After activating any conda environment conda commands stop working

Question

I've done a fresh install of miniconda on my mac. If I run type conda in my terminal i get /Users/myusername/miniconda3/bin/conda . I can create an conda environment and then activate it with source activate myenv . After this command, conda commands will give this response

(myenv) ➜  ~ conda list
local:3: command not found: any-json
usage: conda [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled
                 after the git config command. Writes to the user .condarc
                 file (/Users/myusername/.condarc) by default.
    create       Create a new conda environment from a list of specified
                 packages.
    help         Displays a list of available conda commands and their help
                 strings.
    info         Display information about current conda install.
    install      Installs a list of packages into a specified conda
                 environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove. See conda remove --help.
    search       Search for packages and display associated information. The
                 input is a MatchSpec, a query language for conda packages.
                 See examples below.
    update       Updates conda packages to the latest compatible version. This
                 command accepts a list of package names and updates them to
                 the latest versions that are compatible with all other
                 packages in the environment. Conda attempts to install the
                 newest versions of the requested packages. To accomplish
                 this, it may update some packages that are already installed,
                 or install additional packages. To prevent existing packages
                 from updating, use the --no-update-deps option. This may
                 force conda to install older versions of the requested
                 packages, and it does not prevent additional dependency
                 packages from being installed. If you wish to skip dependency
                 checking altogether, use the '--force' option. This may
                 result in an environment with incompatible packages, so this
                 option must be used with great caution.
    upgrade      Alias for conda update. See conda update --help.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

Now, if I run type conda again I get conda is a shell function from /Users/myusername/miniconda3/etc/profile.d/conda.sh as response instead. If I open up a new terminal, conda commands will work again as before I did run `source activate myenv``

I'm wondering what can be causing this problem and how to fix it.

Maybe worth mentioning that I've added export PATH=/Users/myusername/miniconda3/bin:$PATH to my .zshrc file as I'm running zshell.

Edit 1

Using conda activate gives me the following error

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with

    $ echo ". /Users/myusername/miniconda3/etc/profile.d/conda.sh" >> ~/.bash_profile

or, for all users, enable conda with

    $ sudo ln -s /Users/myusername/miniconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh

The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH.  To do so, run

    $ conda activate

in your terminal, or to put the base environment on PATH permanently, run

    $ echo "conda activate" >> ~/.bash_profile

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bash_profile file.  You should manually remove the line that looks like

    export PATH="/Users/myusername/miniconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^

If I do as the error message tells me to do, which is adding the line . /Users/myusername/miniconda3/etc/profile.d/conda.sh . /Users/myusername/miniconda3/etc/profile.d/conda.sh to my .zshrc file, then conda commands don't work. Eg conda activate gives me the same message as for conda list which I pasted in the beginning of my question.

Edit 2 I've found a solution. In the bash script located in /Users/myusername/miniconda3/etc/profile.d/conda.sh there is a function called conda which looks like this

    conda() {
        if [ "$#" -lt 1 ]; then
            $_CONDA_EXE
        else
            /local cmd="$1"
            shift
            case "$cmd" in
                activate)
                    _conda_activate "$@"
                    ;;
                deactivate)
                    _conda_deactivate "$@"
                    ;;
                install|update|uninstall|remove)


           $_CONDA_EXE "$cmd" "$@" && _conda_reactivate
                ;;
            *)
                $_CONDA_EXE "$cmd" "$@"
                ;;
        esac
    fi
}

When debugging this function I noticed that the cmd variable was empty. But if I change the line /local cmd="$1" to local cmd="$1" all my problems are solved. I don't know why. Does anyone have any ideas why? what does this backslash do?

Answer 1

Modify PATH in your ~/.bash_profile file.

You should manually remove the line that looks like

export PATH="/Users/myusername/miniconda3/bin:$PATH"

The above line should NO LONGER be in your ~/.bash_profile file!

Reference:

1. https://github.com/conda/conda/issues/7980