Python 3.11

[vadim-cherepanov]

Hi,

The README.md manual instructions say to install Python 3.9 in the conda environment, but then pip install . fails because the requirement in the TOML file updated a two weeks ago requires Python >=3.11. I am not sure if Python 3.11+ would break anything else, but if not, can README.md be updated accordingly?

Thanks!
Vadim

[ink-github]

I get the same message when running pip install . inside samap_directory.

pip is looking at multiple versions of sc-samap to determine which version is compatible with other requirements. This could take a while.
ERROR: Package 'sc-samap' requires a different Python: 3.9.23 not in '>=3.11'

I updated my environment to include python = 3.11 and the pip install works smoothly now. Going to try running SAMap to see if any issues arise.

[atarashansky]

Thanks for flagging this — you're correct. SAMap v3.0.0 requires Python ≥3.11 (bumped as part of the PR #170 modernization), and the README's conda instructions haven't been updated yet.

As @ink-github confirmed, installing with Python 3.11 works fine. We've tested v3.0.0 on 3.11 and 3.12 — nothing breaks.

The README has been updated to reflect the new requirement. Simplified install:

conda create -n SAMap -c conda-forge python=3.12 pip
conda activate SAMap
pip install sc-samap

Or for development from source:

conda create -n SAMap -c conda-forge python=3.12 pip
conda activate SAMap
git clone https://github.com/atarashansky/SAMap.git
cd SAMap
pip install -e .

Closing — thanks again!