GNU bug report logs -
#52906
python-biopython conflicts with python-numpy
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Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Thu, 30 Dec 2021 21:24:02 UTC
Severity: normal
Done: Ricardo Wurmus <rekado <at> elephly.net>
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bug#52906
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(Thu, 30 Dec 2021 21:24:02 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Hi,
Using 7022eb6, the package ’python-biopython’ propagates
’python-numpy’, i.e., python-numpy <at> 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 <at> 1.21.3 /gnu/store/ggrkk9l67fjn1cj7alr8vx40xv08a6h0-python-numpy-1.21.3
guix package: error: second entry: python-numpy <at> 1.20.3 /gnu/store/wgsmkn68q8h178sqc7ywjcdr330z9rb6-python-numpy-1.20.3
guix package: error: ... propagated from python-biopython <at> 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
[0001-gnu-Rename-last-python-numpy-as-python-numpy-next.patch (text/x-diff, inline)]
From 962d942ffcba7893ab15c30dc602e51462d9b09a Mon Sep 17 00:00:00 2001
From: zimoun <zimon.toutoune <at> 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
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bug#52906
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(Thu, 30 Dec 2021 23:56:02 GMT)
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Message #8 received at 52906 <at> debbugs.gnu.org (full text, mbox):
On Thu, Dec 30, 2021 at 10:13:48PM +0100, zimoun wrote:
> $ 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 <at> 1.21.3 /gnu/store/ggrkk9l67fjn1cj7alr8vx40xv08a6h0-python-numpy-1.21.3
> guix package: error: second entry: python-numpy <at> 1.20.3 /gnu/store/wgsmkn68q8h178sqc7ywjcdr330z9rb6-python-numpy-1.20.3
> guix package: error: ... propagated from python-biopython <at> 1.76
> hint: Try upgrading both `python-numpy' and `python-biopython', or remove one of
> them from the profile.
> --8<---------------cut here---------------end--------------->8---
See also <https://issues.guix.gnu.org/52859>,
"tests/guix-pack-relocatable fails / numpy propagation collision".
> 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.
Agreed, the stack should be kept consistent.
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bug#52906
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(Fri, 31 Dec 2021 10:19:02 GMT)
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Message #11 received at 52906 <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> Hi,
>
> Using 7022eb6, the package ’python-biopython’ propagates
> ’python-numpy’, i.e., python-numpy <at> 1.20.
Back then we reverted to numpy 1.20.x as the default because of numba,
which did not work with 1.21. I’m now upgrading numba (and llvmlite) to
a more recent release candidate, which should bring compatibility with
numpy 1.21.
If that works we’ll make python-numpy-next the new python-numpy.
Your patch is an acceptable workaround. Arguably this should have been
done when I made numpy 1.20 the default on the core-updates-frozen
branch. I’ll apply your patch later today unless the switch to numpy
1.21 as the default is successful.
--
Ricardo
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(Fri, 31 Dec 2021 10:52:01 GMT)
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Message #14 received at 52906 <at> debbugs.gnu.org (full text, mbox):
Hi Ricardo,
On Fri, 31 Dec 2021 at 11:18, Ricardo Wurmus <rekado <at> elephly.net> wrote:
> zimoun <zimon.toutoune <at> gmail.com> writes:
> Back then we reverted to numpy 1.20.x as the default because of numba,
> which did not work with 1.21. I’m now upgrading numba (and llvmlite) to
> a more recent release candidate, which should bring compatibility with
> numpy 1.21.
>
> If that works we’ll make python-numpy-next the new python-numpy.
I think that it could nice to have "python-numpy-next". Now, because
we are right after a core-updates, the last Numpy version and the one
we use as scientific Python stack are really close. But it will not
necessary the case between 2 core-updates merges. Well, my point is
to have the core-updates package python-numpy used by all the
scientific Python stack and the leaf package python-numpy-next where
updates can happen on master, it can be used with transformations
etc., especially by scientific Python developper.
Cheers,
simon
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(Fri, 31 Dec 2021 12:45:01 GMT)
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Message #17 received at 52906 <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> Hi Ricardo,
>
> On Fri, 31 Dec 2021 at 11:18, Ricardo Wurmus <rekado <at> elephly.net> wrote:
>> zimoun <zimon.toutoune <at> gmail.com> writes:
>
>> Back then we reverted to numpy 1.20.x as the default because of numba,
>> which did not work with 1.21. I’m now upgrading numba (and llvmlite) to
>> a more recent release candidate, which should bring compatibility with
>> numpy 1.21.
>>
>> If that works we’ll make python-numpy-next the new python-numpy.
>
> I think that it could nice to have "python-numpy-next". Now, because
> we are right after a core-updates, the last Numpy version and the one
> we use as scientific Python stack are really close. But it will not
> necessary the case between 2 core-updates merges. Well, my point is
> to have the core-updates package python-numpy used by all the
> scientific Python stack and the leaf package python-numpy-next where
> updates can happen on master, it can be used with transformations
> etc., especially by scientific Python developper.
Yes, it’s a good idea to have it anyway.
I just realized that switching over to the new numpy is going to cause
more than a 1000 rebuilds. So I’ll apply your patch on the master
branch and build out the numpy upgrade on a separate branch.
Thank you!
--
Ricardo
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(Fri, 31 Dec 2021 12:52:01 GMT)
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:
bug acknowledged by developer.
(Fri, 31 Dec 2021 12:52:01 GMT)
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Message #22 received at 52906-done <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> Attached a proposed patch.
I applied it with a small change: I also had to override the name as
“python-numpy” in the derived packages.
Thanks!
--
Ricardo
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(Fri, 31 Dec 2021 13:17:02 GMT)
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Message #25 received at 52906 <at> debbugs.gnu.org (full text, mbox):
Hi,
On Fri, 31 Dec 2021 at 13:44, Ricardo Wurmus <rekado <at> elephly.net> wrote:
> I just realized that switching over to the new numpy is going to cause
> more than a 1000 rebuilds. So I’ll apply your patch on the master
> branch and build out the numpy upgrade on a separate branch.
Thanks! A separate wip-* branch?
Cheers,
simon
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(Fri, 31 Dec 2021 20:20:02 GMT)
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Message #28 received at 52906 <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> Hi,
>
> On Fri, 31 Dec 2021 at 13:44, Ricardo Wurmus <rekado <at> elephly.net> wrote:
>
>> I just realized that switching over to the new numpy is going to cause
>> more than a 1000 rebuilds. So I’ll apply your patch on the master
>> branch and build out the numpy upgrade on a separate branch.
>
> Thanks! A separate wip-* branch?
Yes, I wanted to build this out on wip-upgrade-numpy or something
similar. I’d like to avoid entangling this with other upgrades on a
core-updates or staging branch.
--
Ricardo
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This bug report was last modified 2 years and 59 days ago.
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