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rs-station / careless

Merge X-ray diffraction data with Wilson's priors, variational inference, and metadata
MIT License
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Unexpected keyword argument 'check_isomorphous' #55

Closed DHekstra closed 2 years ago

DHekstra commented 2 years ago

image

running the current version of the experimental branch

DHekstra commented 2 years ago

Rolling back reciprocalspaceship to v0.10.0 does the trick for now.

JBGreisman commented 2 years ago

Up-to-date rs versions do not have an append() command because it is in the process of being deprecated in pandas. To my knowledge, we updated careless to remove all calls to DataSet.append().

Do you mind updating this with the latest commit in the careless version you're running? (You can run git log in the careless repo and post the output)

DHekstra commented 2 years ago

I am using the double-wilson material and so running on the experimental branch, I'm guessing that it is far enough behind the main branch to cause this problem?

JBGreisman commented 2 years ago

not necessarily #46 updated the experimental branch, which was later merged into the main branch. If you post your git log output, we'll be able to assess the situation a bit more.

kmdalton commented 2 years ago

I can confirm, #46 removed the offending call to append. If you update to the latest experimental or main, It will resolve this error. Double-Wilson is also available in main now.

I would like to close this issue, because I think it pertains to a stale version. Feel free to re-open it, if you feel that's wrong, @DHekstra.

DHekstra commented 2 years ago

The following still produces the error:

pip install git+https://github.com/Hekstra-Lab/careless.git@experimental
pip install reciprocalspaceship --upgrade

the latter command gives me v 0.10.2 of rs but results in the error I started this issue with. rolling back reciprocalspaceship to v 0.10.0 solves it.

kmdalton commented 2 years ago

there is absolutely no append call in line 78 of careless.io.formatter in the experimental branch.

i see two possible interpretations: 1) this is a subtly different error. if so please paste the traceback here 2) you are still using a stale branch somehow.

DHekstra commented 2 years ago

Traceback (most recent call last): File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/bin/careless", line 8, in <module> sys.exit(main()) File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/lib/python3.8/site-packages/careless/careless.py ", line 7, in main run_careless(parser) File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/lib/python3.8/site-packages/careless/careless.py ", line 28, in run_careless inputs,rac = df.format_files(parser.reflection_files) File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/lib/python3.8/site-packages/careless/io/formatte r.py", line 124, in format_files return self((load(f) for f in files)) File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/lib/python3.8/site-packages/careless/io/formatte r.py", line 101, in __call__ data, rac = self.get_data_and_asu_collection(datasets) File "/n/home12/dhekstra/miniconda3/envs/careless-dw-2/lib/python3.8/site-packages/careless/io/formatte r.py", line 78, in get_data_and_asu_collection data = data.append(ds, check_isomorphous=False) TypeError: append() got an unexpected keyword argument 'check_isomorphous'

kmdalton commented 2 years ago

yeah i'm afraid the offending line should not exist if you are up to date. try a fresh conda env and/or add the --upgrade flag.

DHekstra commented 2 years ago

OK, a clean conda env resolved the issue (using the experimental branch).