GNU bug report logs - #77542
[PATCH python-team 00/38] Further patches on python-team.

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

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: guix-patches <at> gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH python-team 00/38] Further patches on python-team. 
Date: Fri,  4 Apr 2025 21:06:56 +0200

As usual. A few notes:
- clipper2 was added for cura IIRC, which requires it but isn't ready yet / requires more work.
- I couldn't test python-pytensor update because of build times, so it might still break.

Nicolas Graves (38):
  gnu: Add clipper2.
  gnu: labelme: Add missing native-inputs.
  gnu: scregseg: Add missing native-inputs.
  gnu: autokey: Add missing native-inputs.
  gnu: mageck: Add missing native-inputs.
  gnu: python-pytroch-geometric: Skip failing tests.
  gnu: Add string-view-lite.
  gnu: python-pytensor: Update to 2.30.1.
  gnu: python-vaex-core: Update to 4.17.1.
  gnu: Remove pybind11-2.3.
  gnu: python-property-cached: Fix build.
  gnu: python-attr: Update to 0.3.2.
  gnu: python-serpent: Update to 1.41.
  gnu: python-pyro4: Update to 4.82.
  gnu: python-lcapy: Add missing native-inputs.
  gnu: python-linear-operator: Update to 0.6.
  gnu: gpytorch: Remove uneeded inputs.
  gnu: python-botorch: Add missing native-inputs.
  gnu: python-gpytorch: Update to 1.14.
  gnu: python-botorch: Update to 0.13.0.
  gnu: python-pgmpy: Update to 1.0.0.
  gnu: python-qasync: Ignore failing test.
  gnu: python-bed-reader: Fix build and enable tests.
  gnu: python-pysnptools: Fix build and enable tests.
  gnu: Add python-poetry-core-next.
  gnu: python-duniterpy: Update to 1.2.1.
  gnu: python-pgpy: Fix tests.
  gnu: python-furl: Update to 2.1.4.
  gnu: python-rq: Update to 2.3.1.
  gnu: python-crontab: Update to 3.2.0.
  gnu: python-stone: Update to 3.3.9.
  gnu: python-rq-scheduler: Update to 0.14.
  gnu: python-port-for: Update to 0.7.4.
  gnu: Remove python-cookies.
  gnu: python-django-rq: Update to 3.0.0.
  gnu: python-flask-seasurf: Update to 2.0.0.
  gnu: python-country-converter: Add missing native-input.
  gnu: python-itemloaders: Update to 1.3.2.

 gnu/local.mk                                  |   3 +
 gnu/packages/bioinformatics.scm               | 280 ++++++++++++++----
 gnu/packages/cpp.scm                          |  56 +++-
 gnu/packages/databases.scm                    |  67 +++--
 gnu/packages/django.scm                       |  28 +-
 gnu/packages/engineering.scm                  |   4 +-
 gnu/packages/finance.scm                      |  40 +--
 gnu/packages/image-processing.scm             |   3 +-
 gnu/packages/iso-codes.scm                    |   3 +-
 gnu/packages/machine-learning.scm             |  56 ++--
 .../python-bed-reader-use-store-samples.patch | 147 +++++++++
 .../python-property-cached-asyncio-3_11.patch | 201 +++++++++++++
 .../python-vaex-core-fix-tsl-use.patch        |  67 +++++
 gnu/packages/python-build.scm                 |  10 +
 gnu/packages/python-crypto.scm                |  15 +-
 gnu/packages/python-science.scm               |  87 +++---
 gnu/packages/python-web.scm                   |  60 ++--
 gnu/packages/python-xyz.scm                   | 186 ++++++------
 gnu/packages/statistics.scm                   |  16 +-
 19 files changed, 987 insertions(+), 342 deletions(-)
 create mode 100644 gnu/packages/patches/python-bed-reader-use-store-samples.patch
 create mode 100644 gnu/packages/patches/python-property-cached-asyncio-3_11.patch
 create mode 100644 gnu/packages/patches/python-vaex-core-fix-tsl-use.patch

