I've noticed that when creating a conda environment from an environment.yaml file that explicitly specifies channels, conda (and also mamba) seems to extend the list of channels with whatever is defined in .condarc/.mambarc.
This is surprising - after all the key is channels not additional_channels.
Is there some way to make conda/mamba ignore the "default" channels configured outside of the environment file in question?
To be concrete, here's a minimal reproducible example.
My .condarc/.mambarc look like this:
channels:
- conda-forge
- bioconda
yet I want bioconda to be entirely ignored when installing the following environment.yaml:
name: testenv
channels:
- conda-forge
dependencies:
- python
The solution is to add the magic nodefaults channel to the channel list:
name: testenv
channels:
- conda-forge
- nodefaults # adding this is the solution
dependencies:
- python
Another less ideal option is to pass the --override-channels CLI flag when creating the environment.
conda create -n testenv -f testenv.yaml --override-channels
I tried adding both override_channels: true and override-channels: true to the environment spec, but that didn't have any effect.
Thanks to @merv for pointing out the workaround in this Github issue