Setup-miniconda: Having troubles activating an environment

Replace with:

    - uses: conda-incubator/setup-miniconda@v2
        with:
          environment-file: environment.yaml
          activate-environment: <name stated in environment.yaml>
          auto-activate-base: false
    - run: conda info

Thanks @jaimergp . What about the case that I don't have an environment name specified in environment.yaml ?

Can't you add any name to the file? If it's not in your repo, maybe patch it with echo "name: test" >> environment.yaml before using setup-miniconda?

@jaimergp Sure I could add in the CI recipe itself. I don't like to do it generally, I think it is needlessly limiting to specify the name in the environment file, and as far as I know it is perfectly fine for conda not to specify it.

More widely, shouldn't the action be able to deal with my setup too?

Hi @tdegeus thanks for the report. @jaimergp I can't recall now if we add the name "test" by default to the yaml file if name is not in there.

We need to double check.

It seems indeed that the 'default' environment name is test in this case @goanpeca . But with the commands above I still don't get a correctly activated environment. Here are the details for https://github.com/tdegeus/shelephant/pull/12

    steps:
    - uses: actions/checkout@v2
    - uses: conda-incubator/setup-miniconda@v2
      with:
        environment-file: environment.yaml
        activate-environment: test
        auto-activate-base: false
    - run: conda info

The last command outputs:

      active environment : None
        user config file : /home/runner/.condarc
  populated config files : /home/runner/.condarc
           conda version : 4.8.3
     conda-build version : not installed
          python version : 3.8.3.final.0
        virtual packages : __glibc=2.27
        base environment : /usr/share/miniconda  (writable)
            channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                           https://conda.anaconda.org/conda-forge/noarch
                           https://repo.anaconda.com/pkgs/main/linux-64
                           https://repo.anaconda.com/pkgs/main/noarch
                           https://repo.anaconda.com/pkgs/r/linux-64
                           https://repo.anaconda.com/pkgs/r/noarch
           package cache : /home/runner/conda_pkgs_dir
        envs directories : /usr/share/miniconda/envs
                           /home/runner/.conda/envs
                platform : linux-64
              user-agent : conda/4.8.3 requests/2.23.0 CPython/3.8.3 Linux/5.4.0-1031-azure ubuntu/18.04.5 glibc/2.27
                 UID:GID : 1001:116
              netrc file : None
            offline mode : False

Indeed if I look after the lines that install the packages in environment.yaml it is outputted that

# To activate this environment, use
#
#     $ conda activate test
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Suggesting that the environment was not activated.

@tdegeus because of how github actions work, you need to specify extra arguments for the actions as described in the README for the different shells.

      - name: Conda info
        shell: bash -l {0}
        run: conda info

If you do not use shell: bash -l {0} assuming you are using bash, then the action will not be able to activate the environments correctly.

This is a knowns limitation, you can read more here

@goanpeca So I'd have to do that for every line in which I want to use the environment?

Before, I used some action that didn't have this limitation:

    - uses: s-weigand/setup-conda@v1
    - run: conda --version
    - run: conda env update -n base --file environment.yaml

@tdegeus

So I'd have to do that for every line in which I want to use the environment?

Yes or use a default shell if all your stepps will use the same one, as explained on:
https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#jobsjob_iddefaultsrun

Before, I used some action that didn't have this limitation:

Yes, that action is not properly activating environments.

@tdegeus https://github.com/conda-incubator/setup-miniconda/pull/96 adds information on what I explained on the comment.

I think we can close the issue. If this is not the case, please let us know what else we can do to improve the action.

Thanks again for the feedback :-)

Great @goanpeca , thanks for the help and for the PR!!

If I may give a personal experience on the readme while we close this question:

• It would be great to document that the default environment name for my case is test, I don't think I found that anywhere.
• Personally it would (have) help(ed) me to have a few typical examples that are complete (e.g. a Python and a CMake test). Then some of the pitfalls that I encountered would have been more obvious to me (of course, everything is there, it's just that one is from time to time a lazy reader, and it helps when things are presented 'in your face').