From: zimoun <zimon.toutoune@gmail.com>
To: 52906@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: bug#52906: python-biopython conflicts with python-numpy
Date: Thu, 30 Dec 2021 22:13:48 +0100 [thread overview]
Message-ID: <86o84xpzhv.fsf@gmail.com> (raw)
[-- Attachment #1: Type: text/plain, Size: 1979 bytes --]
Hi,
Using 7022eb6, the package ’python-biopython’ propagates
’python-numpy’, i.e., python-numpy@1.20.3.
However, because Guix installs by default the last version and:
--8<---------------cut here---------------start------------->8---
$ guix package -A | grep 'python-numpy ' | cut -f1,2
python-numpy 1.21.3
python-numpy 1.20.3
--8<---------------cut here---------------end--------------->8---
then this manifests.scm leads to an error,
--8<---------------cut here---------------start------------->8---
$ cat /tmp/manifest.scm
(specifications->manifest
(list "python-numpy"
"python-biopython"))
$ guix package -m /tmp/manifest.scm -p /tmp/fail
The following packages will be installed:
python-biopython 1.76
python-numpy 1.21.3
guix package: error: profile contains conflicting entries for python-numpy
guix package: error: first entry: python-numpy@1.21.3 /gnu/store/ggrkk9l67fjn1cj7alr8vx40xv08a6h0-python-numpy-1.21.3
guix package: error: second entry: python-numpy@1.20.3 /gnu/store/wgsmkn68q8h178sqc7ywjcdr330z9rb6-python-numpy-1.20.3
guix package: error: ... propagated from python-biopython@1.76
hint: Try upgrading both `python-numpy' and `python-biopython', or remove one of
them from the profile.
--8<---------------cut here---------------end--------------->8---
which is annoying.
I propose to refer as name “python-numpy” the symbol python-numpy which
leads to a consistent scientific Python stack. And to refer as name
“python-numpy-next” the symbol python-numpy-next.
For instance, it is already the case for emacs-next or for the
Bioconductor package r-cistopic.
Doing so, adventurous people can use python-numpy-next (or recompile all
the scientific Python stack using it), or update it directly on master
(for testing say) without going to a core-update cycle.
WDYT?
Attached a proposed patch.
Cheers,
simon
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From 962d942ffcba7893ab15c30dc602e51462d9b09a Mon Sep 17 00:00:00 2001
From: zimoun <zimon.toutoune@gmail.com>
Date: Thu, 30 Dec 2021 22:04:49 +0100
Subject: [PATCH] gnu: Rename last 'python-numpy' as 'python-numpy-next'.
* gnu/packages/python-xyz.scm (python-numpy-next): Rename.
---
gnu/packages/python-xyz.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7ca0b1668d..047bb4cbb8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5366,11 +5366,9 @@ (define-public python2-cython
""))
#t)))))))))
-;; NOTE: when upgrading numpy please make sure that python-pandas and
-;; python-scipy still build, as these three packages are often used together.
(define-public python-numpy-next
(package
- (name "python-numpy")
+ (name "python-numpy-next")
(version "1.21.3")
(source
(origin
@@ -5481,6 +5479,8 @@ (define-public python-numpy-1.20
(substitute-keyword-arguments (package-arguments python-numpy-next)
((#:tests? _ #t) #f)))))
+;; NOTE: when upgrading numpy please make sure that python-pandas and
+;; python-scipy still build, as these three packages are often used together.
(define-public python-numpy python-numpy-1.20)
;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of
base-commit: 002442b2209b0953dd209e6219696a8758ceceb2
--
2.34.0
next reply other threads:[~2021-12-30 21:24 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-12-30 21:13 zimoun [this message]
2021-12-30 23:55 ` bug#52906: python-biopython conflicts with python-numpy Leo Famulari
2021-12-31 10:14 ` Ricardo Wurmus
2021-12-31 10:51 ` zimoun
2021-12-31 12:43 ` Ricardo Wurmus
2021-12-31 13:16 ` zimoun
2021-12-31 20:18 ` Ricardo Wurmus
2021-12-31 12:50 ` Ricardo Wurmus
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