Install via conda environment file

[niksirbi]

Hey @viktorpm, because we have many conda dependencies, I've included a conda environment file and updated the installation instructions accordingly. It would be great if you could test whether this works on your side.

[codecov]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (09d264f) 0.00% compared to head (8fe2aea) 0.00%.

Additional details and impacted files

@@          Coverage Diff          @@
##            main      #7   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files          1       1           
  Lines          5       5           
=====================================
  Misses         5       5           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[viktorpm]

I started from scratch: removed the existing environment, cloned the repo and manually downloaded the environment.yaml file. The environment was not created. I got this message:
Collecting package metadata (repodata.json): done Solving environment: \ Killed

[viktorpm]

Couldn't create conda environment

[adamltyson]

FYI this works for me. @viktorpm are you using Windows?

[viktorpm]

FYI this works for me. @viktorpm are you using Windows?

@adamltyson, I'm using WSL but I could install everything previously

I could do it again with this command:
conda create -n template-builder -c aramislab -c conda-forge python=3.10 ants parallel
conda activate template-builder

[niksirbi]

I'm using WSL but I could install everything previously

What has also changed is that I have added napari as a dependency. Maybe that is causing a dependency resolution conflict. Did conda take very long to solve the environment?

@niksirbi, yes it took ages and I guess it timed out. Should I install Napari separately?

[niksirbi]

@viktorpm Unfortunately this tends to happen sometimes, conda is sometimes very slow to resolve dependencies. Maybe it's a good opportunity to install mamba, which is basically the same as conda, but much faster (you can use all the same commands as before, just replace conda with mamba).

If this solves the problem, I might update the instructions to recommend mamba as the default option.

@niksirbi It solved the problem. I removed Miniconda, installed Mamba and ran this command:
mamba env create -f environment.yaml -n template-builder

It quickly created the environment with all the dependencies