+ have changed, leading to errors like::
+
+ Expected:
+ 2.5264364698914e-06
+ Got:
+ np.float64(2.5264364698914e-06)
+
If `doctestplus <https://pypi.org/project/pytest-doctestplus/>` is installed
(and it probably is because it's part of
`sphinx-astropy <https://pypi.org/project/sphinx-astropy/>`,
Index: sherpa-4.16.1/docs/install.rst
===================================================================
--- sherpa-4.16.1.orig/docs/install.rst
+++ sherpa-4.16.1/docs/install.rst
@@ -34,17 +34,14 @@ Requirements
Sherpa has the following requirements:
* Python 3.9 to 3.11
-* NumPy (the exact lower limit has not been determined,
- 1.21.0 or later will work, earlier version may work)
+* NumPy (version 2.0 should work but there has been limited testing)
* Linux or OS-X (patches to add Windows support are welcome)
Sherpa can take advantage of the following Python packages
if installed:
* :term:`Astropy`: for reading and writing files in
- :term:`FITS` format. The minimum required version of astropy
- is version 1.3, although only versions 2 and higher are used in testing
- (version 3.2 is known to cause problems, but version 3.2.1 is okay).
+ :term:`FITS` format.
* :term:`matplotlib`: for visualisation of
one-dimensional data or models, one- or two- dimensional
error analysis, and the results of Monte-Carlo Markov Chain

36
python-sherpa.changes
View File

@ -1,3 +1,39 @@
-------------------------------------------------------------------
Fri Dec 6 12:40:33 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Update to 4.17.0
* This release of Sherpa includes various enhancements,
documentation updates, bug fixes, and infrastructure changes.
## enhancements:
* add calc_model and calc_source functions to return an evaluated
model/source array
* added wstat to plot_pvalue for the likelihood ratio test
* changed XSpec interface to use FunctionUtility C++ API instead
of XSFortran API
* improved support for PHA data starting at channel 0 and
handling of STAT_ERR and SYS_ERR PHA columns which are set to 0
* improved guess for complex models
* improved filtering handling
* several updates to enhance plotting capabilities and layout
## documentation changes:
* added paper citations to front page of Sherpa Read the Docs
documentation
* cleaned up various typos and URL references
* added examples such as use of set_x/y_label
## infrastructure and testing:
* improved test coverage
* many updates to CI
* drop support for Python 3.9 and numpy <1.24
* initial/experimental support for Python 3.12
## bug fixes:
* fixed an issue with plotting 1D data with asymmetric errs after
filter
* include the default identifier in save_all output if it has
been changed
- Drop numpy2.patch
- Add sherpa-pr2188-np2docstrings.patch gh#sherpa/sherpa#2188
- Add sherpa-suse-libdir.patch
-------------------------------------------------------------------
Thu Sep 12 06:18:49 UTC 2024 - Markéta Machová <mmachova@suse.com>

