Script 'mail_helper' called by obssrc
Hello community,
here is the log from the commit of package python-fabio for openSUSE:Factory
checked in at 2022-06-15 00:33:06
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-fabio (Old)
and /work/SRC/openSUSE:Factory/.python-fabio.new.1548 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-fabio"
Wed Jun 15 00:33:06 2022 rev:4 rq:982582 version:0.14.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-fabio/python-fabio.changes
2022-04-21 15:48:57.344335276 +0200
+++ /work/SRC/openSUSE:Factory/.python-fabio.new.1548/python-fabio.changes
2022-06-15 00:34:02.458680046 +0200
@@ -1,0 +2,12 @@
+Fri Jun 10 19:19:12 UTC 2022 - Yogalakshmi Arunachalam <yarunacha...@suse.com>
+
+- Update to 0.14.0:
+ * fix infinite loop when iterating over lima/eiger image files (#468)
+ * fix typo when saving in pilatus/CBF format (#471)
+ * fix noisy test on densification (#440)
+ * limit version of setuptools (related to the PEP517 and associated
regressions)
+ * Change logo in documentation
+ * Support for Python versions 3.6 to 3.10, tested on amd64, ppc64le and arm64
+ * Linux is officially the main platform, Windows and MacOS are supported in
best effort mode.
+
+-------------------------------------------------------------------
Old:
----
fabio-0.13.0.tar.gz
New:
----
fabio-0.14.0.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-fabio.spec ++++++
--- /var/tmp/diff_new_pack.fHMPBM/_old 2022-06-15 00:34:03.330681327 +0200
+++ /var/tmp/diff_new_pack.fHMPBM/_new 2022-06-15 00:34:03.334681332 +0200
@@ -20,7 +20,7 @@
%define skip_python2 1
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-fabio
-Version: 0.13.0
+Version: 0.14.0
Release: 0
Summary: Image IO for images produced by 2D X-ray detectors
License: BSD-3-Clause AND GPL-2.0-or-later AND LGPL-3.0-or-later AND MIT
++++++ fabio-0.13.0.tar.gz -> fabio-0.14.0.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/.github/workflows/python-package.yml
new/fabio-0.14.0/.github/workflows/python-package.yml
--- old/fabio-0.13.0/.github/workflows/python-package.yml 2022-01-14
09:57:50.000000000 +0100
+++ new/fabio-0.14.0/.github/workflows/python-package.yml 2022-06-02
16:10:13.000000000 +0200
@@ -15,7 +15,7 @@
runs-on: ubuntu-latest
strategy:
matrix:
- python-version: ['3.6', '3.7', '3.8', '3.9']
+ python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
steps:
- uses: actions/checkout@v2
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/doc/source/Changelog.rst
new/fabio-0.14.0/doc/source/Changelog.rst
--- old/fabio-0.13.0/doc/source/Changelog.rst 2022-01-14 09:57:50.000000000
+0100
+++ new/fabio-0.14.0/doc/source/Changelog.rst 2022-06-02 16:10:13.000000000
+0200
@@ -1,6 +1,16 @@
Changelog
=========
+FabIO-0.14.0 (06/2022):
+.......................
+- fix infinite loop when iterating over lima/eiger image files (#468)
+- fix typo when saving in pilatus/CBF format (#471)
+- fix noisy test on densification (#440)
+- limit version of setuptools (related to the PEP517 and associated
regressions)
+- Change logo in documentation
+- Support for Python versions 3.6 to 3.10, tested on amd64, ppc64le and arm64
+- Linux is officially the main platform, Windows and MacOS are supported in
best effort mode.
+
FabIO-0.13.0 (01/2022):
.......................
