mamba on windows "mamba: command not found"

[AndrewAnnex]

on a currently private repo I am trying to use mamba to build on mac/linux/windows but I am running into a command not found error on the windows worker, seems like mamba is not available even after successful install as show in the logs.

partial config:

test_runner:
    name: (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
        python-version: ["3.8"]
    steps:
      - uses: actions/checkout@v2
      - name: setup miniconda
        uses: goanpeca/setup-miniconda@v1
        with:
          mamba-version: "*"
          python-version: ${{ matrix.python-version }}
          channels: conda-forge,defaults
          channel-priority: true
          activate-environment: pangeo_test
          auto-update-conda: true
          use-only-tar-bz2: true
      - name: conda info
        shell: bash -l {0}
        run: |
          conda info
      - name: mamba install packages
        shell: bash -l {0}
        run: mamba install ... (command not found error here)

[jaimergp]

Would it be possible to post a reproducible case for a public repo? I can look into it!

[AndrewAnnex]

Hey Jamie, I think that code block above is effectively a reproducible example. It has been a while since I looked at this but in that project I hit the mamba issue before anything relating to my code. I could make a new public repo with that GitHub action configured as well if that will help

…

-Andrew Annex

On Sep 14, 2020, at 5:22 PM, Jaime Rodríguez-Guerra ***@***.***> wrote:  Would it be possible to post a reproducible case for a public repo? I can look into it! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[jaimergp]

I could make a new public repo with that GitHub action configured as well if that will help

Yeah, that will help immensely, thanks!

[AndrewAnnex]

@jaimergp I made a demo repo and see that the issue is occuring in this runner: https://github.com/AndrewAnnex/test_setup_miniconda_github_action/runs/1140527924

It looks like maybe the "activate-environment" flag is the issue, it is installing mamba to the base environment, but since I don't have an environment yaml file and I specify to create a new environment and activate it, the scripts don't seem to install mamba elsewhere like it does with the ubuntu workers.

I think making an environment yaml with mamba as a dependency would fix that, but I don't know if mamba would be used to bootstrap that new environment so I think I would loose the benefits of mamba...

[jaimergp]

Thanks! I'll add this to my list... it's definitely interesting!

[jaimergp]

Behavior should be the same on Ubuntu (we only install mamba on base), so there's definitely a %PATH% issue there...

${MINICONDA}/condabin should always be on PATH, and that's where both conda and mamba are called from. This is independent of activated environments. On Windows, the absolute path to mamba is C:\Miniconda\condabin\mamba.bat and it's being used in the setup steps. You could try using that abs path instead, but let's see if we can have mamba working.

printenv reveals that PATH does contain it: https://github.com/AndrewAnnex/test_setup_miniconda_github_action/runs/1140527924#step:4:158

The only difference I see is that you are using inline YAML instead of the "paragraph YAML" pipe style. It shouldn't have any difference, but I've seen weirder things happen. Just to make sure, can you do this:

      - name: mamba install packages
        shell: bash -l {0}
        run: |
          conda install jupyter
          mamba install jupyterlab

[jaimergp]

@AndrewAnnex this should be fixed in the next release. In the meantime, it seems that Bash on Windows requires the .bat extension, so you'd need to use mamba.bat install xxx. Next version includes a patch to workaround that requirement.

[AndrewAnnex]

Great! thanks for letting me know!

…

-Andrew Annex

On Nov 17, 2020, at 4:45 PM, Jaime Rodríguez-Guerra ***@***.***> wrote:  @AndrewAnnex this should be fixed in the next release. In the meantime, it seems that Bash on Windows requires the .bat extension, so you'd need to use mamba.bat install xxx. Next version includes a patch to workaround that requirement. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.