Update GitHub Actions to the latest versions to avoid Node20.js deprecation warnings

[yantosca]

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Describe the update

GitHub Actions is retiring Node20.js from all of its runners in June 2026:

gnu (Debug)Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

Therefore we have updated all of the GitHub Actions workflow files to check out the latest version of each action.

Old version	New version
actions/checkout@v4	actions/checkout@v6
actions/setup-micromamba@v2	actions/setup-micromamba@v3
actions/setup-python@v5	actions/setup-python@v6
actions/stale@v5	actions/stale@v10

We have also removed Python 3.9 from GitHub actions that test building python environments and have also added Python 3.14.

Expected changes

• This is a no-diff-to-benchmark update that will only affect GitHub actions.
• This will allow our GitHub Actions to proceed as normal after GitHub removes Node20.js support in June.
• This will make our setup more future-proof against further GitHub Actions system changes.