- Allow files to be larger than 2GB (Thanks Wout)
Binary files old/fabio-0.13.0/doc/source/img/logo.png and
new/fabio-0.14.0/doc/source/img/logo.png differ
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/cbfimage.py
new/fabio-0.14.0/fabio/cbfimage.py
--- old/fabio-0.13.0/fabio/cbfimage.py 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/fabio/cbfimage.py 2022-06-02 16:10:13.000000000 +0200
@@ -2,7 +2,7 @@
#
# Project: FabIO X-ray image reader
#
-# Copyright (C) 2010-2020 European Synchrotron Radiation Facility
+# Copyright (C) 2010-2022 European Synchrotron Radiation Facility
# Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -326,7 +326,7 @@
nonCifHeaders.append("%s %s" % (key, self.header[key]))
if self.pilatus_headers is not None:
# regenerate the Pilatus header and set the convention
- self.cif["_array_data.header_content"] = str(self.pilatus_headers)
+ self.cif["_array_data.header_contents"] = str(self.pilatus_headers)
self.cif["_array_data.header_convention"] = "PILATUS_1.2"
if len(nonCifHeaders) > 0:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/edfimage.py
new/fabio-0.14.0/fabio/edfimage.py
--- old/fabio-0.13.0/fabio/edfimage.py 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/fabio/edfimage.py 2022-06-02 16:10:13.000000000 +0200
@@ -45,6 +45,11 @@
"""
+__authors__ = ["J??r??me Kieffer", "Jon Wright", "Henning O. Sorensen", "Erik
Knudsen"]
+__contact__ = "jerome.kief...@esrf.fr"
+__license__ = "MIT"
+__copyright__ = "ESRF"
+__date__ = "01/06/2022"
import os
import re
@@ -1214,45 +1219,45 @@
def getframe(self, num):
""" returns the file numbered 'num' in the series as a FabioImage """
- newImage = None
+ new_image = None
if self.nframes == 1:
logger.debug("Single frame EDF; having FabioImage default
behavior: %s" % num)
- newImage = fabioimage.FabioImage.getframe(self, num)
- newImage._file = self._file
+ new_image = fabioimage.FabioImage.getframe(self, num)
+ new_image._file = self._file
elif num < self.nframes:
logger.debug("Multi frame EDF; having EdfImage specific behavior
frame %s: 0<=frame<%s" %
(num, self.nframes))
- newImage = self.__class__(frames=self._frames)
- newImage.currentframe = num
- newImage.filename = self.filename
- newImage._file = self._file
+ new_image = self.__class__(frames=self._frames)
+ new_image.currentframe = num
+ new_image.filename = self.filename
+ new_image._file = self._file
else:
raise IOError("EdfImage.getframe: Cannot access frame %s:
0<=frame<%s" %
(num, self.nframes))
- return newImage
+ return new_image
def previous(self):
""" returns the previous file in the series as a FabioImage """
- newImage = None
+ new_image = None
if self.nframes == 1:
- newImage = fabioimage.FabioImage.previous(self)
+ new_image = fabioimage.FabioImage.previous(self)
else:
- newFrameId = self.currentframe - 1
- newImage = self.getframe(newFrameId)
- return newImage
+ new_idx = self.currentframe - 1
+ new_image = self.getframe(new_idx)
+ return new_image
def next(self):
"""Returns the next file in the series as a fabioimage
:raise IOError: When there is no next file or image in the series.
