Bug#1053649: python3-numpy fails to install due to file clash with python-numpy

[Wookey]

Package: python3-numpy
Version: 1:1.24.2-1
Severity: important

I am upgrading a system (laptop) from bullseye to bookworm. Everything
was upgraded fully in bullseye, and all foreign (-dmo) packages
removed before starting the upgrade. There were some old packages
onthe system, include quite a few pthon-* (python2) packages.

I did
apt upgrade --without-new-pkgs
first (as recomended on debian.org/releases/bookworm/amd64/release-notes/ch-upgrading.en.html) and that went fine, but the subsequent
apt full-upgrade
failed with:
Preparing to unpack .../python3-numpy_1%3a1.24.2-1_amd64.deb ...
Unpacking python3-numpy (1:1.24.2-1) ...
dpkg: error processing archive /var/cache/apt/archives/python3-numpy_1%3a1.24.2-1_amd64.deb
(--unpack):
trying to overwrite '/usr/bin/f2py', which is also in package python-numpy 1:1.16.2-1
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
Errors were encountered while processing:
/var/cache/apt/archives/python3-numpy_1%3a1.24.2-1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)


trying to remove python-numpy didn't work either:
sudo dpkg -r python-numpy
dpkg: dependency problems prevent removal of python-numpy:
python-gtk2 depends on python-numpy (>= 1:1.13.1).
python-gtk2 depends on python-numpy-abi9; however:
Package python-numpy-abi9 is not installed.
Package python-numpy which provides python-numpy-abi9 is to be removed.
python-gtk2 depends on python-numpy (>= 1:1.13.1).
python-gtk2 depends on python-numpy-abi9; however:
Package python-numpy-abi9 is not installed.
Package python-numpy which provides python-numpy-abi9 is to be removed.

removing 2 packages together:
sudo dpkg -r python-numpy python-gtk2
[sudo] password for tess:
(Reading database ... 365279 files and directories currently installed.)
Removing python-gtk2 (2.24.0-5.1+b1) ...
Removing python-numpy (1:1.16.2-1) ...

worked, and then I was able to carry on with
apt --fix-broken-install

This was a totally normal upgrade (albeit with a few old packages lyng around) , so should have worked.
I guess there should be a conflict added to prevent this, which would force the old python-numpy to be removed before the new python3-numpy goes in?

Cheers.

-- System Information:
Debian Release: 12.2
Architecture: amd64 (x86_64)

Kernel: Linux 5.10.0-26-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages python3-numpy depends on:
ii libblas3 [libblas.so.3] 3.11.0-2
ii libc6 2.36-9+deb12u2
ii liblapack3 3.11.0-2
iU python3 3.11.2-1+b1
ii python3-pkg-resources 66.1.1-1
ii python3.9 3.9.2-1

[A. F. Cano]

In my case, this is what worked:

sudo dpkg -r python-numpy python-gtk2 python-collada zenmap
(Reading database ... 1421314 files and directories currently installed.)
Removing python-collada (0.4-3) ...
Removing zenmap (7.70+dfsg1-6+deb10u2) ...

Removing python-gtk2 (2.24.0-5.1+b1) ...
Removing python-numpy (1:1.16.2-1) ...

Processing triggers for doc-base (0.11.1) ...
Processing 2 removed doc-base files, 1 added doc-base file...
Registering documents with dwww...
Processing triggers for man-db (2.9.4-2) ...
Processing triggers for gnome-menus (3.36.0-1) ...
Processing triggers for desktop-file-utils (0.26-1) ...
Processing triggers for mailcap (3.69) ...

Not doing the 4 at the same time would make dpkg complain about
dependencies.