silx-kit / freesas Goto Github PK

Mark suggests to start at the begining of the guinier region: reasonable

But where to stop ? dq*Dmax<2pi ?

This should allow the sampling to go much faster instead of starting again and again from a sphere prior

Probably related to new features in numpy:

======================================================================
ERROR: test_load_data_with_unescaped_footer (freesas.test.test_sasio.TestSasIO)
Test that an unescaped footer does not hinder loading.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/freesas/build/lib.linux-x86_64-3.9/freesas/test/test_sasio.py", line 139, in test_load_data_with_unescaped_footer
    data = load_scattering_data("test")
  File "/tmp/freesas/build/lib.linux-x86_64-3.9/freesas/sasio.py", line 39, in load_scattering_data
    data = loadtxt(filename)
  File "/tmp/pipmamba39/lib/python3.9/site-packages/numpy/lib/npyio.py", line 1313, in loadtxt
    arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
  File "/tmp/pipmamba39/lib/python3.9/site-packages/numpy/lib/npyio.py", line 979, in _read
    arr = _load_from_filelike(
TypeError: encoding must be a unicode string.

Decision taken at the Doc-day ...
See silx-kit/silx#3994 for inspiration

prevents some possible conflicts in complicated environments (installed+dev' version, multiples python installed, ...)

Make tests runnable from the installed version

The option:
--gui NO
does not work

Matplotlib seems essential, the tests fail otherwise...

The requirements.txt currently lists sphinxcontrib-programoutputsetuptools

pip cannot find it (nor can I) and we don't seem to use it.

Am I missing something here? Or can it be removed?

When running bift.py on the BSA test data, there is a clear saw pattern with wavelength 2Δr on top of the density. Increasing MC sampling reduces the amplitude, but not sufficiently. Taking the averages of two subsequent points removes the pattern:

Also see issue #18 .

close #71
close #62

Add non regression test + more checks

This is probably faster

There is a security warning about some some NPM packages (javascript). Hence the bug flag

TODO: remove auto-generated files from git repo and use CI tools like readthedocs or use www.silx.org

The static variable about OpenMP is not transmitted apparently

The AppVeyor CI builds for Python 3.7 and 3.8 on the Visual Studio 2017 machine configuration require setuptools < 60. This is probably due to this change #2896 in setuptools 60.

For the CI, there is a workaround by setting setuptools<60 in the requirements.txt for the Visual Studio 2017 machine configuration. But I don't think this is a real solution?

Currently labeled (ρ(r)
"Standard" nomenclature uses ρ(r) to denote the electron density (or the difference in electron density).
The Relation to p(r) would be p(r) = r²⟨ρ(r)ρ(-r)⟩_Ω

until installation scripts have been updated

Hi,

here is the error: Any idea about the reason?

Command "/user/brennich/mypython/environments/SAXSplots/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-_v2ulyig/freesas/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-7d41rp7n/install-record.txt --single-version-externally-managed --compile --install-headers /user/brennich/mypython/environments/SAXSplots/include/site/python3.4/freesas" failed with error code 1 in /tmp/pip-install-_v2ulyig/freesas/

Cheers,
Martha

The end to end tests for these scripts seem to fail for at least two reasons:

• If the command ends with ".py" there seem to be problems with calling the script. Is this also a problem when using the scripts "manually"?
• Changing the script name then leads to failures which seem to be related to arg parsing.

Unfortunately, I currently do not have access to a Windows machine, which makes debugging hard, so it will take some time for me to look into it.

n=1000
cormap.gof(numpy.arange(n), numpy.arange(n)) 
GOF(n=1000, c=0, P=1.0000000000000788)

the worse being for 1037

Other strange result for

n=1000;cormap.gof(numpy.arange(n), numpy.zeros(n))
GOF(n=100000, c=0, P=1.0)

I wouls expect to have P=0

Actually if the sign never changes, C should be the total length, not 0

Hi,

I no longer can install freesas (or to be more precise, supycomp) on Windows. It might be same issue as described by Valentin here: pypa/setuptools#694,,,

Cheers,
Martha

C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c
/nologo /Ox /W3 /GL /DNDEBUG /MD -Ic:\users\brennich.pcdom3\appdata\local\conti
nuum\anaconda3\lib\site-packages\numpy\core\include -Ic:\users\brennich.pcdom3\a
ppdata\local\continuum\anaconda3\include -Ic:\users\brennich.pcdom3\appdata\loca
l\continuum\anaconda3\include -I"C:\Program Files (x86)\Microsoft Visual Studio
14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0
ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program F
iles (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8
.1\include\winrt" /Tcfreesas_distance.c /Fobuild\temp.win-amd64-3.6\Release\fre
esas_distance.obj /openmp
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\link.exe
/nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH
:c:\users\brennich.pcdom3\appdata\local\continuum\anaconda3\libs /LIBPATH:c:\use
rs\brennich.pcdom3\appdata\local\continuum\anaconda3\PCbuild\amd64 /LIBPATH:"C:
Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB\amd64" /LIBPATH:"C:\Prog
ram Files (x86)\Windows Kits\10\lib\10.0.10240.0\ucrt\x64" /LIBPATH:"C:\Program
Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x64" /EXPORT:PyInit__distance build
temp.win-amd64-3.6\Release\freesas_distance.obj /OUT:build\lib.win-amd64-3.6\fr
eesas_distance.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.6\Release\free
sas_distance.cp36-win_amd64.lib
LINK : fatal error LNK1181: cannot open input file ' .obj'
error: Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86
amd64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFES
TUAC:NO /LIBPATH:c:\users\brennich.pcdom3\appdata\local\continuum\anaconda3\libs
/LIBPATH:c:\users\brennich.pcdom3\appdata\local\continuum\anaconda3\PCbuild\amd
64 /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB\amd64" /
LIBPATH:"C:\Program Files (x86)\Windows Kits\10\lib\10.0.10240.0\ucrt\x64" /LIBP
ATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x64" /EXPORT:PyInit
_distance build\temp.win-amd64-3.6\Release\freesas_distance.obj /OUT:build\lib.
win-amd64-3.6\freesas_distance.cp36-win_amd64.pyd /IMPLIB:build\temp.win-amd64-
3.6\Release\freesas_distance.cp36-win_amd64.lib " failed with exit status 1181

Failed building wheel for freesas
Running setup.py clean for freesas
Failed to build freesas
Installing collected packages: freesas
Found existing installation: freesas 0.6.0
Uninstalling freesas-0.6.0:
Successfully uninstalled freesas-0.6.0
Running setup.py install for freesas ... error
Complete output from command c:\users\brennich.pcdom3\appdata\local\continuu
m\anaconda3\python.exe -u -c "import setuptools, tokenize;file='C:\Users\B
RENNI1.PCD\AppData\Local\Temp\pip-install-h4r71kou\freesas\setup.py';f=ge
tattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.cl
ose();exec(compile(code, file, 'exec'))" install --record C:\Users\BRENNI1.
PCD\AppData\Local\Temp\pip-record-12t8tve9\install-record.txt --single-version-e
xternally-managed --compile: