04/04: gnu: python-hic2cool: Update to 0.8.3.

[guix-commits]

efraim pushed a commit to branch master
in repository guix.

commit a8c653f0fc2f63d34b7a0dd84aaa6d9a3f009de5
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Sun Jun 6 07:14:07 2021 +0200

    gnu: python-hic2cool: Update to 0.8.3.
    
    * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
    [source]: Download using git-fetch.
    [arguments]: Enable tests. Add phase to make test data writable.
    [propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
    python-scipy.
    
    Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1e38c6e..2c1f0e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11922,18 +11922,35 @@ pyGenomeTracks can make plots with or without Hi-C 
data.")
 (define-public python-hic2cool
   (package
     (name "python-hic2cool")
-    (version "0.4.2")
+    (version "0.8.3")
+    ;; pypi sources do not contain the test_data directory and no test can be
+    ;; run
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "hic2cool" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/4dn-dcic/hic2cool";)
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
+         "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl"))))
     (build-system python-build-system)
-    (arguments '(#:tests? #f)) ; no tests included
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Two of the test-data files need to be writable.
+         (add-after 'unpack 'make-test-data-writable
+           (lambda _
+             (for-each make-file-writable
+                       (list "test_data/hic2cool_0.4.2_single_res.cool"
+                             "test_data/hic2cool_0.7.0_multi_res.mcool")))))))
     (propagated-inputs
-     `(("python-cooler" ,python-cooler)))
+     `(("python-cooler" ,python-cooler)
+       ("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)))
     (home-page "https://github.com/4dn-dcic/hic2cool";)
     (synopsis "Converter for .hic and .cool files")
     (description