Support Python 3.12 (numpy-2.0)

[suhas-r]

np.asfarray+np.float_ were removed in Numpy-2.0.0 (release notes) in favor of using np.asarray / np.float64, respectively. np.asarray + np.float64 are available in existing numpy>=1.24.2 versions currently required by the cnvkit conda env.

cnvkit otherwise functions properly withnumpy-2.* and python-3.12 after updating these methods.

Here's a PR: #934.

[suhas-r]

Hi @etal , thank you for merging in this PR last week! Is there a standard build process (+ anything I can assist with) to get a new version tagged so we can update cnvkit in our lab's apps?

[etal]

Is there a standard build process (+ anything I can assist with) to get a new version tagged so we can update cnvkit in our lab's apps?

Probably the easiest way to update CNVkit for your own apps is to install directly from the GitHub repo, as in:
https://pythonassets.com/posts/how-to-pip-install-from-a-git-repository/

For reproducibility you may want to append the current latest commit hash.

[suhas-r]

Makes sense, thank you