67
python-sherpa.spec
View File

@ -16,22 +16,23 @@
#
# requires distutils and setuptools < 60, which does not backport distutils. Unsuitable for python312
# Track upstream progress in https://github.com/sherpa/sherpa/pull/1949
%define skip_python312 1
Name: python-sherpa
Version: 4.16.1
Version: 4.17.0
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/2069 Allow the tests to pass with NumPy 2.0
Patch: numpy2.patch
BuildRequires: %{python_module devel >= 3.8}
BuildRequires: %{python_module numpy-devel >= 1.19}
# PATCH-FIX-UPSTREAM sherpa-pr2188-np2docstrings.patch gh#sherpa/sherpa#2188
Patch0: https://github.com/sherpa/sherpa/pull/2188.patch#/sherpa-pr2188-np2docstrings.patch
# PATCH-FIX-OPENSUSE sherpa-suse-libdir.patch -- UPSTREAM struggles with library paths, see e.g. gh#sherpa/sherpa#2159 code@bnavigator.de
Patch1: sherpa-suse-libdir.patch
BuildRequires: %{python_module devel >= 3.9}
BuildRequires: %{python_module numpy-devel}
BuildRequires: %{python_module pip}
BuildRequires: %{python_module setuptools >= 64}
BuildRequires: %{python_module tomli if %python-base < 3.11}
BuildRequires: %{python_module wheel}
BuildRequires: bison
BuildRequires: fdupes
@ -39,14 +40,15 @@ BuildRequires: fftw3-devel
BuildRequires: flex
BuildRequires: gcc-c++
BuildRequires: python-rpm-macros
Requires: python-numpy >= 1.19
BuildRequires: wcslib-devel
Requires: python-numpy
Requires(post): update-alternatives
Requires(postun): update-alternatives
ExcludeArch: %{ix86} %{arm}
# SECTION test requirements
BuildRequires: %{python_module pytest >= 5}
BuildRequires: %{python_module pytest >= 8}
# doctestplus tests don’t look ready gh#sherpa/sherpa#1719
# BuildRequires: %{python_module pytest-doctestplus}
# BuildRequires: %%{python_module pytest-doctestplus}
BuildRequires: %{python_module pytest-xdist}
BuildRequires: %{python_module pytest-xvfb}
# Highly recommended by upstream when building from source
@ -62,23 +64,19 @@ data, using a variety of statistics and optimization methods.
%prep
%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.*$|fftw-include-dirs=%{_includedir}|" setup.cfg
sed -i "s|#fftw-lib-dirs.*$|fftw-lib-dirs=%{_libdir}|" setup.cfg
sed -i "s|#fftw-libraries|fftw-libraries|" setup.cfg
sed -i -e 's|@_LIB@|%{_lib}|' setup.cfg helpers/sherpa_config.py
rm -r extern/fftw-*
# adjust the "install path" for stk.so and group.so for the build phase
sed -i "/pydir =/ s/libdir,/self.install_dir, '%{_lib}',/" helpers/sherpa_config.py
# Remove shebangs
sed -i "1{/\\/usr\\/bin\\/env python/d}" \
sherpa/optmethods/ncoresde.py \
sherpa/optmethods/ncoresnm.py \
sherpa/optmethods/opt.py \
sherpa/utils/akima.py
%build
cp -r extern extern0
%{python_expand #
# use the python3X bundled setuptools instead of setuptools 60+ from the distribution
# https://sherpa.readthedocs.io/en/latest/install.html#building-from-source
mkdir -p build
$python -m venv build/buildenv --system-site-packages
build/buildenv/bin/pip wheel --no-deps --disable-pip-version-check --use-pep517 --no-build-isolation --progress-bar off --verbose . -w build/
%{python_expand # rebuild and install extern/ into build/ for every wheel
%$python_pyproject_wheel
rm -r extern
cp -r extern0 extern
}
@ -90,27 +88,24 @@ cp -r extern0 extern
%python_clone -a %{buildroot}%{_bindir}/sherpa_smoke
%python_expand %fdupes %{buildroot}%{$python_sitearch}
%{python_expand # REMOVE HASHBANGS FROM NON-EXEC FILES
sed -i "1{/\\/usr\\/bin\\/env python/d}" %{buildroot}%{$python_sitearch}/sherpa/optmethods/ncoresde.py
sed -i "1{/\\/usr\\/bin\\/env python/d}" %{buildroot}%{$python_sitearch}/sherpa/optmethods/ncoresnm.py
sed -i "1{/\\/usr\\/bin\\/env python/d}" %{buildroot}%{$python_sitearch}/sherpa/optmethods/opt.py
sed -i "1{/\\/usr\\/bin\\/env python/d}" %{buildroot}%{$python_sitearch}/sherpa/utils/akima.py
}
%check
# avoid conftest import mismatch
mv sherpa sherpa_temp
export PYTHONPATH=$PWD/sherpa-test-data-%{version}
# unclosed resource warnings by pytest although the tests use Path.to_text which should have closed it.
donttest="test_save"
donttest="test_Griewank"
# precision issues
%ifnarch x86_64
donttest+=" or (test_regproj and sherpa.plot.dummy_backend)"
donttest+=" or (test_fit_single and Chi2XspecVar)"
%endif
donttest+=" or test_Griewank"
# Tests must not be run in parallel https://github.com/sherpa/sherpa/issues/2031
%pytest_arch -n1 --pyargs sherpa -k "not ($donttest)"
# gh#sherpa/sherpa#1923
donttest+=" or test_integrate1d_basic_epsabs"
# flaky
donttest+=" or test_scaling_staterr"
donttest+=" or (test_Shekel7 and montecarlo)"
# docstring mismatches
python313_donttest=" or test_show_fit or test_modify_doctring or test_modelwrapper_str_with_doc"
%pytest_arch --pyargs sherpa -n auto --dist=loadgroup -r fE -k "not ($donttest ${$python_donttest})"
%post
%python_install_alternative sherpa_smoke

