Bump biopython from 1.79 to 1.88 - #26

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4, actions/setup-python@v5, conda-incubator/setup-miniconda@v3. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

`auto-activate-base` is deprecated. Please use `auto-activate`. If your installer does not use the `base` environment as the default environment, also add `activate-environment: base`.

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. mdtraj 1.10.3 requires netCDF4, which is not installed.

warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.

warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used. warning libmamba Please make sure you understand Anaconda Terms of Services. warning libmamba See: https://legal.anaconda.com/policies/en/