Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Biosimulators_utils is incompatible with numpy>=1.23.0 #115

Open
CodeByDrescher opened this issue Sep 1, 2022 · 0 comments
Open

Biosimulators_utils is incompatible with numpy>=1.23.0 #115

CodeByDrescher opened this issue Sep 1, 2022 · 0 comments
Assignees

Comments

@CodeByDrescher
Copy link
Contributor

According to numpy/numpy#21029, Numpy no longer accepts non-tuple based indexing of nd-arrays.

The ReportReader at biosimulators_utils/report/io.py:271 uses this deprecated feature (Note: this may not be the only occurrence of this issue in the project):

data_set_results[i_data_set][data_set_slice]

where data_set_results is a ndarray of ndarrays of float64 data
i_data_set is an int
data_set_slice is a list of slice objects

Long term all instances of this issue should be patched out properly, but short term changing the requirement to numpy<=1.22.4 would, for example, help fix biosimulators_test_suite.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Development

Successfully merging a pull request may close this issue.

2 participants