ERROR: Will not install to the user site because it will lack sys.path precedence ... using venv inside docker

I am having troubles building docker from ubuntu:24.04, Python version 3.12.3 and pip 25.1.1. Since the recent (I think) defualt pip behavior throwing

error: externally-managed-environment 

when calling system-python/pip to install packages, i tried to manage python packages with venv also inside docker.

Then as I usually do i run the container (now with with the /opt/venv) via singularity as non-sudo, providing the target home (e.g., singularity shell -H /home/davide/test docker://myImage)

But now, trying to install additional packages the /opt/venv/bin/pip do not fall-back on local installation in /home/davide/test/.local (as it used to) when /opt/ is found not-writable and fails as follows

pip3 install scanpy
ERROR: Will not install to the user site because it will lack sys.path precedence to numpy in /opt/venv/lib/python3.12/site-packages

here the minimal dockerfile to reproduce the problem

FROM ubuntu:24.04

# general environmental variables
ENV DEBIAN_FRONTEND=noninteractive

SHELL ["/bin/bash", "-o", "pipefail", "-c"]
WORKDIR /

RUN apt-get update -y  && apt-get install -y python3 python3-venv python-is-python3 python3-pip

COPY config/requirements.txt /opt/requirements.txt
RUN python3 -m venv --system-site-packages /opt/venv && \
    /opt/venv/bin/pip install --no-cache-dir --upgrade pip setuptools && \
    /opt/venv/bin/pip install --no-cache-dir -r /opt/requirements.txt

ENV PATH=/opt/venv/bin:${PATH}
ENV PIP_USER=yes

ENTRYPOINT []

with requiirements.txt only having scipy

Some info from the container launched via singularity:

Singularity> python -m site
sys.path = [
    '/home/davide/test',
    '/usr/lib/python312.zip',
    '/usr/lib/python3.12',
    '/usr/lib/python3.12/lib-dynload',
    '/opt/venv/lib/python3.12/site-packages',
    '/usr/local/lib/python3.12/dist-packages',
    '/usr/lib/python3/dist-packages',
]
USER_BASE: '/home/davide/test/.local' (doesn't exist)
USER_SITE: '/home/davide/test/.local/lib/python3.12/site-packages' (doesn't exist)
ENABLE_USER_SITE: True

Singularity> which python
/opt/venv/bin/python


Singularity> ls -ltr /opt/venv/bin/
total 17
lrwxrwxrwx 1 root root    7 Jul 30 16:53 python3.12 -> python3
lrwxrwxrwx 1 root root   16 Jul 30 16:53 python3 -> /usr/bin/python3
lrwxrwxrwx 1 root root    7 Jul 30 16:53 python -> python3
-rw-r--r-- 1 root root 2180 Jul 30 16:53 activate.fish
-rw-r--r-- 1 root root  905 Jul 30 16:53 activate.csh
-rw-r--r-- 1 root root 2006 Jul 30 16:53 activate
-rw-r--r-- 1 root root 9033 Jul 30 16:53 Activate.ps1
-rwxr-xr-x 1 root root  226 Jul 30 16:53 pip3.12
-rwxr-xr-x 1 root root  226 Jul 30 16:53 pip3
-rwxr-xr-x 1 root root  226 Jul 30 16:53 pip
-rwxr-xr-x 1 root root  221 Jul 30 16:53 numpy-config
-rwxr-xr-x 1 root root  221 Jul 30 16:53 f2py

I might be missing something basic, but I’m struggling to figure this out. Thanks in advance for any help! :)