Upgrade d3 or use different graphing library for display (not capture)

[jywarren]

Refactoring and using a new graphing library would be a lot of work, because we use d3 in the calibration routines and they are pixel-level CSS tuned with multiple complex drag interactions -- see https://publiclab.org/wiki/spectral-workbench-calibration#Video

However, we have identified a problem with d3 v3.5.17 and have had to revert to v3.4.0. The error is:

Uncaught TypeError: Cannot read property 'id' of undefined
    at SVGGElement.<anonymous> (spectral-workbench.js:5374)
    at SVGGElement.o (d3.min.js:1)
    at d3.min.js:3
    at Y (d3.min.js:1)
    at Array.Co.each (d3.min.js:3)
    at Array.Co.attr (d3.min.js:3)
    at _graph.load (spectral-workbench.js:5373)
    at Object.success (spectral-workbench.js:127)
    at c (jquery.min.js:2)
    at Object.fireWith [as resolveWith] (jquery.min.js:2)

The revert is in #175, after initially bumping in #165.

---

Perhaps we could stop using nvd3 (https://nvd3.org/) which is not compatible with modern d3 (v5 for example and maybe v4), and then could get d3 up to a more recent version.

But we should really start by moving the calibration routine out of the Ruby on Rails SpectralWorkbench.org project and into this repo. The script for calibration UI (as in the video linked at top) is:

https://github.com/publiclab/spectral-workbench/blob/98dbde7a881788f7bd48db59eee616d6de70054b/app/assets/javascripts/analyze.js#L52-L60

https://github.com/publiclab/spectral-workbench/blob/98dbde7a881788f7bd48db59eee616d6de70054b/app/assets/javascripts/analyze.js#L122-L143

Lot of work here, but worthwhile!

[jywarren]

Ahhh, i see-- we upgraded d3 to v3.5.x to get past this issue in v3.4.13 -- #162 (comment)

So, that issue is blocking us...

[jywarren]

Noting this was caught by @sidntrivedi012 in #77 (comment)

and it's actually d3's dependency of an old version of jsdom that is requiring contextify and causing the error.

Here is where d3 upgraded to a newer jsdom: d3/d3#570

[jywarren]

Oh, that's not right, that's d3 v2.8.0... looking deeper...

[jywarren]

OK, then here, they went to JSDOM 7/8: d3/d3#2596

[jywarren]

And here, they mention specifically the d3 v3.4 and v3.5 threshold: d3/d3#2578 (comment) and jsdom as a dev dependency...

[jywarren]

We could try requiring [email protected] ...

[jywarren]

OK, first version of d3 to make JSDOM optional is actually v3.5.4 (d3/d3#2225)... trying in #175