-- 
2.49.0

Message #8 received at 77542 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 77542 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH python-team 00/38] Further patches on python-team.
Date: Sat, 05 Apr 2025 08:08:02 +0100

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

Hi,

They must lagged somewhere, no patches on the bug tracker either
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=77542

--
Oleg

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Message #11 received at 77542 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>, 77542 <at> debbugs.gnu.org
Subject: Re: [bug#77542] [PATCH python-team 00/38] Further patches on
 python-team.
Date: Sat, 05 Apr 2025 11:13:04 +0200

It's 77541, sorry ;)

On 2025-04-05 08:08, Sharlatan Hellseher wrote:

> Hi,
>
> They must lagged somewhere, no patches on the bug tracker either
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=77542
>
> --
> Oleg

-- 
Best regards,
Nicolas Graves

Message #14 received at 77542 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 77542 <at> debbugs.gnu.org
Cc: ngraves <at> ngraves.fr
Subject: [PATCH python-team 00/38] Further patches on python-team.
Date: Sat, 05 Apr 2025 15:59:03 +0100

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

Hi Nicolas,

I could build all proposed patches successfully. python-pytensor was
downgraded to make it compatible with current version of python-scipy
which I avoid to refresh, let's do it in the next iteration of
python-team and concentrate on the failing ones in the current.

/gnu/store/424c967mkwcyaq58lgcq0p4kv9bg0bpd-clipper2-1.5.2
/gnu/store/xg3b83c7b9384cby31wfas9b5zl6pjjj-python-poetry-core-2.1.2
/gnu/store/v1v7dxf6hv3bf3w1q3cgyy6pdy50cwzx-string-view-lite-1.8.0
/gnu/store/jcscrrwqx3d0sss9il769pa9zdrshjnm-autokey-0.96.0
/gnu/store/wv9hh9ayn5z03a2vc77b5lyfydrvr878-labelme-5.2.1
/gnu/store/yc6sd9rhbcf7h1a2z9662rh22nry29nw-mageck-0.5.9.5
/gnu/store/z9r7n04ln5r4y5s1jcfmzrnkysj2a37z-python-attr-0.3.2
/gnu/store/4pv6wfrap959l7z4qyy45a0jpvanlh8z-python-bed-reader-1.0.6
/gnu/store/ysil15a6zknh5c3rlcnvjy32mp1kayjd-python-botorch-0.13.0
/gnu/store/5wrcfk8myyqyvwar5yg819fwln60y5h7-python-country-converter-1.2
/gnu/store/gzzppyb3d9kl5dm26n528qp3l808gq4l-python-crontab-3.2.0
/gnu/store/25hasb3xa8vblyzgs37zfzgbkqxa1ch3-python-django-rq-3.0.0
/gnu/store/iddwmfzskxks4v0dvznv5fffk6hyy6n6-python-duniterpy-1.2.1
/gnu/store/wm9alrf69h2yxw3dmbamknir4shxmpsq-python-flask-seasurf-2.0.0
/gnu/store/vv79rqkdmxxbl8cb9rbk8s46xkw189vd-python-furl-2.1.4
/gnu/store/b4ays94g46shz0khzdm2mgpg695qvvc2-python-gpytorch-1.14
/gnu/store/1ldxzdd51bf1sqrvpmzq458vwh9wl6zm-python-itemloaders-1.3.2
/gnu/store/03i1r1bqjc45kq07ijgkqzzlm3vq858g-python-lcapy-1.24
/gnu/store/9kvzq38ffmng76mr9s93i1h9lpnbnzm3-python-linear-operator-0.6
/gnu/store/xzhllld70mbr09mqbhd15vczkariir3b-python-pgmpy-1.0.0
/gnu/store/z7i9bfr0sh1lbbr1jg8qkylvgrrmv5x9-python-pgpy-0.6.0
/gnu/store/kapbm1cyp0krwa6a4b79y2ycj9q2iws8-python-port-for-0.7.4
/gnu/store/b3xhskqmr2317flcrir6blmh3mqw9px8-python-property-cached-1.6.4
/gnu/store/cq7jnq7wdcw7gvhnc6n4338v3amhhqj5-python-pyro4-4.82
/gnu/store/i0gz00w673khq4y2zqi0nz0ksazbbg7b-python-pysnptools-0.5.14
/gnu/store/wfb4svky47l66y6fb8r0avwc88qn6mci-python-pytensor-2.28.3
/gnu/store/63kflm6c358xiv6qilxp0cmwq1fmxmc2-python-pytorch-geometric-2.6.1
/gnu/store/dqzwsgj2cfkx63yvawys5ahvs8ik0gpa-python-qasync-0.27.1
/gnu/store/hsqz5mzh11mgsqkwg7hl9dpmdz82m66a-python-rq-2.3.1
/gnu/store/w1d9g1vz2saj70540kazy0s90x7jzgv2-python-rq-scheduler-0.14
/gnu/store/4rykyk29gjw3ga2hxyfkzw4v7ik7yzw4-python-serpent-1.41
/gnu/store/rpnghqljbjq6ky58c3gil40awrl25hqs-python-stone-3.3.9
/gnu/store/hjjib64r4p0av2pw1q6nyz7anc63xqaq-python-vaex-core-4.18.1
/gnu/store/frxzhn9lhgwg5llwgsdf0c5kcshsnzk4-scregseg-0.1.3