3
sherpa-4.16.1.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:ed4dfba237c4a6b60b4141e5619b53b25cb9e23be26cbcd7dbf00f8822d4669c
size 13738921

3
sherpa-4.17.0.tar.gz Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:f22f9dcb1b6326508d4142ea88931492972782fd292871ed942d1a212e70091a
size 13985328

248
sherpa-pr2188-np2docstrings.patch Normal file
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@ -0,0 +1,248 @@
From 388a7b3c87b8068c572041aeb57d2136a583e83b Mon Sep 17 00:00:00 2001
From: Douglas Burke <dburke.gw@gmail.com>
Date: Tue, 29 Oct 2024 14:35:02 -0400
Subject: [PATCH] TEST: address numpy 2 changes to output for docstring tests
The str/repr output in NumPy 2 is much-more verbose and no-longet
matches the behaviour of the associated Python types. This breaks
a number of doctests, which had things like
>>> (a == b).all()
True
>>> x.val
3.4
which now fails for "textual" reasons even though the values are
the same. The simplest approach is just to print the values, so
we now have
>>> print((a == b).all())
True
>>> print(x.val)
3.4
It is not ideal, but is a simple fix that works with versions 1
and 2 of NumPy.
---
sherpa/astro/data.py | 14 +++++++-------
sherpa/data.py | 8 ++++----
sherpa/models/basic.py | 24 ++++++++++++------------
sherpa/models/model.py | 2 +-
sherpa/models/parameter.py | 10 +++++-----
5 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/sherpa/astro/data.py b/sherpa/astro/data.py
index 15f91fad72..87db02f617 100644
--- a/sherpa/astro/data.py
+++ b/sherpa/astro/data.py
@@ -2563,9 +2563,9 @@ def _get_ebins(self,
>>> pha.ungroup()
>>> pha.units = 'channel'
>>> clo, chi = pha._get_ebins()
- >>> (clo == pha.channel).all()
+ >>> print((clo == pha.channel).all())
True
- >>> (chi == clo + 1).all()
+ >>> print((chi == clo + 1).all())
True
>>> pha.units = 'energy'
@@ -2574,7 +2574,7 @@ def _get_ebins(self,
True
>>> elo[0:5]
array([0.00146, 0.0146 , 0.0292 , 0.0438 , 0.0584 ])
- >>> (elo[1:] == ehi[:-1]).all()
+ >>> print((elo[1:] == ehi[:-1]).all())
True
>>> pha.group()
@@ -2587,7 +2587,7 @@ def _get_ebins(self,
>>> pha.units = 'wave'
>>> wlo, whi = pha._get_ebins()
- >>> (wlo == glo).all()
+ >>> print((wlo == glo).all())
True
"""
@@ -2702,7 +2702,7 @@ def _get_indep(self,
array([0.1 , 0.11, 0.12, 0.13, 0.14])
>>> ehi[0:5]
array([0.11 , 0.12 , 0.13 , 0.14 , 0.15000001])
- >>> (elo[1:] == ehi[:-1]).all()
+ >>> print((elo[1:] == ehi[:-1]).all())
True
>>> pha.units = 'wave'
@@ -2711,7 +2711,7 @@ def _get_indep(self,
array([112.71289825, 103.32015848, 95.37245534, 88.56013348])
>>> whi[0:4]
array([123.98418555, 112.71289825, 103.32015848, 95.37245534])
- >>> (wlo[:-1] == whi[1:]).all()
+ >>> print((wlo[:-1] == whi[1:]).all())
True
"""
@@ -3425,7 +3425,7 @@ def apply_grouping(self, data, groupfunc=np.sum):
>>> v1 = pha.apply_grouping(dvals)
>>> pha.notice(1.2, 4.5)
>>> v2 = pha.apply_grouping(dvals)
- >>> np.all(v1 == v2)
+ >>> print(np.all(v1 == v2))
True
"""
diff --git a/sherpa/data.py b/sherpa/data.py
index 30fe9dbf0f..daf79d93e2 100644
--- a/sherpa/data.py
+++ b/sherpa/data.py
@@ -2042,8 +2042,8 @@ def notice(self,
>>> x = np.arange(0.4, 2.6, 0.2)
>>> y = np.ones_like(x)
>>> d = Data1D('example', x, y)
- >>> d.x[0], d.x[-1]
- (0.4, 2.4000000000000004)
+ >>> print(d.x[0], d.x[-1])
+ 0.4 2.4000000000000004
>>> d.notice()
>>> d.get_filter(format='%.1f')
'0.4:2.4'
@@ -2326,8 +2326,8 @@ def notice(self,
