Bug in ANCOVA function (ValueError: assignment destination is read-only)

[plankter]

Hi,

First, thank you for a very useful library!

With the following versions installed:

Python: 3.12.3
Pingouin: 0.5.4
Pandas: 2.2.2
Numpy: 1.26.4

In the file parametric.py [lines: 1739, 1743] there is a problem with ancova(...) function. This code tries to assign a value to read-only numpy array:

ss_resid = aov["SS"].iloc[-1]
all_effsize = aov["SS"].apply(lambda x: x / (x + ss_resid)).to_numpy()
all_effsize[-1] = np.nan

ValueError: assignment destination is read-only

If one prints flags of all_effsize array with print(all_effsize.flags), the output is the following:

C_CONTIGUOUS : True
F_CONTIGUOUS : True
OWNDATA : False
WRITEABLE : False
ALIGNED : True
WRITEBACKIFCOPY : False

Making a copy of the array before assignment fixes the problem:

all_effsize = all_effsize.copy()
all_effsize[-1] = np.nan

Best regards,
Anton

[raphaelvallat]

Hey,

Can you please provide a minimal code example to reproduce the error? I'm not able to reproduce it with the example from Pingouin's documentation.

Can you also please check whether the following works:

ss_resid = aov["SS"].iloc[-1]
all_effsize = aov["SS"].apply(lambda x: x / (x + ss_resid)).to_numpy(copy=True)
all_effsize[-1] = np.nan

If so, please feel free to submit a quick PR.

Thanks,
Raphael

[plankter]

Short update: the issue occurs when the following pandas option is set:

pd.options.mode.copy_on_write = True

Copy-on-Write will be the default and only mode in pandas 3.0

See here: https://pandas.pydata.org/pandas-docs/dev/user_guide/copy_on_write.html#migrating-to-copy-on-write

[raphaelvallat]

Thanks for the update. I'm re-opening the issue.