ANMD and ClustENM fixes and test fixes - #2269

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/cache@v4, actions/checkout@v4, mamba-org/setup-micromamba@v1. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

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