What is the right way to update Anaconda and Conda base & environments?

Question

Just wondering as what is the right way to update Anaconda and Conda installation and virtual environments. Here is my confusion step by step:

1. When I run command <

Answer 1

The other way in is simply,

anaconda-navigator

The resulting GUI image is below, the only difference with respect to this question is where you see "Installed", there is a drop down menu for for "Updatable" and therein you simply click the dependencies for updating for any given environment.

General info

I'm sure everyone knows this, but for anyone who doesn't Anaconda navigator is a point and click GUI already part of the Anaconda and is simply brilliant for managing, installing, updating and deleting all the dependencies.

With respect to the question it is great for managing all the dependencies inside new envs, creating new envs, loading new channels. It works great remotely via X11 if you have Anaconda loaded on a remote cluster/server.

The bonus for me is that I've never known it fail.

Answer 2

You're not doing anything wrong per se, but it just doesn't make much sense to ever run conda update anaconda and conda update --all right after each other on the same env - they represent two completely different configurations.

Update Anaconda

Anaconda is a Python distribution that bundles together a ton of packages. Presumably, a bunch of testing goes into verifying that all the package versions and builds are compatible with each other. Because this takes time to do, the Anaconda team only releases new distributions (i.e., a new anaconda version) every couple months or so. If you want a stable set of packages that have been tested for interoperability, then do conda update anaconda.

Update All

In between Anaconda releases, new versions of many packages are still released on the Anaconda channel, and if you run conda update --all you're going to inevitably get ahead of the versions specified in the anaconda bundle. If you want the newest individual package releases and don't mind potentially working with package builds that aren't thoroughly tested for integration, then run conda update --all.

It may be worth noting that people who prioritize having access to the latest versions of packages often seem to prefer Conda Forge, because it tends to have more frequent package releases. However, in my opinion, there's almost no point to installing Anaconda if you're going to switch most packages to Conda Forge anyway. Instead, just install Miniconda and only install what you want from Conda Forge at the start.

Update None

Personally, I will rarely run conda update on an env once I've harden the requirements for a project. Every time you update an env, you risk breaking code that you've already written. Instead, Conda makes it quite easy to create new envs, and if they have a lot of overlap with other envs, then the envs can be quite light due to sharing packages across envs via hardlinking.

Update Conda

The one exception to everything above is the conda package, which is the very infrastructure you're using to manage packages and envs. That, one should update just like any other package manager (e.g., a pip or a homebrew).

Answer 3

Found the answers in this useful post by Anaconda

Keeping Anaconda Up To Date

Below is a question that gets asked so often that I decided it would be helpful to publish an answer explaining the various ways in which Anaconda can be kept up to date. The question was originally asked on StackOverflow.

I have Anaconda installed on my computer and I’d like to update it. In Navigator I can see that there are several individual packages that can be updated, but also an anaconda package that sometimes has a version number and sometimes says custom. How do I proceed?

The Answer

What 95% of People Actually Want In most cases what you want to do when you say that you want to update Anaconda is to execute the command:

conda update --all

This will update all packages in the current environment to the latest version—with the small print being that it may use an older version of some packages in order to satisfy dependency constraints (often this won’t be necessary and when it is necessary the package plan solver will do its best to minimize the impact).

This needs to be executed from the command line, and the best way to get there is from Anaconda Navigator, then the “Environments” tab, then click on the triangle beside the root environment, selecting “Open Terminal”:

This operation will only update the one selected environment (in this case, the root environment). If you have other environments you’d like to update you can repeat the process above, but first click on the environment. When it is selected there is a triangular marker on the right (see image above, step 3). Or, from the command line, you can provide the environment name (-n envname) or path (-p /path/to/env). For example, to update your dspyr environment from the screenshot above:

conda update -n dspyr --all

Update Individual Packages

If you are only interested in updating an individual package then simply click on the blue arrow or blue version number in Navigator, e.g. for astroid or astropy in the screenshot above, and this will tag those packages for an upgrade. When you are done you need to click the “Apply” button:

Or from the command line:

conda update astroid astropy

Updating Just the Packages in the Standard Anaconda Distribution

If you don’t care about package versions and just want “the latest set of all packages in the standard Anaconda Distribution, so long as they work together,” then you should take a look at this gist.

Why Updating the Anaconda Package is Almost Always a Bad Idea

In most cases, updating the Anaconda package in the package list will have a surprising result—you may actually downgrade many packages (in fact, this is likely if it indicates the version as custom). The gist above provides details.

Leverage conda Environments

Your root environment is probably not a good place to try and manage an exact set of packages—it is going to be a dynamic working space with new packages installed and packages randomly updated. If you need an exact set of packages, create a conda environment to hold them. Thanks to the conda package cache and the way file linking is used, doing this is typically fast and consumes very little additional disk space. For example:

conda create -n myspecialenv -c bioconda -c conda-forge python=3.5 pandas beautifulsoup seaborn nltk

The conda documentation has more details and examples.

pip, PyPI, and setuptools?

None of this is going to help with updating packages that have been installed from PyPI via pip, or any packages installed using python setup.py install. conda list will give you some hints about the pip-based Python packages you have in an environment, but it won’t do anything special to update them.

Commercial Use of Anaconda or Anaconda Enterprise

It’s pretty much exactly the same story, with the exception that you may not be able to update the root environment if it was installed by someone else (say, to /opt/anaconda/latest). If you’re not able to update the environments you are using, you should be able to clone and then update:

conda create -n myenv --clone root
conda update -n myenv --all