>>> xlo, xhi = edges[:-1], edges[1:]
>>> y = np.ones_like(xlo)
>>> d = Data1DInt('example', xlo, xhi, y)
- >>> d.xlo[0], d.xhi[-1]
- (0.4, 2.400000000000001)
+ >>> print(d.xlo[0], d.xhi[-1])
+ 0.4 2.400000000000001
>>> d.get_filter(format='%.1f')
'0.4:2.4'
>>> d.notice(0.8, 1.9)
diff --git a/sherpa/models/basic.py b/sherpa/models/basic.py
index c1061e033a..d5280eda0f 100644
--- a/sherpa/models/basic.py
+++ b/sherpa/models/basic.py
@@ -539,14 +539,14 @@ class Gauss1D(RegriddableModel1D):
>>> m1.pos, m2.pos = 10, 10
>>> m1.ampl, m2.ampl = 10, 10
>>> m1.fwhm, m2.fwhm = 5, 5
- >>> m1(10)
+ >>> print(m1(10))
10.0
- >>> m2(10)
+ >>> print(m2(10))
1.8788745573993026
>>> m1.fwhm, m2.fwhm = 1, 1
- >>> m1(10)
+ >>> print(m1(10))
10.0
- >>> m2(10)
+ >>> print(m2(10))
9.394372786996513
The normalised version will sum to the amplitude when given
@@ -558,9 +558,9 @@ class Gauss1D(RegriddableModel1D):
>>> m1.fwhm, m2.fwhm = 12.2, 12.2
>>> grid = np.arange(-90, 110, 0.01)
>>> glo, ghi = grid[:-1], grid[1:]
- >>> m1(glo, ghi).sum()
+ >>> print(m1(glo, ghi).sum())
129.86497637060958
- >>> m2(glo, ghi).sum()
+ >>> print(m2(glo, ghi).sum())
10.000000000000002
"""
@@ -1923,12 +1923,12 @@ class TableModel(ArithmeticModel):
>>> d.staterror = [.2, .2, .2, .2, .2]
>>> tm1 = TableModel('tabmodel')
>>> tm1.load(None, [.6, .2, 1.1, .2, .5])
- >>> tm1.ampl.val
+ >>> print(tm1.ampl.val)
1.0
>>> tm1.fold(d)
>>> fit1 = Fit(d, tm1)
>>> res1 = fit1.fit()
- >>> tm1.ampl.val
+ >>> print(tm1.ampl.val)
1.9894736842102083
In this case the `fold` method is necessary, to ensure that the
@@ -1941,11 +1941,11 @@ class TableModel(ArithmeticModel):
>>> tm2 = TableModel('tabmodel')
>>> tm2.load(None, [.6, .2, 1.1, .2, .5])
>>> tm2.fold(d)
- >>> tm2.ampl.val
+ >>> print(tm2.ampl.val)
1.0
>>> fit2 = Fit(d, tm2)
>>> res2 = fit2.fit()
- >>> tm2.ampl.val
+ >>> print(tm2.ampl.val)
1.9866666666663104
The masking also holds if the notice or ignore method has been
@@ -1957,11 +1957,11 @@ class TableModel(ArithmeticModel):
>>> tm3 = TableModel('tabmodel')
>>> tm3.load(None, [.6, .2, 1.1, .2, .5])
>>> tm3.fold(d)
- >>> tm3.ampl.val
+ >>> print(tm3.ampl.val)
1.0
>>> fit3 = Fit(d, tm3)
>>> res = fit3.fit()
- >>> tm3.ampl.val
+ >>> print(tm3.ampl.val)
1.9866666666663104
"""
diff --git a/sherpa/models/model.py b/sherpa/models/model.py
index 5b89181d28..020ef7a30f 100644
--- a/sherpa/models/model.py
+++ b/sherpa/models/model.py
@@ -152,7 +152,7 @@
>>> m1.ampl = 10
>>> m2.ampl = 12
- >>> m3.ampl.val
+ >>> print(m3.ampl.val)
11.0
>>> m3.ampl.link
<BinaryOpParameter '(gauss1d.ampl + gmdl.ampl) / 2'>
diff --git a/sherpa/models/parameter.py b/sherpa/models/parameter.py
index 3e1ee5215a..09af7c9bcf 100644
--- a/sherpa/models/parameter.py
+++ b/sherpa/models/parameter.py
@@ -60,7 +60,7 @@
The `val` attribute is used to retrieve or change the parameter value:
- >>> p.val
+ >>> print(p.val)
2.0
>>> p.val = 3
@@ -72,9 +72,9 @@
for these are the 32-bit floating point maximum value, and it's
negative:
- >>> p.max
+ >>> print(p.max)
3.4028234663852886e+38
- >>> p.min
+ >>> print(p.min)
-3.4028234663852886e+38
Setting a value outside this range will raise a
@@ -578,9 +578,9 @@ def _set_link(self, link: Optional[Parameter]) -> None:
>>> a = Parameter("mdl", "a", 2)
>>> b = Parameter("mdl", "b", 1)
>>> b.link = 10 - a
->>> a.val
+>>> print(a.val)
2.0
->>> b.val
+>>> print(b.val)
8.0
""")