"""
- newImage = None
+ new_image = None
if self.nframes == 1:
- newImage = fabioimage.FabioImage.next(self)
+ new_image = fabioimage.FabioImage.next(self)
else:
- newFrameId = self.currentframe + 1
- newImage = self.getframe(newFrameId)
- return newImage
+ new_idx = self.currentframe + 1
+ new_image = self.getframe(new_idx)
+ return new_image
def write(self, fname, force_type=None, fit2dMode=False):
"""
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/eigerimage.py
new/fabio-0.14.0/fabio/eigerimage.py
--- old/fabio-0.13.0/fabio/eigerimage.py 2022-01-14 09:57:50.000000000
+0100
+++ new/fabio-0.14.0/fabio/eigerimage.py 2022-06-02 16:10:13.000000000
+0200
@@ -45,7 +45,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
-__date__ = "10/05/2021"
+__date__ = "01/06/2022"
import logging
logger = logging.getLogger(__name__)
@@ -226,18 +226,33 @@
new_img._nframes = self.nframes
new_img.currentframe = num
else:
- raise IOError("getframe %s out of range [%s %s[" % (num, 0,
self.nframes))
+ raise IOError(f"getframe {num} out of range [0
{self.nframes}[")
else:
new_img = FabioImage.getframe(self, num)
return new_img
def previous(self):
- """ returns the previous frame in the series as a fabioimage """
- return self.getframe(self.currentframe - 1)
+ """ returns the previous file in the series as a FabioImage """
+ new_image = None
+ if self.nframes == 1:
+ new_image = FabioImage.previous(self)
+ else:
+ new_idx = self.currentframe - 1
+ new_image = self.getframe(new_idx)
+ return new_image
def next(self):
- """ returns the next frame in the series as a fabioimage """
- return self.getframe(self.currentframe + 1)
+ """Returns the next file in the series as a fabioimage
+
+ :raise IOError: When there is no next file or image in the series.
+ """
+ new_image = None
+ if self.nframes == 1:
+ new_image = FabioImage.next(self)
+ else:
+ new_idx = self.currentframe + 1
+ new_image = self.getframe(new_idx)
+ return new_image
def close(self):
if self.h5 is not None:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/ext/dense.pyx
new/fabio-0.14.0/fabio/ext/dense.pyx
--- old/fabio-0.13.0/fabio/ext/dense.pyx 2022-01-14 09:57:50.000000000
+0100
+++ new/fabio-0.14.0/fabio/ext/dense.pyx 2022-06-02 16:10:13.000000000
+0200
@@ -31,7 +31,7 @@
"""Densification of sparse frame format
"""
__author__ = "J??r??me Kieffer"
-__date__ = "10/05/2021"
+__date__ = "02/06/2022"
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
@@ -44,7 +44,7 @@
int64_t, uint64_t
from libc.math cimport isfinite, log, sqrt, cos, M_PI
from libc.stdlib cimport RAND_MAX
-cimport cython
+cimport cython
ctypedef fused any_t:
double
@@ -221,15 +221,16 @@
return numpy.asarray(ary).reshape(shape)
-def densify(float[:,::1] mask,
- float[::1] radius,
+def densify(cython.floating[:,::1] mask,
+ cython.floating[::1] radius,
uint32_t[::1] index,
any_t[::1] intensity,
any_t dummy,
dtype,
float[::1] background,
float[::1] background_std=None,
- normalization=None):
+ normalization=None,
+ seed = None):
"""
Densify a sparse representation to generate a normal frame
@@ -241,7 +242,8 @@
:param dummy: numerical value for masked-out pixels in dense image
:param dtype: dtype of intensity.
:param background_std: 1D array with the background std at given distance
from the center --> activates the noisy mode.
- :param
+ :param normalization: normalization array: renormalize all data with this
factor (pixel-wise)
+ :param seed: seed for the random number-generator, used only when
regenerating noisy background
:return: dense frame as 2D array
"""
cdef:
@@ -267,15 +269,16 @@
noisy = False
else:
noisy=True
- try:
- value = time.time_ns()
- except Exception:
- value = int(time.time()*1e9)
- mt = MT(value)
+ if seed is None:
+ try:
+ seed = time.time_ns()
+ except Exception:
+ seed = int(time.time()*1e9)
+ mt = MT(seed)
with nogil:
start = radius[0]
- idelta = (size - 1)/(radius[size-1] - start)
+ idelta = <double>(size - 1)/(radius[size-1] - start)
#Linear interpolation
for i in range(height):
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/limaimage.py
new/fabio-0.14.0/fabio/limaimage.py
--- old/fabio-0.13.0/fabio/limaimage.py 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/fabio/limaimage.py 2022-06-02 16:10:13.000000000 +0200
@@ -33,7 +33,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
-__date__ = "07/05/2021"
+__date__ = "01/06/2022"
import logging
logger = logging.getLogger(__name__)
@@ -194,18 +194,33 @@
new_img._nframes = self.nframes
new_img.currentframe = num
else:
- raise IOError("getframe %s out of range [%s %s[" % (num, 0,
self.nframes))
+ raise IOError(f"getframe({num}) out of range [0,
{self.nframes}[")
else:
new_img = FabioImage.getframe(self, num)
return new_img
def previous(self):
- """ returns the previous frame in the series as a fabioimage """
- return self.getframe(self.currentframe - 1)
+ """ returns the previous file in the series as a FabioImage """
+ new_image = None
+ if self.nframes == 1:
+ new_image = FabioImage.previous(self)
+ else:
+ new_idx = self.currentframe - 1
+ new_image = self.getframe(new_idx)
+ return new_image
def next(self):
- """ returns the next frame in the series as a fabioimage """
- return self.getframe(self.currentframe + 1)
+ """Returns the next file in the series as a fabioimage
+
+ :raise IOError: When there is no next file or image in the series.
