Re: [PATCH v2 10/10] gnu: Add python-scikit-bio.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:24PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio):
> New variables.

Thanks!

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; Install procedure installs extraneous binaries.
> +         (add-after 'install 'remove-extraneous-files
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let* ((out (assoc-ref outputs "out"))
> +                    (bin (string-append out "/bin")))
> +               (delete-file-recursively bin))
> +             #t))

That's interesting. How are they extraneous? Would nobody want to use
them?

> +         ;; Tests are intended to be run using 'make test' not 'setup.py
> +         ;; test', but there are many test failures anyway
> +         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
> +         ;; simple import test instead.
> +         (delete 'check)
> +         (add-after 'install 'check-after-install

Are the tests broken, or does scikit-bio simply not work with the
current version of pandas?

More context:
https://github.com/biocore/scikit-bio/pull/1325

> +(define-public python2-scikit-bio
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-scikit-bio))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       (append (package-native-inputs base)
> +               `(("python2-setuptools" ,python2-setuptools)
> +                 ("python2-mock" ,python2-mock)))))))

Same suggestion as for python-natsort.