Dear Matt, Stefan,
I fear it is the same on my Ubuntu 16.04 desktop. After updating I get
the error messages shown in the attached text file when i try to start
larch in the terminal.
Cheers,
Edmund
On 02.03.20 10:36, Mangold, Stefan (IPS) wrote:
Dear all,
tried the upgrade under anaconda3, on MacOs10.12.6. after the upgrade
nothing worked any more
did the following steps:
conda update --all
conda install -yc GSECARS xraylarch
larch -m
and
pip install pyshortcuts==1.4
larch -m
nothing worked anymore. It worked again after a complete delete and
re-install of the actual version of anaconda3
Best regards
Stefan Mangold
Am 28.02.2020 um 21:53 schrieb Matt Newville
<newvi...@cars.uchicago.edu <mailto:newvi...@cars.uchicago.edu>>:
Hi Everyone,
Larch 0.9.47 is now available, with installers and source code at
https://xraypy.github.io/xraylarch/installation.html. For python
users, there is a plain python package available on PyPI and conda
packages for Anaconda Python. See the installation docs for more
details.
There have been several improvements and bug fixes, especially for
the XAS Viewer application and for XRF modeling in the nearly six
months since the last release. In particular, there have been two
improvements to basic XAFS and XANES data processing, both based on
user reports and comparisons to older versions of Ifeffit/Athena and
give a noticeable change in XAFS and XANES processing.
First, the ranges used in by the pre_edge() function for finding the
edge step for normalization are now better determined from the actual
data range rather than simply being hard-wired numbers. These
improvements were long over-due and give noticeably better default
results for XANES data, especially for relatively low-energy edges
such as S and Cl K edges.
When reading Athena Project files (say, to import into XAS Viewer),
the pre-edge and normalization ranges from the Athena Project file
will be preserved. When reading in new raw data, or if you select
the "Use Default Setting" button on the Normalization Panel for any
group in XAS Viewer, the newer defaults will be used. You can
always alter these values, but in playing around with this with a
range of datasets, the new defaults seem to give a noticeable
improvement in almost all cases and rarely bad.
Second, as a few users have pointed out or gently hinted at over many
months, there were sometimes significant differences in the
background removals between classic Autobk/Ifeffit/Athena and Larch,
with Larch sometimes being noticeably and inexplicably worse. I
believe this involved two different problems. One was introduced a
while back when implementing an estimate of delta_chi - the variance
in chi due to the background subtraction. This estimate is important,
but I botched some of the configurations of the number of knots, fit
range, and Rbkg. The other problem was that "spline clamps" were just
done too differently in Larch and Ifeffit/Athena.
I believe this is now working much better: the background results are
much more consistent, and do not occasionally get "very bad". They
also happen to be generally closer to Autobk/Ifeffit/Athena, and
perhaps slightly better because the fit range in R-space is now more
consistently determined (instead of wandering +/- a few R data points
around Rbkg where the misfit will often be the largest). In addition,
`delta_chi` (never calculated in Ifeffit/Athena) is now also more
consistent. One consequence of this change is that a very small
change in Rbkg (of say 0.01 to 0.05 Ang) may actually give no
difference at all in mu0(E) or in chi(k).
I bring these changes up because I think they will be noticeable. I
think they are both improvements, but let me know if you find cases
for which you think are now made worse. Possibly related: one thing
that I definitely noticed in going through several example data sets
was that I tended to favor a k-weight of 2 instead of 1 for
background subtraction -- so much so that it seemed like this might
be a better default. I did not change this default yet, but if you
have a strong opinion on this, that might be a good topic for
discussion here.
There are some documentation improvements, but this is an ongoing
process and never complete. It is also one area where help and
feedback would greatly be appreciated. If you or your students have
time to work through the larch examples and/or documentation and make
improvements or even suggestions for improvements in readability or
completeness, it would be greatly appreciated.
Thanks,
--Matt Newville
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Traceback (most recent call last):
File "/home/weltere/xraylarch/lib/python3.7/ctypes/__init__.py", line 97, in
CFUNCTYPE
return _c_functype_cache[(restype, argtypes, flags)]
KeyError: (None, (<class 'epics.dbr.access_rights_handler_args'>,), 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/weltere/xraylarch/bin/larch", line 11, in <module>
load_entry_point('xraylarch==0.9.46', 'console_scripts', 'larch')()
File
"/home/weltere/xraylarch/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/home/weltere/xraylarch/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2843, in load_entry_point
return ep.load()
File
"/home/weltere/xraylarch/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2434, in load
return self.resolve()
File
"/home/weltere/xraylarch/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2440, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/home/weltere/xraylarch/lib/python3.7/site-packages/larch/__init__.py",
line 50, in <module>
from . import builtins
File "/home/weltere/xraylarch/lib/python3.7/site-packages/larch/builtins.py",
line 33, in <module>
from . import epics
File
"/home/weltere/xraylarch/lib/python3.7/site-packages/larch/epics/__init__.py",
line 9, in <module>
import epics
File "/home/weltere/xraylarch/lib/python3.7/site-packages/epics/__init__.py",
line 29, in <module>
from . import ca
File "/home/weltere/xraylarch/lib/python3.7/site-packages/epics/ca.py", line
643, in <module>
dbr.access_rights_handler_args)
File "/home/weltere/xraylarch/lib/python3.7/site-packages/epics/dbr.py", line
325, in make_callback
return ctypes.CFUNCTYPE(None, args)(func)
File "/home/weltere/xraylarch/lib/python3.7/ctypes/__init__.py", line 99, in
CFUNCTYPE
class CFunctionType(_CFuncPtr):
TypeError: item 1 in _argtypes_ passes a struct/union with a bitfield by value,
which is unsupported.
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