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Update rms notebooks #75
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Looks good, just a couple of thoughts on what could be done to make it a little bit clearer.
doc/source/examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
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@@ -108,12 +117,12 @@ | |||
"name": "stderr", | |||
"output_type": "stream", | |||
"text": [ | |||
"Step 98/98 [100.0%]\n" | |||
"Step 102/102 [100.0%]\n" |
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locally this progress bar doesn't show up with the current code, you need to passs verbose=True
to run()
. Also as of v1.0 the progress bar should be tdqm not the old progress meter.
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I'm ok with it not showing up unless you think it's necessary? Re-ran with 1.0 to get rid of the bar.
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As long as we show off the progress bar somewhere it doesn't matter. That being said, maybe a "unified style" might be favourable, i.e. all progress bars or all no progress bars.
doc/source/examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
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Sorry, I completely forgot to review the second notebook.
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The new background sections look really awesome!
Just a couple of comments & thoughts.
doc/source/examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
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RTD is still segfaulting because it still installs MDAnalysis via conda (see MDAnalysis/mdanalysis#2818) so I've revived my fork. Notebooks: |
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LGTM!
Unfortunately can't comment directly on the diff for RMSF, here are some minor comments:
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"If you use these datasets from MDAnalysisData, it may take some time to download." sounds a bit awkwardly worded for me, how about "Note: downloading these datasets from MDAnalysisData may take some time".
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"where x is the coordinates" do we want to be a bit more specific here and say "of particle i" and something along the lines of "where <> indicates the ensemble average".
Note: just restarting the Travis build to test something out. I've been finding that the astropy Travis build has started failing elsewhere similarly to when we were using standard conda environments. Just checking it's not also an issue here. Edit: well at least it's not the same issue, but it does fail :( https://travis-ci.com/github/MDAnalysis/UserGuide/builds/174744621 |
This happens after the pages are built and a sitemap is generated; what is Python even doing at that point? |
Garbage collecting and possibly running into a bug in the XDRReader?? |
Not getting the same issue, but it looks like the problem might be down to numpy==1.19.0. (see #95). It might be worth testing if pinning to 1.18.5 fixes the CI @lilyminium |
RMS notebook updated for 1.0:
weights_groupselections
Built: https://mdauserguide.readthedocs.io/en/rms-1.0/
Notebooks:
https://mdauserguide.readthedocs.io/en/rms-1.0/examples/analysis/alignment_and_rms/rmsd.html
https://mdauserguide.readthedocs.io/en/rms-1.0/examples/analysis/alignment_and_rms/pairwise_rmsd.html