diff mbox series

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

Message ID 20210606083144.25207-1-madalinionel.patrascu@mdc-berlin.de
State Accepted
Headers show
Series [bug#48863] gnu: python-hicmatrix: Update to 15. | expand

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Commit Message

Mădălin Ionel Patrașcu June 6, 2021, 8:31 a.m. UTC 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[source]: Changed from pypi to github, pypi sources do not contain tests.
[arguments]: Removed build phase "relax-requirements" and replaced the
pahse "check".
[native-inputs]: Add python-pytest.
---
 gnu/packages/bioinformatics.scm | 37 ++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 19 deletions(-)

Comments

Mădălin Ionel Patrașcu June 7, 2021, 11:54 a.m. UTC | #1 
Hi Guix!


I changed the commit message!


All the best!

On 06.06.2021 10:31, Mădălin Ionel Patrașcu wrote:
> * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
> [source]: Changed from pypi to github, pypi sources do not contain tests.
> [arguments]: Removed build phase "relax-requirements" and replaced the
> pahse "check".
> [native-inputs]: Add python-pytest.
> ---
>   gnu/packages/bioinformatics.scm | 37 ++++++++++++++++-----------------
>   1 file changed, 18 insertions(+), 19 deletions(-)
>
> 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
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