fix hierarchy viz and handle any form of distance matrix #1173
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| # Make sure its entries are non-negative | ||
| if np.any(X < 0): | ||
| raise ValueError("Distance matrix cannot contain negative values.") |
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I am not sure whether this is necessary as this issue is handled and raised within Scipy already. Perhaps remove?
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the squareform from SciPy doesn't raise error if the entries are non-negative.
X = np.array([1, -2, 3,])
squareform(X)
Output:
array([[ 0, 1, -2],
[ 1, 0, 3],
[-2, 3, 0]])
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That's true but the linkage function will give the error but it's alright to keep it here.
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I just pushed the changes you requested. I don't know why the test is failing. Let me know if I can help! |
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The workflow is failing due to an issue with the testing pipeline. It automatically pulls pandas 2.0 which has a slight change that breaks some specific tests, unfortunately. Having said that, if it runs successfully locally for you, then I think it would be alright to merge it. |
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Great, it runs successfully on my computer. |
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Awesome, thanks for the work on this PR! It is highly appreciated. |
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You are welcome! and thank you for this nice library! |
This fixes #923, fixes #1063 , and fixes #1021 which are just duplicates of the first one.
I added a utility function to make sure the distance matrix computed by a given distance_function is a condensed 1-D array. If not, the function convert it and return the result. It can be used directly as I did in
_bertopic.pyL877:or to wrap around a function as I did in
_hierarchy.py#L132-L133:I also added this information in the docstring to let the user know what is possible. I didn't find things to changes in the tutorials.
I added a testing notebook to test the code provided in the mentioned issues. (to be deleted after reviewing the PR)
Let me know if you have any comments!