63
sherpa-suse-libdir.patch Normal file
View File

@ -0,0 +1,63 @@
diff -ur sherpa-4.17.0.orig/helpers/sherpa_config.py sherpa-4.17.0/helpers/sherpa_config.py
--- sherpa-4.17.0.orig/helpers/sherpa_config.py 2024-12-06 15:08:24.931381043 +0100
+++ sherpa-4.17.0/helpers/sherpa_config.py 2024-12-06 16:38:48.368539972 +0100
@@ -79,7 +79,7 @@
def finalize_options(self):
incdir = os.path.join(self.install_dir, 'include')
libdir = os.path.join(self.install_dir, 'lib')
- pydir = os.path.join(libdir, f'python{version}', 'site-packages')
+ pydir = os.path.join(self.install_dir, '@_LIB@', f'python{version}', 'site-packages')
if self.fftw_include_dirs is None:
self.fftw_include_dirs = incdir
@@ -144,7 +144,7 @@
# normal installs: editable installs do not seem to care about
# the data_files setting.
#
- libdir = os.path.join('lib',
+ libdir = os.path.join('@_LIB@',
f'python{version}',
'site-packages')
dfiles = []
diff -ur sherpa-4.17.0.orig/setup.cfg sherpa-4.17.0/setup.cfg
--- sherpa-4.17.0.orig/setup.cfg 2024-12-06 15:08:24.934714481 +0100
+++ sherpa-4.17.0/setup.cfg 2024-12-06 16:38:22.761072281 +0100
@@ -20,15 +20,15 @@
# FFTW Library
# Uncomment to use a local installation
-#fftw=local
+fftw=local
# If fftw=local uncomment the following lines and
# change the default location of libraries and the name
# of the library to be linked (usually fftw3)
# (include multiple values by separating them with spaces)
-#fftw-include_dirs=build/include
-#fftw-lib-dirs=build/lib
-#fftw-libraries=fftw3
+fftw-include_dirs=include
+fftw-lib-dirs=@_LIB@
+fftw-libraries=fftw3
# Region Library
# Uncomment to use a local installation
@@ -50,13 +50,10 @@
#region-use-cxc-parser=False
# WCS Subroutines
-# Uncomment to use a local installation
-#wcs=local
-
-# Uncomment and change default location if needed
-#wcs-include-dirs=build/include
-#wcs-lib-dirs=build/lib
-#wcs-libraries=wcs
+# sherpa is not compatible with wcs.h from system. Make it build and find vendored wcssubs in extern/
+wcs-include-dirs=build/include
+wcs-lib-dirs=build/lib
+wcs-libraries=wcs
[build_sphinx]
Nur in sherpa-4.17.0: sherpa-suse-libdir.patch.

3
sherpa-test-data-4.16.1.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:c61443bf3530e42322cec52887cc2f170c2d5d9aaba2822e107da2626c269a1c
size 137775313

3
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View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:215d3465c7a9d1b4307ec5eeb1f489a1251de9cee71e75e7162f491ad6037126
size 137775257