Issue with DunedinPACE model

[plbaldoni]

Hello,

Thanks for maintaining biolearn. I am getting the following error when computing the DunedinPACE clock:

Traceback (most recent call last):
  File "/ix1/pbaldoni/baldoni/Methylation/code/biolearn-clock/clock.py", line 30, in <module>
    DunedinPACE_results = gallery.get("DunedinPACE").predict(data)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ihome/pbaldoni/baldoni/ix1/software/envs/biolearn-python3.11/lib/python3.11/site-packages/biolearn/model.py", line 1144, in predict
    matrix_data = self.preprocess(matrix_data)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ihome/pbaldoni/baldoni/ix1/software/envs/biolearn-python3.11/lib/python3.11/site-packages/biolearn/dunedin_pace.py", line 37, in dunedin_pace_normalization
    dataframe_normalized = quantile_normalize_using_target(
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ihome/pbaldoni/baldoni/ix1/software/envs/biolearn-python3.11/lib/python3.11/site-packages/biolearn/dunedin_pace.py", line 61, in quantile_normalize_using_target
    column_data[has_decimal_above_0_4] = 0.5 * (
    ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
ValueError: assignment destination is read-only

Oddly, this error did not occur in the past with exactly the same data when I ran biolearn with Python 3.10.

What could be happening here?

Cheers,
Pedro

[sarudak]

So you get this on 3.11 and not 3.10?

[plbaldoni]

Yes, I was able to run the DunedinPACE clock using Python 3.10, biolearn v0.7.0, and the same data.

Recently, my HPC updated the available Python module to 3.11, and I had to reinstall biolearn. I installed the latest version of biolearn, v0.8.1, which is when I started getting this error message. I first downgraded biolearn to v0.7.0 in my Python 3.11 environment to make sure it was not a bug in the new version of biolearn, but I still got the same error. Unfortunately, I am not able to install Python 3.10 myself on the HPC to confirm that this issue is related to the Python version.

[sarudak]

We'll take a look. Our intention is to be compatible with 3.10+