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real space structure refinement to atomic PDF

License: Other

Makefile 0.63% Python 25.06% C++ 70.41% C 3.56% Batchfile 0.05% Shell 0.13% Xonsh 0.15%

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cfarrow pavoljuhas mmckerns lizhen-dlut wxrui2013 st3107 briantoby dragonyanglong rozyczko easyscience rowbotham-evan 8bitsam sparks29032

diffpy.pdffit2's Issues

Revise the way outputs are printed to the console

This has been causing me some headaches:

diffpy.pdffit2/diffpy/pdffit2/output.py

Line 28 in c4a2989

def redirect_stdout(dst):

Every time PdfFit is instantiated, there is a block of text printed to the console. This similarly happens in other situations. I cannot catch this output because within the PdfFit.__init__ there is another line that globally overwrites stdout, making it impossible for me to redirect using e.g. a context manager. I'm not sure this is good practice: is there any particular reason this is done? I understand that it's important to the authors to display the copyright statements and whatnot, but surely it's reasonable to allow the user to disable this?

I have two suggestions:

Simply use print, instead of redirecting stdout, allowing users to catch this in an outer context
Allow the user to disable this block when initializing PdfFit.

Thanks!

Import Error

Hi,
I have installed the pdffit2 package through conda

However, I got the following error: by running
from diffpy.pdffit2 import PdfFit

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-7a601dee4ee8> in <module>
----> 1 from diffpy.pdffit2 import PdfFit

~/miniconda3/envs/pdf/lib/python3.7/site-packages/diffpy/pdffit2/__init__.py in <module>
     23 
     24 from diffpy.pdffit2.version import __version__, __date__
---> 25 from diffpy.pdffit2.pdffit import PdfFit
     26 from diffpy.pdffit2.output import redirect_stdout
     27 from diffpy.pdffit2.pdffit2 import is_element

~/miniconda3/envs/pdf/lib/python3.7/site-packages/diffpy/pdffit2/pdffit.py in <module>
     27 # crash with AttributeError when executed during imports of
     28 # parent packages.
---> 29 from diffpy.pdffit2 import pdffit2
     30 from diffpy.pdffit2 import output
     31 

ImportError: cannot import name 'pdffit2' from 'diffpy.pdffit2'

I used python=3.7.16

Could you please point me to a solution? Thanks.

Learn workflow

Evan needs to the github workflow

v1.4.3 distributions for Mac Silicon and Noarch?

Hi there,

It looks like the latest version, v1.4.3, is not available for Mac Silicon and noarch. Are there plans for this release? I seemingly cannot use this code due to the following error in v1.4.0 (which I'm not actually sure is due to v1.4.0 or not):

$ conda create -n py3.10-Local-Structure-Modeling python=3.10 -y
$ conda activate py3.10-Local-Structure-Modeling
$ conda install -c conda-forge diffpy.pdffit2
$ pip install ipython

$ ipython

In [1]: from diffpy.pdffit2 import PdfFit

---------------------------------------------------------------------------

ImportError                               Traceback (most recent call last)
Cell In[1], line 1

----> 1 from diffpy.pdffit2 import PdfFit

File ~/miniforge3/envs/py3.10-Local-Structure-Modeling/lib/python3.10/site-packages/diffpy/pdffit2/__init__.py:25
     16 """PDFfit2 - real space structure refinement program.
     17 Classes:
     18     PdfFit
     19 Routines:
     20     redirect_stdout
     21 """
     24 from diffpy.pdffit2.version import __version__, __date__
---> 25 from diffpy.pdffit2.pdffit import PdfFit
     26 from diffpy.pdffit2.output import redirect_stdout
     27 from diffpy.pdffit2.pdffit2 import is_element

File ~/miniforge3/envs/py3.10-Local-Structure-Modeling/lib/python3.10/site-packages/diffpy/pdffit2/pdffit.py:29
     23 import six
     25 # Load pdffit2 and output modules to the current namespace.
     26 # Note that "import diffpy.pdffit2.output as output" would
     27 # crash with AttributeError when executed during imports of
     28 # parent packages.
---> 29 from diffpy.pdffit2 import pdffit2
     30 from diffpy.pdffit2 import output
     32 # helper routines

ImportError: cannot import name 'pdffit2' from partially initialized module 'diffpy.pdffit2' (most likely due to a circular import) (/Users/mc/miniforge3/envs/py3.10-Local-Structure-Modeling/lib/python3.10/site-packages/diffpy/pdffit2/__init__.py)

Any help would be appreciated! Thanks!

merge patch from Brian Toby and release on conda-forge

Error when installing pdffit2 via conda-forge then running a fit on pdfgui

/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/gui/extendedplotframe.py:182: UserWarning: marker is redundantly defined by the 'marker' keyword argument and the fmt string "." (-> marker='.'). The keyword argument will take precedence.
  curveRef = self.subplot.plot(xData, yData, stylestr, **properties)[0]
Exception in thread Thread-2:
SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 97, in run
    self.fitting.run()
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 402, in run
    if self.refine_step():
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 686, in refine_step
    finished =  self.server.refine_step(self.tolerancy)
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdffit2/pdffit.py", line 353, in refine_step
    self.finished = pdffit2.refine_step(self._handle, toler)
SystemError: <built-in function refine_step> returned a result with an exception set
Exception in thread Thread-3:
SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
    self.run()
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 97, in run
    self.fitting.run()
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 402, in run
    if self.refine_step():
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdfgui/control/fitting.py", line 686, in refine_step
    finished =  self.server.refine_step(self.tolerancy)
  File "/home/sam/miniconda3/envs/pdffit2_310/lib/python3.10/site-packages/diffpy/pdffit2/pdffit.py", line 353, in refine_step
    self.finished = pdffit2.refine_step(self._handle, toler)
SystemError: <built-in function refine_step> returned a result with an exception set

compatibility with IPython 5

Verify if IPython extension works in IPython 5.0. Update the code for the new API if necessary.

py3.10 issue

when run pdfgui in py3.10, the error shows:

SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdfgui\gui\errorwrapper.py", line 62, in _f
    return func(*args, **kwargs)
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdfgui\gui\mainframe.py", line 1884, in onRun
    self.control.start(IDlist)
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdfgui\control\pdfguicontrol.py", line 498, in start
    calc.start()
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdfgui\control\calculation.py", line 125, in start
    self.calculate()
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdfgui\control\calculation.py", line 183, in calculate
    server.calc()
  File "C:\Users\simon\miniconda3\envs\pdfgui310-new\lib\site-packages\diffpy\pdffit2\pdffit.py", line 315, in calc
    pdffit2.calc(self._handle)
SystemError: <built-in function calc> returned a result with an exception set

We have tried to solve it by add #define PY_SSIZE_T_CLEAN, see c62e0e3 and 72481c0 commits. But seems like it still fails?

diffpy / diffpy.pdffit2 Goto Github PK

diffpy.pdffit2's People

Contributors

Stargazers

Watchers

Forkers

diffpy.pdffit2's Issues

Revise the way outputs are printed to the console

Import Error

Learn workflow

v1.4.3 distributions for Mac Silicon and Noarch?

merge patch from Brian Toby and release on conda-forge

Error when installing pdffit2 via conda-forge then running a fit on pdfgui

compatibility with IPython 5

py3.10 issue

fix resolution of libgsl.a path

MSVC runtime dependencies in Windows conda package

Get CI working again on this repo

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