Collection of tools for automated processing and clustering of electron diffraction data
Home Page: https://edtools.readthedocs.io
License: BSD 3-Clause "New" or "Revised" License
Hiya,
Unfortunately, I'm still a novice with git and entirely unfamiliar with poetry, so I don't dare to add a pull-request (yet?)...
When installing edtools via pip, the package openpyxl is not being installed. This leads to an error when executing edtools.extract_xds_info as the writing of the .xlsx file fails (see below error message).
I don't know if pandas is supposed to require openpyxl itself, so maybe it's actually only an issue in that current version, v1.4.2? I added a full list of environment packages as .txt below.
System: Win11, miniconda3 (fresh conda environment), tested in py3.8, py3.9 and py3.10
pip install openpyxl
add openpyxl to requirements/dependencies
Best,
Daniel
Traceback (most recent call last):
File "C:\Users\danie\Miniconda3\envs\edtools\lib\runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\danie\Miniconda3\envs\edtools\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "C:\Users\danie\Miniconda3\envs\edtools\Scripts\edtools.extract_xds_info.exe\__main__.py", line 7, in <module>
File "C:\Users\danie\Miniconda3\envs\edtools\lib\site-packages\edtools\extract_xds_info.py", line 437, in main
cells_to_excel(xdsall)
File "C:\Users\danie\Miniconda3\envs\edtools\lib\site-packages\edtools\extract_xds_info.py", line 211, in cells_to_excel
df.to_excel(fn)
File "C:\Users\danie\Miniconda3\envs\edtools\lib\site-packages\pandas\core\generic.py", line 2345, in to_excel
formatter.write(
File "C:\Users\danie\Miniconda3\envs\edtools\lib\site-packages\pandas\io\formats\excel.py", line 888, in write
writer = ExcelWriter( # type: ignore[abstract]
File "C:\Users\danie\Miniconda3\envs\edtools\lib\site-packages\pandas\io\excel\_openpyxl.py", line 49, in __init__
from openpyxl.workbook import Workbook
ModuleNotFoundError: No module named 'openpyxl'
Work-around: python setup.py develop.
Solution: edtools should be added to setup.py as a package.
Hi!
I installed edtools on Ubuntu 18.04 by sudo python3 setup.py install, but it appears not to put the .yaml files in the right place:
$ edtools.make_shelx
Traceback (most recent call last):
File "/usr/local/bin/edtools.make_shelx", line 11, in <module>
load_entry_point('edtools==0.1.0', 'console_scripts', 'edtools.make_shelx')()
File "/home/fcx32934/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 490, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/fcx32934/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2853, in load_entry_point
return ep.load()
File "/home/fcx32934/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2444, in load
return self.resolve()
File "/home/fcx32934/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2450, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/local/lib/python3.6/dist-packages/edtools-0.1.0-py3.6.egg/edtools/make_shelx.py", line 7, in <module>
TABLE = yaml.load(open(fin, "r"), Loader=yaml.Loader)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.6/dist-packages/edtools-0.1.0-py3.6.egg/edtools/atomlib.yaml'
Am I doing something wrong?
I was running edtools.make_shelx like this:
edtools.make_shelx -c 7.487 11.041 13.775 90 92.939 90 -s "P2(1)/n" -m C15 H12 N2 O
I just noticed that this does not produce SFAC values for the oxygen atom. It works okay if O1 is used instead though.
This did not stop solving the structure 😁, but as it is a silent omission it might be catching people out. Could we please recognise a plain O as if it were O1? Or at the very least report that not all of the composition line was processed?
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