Anaconda Inc. (the company) has begun to threaten legal action against against commercial companies and has also advised non-profits to purchase licenses to the Anaconda software/distribution channels. While the situation is being resolved, some institutions have blocked the anaconda.org domain completely.

In the art style of 1990s Disney, cel shading: A mysterious blacksmith in a dark, forge-like setting. She wears a sleek, gold-plated helmet embossed with the symbol of a snake and an armored robe with intricate designs. Sparks fly as she hammers a molten weapon on an anvil, which begins to take the shape of a coiled snake. The forge’s flames cast a warm glow, reflecting off her helmet and tools. The snake is a python with a green sheen.
The way of the Mambalorian is miniforge distribution. This is the way.

This has been brewing for a number of years. The first change happened back in 2020, and the second happened very recently in March 2024 that affects “government entities and non-profit entities with over 200 employees or contractors”. This is problematic due the wording around ‘employees’ - many organisations have hundreds of employees but few users of conda software.

In order to avoid any potential problems, avoiding defaults channel is the best course of action.

Before we dive in, a quick recap on definitions:

  • Anaconda Inc. is the commercial entity behind the conda, miniconda, and the Anaconda.Navigator software suite.
  • Anaconda Inc. curates a set of packages which are available through specific channels - also known as defaults channel
  • Miniforge is a non-Anaconda community-developed installer specific to conda-forge channel
  • mamba is a drop in replacement to conda.
  • Far more detailed information on all the different channels/distributions can be found here.

All the hoohah surrounds the curated Anaconda channels, commonly referred to as defaults channel. Note: When installing conda/miniconda software, the defaults channel is added to your global channels list. You could inadvertently be using Anaconda services without intending to.

How to’s

Below is guidance on how to best deal with defaults channel.

Safest: Fresh Install of Miniforge distribution

  1. Install the conda-forge distribution miniforge3 - instructions here, this will also install mamba.
  2. Add the channels bioconda and nodefaults [in that order] as global defaults:
  conda config --add channels bioconda nodefaults

Adding the nodefaults channel to the global conda config will disable defaults in all newly created environments, see also the docs and below.

That’s it!

Best: Current Miniforge install:

Note miniconda users: The below solution is only for miniforge installs. See below for more details.

  1. To check if your installation (regardless if that’s anaconda, miniconda, miniforge, etc.) has the defaults channel in your global configuration :
  conda config --show channels
  # or more informative: 
  conda config --get
  1. Now remove defaults: 
      conda config --remove channels defaults
  2. Check defaults is removed: 
      conda config --show channels

  3. Double check that defaults is not accessible, this should fail to install anaconda-fonts:

      # This will access defaults channel!
  conda install fonts-anaconda

If the above succeeds, see below.

Done!

Dangerous: Conda/Miniconda

It’s tricky to fully decouple your conda usage from the defaults channel, because it is hard-coded in some places the miniconda code.

During the writing of this post, a colleague could not stop their miniconda installation from using the defaults channel, even when defaults was not in the channels list (we double and triple checked everything). After testing, several people also observed the same issue. We (thanks James and Helena) eventually tracked the bug to (we think) the miniconda + libmamba solver.

The conda developers have deprecated the implicit adding defaults and are moving to remove it completely.

The safest option is to install the conda-forge distribution. This has the added benefit of installing mamba from the very beginning and is the recommended method of installation by the mamba devs.

To test your setup, remove the defaults channel (see above) try to install fonts-anaconda, which is accessible only via defaults. Warning: this will access the Anaconda defaults channel! Also check to see if you are using the classic or libmamba solver by running conda config --show | grep "solver:"

It is far simpler to install miniforge3.

Protecting against defaults channel

It’s possible to protect users of your pipelines/tools by including nodefaults channel in a conda.yaml file. For example:

channels:
  - conda-forge
  - bioconda
  - nodefaults

This will override the defaults channel if it exists in the users global config. Unfortunately, this is specific to conda env subcommand, therefore it will not work for conda install or conda create when added to global config. There is an open issue on github for this feature.

FAQs + FYIs

- How can I transition safely from defaults channel?

If you are worried removing defaults will break your current setup, conda-forge has great documentation on how to test and transition from your addiction to defaults.

- Be wary of foreign conda.yaml files in software/pipelines

Lots of pipelines/tools will use conda.yaml to enable easy installation of dependencies. It’s very likely defaults could be in a conda.yaml file because it’s been the… default to include it.

Unfortunately as far as I know, there is no setting or method available to protect against a conda.yaml using a package from defaults.

There is a feature request for nodefaults to apply everywhere.

I suggest always double checking foreign conda.yaml files before installing.

- Will removing defaults interfere with the install of bioinfo tools?

Very unlikely. conda-forge transitioned away from Anaconda’s defaults channel in 2021 and has continued to diverge in both names and recipes. There is a slight chance it may cause issues for old pre 2020/2021 recipes but this is rare as recipes have continually been updated. Not too worry though, conda-forge is community driven, feel free to contribute if you run into any problems!

Anecdotally, several people including myself have been operating without defaults channel for over a year. We’ve not had any issues.

- What about bioconda packages?

bioconda channel has always had strong dependencies on conda-forge. Therefore, dropping defaults will have little to no effect. If you are worried see above on how to transition from defaults.

- How can I see if packages were installed from defaults?

Run this command to show the source of packages in the current actived environment:

  conda list --show-channel-urls | grep "defaults"

Add --name ENV to inspect a specific environment without activing it.

If nothing appears, you’re golden!

- My institution has blocked anaconda.org. What do I do?!

Prefix.dev, the German company behind the all-in-one pixi software manager has setup mirrors of both conda-forge and bioconda channels:

https://prefix.dev/channels/conda-forge
https://prefix.dev/channels/bioconda

Follow these instructions to configure the mirrors.

- Be careful of channel leakage

I came across this interesting issue on github defaults channels leak into environments config. The summary is that due to how conda merges (not replaces) config files, your primary .condarc file could leak into other envs. More info on conda’s configuration engine can be found here and the documentation is here.

Again, the safest option is to remove defaults from your .condarc (see above).

Questions? Ask in the comments below!

See Also