T020: update deprecated code fix broken ci

[dominiquesydow]

Description

T020 fails with cryptic message in CI under MacOS:

UserWarning: Reload offsets from trajectory
 ctime or size or n_atoms did not match
  warnings.warn("Reload offsets from trajectory\n "

Try to fix this by rerunning on local MacOS & fix warnings etc. along the way.

Note: I recommend merging #362 first, only then this PR (as this PR branches off t019-exclude-windows-from-ci).

Todos

• Fix code with deprecation warnings from MDAnalysis
  • Instance 1

    rmsd_analysis = rms.RMSD(...)
    rmsd_analysis.run()
    rmsd_analysis.rmsd → rmsd_analysis.results.rmsd
    

  • Instance 2

    pairwise_rmsd = diffusionmap.DistanceMatrix(...)
    pairwise_rmsd.run()
    pairwise_rmsd.dist_matrix → pairwise_rmsd.results.dist_matrix
    

  • Instance 3

    hbonds = HBA(...)
    hbonds.run()
    hbonds.hbonds → hbonds.results.hbonds
    

• Rerun notebooks manually (take care of 3D viewer views)
• Update xtc_offsets.npz file and add xtc_offsets.lock (from manual rerun), see notes in docs --> CI fail remains
• Remove both files, see commit f2878ee --> CI fail gone? yes, it seems so (passing CI)
• Run CI only for T020 (to be faster) & revert back those changes from commit eb45383

Status

• Ready to go

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[dominiquesydow]

@mbackenkoehler, this PR should be ready as well - I think the problem was the xtc offset file, I removed it now & also updated the notebooks that showed a couple of deprecation warnings.
I just kicked off the CI on all notebooks (minus T019 on Windows).

I recommend merging first this PR:
#362
and then this PR will update automatically asking to merge on dev (at the moment asking to merge onto 019-exclude-windows-from-ci), which you should then be able to do without conflicts.

[mbackenkoehler]

I re-ran the test on dev and now - for some reason... - T018 is failing as well. So this is clearly not the culprit ;)