+ """
+ new_image = None
+ if self.nframes == 1:
+ new_image = FabioImage.next(self)
+ else:
+ new_idx = self.currentframe + 1
+ new_image = self.getframe(new_idx)
+ return new_image
def close(self):
if self.h5 is not None:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/sparseimage.py
new/fabio-0.14.0/fabio/sparseimage.py
--- old/fabio-0.13.0/fabio/sparseimage.py 2022-01-14 09:57:50.000000000
+0100
+++ new/fabio-0.14.0/fabio/sparseimage.py 2022-06-02 16:10:13.000000000
+0200
@@ -37,7 +37,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "2020 ESRF"
-__date__ = "10/05/2021"
+__date__ = "02/06/2022"
import logging
logger = logging.getLogger(__name__)
@@ -66,7 +66,8 @@
dummy,
background,
background_std=None,
- normalization=None):
+ normalization=None,
+ seed=None):
"""Generate a dense image of its sparse representation
:param mask: 2D array with NaNs for mask and pixel radius for the valid
pixels
@@ -82,6 +83,8 @@
"""
dense = numpy.interp(mask, radius, background)
if background_std is not None:
+ if seed is not None:
+ numpy.random.seed(seed)
std = numpy.interp(mask, radius, background_std)
numpy.maximum(0.0, numpy.random.normal(dense, std), out=dense)
if normalization is not None:
@@ -91,7 +94,8 @@
flat[index] = intensity
dtype = intensity.dtype
if numpy.issubdtype(dtype, numpy.integer):
- dense = numpy.round(dense)
+ #dense = numpy.round(dense) # Foolded by banker's rounding !!!!
+ dense += 0.5
dense = numpy.ascontiguousarray(dense, dtype=dtype)
dense[numpy.logical_not(numpy.isfinite(mask))] = dummy
return dense
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/fabio/test/test_densification.py
new/fabio-0.14.0/fabio/test/test_densification.py
--- old/fabio-0.13.0/fabio/test/test_densification.py 2022-01-14
09:57:50.000000000 +0100
+++ new/fabio-0.14.0/fabio/test/test_densification.py 2022-06-02
16:10:13.000000000 +0200
@@ -32,7 +32,7 @@
__contact__ = "jerome.kief...@esrf.fr"
__license__ = "MIT"
__copyright__ = "2020 ESRF"
-__date__ = "28/04/2021"
+__date__ = "02/06/2022"
import unittest
import numpy
@@ -66,13 +66,15 @@
self.assertAlmostEqual(N.std(), sigma, 1)
def test_cython(self):
+ seed = 0
shape = 256, 256
nframes = 8
vsize = 181 # This is cheated to avoid interpolation issues with
rounding 128*sqrt(2)
y, x = numpy.ogrid[-shape[0] // 2:-shape[0] // 2 + shape[0],
-shape[1] // 2:-shape[1] // 2 + shape[1]]
- r2d = numpy.sqrt(x * x + y * y).astype(numpy.float32)
- radius = numpy.linspace(0, r2d.max(), vsize).astype(numpy.float32)
+ # To make this test "robust", those two radial position arrays needs
to be in float64 ... in production float32 is more common
+ r2d = numpy.sqrt(x * x + y * y).astype(numpy.float64)
+ radius = numpy.linspace(0, r2d.max(), vsize).astype(numpy.float64)
npeak = numpy.random.randint(90, 110, size=nframes)
scale = numpy.random.randint(90, 110, size=nframes)
osc = numpy.random.randint(40, 100, size=nframes)
@@ -92,6 +94,7 @@
f.ravel()[index[indptr[i]:indptr[i + 1]]] =