I'll give it a go to check it with -P1 before pushing, 
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build -M8 -P1 clipper2 -P1 python-poetry-core <at> 2
 -P1 string-view-lite -P1 autokey -P1 labelme -P1 mageck -P1
 python-attr -P1 python-bed-reader -P1 python-botorch -P1
 python-country-converter -P1 python-crontab -P1 python-django-rq -P1
 python-duniterpy -P1 python-flask-seasurf -P1 python-furl -P1
 python-gpytorch -P1 python-itemloaders -P1 python-lcapy -P1
 python-linear-operator -P1 python-pgmpy -P1 python-pgpy -P1
 python-port-for -P1 python-property-cached -P1 python-pyro4 -P1
 python-pysnptools -P1 python-pytensor -P1 python-pytorch-geometric -P1
 python-qasync -P1 python-rq -P1 python-rq-scheduler -P1 python-serpent
 -P1 python-stone -P1 python-vaex-core -P1 scregseg
--8<---------------cut here---------------end--------------->8---

--
Oleg

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Message #19 received at 77542-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 77542-done <at> debbugs.gnu.org
Subject: [PATCH python-team 00/38] Further patches on python-team.
Date: Sat, 05 Apr 2025 22:07:20 +0100

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

Hi,

I've fixed some failing packages in the chain but have no chance to
check how to deal with these two:
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build -M8 -P1 -k clipper2 -P1 python-poetry-core <at> 2
 -P1 string-view-lite -P1 autokey -P1 labelme -P1 mageck -P1
 python-attr -P1 python-bed-reader -P1 python-botorch -P1
 python-country-converter -P1 python-crontab -P1 python-django-rq -P1
 python-duniterpy -P1 python-flask-seasurf -P1 python-furl -P1
 python-gpytorch -P1 python-itemloaders -P1 python-lcapy -P1
 python-linear-operator -P1 python-pgmpy -P1 python-pgpy -P1
 python-port-for -P1 python-property-cached -P1 python-pyro4 -P1
 python-pysnptools -P1 python-pytensor -P1 python-pytorch-geometric -P1
 python-qasync -P1 python-rq -P1 python-rq-scheduler -P1 python-serpent
 -P1 python-stone -P1 python-vaex-core -P1 scregseg 2>&1 | grep "drv failed"

build of /gnu/store/bcj5hy335qcx92w6jb7f68a7759dbvs7-silkaj-0.10.0.drv failed
build of /gnu/store/mr1pl70mgjwh7m1lark373crk5pl1lys-python-django-3.1.14.drv failed
--8<---------------cut here---------------end--------------->8---

* python-django-3.1.14
Maybe we can get read of it?

* silkaj-0.10.0
Requires a fresh https://github.com/python-pendulum/pendulum, requires
Rust, fails to build due to https://github.com/python-pendulum/pendulum/issues/857

Pushed to python-team.

--
Oleg

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