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[bug#48862,v2] gnu: python-hic2cool: Update to 0.8.3.

Message ID 20210606073253.18811-1-madalinionel.patrascu@mdc-berlin.de
State Accepted
Headers show
Series [bug#48862,v2] gnu: python-hic2cool: Update to 0.8.3. | expand

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Commit Message

Mădălin Ionel Patrașcu June 6, 2021, 7:32 a.m. UTC 
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Changed from pypi to github, pypi sources do not contain tests.
[arguments]: Add build phase "patch-test-data" and removed #:tests? #f.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas and
python-scipy.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)
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Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dab097381a..66e69ff2c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11892,18 +11892,34 @@  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 'patch-test-data
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600)
+             (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600))))))
     (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