Pinned environment.yaml should not include channel defaults

[nkaretnikov]

Context

The generated yaml file includes defaults even when the spec doesn't:

Repro

channels:
- conda-forge
dependencies:
- python ==3.9
- pip:
  - flask
description: ''
name: test
prefix: null
variables: null

channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- ca-certificates=2024.2.2=hbcca054_0
- ld_impl_linux-64=2.40=h55db66e_0
- libffi=3.3=h58526e2_2
- libgcc-ng=13.2.0=hc881cc4_6
- libgomp=13.2.0=hc881cc4_6
- libsqlite=3.45.3=h2797004_0
- libstdcxx-ng=13.2.0=h95c4c6d_6
- libzlib=1.2.13=hd590300_5
- ncurses=6.4.20240210=h59595ed_0
- openssl=1.1.1w=hd590300_0
- pip=24.0=pyhd8ed1ab_0
- python=3.9.0=hffdb5ce_5_cpython
- readline=8.2=h8228510_1
- setuptools=69.5.1=pyhd8ed1ab_0
- sqlite=3.45.3=h2c6b66d_0
- tk=8.6.13=noxft_h4845f30_101
- tzdata=2024a=h0c530f3_0
- wheel=0.43.0=pyhd8ed1ab_1
- xz=5.2.6=h166bdaf_0
- zlib=1.2.13=hd590300_5
- pip:
  - blinker==1.7.0
  - click==8.1.7
  - flask==3.0.3
  - importlib-metadata==7.1.0
  - itsdangerous==2.2.0
  - jinja2==3.1.3
  - markupsafe==2.1.5
  - werkzeug==3.0.2
  - zipp==3.18.1
name: /home/test/.local/share/conda-store/state/default/c289b5a3-1714091897-1-test
prefix: /home/test/.local/share/conda-store/state/default/c289b5a3-1714091897-1-test

This is because conda/mamba env export includes this channel by default. There's an option --override-channels, which should help, I think, but it requires passing at least one -c / --channel flag, which would require extracting channels from the specification.

See action_generate_conda_export and api_get_build_yaml.

Value and/or benefit

Export matches the spec.

Anything else?

No response

[jonzeper]

We just realized that we've been unintentionally installing some packages from Anaconda's pkgs/main for some time, I guess due to this.

I wasn't able to reproduce the issue using mamba on its own. If I create an environment and export it with mamba env export, it does not add defaults. It seems to only happen when conda-store builds the environment. Not sure why - I tried to troubleshoot a bit but didn't get anywhere. Ended up setting the env var CONDA_CHANNELS=conda-forge as a quick fix on our deployment to restrict available channels.

Anyway, just wanted to throw an upvote for fixing this, and maybe should be considered a bug?
nbconvert=6.5.4 is a good test case -- it exists on pkgs/main but not conda-forge

[trallard]

@jaimergp do you have any insights on the cleanest way to resolve this?

[jaimergp]

The cleanest would be "waiting" til deprecations introduced in conda/conda#14227 are effective by March. It seems that users expect the channels list in their environment.yml file to be the only source of channel information (reasonably so!), so we just need to make sure the input and output YAMLs match this part.

I'd say conda/conda#12356 is the cause behind, but we need to figure it out. The canonical workaround is to run conda config --remove channels defaults if defaults is not in the env.yml.