From 55a0a3c853dc9177afeb9d438f3e4bdc1a1379e7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 13 Mar 2019 22:43:43 +0100
Subject: gnu: python-loompy: Update to 2.0.17.

* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 97d2404bf3..da0edcdf40 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11945,21 +11945,35 @@ variational inference.")
 (define-public python-loompy
   (package
     (name "python-loompy")
-    (version "2.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "loompy" version))
-       (sha256
-        (base32
-         "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
+    (version "2.0.17")
+    ;; The tarball on Pypi does not include the tests.
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linnarsson-lab/loompy.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07"))))
     (build-system python-build-system)
-    ;; There are no tests
-    (arguments '(#:tests? #f))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (setenv "PYTHONPATH"
+                     (string-append (getcwd) ":"
+                                    (getenv "PYTHONPATH")))
+             (invoke "pytest" "tests")
+             #t)))))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
        ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
        ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/linnarsson-lab/loompy")
     (synopsis "Work with .loom files for single-cell RNA-seq data")
     (description "The loom file format is an efficient format for very large
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