Python dependency is missing in the Getting Started section

[edoumazane]

Hi, Thank you for developing Abba, it's a very nice tool.

I have a concern about the getting started section. The instructions are as follows:

• create an environment without python
• activate it
• call pip install abba-python

On my system, this results in installing all abba-python dependencies in system's pip.

I assume this is not the intended behavior and it may result in very unexpected problems.

I would suggest adding python and using a YML file that can be passed to conda, such as:

# Run conda env create -f <path to this file> to create the environment
# Run conda env update -f <path to this file> to update the environment
name: abba-env
channels:
  - conda-forge
dependencies:
  - openjdk=8
  - python=3.10 
  - pip
  - ipykernel
  - ipywidgets
  - maven
  - pip:
    - abba-python 

(i had to install maven)

[NicoKiaru]

Thanks a lot! I am happy to get some advice because I'm struggling a lot with these things. Still I thought that install commands executed within an environment would be contained to this environment. Is this not true ?

As for maven, it should come with pip install abba-python, no ? Maven is a common issue I have because it's usually installed on my computers - because of the Java development I do. Thus I fail to detect when it could be missing.

Which OS do you have ?

[edoumazane]

Happy if i can help! I have Linux ubuntu 20.04.

No, when a program is not installed in an environment, it will look at the system level (actually it just follows the order of priority indicated by the $PATH). In Linux/Mac you can always which <command> (like which pip) to see where is the executable you call. You don't have pip in the environment if you don't install python. If system's pip is called, the packages are installed at the system level. It really can mess up some things. I'm not sure but at least in some cases, when solving an environment, if a dependency package is already at the system level, it might skip installing that package in the environment.

For maven, i had an error at pip install abba-python that mentionned it was missing. But i didn't have it installed at the system level. So i installed it in the environment.

[NicoKiaru]

Ok. Do you think you could make a PR and fix this issue ? I'd be happy to merge it.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/abba-export-qupath-import-error/88166/4

[NicoKiaru]

Quick question @doumazane : is this repo working with python 3.10 in your configuration ? I thought I was locked to 3.8, but that's good news if not.

[edoumazane]

• For what i did it worked fine with python 3.10!
• I noticed conda installs python 3.12 if not pinned but then it does not go through the pip installation of abba_python, with an error that involves jpype. But with 3.10 it's fine.
• I also noticed that this time i did not have to specify maven in the conda dependencies
• I'm preparing a PR.

[GuillaumeLeGoc]

I wrote a quick fix for the instructions in the meantime.