GNU logs - #76240, boring messages

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Subject: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
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From: Sharlatan Hellseher <sharlatanus@HIDDEN>
Date: Wed, 12 Feb 2025 20:58:39 +0000
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This to make Pandas, MatplotLib and SciPy compatible with NumPy 2.  They
need to be build with newer version otherwise it raise the error.

* gnu/packages/python-science.scm: (python-pandas-with-numpy-2,
python-scipy-with-numpy-2): New variables.

* gnu/packages/python-xyz.scm (python-matplotlib-with-numpy-2): New variable.

Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52
---
 gnu/packages/python-science.scm | 19 +++++++++++++++++++
 gnu/packages/python-xyz.scm     | 21 +++++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 1f4cdb239a1..0332546d22d 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -475,6 +475,14 @@ (define-public python-scipy
 routines such as routines for numerical integration and optimization.")
     (license license:bsd-3)))

+(define-public python-scipy-with-numpy-2
+  (package
+    (inherit python-scipy)
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-scipy)
+       (replace "python-numpy" python-numpy-2)
+       (replace "python-matplotlib" python-matplotlib-with-numpy-2)))))
+
 (define-public python-scikit-allel
   (package
     (name "python-scikit-allel")
@@ -1479,6 +1487,17 @@ (define-public python-pandas-2

 (define-public python-pandas python-pandas-2)

+(define-public python-pandas-with-numpy-2
+  (package
+    (inherit python-pandas)
+    (native-inputs
+     (modify-inputs (package-native-inputs python-pandas)
+       (replace "python-numpy" python-numpy-2)
+       (replace "python-matplotlib" python-matplotlib-with-numpy-2)))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-pandas)
+       (replace "python-matplotlib" python-matplotlib-with-numpy-2)))))
+
 (define-public python-pandas-stubs
   (package
     (name "python-pandas-stubs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a4017fffe48..1fc6ebdb0b4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10462,6 +10462,27 @@ (define-public python-matplotlib
 toolkits.")
     (license license:psfl)))

+(define-public python-matplotlib-with-numpy-2
+  (package
+    (inherit python-matplotlib)
+    (version "3.8.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "matplotlib" version))
+       (sha256
+        (base32 "1spzglb3hh3959z72iwspm9dsbf5zz2q3hri1sb5ihcybrykkb4a"))))
+    (arguments
+     (substitute-keyword-arguments
+         (package-arguments python-matplotlib)
+       ((#:tests? _ #t) #f)
+       ((#:phases phases #~%standard-phases)
+        #~(modify-phases #$phases
+            (delete 'sanity-check)))))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-matplotlib)
+       (replace "python-numpy" python-numpy-2)))))
+
 (define-public python-matplotlib-documentation
   (package
     (inherit python-matplotlib)

base-commit: c9abfacd9f58f7365668b67a8125640b7497932a
prerequisite-patch-id: a2254ccef49d23b75149b22b200b6156097b673f
prerequisite-patch-id: 4e4a0833f7c017f2922344883800161335290814
prerequisite-patch-id: 97653359db283a3832359fc4cd0dc1741a2f51bc
prerequisite-patch-id: 2eac1b43f9e9050e8467c89cd384da43bff63305
-- 
2.47.1

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From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: Sharlatan Hellseher <sharlatanus@HIDDEN>
Subject: bug#76240: Acknowledgement ([PATCH] gnu: Add NumPy 2 related
 variants.)
Message-ID: <handler.76240.B.173939393822472.ack <at> debbugs.gnu.org>
References: <e2de75ba2392dbb0aa6021befea7d9a6b8c17959.1739393772.git.sharlatanus@HIDDEN>
X-Gnu-PR-Message: ack 76240
X-Gnu-PR-Package: guix-patches
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Date: Wed, 12 Feb 2025 20:59:02 +0000

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Message sent to guix-patches@HIDDEN:

Subject: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
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To: Sharlatan Hellseher <sharlatanus@HIDDEN>
Cc: Tanguy Le Carrour <tanguy@HIDDEN>, Munyoki Kilyungi <me@HIDDEN>, Lars-Dominik Braun <lars@HIDDEN>, 76240 <at> debbugs.gnu.org, jgart <jgart@HIDDEN>, Marius Bakke <marius@HIDDEN>
From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
In-Reply-To: <e2de75ba2392dbb0aa6021befea7d9a6b8c17959.1739393772.git.sharlatanus@HIDDEN>
 (Sharlatan Hellseher's message of "Wed, 12 Feb 2025 20:58:39 +0000")
References: <e2de75ba2392dbb0aa6021befea7d9a6b8c17959.1739393772.git.sharlatanus@HIDDEN>
Date: Fri, 14 Feb 2025 13:59:47 +0100
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Hi!

