dash-bio docs posts

[olayway]

added dash-bio docs posts for dash-graphing-library:

• AlignmentChart
• Circos
• Clustergram
• Molecular Visualizations
• VolcanoPlot

Couldn't assign @emmeb as a reviewer, so I'm tagging instead. @smallstepman for visibility.

[nicolaskruchten]

Unfortunately this straightforward approach will not work to display or document dash apps in this framework... let's discuss on Slack after the launch webinar on Wednesday :)

[smallstepman]

We were worried about same thing, tho we thought we'll try simplistic approach first ^^. We saw other dash examples use iframe wrapped inside ```python no_display=true .... We're happy to redo this PR to follow same convention, however we'd need some general direction (e.g. where to deploy each of the dash-bio examples - dash gallery or somewhere else)

[smallstepman]

ready for initial PR @emmeb

We probably need more stuff in Alignment Viewer but we've ran out of ideas and time - I tried implementing table similar to the one in Alignment Viewer, but with 40*300 cells to dispaly the performance was bismal, I briefly looked at heatmap, but seems like we wouldn't be able to display any letters on top of color map.
Let me know if you have other ideas.

I definitely skimped on the amount of text/content, sorry for that, I hope you could help me with that?

[emmeb]

Overall this looks great! Going to send over some text to add to all the sections. Couple of small fixes:

1. I think this section is missing from the plotly.com/python page -- I don't see it in the index/sidebar. Could it be placed under AI/Machine Learning?
2. On the Dash Bio main page, I don't see any images relating to the plots. Could these be added?
3. For the embedded apps -- could you use the first example in each dash-bio page (these are the fanciest ones)
   -- alignment chart: https://dash.gallery/dash-alignment-chart/
   -- volcano: https://dash.gallery/dash-volcano-plot/
   -- clustogram: https://dash.gallery/dash-clustergram/
   -- manhattan: https://dash.gallery/dash-manhattan-plot/
   Thank you!

[emmeb]

permalink: python/manhattan-plot/
thumbnail: thumbnail/manhttan-plot.png

[HammadTheOne]

Note - I can add the thumbnails, which are sourced from our S3 bucket, as long as they have the correct path.

Once we know which ones we want to add to begin with, feel free to send me the thumbnails and I can upload them so that they're displayed on the docs.

[smallstepman]

@HammadTheOne we've dumped all image files here

all_static/images/alignment_chart.png 
all_static/images/circos.png 
all_static/images/clustergram.png 
all_static/images/molecule_3d_viewer.png 
all_static/images/volcano_plot.png 

[smallstepman]

@nicolaskruchten please take a look at logs from failing build stage

#!/bin/bash -eo pipefail
cd doc
python3 -m venv venv
. venv/bin/activate
npm install electron@1.8.4
npm install orca
pip install -U pip
pip uninstall -y plotly
pip install -r requirements.txt
if [ "${CIRCLE_BRANCH}" != "doc-prod" ]; then
  pip uninstall -y plotly
  cd ../packages/python/plotly
  pip install -e .
  cd ../../../doc
fi
echo 'export PATH="/home/circleci/project/doc/node_modules/.bin:$PATH"' >> $BASH_ENV
sudo apt-get install -y poppler-utils libxtst6 xvfb libgtk2.0-0 libgconf-2-4 libnss3 libasound2 rename
cd ..


> electron@1.8.4 postinstall /home/circleci/project/doc/node_modules/electron
> node install.js

/home/circleci/project/doc/node_modules/electron/install.js:47
  throw err
  ^

Error: GET https://github.com/electron/electron/releases/download/v1.8.4/SHASUMS256.txt returned 500
    at Request.<anonymous> (/home/circleci/project/doc/node_modules/nugget/index.js:169:61)
    at Request.emit (events.js:400:28)
    at Request.onRequestResponse (/home/circleci/project/doc/node_modules/request/request.js:1059:10)
    at ClientRequest.emit (events.js:400:28)
    at HTTPParser.parserOnIncomingClient [as onIncoming] (_http_client.js:647:27)
    at HTTPParser.parserOnHeadersComplete (_http_common.js:126:17)
    at TLSSocket.socketOnData (_http_client.js:515:22)
    at TLSSocket.emit (events.js:400:28)
    at addChunk (internal/streams/readable.js:290:12)
    at readableAddChunk (internal/streams/readable.js:265:9)
npm WARN enoent ENOENT: no such file or directory, open '/home/circleci/project/doc/package.json'
npm WARN doc No description
npm WARN doc No repository field.
npm WARN doc No README data
npm WARN doc No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! electron@1.8.4 postinstall: `node install.js`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the electron@1.8.4 postinstall script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/circleci/.npm/_logs/2021-10-21T15_40_05_579Z-debug.log


Exited with code exit status 1
CircleCI received exit code 1

please advise if I can help with fixing

[nicolaskruchten]

The build on master ran clean this morning so I suspect something to do with this PR specifically...

[smallstepman]

looks like this branch has been merged with the master after your commits: e91ba8a
perhaps that is the source of the issue?

[nicolaskruchten]

Right, those commits fixed the build on master. Now it's broken in this PR so it seems to me there's a problem with the changeset in this PR...

[smallstepman]

build has successfully passed install dependencies stage (even tho I haven't changed anything that in my imagination would influence that stage) 🤷

sorry for bothering you @nicolaskruchten , looks like it was a false alarm afterall

[smallstepman]

@emmeb

I think this section is missing from the plotly.com/python page -- I don't see it in the index/sidebar. Could it be placed under AI/Machine Learning?

these changes are comming in separate PR: plotly/graphing-library-docs#154

[nicolaskruchten]

OK, build is green, merging. The pages will appear at their target URLs within around 20 minutes. You'll have to complete the graphing-library-docs PR to get the new section up etc though.