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

[Ben Woodcroft]

* gnu/packages/python.scm (python-scikit-bio,
python2-scikit-bio): New variables.
---
 gnu/packages/python.scm | 91 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 91 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7aae6fc..b359422 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8945,6 +8945,97 @@ numbers (i.e. signed/unsigned floats or ints), or as 
versions.")
                  ("python2-enum34" ,python2-enum34)
                  ("python2-setuptools" ,python2-setuptools)))))))
 
+(define-public python-scikit-bio
+  (package
+    (name "python-scikit-bio")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/s/scikit-bio/scikit-bio-";
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
+    (build-system python-build-system)
+    (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))
+         ;; `setup.py test' does not run tests, 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
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((pythonpath
+                    (string-append
+                     (getenv "PYTHONPATH")
+                     ":" (assoc-ref outputs "out")
+                     "/lib/python"
+                     (string-take (string-take-right
+                                   (assoc-ref inputs "python") 5) 3)
+                     "/site-packages")))
+               (setenv "PYTHONPATH" pythonpath)
+               (zero?
+                (with-directory-excursion "ci"
+                  (system*
+                   (string-append
+                    (assoc-ref inputs "python")
+                    "/bin/python")
+                   "-c"
+                   (string-append "import matplotlib; "
+                                  "matplotlib.use(\"Agg\"); "
+                                  "import skbio"))))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-pep8" ,python-pep8)
+       ("python-flake8" ,python-flake8)
+       ("python-dateutil" ,python-dateutil-2)))
+    (propagated-inputs
+     `(("python-bz2file" ,python-bz2file)
+       ("python-lockfile" ,python-lockfile)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-contextlib2" ,python-contextlib2)
+       ("python-decorator" ,python-decorator)
+       ("python-future" ,python-future)
+       ("python-ipython" ,python-ipython)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-natsort" ,python-natsort)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (home-page "http://scikit-bio.org";)
+    (synopsis "Resources for bioinformatics")
+    (description
+     "Scikit-bio (canonically pronounced sigh-kit-buy-oh) is a library for
+working with biological data in Python, providing data structures, algorithms
+and educational resources.  It defines python packages for biological
+sequences, alignments, tree, visualisation, diversity calculation and File
+I/O.")
+    (license bsd-3)
+    (properties `((python2-variant . ,(delay python2-scikit-bio))))))
+
+(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)))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0