Sharlatan Hellseher <sharlatanus@HIDDEN> skribis:

> This to make Pandas, MatplotLib and SciPy compatible with NumPy 2.  They
> need to be build with newer version otherwise it raise the error.
>
> * gnu/packages/python-science.scm: (python-pandas-with-numpy-2,
> python-scipy-with-numpy-2): New variables.
>
> * gnu/packages/python-xyz.scm (python-matplotlib-with-numpy-2): New varia=
ble.
>
> Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52

[...]

> +(define-public python-scipy-with-numpy-2
> +  (package
> +    (inherit python-scipy)
> +    (propagated-inputs

Comment for all of these: it should be =E2=80=98package/inherit=E2=80=99 (t=
o potentially
inherit replacements) and also change the =E2=80=98name=E2=80=99 field to d=
istinguish
it.

Actually, assuming we want to move to NumPy 2.x going forward, I would
suggest keeping the regular name for the -with-numpy-2 variants (like
=E2=80=9Cpython-scipy=E2=80=9D) and choose a different name for the NumPy 1=
.x variants
(like =E2=80=9Cpython-scipy-with-numpy-1=E2=80=9D).

That way, somebody running:

  guix shell python python-numpy python-scipy

will still get a consistent package set.

How does that sound?

Thanks,
Ludo=E2=80=99.

Message sent to guix-patches@HIDDEN:

Subject: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
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To: Sharlatan Hellseher <sharlatanus@HIDDEN>
Cc: Tanguy Le Carrour <tanguy@HIDDEN>, Munyoki Kilyungi <me@HIDDEN>, Lars-Dominik Braun <lars@HIDDEN>, 76240 <at> debbugs.gnu.org, jgart <jgart@HIDDEN>, Marius Bakke <marius@HIDDEN>
From: Ludovic =?UTF-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
In-Reply-To: <878qq8znp8.fsf@HIDDEN> ("Ludovic =?UTF-8?Q?Court=C3=A8s?="'s message of "Fri, 14 Feb 2025 13:59:47 +0100")
References: <e2de75ba2392dbb0aa6021befea7d9a6b8c17959.1739393772.git.sharlatanus@HIDDEN>
 <878qq8znp8.fsf@HIDDEN>
Date: Fri, 21 Feb 2025 12:26:26 +0100
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Hey Oleg,

Ludovic Court=C3=A8s <ludo@HIDDEN> skribis:

> Sharlatan Hellseher <sharlatanus@HIDDEN> skribis:
>
>> This to make Pandas, MatplotLib and SciPy compatible with NumPy 2.  They
>> need to be build with newer version otherwise it raise the error.
>>
>> * gnu/packages/python-science.scm: (python-pandas-with-numpy-2,
>> python-scipy-with-numpy-2): New variables.
>>
>> * gnu/packages/python-xyz.scm (python-matplotlib-with-numpy-2): New vari=
able.
>>
>> Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52
>
> [...]
>
>> +(define-public python-scipy-with-numpy-2
>> +  (package
>> +    (inherit python-scipy)
>> +    (propagated-inputs
>
> Comment for all of these: it should be =E2=80=98package/inherit=E2=80=99 =
(to potentially
> inherit replacements) and also change the =E2=80=98name=E2=80=99 field to=
 distinguish
> it.
>
> Actually, assuming we want to move to NumPy 2.x going forward, I would
> suggest keeping the regular name for the -with-numpy-2 variants (like
> =E2=80=9Cpython-scipy=E2=80=9D) and choose a different name for the NumPy=
 1.x variants
> (like =E2=80=9Cpython-scipy-with-numpy-1=E2=80=9D).
>
> That way, somebody running:
>
>   guix shell python python-numpy python-scipy

This broke =E2=80=98tests/guix-pack-relocatable.sh=E2=80=99 for these reaso=
ns:

--8<---------------cut here---------------start------------->8---
+ guix pack -RR python-numpy python-scipy --no-grafts -n
guix pack: error: profile contains conflicting entries for python-numpy
guix pack: error:   first entry: python-numpy@HIDDEN /gnu/store/i1g6wbcc0ilh=
cc5vy4pi70z58gk1716f-python-numpy-2.2.2R
guix pack: error:   second entry: python-numpy@HIDDEN /gnu/store/2s1jala0jg=
56drh4hc19mrdg6w3gswhm-python-numpy-1.24.4R
guix pack: error:    ... propagated from python-pythran@HIDDEN
guix pack: error:    ... propagated from python-scipy@HIDDEN
hint: Backtrace:
--8<---------------cut here---------------end--------------->8---

Would be nice to address it before we get a deluge of angry bug reports.
:-)

Ludo=E2=80=99.

Last modified: Fri, 21 Feb 2025 11:30:04 UTC

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