setup-micromamba rewrite specification

[jonashaag]

We're going to release a new version of provision-with-micromamba:

• With a new name, setup-micromamba (other suggestions welcome; the action's main task is to set up a Conda environment using Micromamba)
• Rewritten in TypeScript
• Using semantic versioning

We will add a upgrade hint to this repo and maybe add a warning in the GHA output.

Use cases

We'll remove some of the options of provision-with-micromamba, see here for discussion #103.

Here we'll collect some use cases that we want to support. Feel free to make more suggestions.

Env from environment.yml

Options:

• Path to environment.yml (no implicit default of ./environment.yml like in provision-with-micromamba)
• Optional path to .condarc (implicit default to ~/.condarc)

Env from environment.yml with extra specs

Like above, but with an optional extra-specs: x y z option. This is runs

micromamba create -f environment.yml x y z

Env without environment.yml

For tiny CI setups, options:

• Extra specs
• environment-name to substitute the missing name: in environment.yml
• Channels from .condarc

Installing Micromamba only

• Provide create-env: false to skip micromamba create and just download + setup Micromamba.

Creating an empty env

Not sure if we should support this.

Convenience options

Implicit conda-forge

If using only extra specs and no .condarc is given, default to conda-forge? Although this reuqires that we check .condarc.

.condarc as string

Allow syntax like the following?

with:
  condarc: |
    channels:
      - x

Although this is also possible simply by using cat in a preceding step.

Proposal

Derived from the use cases, we offer the following options:

• condarc-file: Path to a .condarc file to consider, defaults to ~/.condarc.
• environment-file: Path to environment file, no default.
• environment-name: Override name: in environment.yml and set name if not passing environment.yml.
• extra-specs: String with extra specs to pass to micromamba create.
• create-args: List of strings that are passed to micromamba create.
• create-env: false to skip micromamba create.
• micromamba-version, cache-*, log-level, installer-url, post-deinit.

[pavelzw]

What will happen when you don't supply anything to environment-file?
Will an env still be created? What will the name be? base?

I think it makes sense to allow the user just to install micromamba without any environment creation steps, maybe by setting create-env: false. One fictional use case would be that the user wants to make sure that a certain package is pushed to a repository and just wants to do micromamba search <package>. This doesn't need an environment.

[pavelzw]

Some thoughts on log-level: GitHub Actions support different log-levels natively. See Workflow commands for GitHub Actions / Setting a debug message.

The debug mode is active when ACTIONS_SETUP_DEBUG=true. You can print debug messages by executing echo "::debug::This is a debug message" (or using the @actions/core debug method). These messages only get printed when ACTIONS_SETUP_DEBUG=true. This can be achieved by setting it in the workflow itself or by enabling debug logging when rerunning a workflow.

Since we probably cannot add ::debug:: in between micromamba logs, I think it would be a good idea to set the log-level to debug when ACTIONS_SETUP_DEBUG=true automatically. Then you do not need to create a separate commit to do this when encountering an error.

See here for an example with debug turned off and here for an example with debug logging.

[pavelzw]

.condarc as string

Allow syntax like the following?

Is this possible in Workflow files?

[pavelzw]

Also, we should use dependabot to upgrade the version of @actions/core. I see far too many actions that still use old versions of this package resulting in node deprecation warnings as well as set-output deprecation warnings. This is the default anyway in actions/typescript-action.

[jonashaag]

What will happen when you don't supply anything to environment-file?
Will an env still be created? What will the name be? base?

Good point, will add environment-name back.

I think it makes sense to allow the user just to install micromamba without any environment creation steps, maybe by setting create-env: false. One fictional use case would be that the user wants to make sure that a certain package is pushed to a repository and just wants to do micromamba search <package>. This doesn't need an environment.

I'm not quite sure about this. I agree that you might want an empty environment but if you want micromamba only you can use micro.mamba.pm/install.sh.

I think it would be a good idea to set the log-level to debug when ACTIONS_SETUP_DEBUG=true automatically

Agreed!

.condarc as string

Allow syntax like the following?

Is this possible in Workflow files?

Yes but the stuff after | is just plain text; no YAML parsing involved.

This is the default anyway in actions/typescript-action.

Perfect!

[pavelzw]

I'm not quite sure about this. I agree that you might want an empty environment but if you want micromamba only you can use micro.mamba.pm/install.sh.

pnpm/action-setup is kind of similar to our use case. They also provide this functionality.

[jonashaag]

OK added it!

[pavelzw]

I think adding some sort of environment information, i.e. which exact package versions were installed, to the step output (maybe even optional to the job summary?) might also be helpful.

[jonashaag]

It’s already there in the „Environment Info“ output, or are you looking for something else?

[pavelzw]

I meant the GITHUB_OUTPUT for a specific step such that you can you can use this output in future Workflow steps, see here.

[pavelzw]

Maybe adding something like init-shell: ['zsh', 'bash'] would also be a nice option to make it easier to manage stateful selfhosted runners.

[pavelzw]

If it is possible to add micromamba as a shell option in GitHub (see ADR 0277), we should explore this option. Having something like

- run: pytest ...
  shell: micromamba

would be a nice to have.

[zacharyburnett]

This would be great for me, as I have recently had issues running provision-with-micromamba on a self-hosted runner, as it overwrites and adds to the .condarc file every time.

[jonashaag]

This would be great for me, as I have recently had issues running provision-with-micromamba on a self-hosted runner, as it overwrites and adds to the .condarc file every time.

Note this: https://github.com/mamba-org/provision-with-micromamba#post-deinit

[mikemhenry]

This proposal looks great, I use this action extensively (I've been switching to this action from the mamba/conda ones whenever I get the chance) and the proposal covers all of my use cases.

[pavelzw]

The first release of setup-micromamba is out, feel free to check it out 🎉