Switch conda to mamba?

Ideas and Suggestions
1

The install docs state to use conda for installing qiime2. Given the large number of dependencies, and the speed & code stability of mamba, maybe it's time to change conda to mamba?

For example, change:

wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml
conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml

to:

wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml
mamba env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml
3 Likes
2

Good to see you again, Nick,

We have had issues with mamba, see
Qiime2 2022.8 can't be installed with mamba and
installing Qiime2 with mamba

Mamba is so much faster, so if it's ready to use in production that would be awesome! Would you be willing to help us out with testing?

3

It's also now possible to use libsolv (the important part that mamba uses) inside of conda directly. See:

https://conda.github.io/conda-libmamba-solver/libmamba-vs-classic/

4 Likes
4

I'd also like to give mamba a vote. I failed to install qiime2 with conda in ubuntu-server 22 environment on my old surface pro4 (which can not work without being plugged :laughing:). It took a very long time for the installation process and I finally gave up. In contrast, mamba worked quite fast and completed the installation just in one try. My very recent installation is version 2023.2.

2 Likes
5

Mamba is so much faster, so if it's ready to use in production that would be awesome! Would you be willing to help us out with testing?

Sure! It would probably be best to include a mamba install in the qiime2 CI testing. It appears that neither a conda nor a mamba install of qiime2 is currently tested in your github actions. Do you want me to send a PR with an updated ci.yml?

1 Like
7

Not yet! Qiime2 has a couple of testing systems, so let's see what the devs recommend!

8

I'll try mamba. Indeed, it is faster.