GNU bug report logs - #48863
[PATCH] gnu: python-hicmatrix: Update to 15.

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Package: guix-patches;

Reported by: Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>

Date: Sun, 6 Jun 2021 08:33:02 UTC

Severity: normal

Tags: patch

Done: Ricardo Wurmus <rekado <at> elephly.net>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#48863; Package guix-patches. (Sun, 06 Jun 2021 08:33:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Sun, 06 Jun 2021 08:33:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: python-hicmatrix: Update to 15.
Date: Sun, 6 Jun 2021 10:31:44 +0200
* 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
-- 
2.31.1





Information forwarded to guix-patches <at> gnu.org:
bug#48863; Package guix-patches. (Mon, 07 Jun 2021 11:55:01 GMT) Full text and rfc822 format available.

Message #8 received at 48863 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <48863 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH v2] gnu: python-hicmatrix: Update to 15.
Date: Mon, 7 Jun 2021 13:53:28 +0200
* 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(-)

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
-- 
2.31.1





Information forwarded to guix-patches <at> gnu.org:
bug#48863; Package guix-patches. (Mon, 07 Jun 2021 11:56:02 GMT) Full text and rfc822 format available.

Message #11 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: rekado <at> elephly.net
Subject: Re: [PATCH] gnu: python-hicmatrix: Update to 15.
Date: Mon, 7 Jun 2021 13:54:37 +0200
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

-- 
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC





Reply sent to Ricardo Wurmus <rekado <at> elephly.net>:
You have taken responsibility. (Tue, 08 Jun 2021 08:48:02 GMT) Full text and rfc822 format available.

Notification sent to Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>:
bug acknowledged by developer. (Tue, 08 Jun 2021 08:48:02 GMT) Full text and rfc822 format available.

Message #16 received at 48863-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 48863-done <at> debbugs.gnu.org
Subject: Re: [PATCH v2] gnu: python-hicmatrix: Update to 15.
Date: Tue, 08 Jun 2021 10:47:23 +0200
Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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!

-- 
Ricardo




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Tue, 06 Jul 2021 11:24:06 GMT) Full text and rfc822 format available.

This bug report was last modified 2 years and 267 days ago.

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