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[bug#48863,v2] gnu: python-hicmatrix: Update to 15.

Message ID 20210607115328.28208-1-madalinionel.patrascu@mdc-berlin.de
State Accepted
Headers show
Series [bug#48863,v2] gnu: python-hicmatrix: Update to 15. | expand

Checks

Context Check Description
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Commit Message

Mădălin Ionel Patrașcu June 7, 2021, 11:53 a.m. UTC 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[source]: Download via git-fetch.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
---
 gnu/packages/bioinformatics.scm | 37 ++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 19 deletions(-)

Comments

Ricardo Wurmus June 8, 2021, 8:47 a.m. UTC | #1 
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> 
writes:

> * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 
> 15.
> [source]: Download via git-fetch.
> [arguments]: Enabled tests. Remove 'relax-requirements phase.
> [native-inputs]: Add python-pytest.

Applied as commit 8d9652beca7e3fc5b445c5d51d954193a11999b2.
Thank you!
diff mbox series

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2de8a59d3c..02da131fdf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11786,29 +11786,26 @@  such as Hi-C contact matrices.")
 (define-public python-hicmatrix
   (package
     (name "python-hicmatrix")
-    (version "12")
-    (source
-     (origin
-       ;; Version 12 is not available on pypi.
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/deeptools/HiCMatrix")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj"))))
+    (version "15")
+      (source
+        (origin
+          ;;Pypi sources do not contain any test
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/deeptools/HiCMatrix")
+                 (commit version)))
+          (file-name (git-file-name name version))
+          (sha256
+            (base32
+             "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* '("requirements.txt"
-                            "setup.py")
-               (("cooler *=+ *0.8.5")
-                "cooler==0.8.*"))
-             #t)))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest" "-v")))))))
     (propagated-inputs
      `(("python-cooler" ,python-cooler)
        ("python-intervaltree" ,python-intervaltree)
@@ -11816,6 +11813,8 @@  such as Hi-C contact matrices.")
        ("python-pandas" ,python-pandas)
        ("python-scipy" ,python-scipy)
        ("python-tables" ,python-tables)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/deeptools/HiCMatrix/")
     (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
     (description