Create new environment regional mom6

[helenmacdonald]

@ashjbarnes and I would like to release the regional mom6 toolbox to gadi in a containerised environment. Can we please be given access to do this?

My understanding is that the steps are:

1. We create a branch
2. We make a new folder called regional-mom6 (or similar) under environments
3. We then make environment.yml and environment_dev.yml files
4. We then do a PR back to main

One quick question - regional mom6 already lists some dependencies here - should we copy these dependencies to environment.yml and environment_dev.yml? Or just add the new dependencies (matplotlib)?

[atteggiani]

Hi Helen,
thank you for opening this issue.

The steps you outlined are correct. However, for the time being, I can go on and open a PR with the new environment.

For that, I will need the following information:

• Name that you want to give to the regional mom6 environment. Note this will be the name the end users will need to type when they want to use the environment (e.g. module load <name>)
• The environment specification file (environment.yml)

Env specification

About the environment specification, it will need to contain the "core" dependencies of the environment (in this case the regional_mom6 package), along with any other needed dependencies that are not already dependencies of the "core" package.
For example, I see the dependecies listed in the linked environment-ci.yml:

dependencies:
  - esmpy
  - numpy
  - xesmf

In this case, all these dependencies are also present within the regional_mom6 package, so they should not be added to the environment specification because they would be automatically installed with the regional_mom6 package.
On the other hand, matplotlib is not present within the regional_mom6 package dependencies, so if you want it in the environment it should be listed separately.

Your environment.yml could look something like:

name: regional_mom6
channels:
  - accessnri
  - conda-forge
dependencies:
  - regional_mom6==0.1
  - matplotlib

This assumes the regional_mom6 package is available as a conda package (probably in the accessnri Anaconda.org channel).
If that is not the case, only during the testing phase the package can be added from github directly using pip:

name: regional_mom6
channels:
  - accessnri
  - conda-forge
dependencies:
  - matplotlib
  - pip:
    - git+https://github.com/COSIMA/regional-mom6.git@main

However, note this env specification would be suitable as the development one (environment_dev.yml), but not for the STABLE environment. Therefore, when the first STABLE environment version is deployed to PRODUCTION, all packages should be specified as conda packages.

If you would like help releasing the regional_mom6 package as a conda package in the accessnri channel, please let me know.

[helenmacdonald]

Thanks @atteggiani – what you propose sounds good. Could we add one more package dependency – the copernicusmarine toolbox (it is available through conda-forge).

At the moment I believe that regional_mom6==0.1 contains some bugs so I think we need the unstable
- git+https://github.com/COSIMA/regional-mom6.git@main to start with.

I don’t have strong preferences on the name – I have come up with these 3:
rm6, rmom6 or regional_mom6

@ashjbarnes do you have a suggestion or preference? If no-one else has a preference then I would go for rmom6 as it is short but long enough to be a bit descriptive.

If you would like help releasing the regional_mom6 package as a conda package in the accessnri channel, please let me know.

I think this is a question for @ashjbarnes – it is currently on conda_forge here but hasn’t been updated in a while. It sounds like we may need to update before we can do a non-bug stable release?

[atteggiani]

Could we add one more package dependency – the copernicusmarine toolbox (it is available through conda-forge).

Sure, that sounds good.

If no-one else has a preference then I would go for rmom6 as it is short but long enough to be a bit descriptive.

I like rmom6 for the name as well.

it is currently on conda_forge here but hasn’t been updated in a while. It sounds like we may need to update before we can do a non-bug stable release?

Well If the regional_mom6 package is already available on conda-forge that's pretty good!
In that case, we can use version 0.1 for now, and it will get updated once there is a more stable version without bugs.
The tests will anyway be carried out mostly with the development version of the environment at this stage.

[helenmacdonald]

Thanks @atteggiani!