GNU bug report logs - #76240
[PATCH] gnu: Add NumPy 2 related variants.

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

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH] gnu: Add NumPy 2 related variants.
Date: Wed, 12 Feb 2025 20:58:39 +0000

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

Message #8 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: Tanguy Le Carrour <tanguy <at> bioneland.org>,
 Munyoki Kilyungi <me <at> bonfacemunyoki.com>, Lars-Dominik Braun <lars <at> 6xq.net>,
 76240 <at> debbugs.gnu.org, jgart <jgart <at> dismail.de>, Marius Bakke <marius <at> gnu.org>
Subject: Re: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
Date: Fri, 14 Feb 2025 13:59:47 +0100

Hi!

Sharlatan Hellseher <sharlatanus <at> gmail.com> 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 variable.
>
> Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52

[...]

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

Comment for all of these: it should be ‘package/inherit’ (to potentially
inherit replacements) and also change the ‘name’ 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
“python-scipy”) and choose a different name for the NumPy 1.x variants
(like “python-scipy-with-numpy-1”).

That way, somebody running:

  guix shell python python-numpy python-scipy

will still get a consistent package set.

How does that sound?

Thanks,
Ludo’.

Message #11 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: Tanguy Le Carrour <tanguy <at> bioneland.org>,
 Munyoki Kilyungi <me <at> bonfacemunyoki.com>, Lars-Dominik Braun <lars <at> 6xq.net>,
 76240 <at> debbugs.gnu.org, jgart <jgart <at> dismail.de>, Marius Bakke <marius <at> gnu.org>
Subject: Re: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
Date: Fri, 21 Feb 2025 12:26:26 +0100

Hey Oleg,

Ludovic Courtès <ludo <at> gnu.org> skribis:

> Sharlatan Hellseher <sharlatanus <at> gmail.com> 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 variable.
>>
>> Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52
>
> [...]
>
>> +(define-public python-scipy-with-numpy-2
>> +  (package
>> +    (inherit python-scipy)
>> +    (propagated-inputs
>
> Comment for all of these: it should be ‘package/inherit’ (to potentially
> inherit replacements) and also change the ‘name’ 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
> “python-scipy”) and choose a different name for the NumPy 1.x variants
> (like “python-scipy-with-numpy-1”).
>
> That way, somebody running:
>
>   guix shell python python-numpy python-scipy

This broke ‘tests/guix-pack-relocatable.sh’ for these reasons:

--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 <at> 2.2.2 /gnu/store/i1g6wbcc0ilhcc5vy4pi70z58gk1716f-python-numpy-2.2.2R
guix pack: error:   second entry: python-numpy <at> 1.24.4 /gnu/store/2s1jala0jg56drh4hc19mrdg6w3gswhm-python-numpy-1.24.4R
guix pack: error:    ... propagated from python-pythran <at> 0.17.0
guix pack: error:    ... propagated from python-scipy <at> 1.12.0
hint: Backtrace:
--8<---------------cut here---------------end--------------->8---

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

Ludo’.

Message #14 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: Tanguy Le Carrour <tanguy <at> bioneland.org>,
 Munyoki Kilyungi <me <at> bonfacemunyoki.com>, Lars-Dominik Braun <lars <at> 6xq.net>,
 76240 <at> debbugs.gnu.org, jgart <jgart <at> dismail.de>, Marius Bakke <marius <at> gnu.org>
Subject: Re: [bug#76240] [PATCH] gnu: Add NumPy 2 related variants.
Date: Mon, 21 Apr 2025 23:58:53 +0200

Hi Oleg,

Did you have a chance to look into this?

Thanks in advance,
Ludo’.

Ludovic Courtès <ludo <at> gnu.org> writes:

> Hey Oleg,
>
> Ludovic Courtès <ludo <at> gnu.org> skribis:
>
>> Sharlatan Hellseher <sharlatanus <at> gmail.com> 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 variable.
>>>
>>> Change-Id: I53878b643ea6f7b35e3d893a18da438c2c111c52
>>
>> [...]
>>
>>> +(define-public python-scipy-with-numpy-2
>>> +  (package
>>> +    (inherit python-scipy)
>>> +    (propagated-inputs
>>
>> Comment for all of these: it should be ‘package/inherit’ (to potentially
>> inherit replacements) and also change the ‘name’ 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
>> “python-scipy”) and choose a different name for the NumPy 1.x variants
>> (like “python-scipy-with-numpy-1”).
>>
>> That way, somebody running:
>>
>>   guix shell python python-numpy python-scipy
>
> This broke ‘tests/guix-pack-relocatable.sh’ for these reasons:
>
> + 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 <at> 2.2.2 /gnu/store/i1g6wbcc0ilhcc5vy4pi70z58gk1716f-python-numpy-2.2.2R
> guix pack: error:   second entry: python-numpy <at> 1.24.4 /gnu/store/2s1jala0jg56drh4hc19mrdg6w3gswhm-python-numpy-1.24.4R
> guix pack: error:    ... propagated from python-pythran <at> 0.17.0
> guix pack: error:    ... propagated from python-scipy <at> 1.12.0
> hint: Backtrace:
>
> Would be nice to address it before we get a deluge of angry bug reports.
> :-)
>
> Ludo’.

Message #17 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76240 <at> debbugs.gnu.org
Cc: ludo <at> gnu.org
Subject: [PATCH] gnu: Add NumPy 2 related variants.
Date: Mon, 21 Apr 2025 23:30:42 +0100

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512


Hi Ludo,

It good timing to check it after python-team is merged. I need to
refresh my thoughts on this as with default NumPy swapped to 2 the whole
Python science stack needs to be rebuild.

I might need some more research.

- --
Thanks,
Oleg
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Message #20 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 76240 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: Add NumPy 2 related variants.
Date: Tue, 22 Apr 2025 15:19:34 +0200

Sharlatan Hellseher <sharlatanus <at> gmail.com> writes:

> It good timing to check it after python-team is merged. I need to
> refresh my thoughts on this as with default NumPy swapped to 2 the whole
> Python science stack needs to be rebuild.

Alright.  If you have ideas on how to fix the failing test in the
meantime, that’d be great; we shouldn’t leave failing tests in place for
this long.

Thanks,
Ludo’.

Message #23 received at 76240 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76240 <at> debbugs.gnu.org
Cc: me <at> bonfacemunyoki.com, tanguy <at> bioneland.org, ludo <at> gnu.org, lars <at> 6xq.net,
 ngraves <at> ngraves.fr
Subject: [PATCH] gnu: Add NumPy 2 related variants.
Date: Thu, 24 Apr 2025 14:33:21 +0100

[Message part 1 (text/plain, inline)]

Hi Ludo,

Tests are activated and all passed without any skippings x86_64 (!!).

Pushed to master as 9801822b8b5643a56551506d04abc7fc504076de.

I've CCed other Python masters to brainstorm migration to NymPy 2+ ;-)

--
Oleg

[signature.asc (application/pgp-signature, inline)]

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