intensity[indptr[i]:indptr[i + 1]]
python = densify(r2d, radius, index[indptr[i]:indptr[i + 1]],
intensity[indptr[i]:indptr[i + 1]], 0, background[i])
cython = cython_densify.densify(r2d, radius,
index[indptr[i]:indptr[i + 1]], intensity[indptr[i]:indptr[i + 1]], 0,
intensity.dtype, background[i], None)
+
self.assertTrue(numpy.all(python == cython), "python == cython #"
+ str(i))
# Rounding errors:
delta = (python.astype(int) - f)
@@ -101,8 +104,8 @@
self.assertLess(len(bad[0]), numpy.prod(shape) / 500, "python
differs from reference on less then 0.2% of the pixel #" + str(i))
# Now consider the noise ...
- python = densify(r2d, radius, index[indptr[i]:indptr[i + 1]],
intensity[indptr[i]:indptr[i + 1]], 0, background[i], noise[i])
- cython = cython_densify.densify(r2d, radius,
index[indptr[i]:indptr[i + 1]], intensity[indptr[i]:indptr[i + 1]], 0,
intensity.dtype, background[i], noise[i])
+ python = densify(r2d, radius, index[indptr[i]:indptr[i + 1]],
intensity[indptr[i]:indptr[i + 1]], 0, background[i], noise[i], seed=seed)
+ cython = cython_densify.densify(r2d, radius,
index[indptr[i]:indptr[i + 1]], intensity[indptr[i]:indptr[i + 1]], 0,
intensity.dtype, background[i], noise[i], seed=seed)
self.assertTrue(abs(python.astype(int) - cython).max() <= 2 *
max(1, noise[i].max()), "python is close to cython #" + str(i))
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/requirements.txt
new/fabio-0.14.0/requirements.txt
--- old/fabio-0.13.0/requirements.txt 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/requirements.txt 2022-06-02 16:10:13.000000000 +0200
@@ -1,4 +1,5 @@
#List of dependecies used by PIP but also by ReadTheDocs to generate the
documentation on the fly
+setuptools<60
numpy
cython
lxml>=4.6.3
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/setup.py new/fabio-0.14.0/setup.py
--- old/fabio-0.13.0/setup.py 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/setup.py 2022-06-02 16:10:13.000000000 +0200
@@ -30,7 +30,7 @@
__contact__ = "jerome.kief...@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "29/04/2021"
+__date__ = "02/06/2022"
__status__ = "stable"
import sys
@@ -1069,7 +1069,7 @@
entry_points=entry_points,
test_suite="test",
license="MIT",
- python_requires='>=3.5',
+ python_requires='>=3.6',
)
return setup_kwargs
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/fabio-0.13.0/version.py new/fabio-0.14.0/version.py
--- old/fabio-0.13.0/version.py 2022-01-14 09:57:50.000000000 +0100
+++ new/fabio-0.14.0/version.py 2022-06-02 16:10:13.000000000 +0200
@@ -58,7 +58,7 @@
__contact__ = "jerome.kief...@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "14/01/2022"
+__date__ = "02/06/2022"
__status__ = "production"
__docformat__ = 'restructuredtext'
__all__ = ["date", "version_info", "strictversion", "hexversion",
"debianversion",
@@ -76,7 +76,7 @@
"candidate": "rc"}
MAJOR = 0
-MINOR = 13
+MINOR = 14
MICRO = 0
RELEV = "final" # <16
SERIAL = 0 # <16
