feat: benchmark 8 spec #1230

wd15 · 2020-11-18T00:48:37Z

Full implementation of benchmark 8

Address #1208

Includes

automated citations using a new notebook extension
fix for equation numbering

This is really a draft as the submission guidelines may need to change based on some test uploads. The actual benchmark 8 landing page is not yet functional for this set of submission guidelines.

TODO

check this against the overleaf document prepared by Wenkun
Ensure link to "Phase Field Benchmark Problems for Nucleation" in notebook is correct
Setup reviewnb
Make phase field upload optional for 8a

Remember to tear down the live site when merging or closing this
pull request.

This change is

commit-lint · 2020-11-18T00:48:41Z

Documentation

new benchmark 8 spec (d78ebe0)
notebooks: change wording (5ef24aa)

Build System

nix: notebook extension with bibtex (4c70e71)
use correct version of notebook-exenstions (6a68835)

Continuous Integration

update surge token (57dc220)

Bug Fixes

broken link to yaml info (d477760)
remove twitter from the frontpage (0f023f0)
update for wenkun review (52ffb10)
add particle count code correctly (a97879e)
link to nucleation paper (65ccdc2)

Tests

switch off htmlproofer for twitter links (e909924)

Code Refactoring

update for tkphd review (81f5ebf)

Contributors

wd15

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Allow equation numbering and bibtex citations in noteobok

pfhub · 2020-11-18T04:07:04Z

The new PFHub live website is ready for review.

pfhub · 2020-11-18T23:26:55Z

The new PFHub live website is ready for review.

wd15 · 2020-11-19T00:48:09Z

@tkphd this is the first draft of BM8. I probably need to modify it again if the paper has changed. I won't merge this until the paper goes to pre-print, but wanted to check that all the tests passed in a PR.

Also, we can test the upload guidelines when I get the BM8 results pages sorted in a separate PR

pfhub · 2021-01-19T23:59:55Z

The new PFHub live website is ready for review.

wd15 · 2021-03-24T16:01:15Z

@wuwenkun, please review this when you get a chance, I've compared with your latest overleaf version and it seems pretty good. Some of the ordering is a little different, but I'm not sure that matters.

wd15 · 2021-03-24T16:03:10Z

@wuwenkun, this is the link for the notebook rendered on the website,

https://random-cat-1230.surge.sh/benchmarks/benchmark8.ipynb/

and the link if you want to make changes to the notebook,

https://github.com/wd15/pfhub/blob/issue1208-bm8/benchmarks/benchmark8.ipynb

wd15 · 2021-03-24T16:04:04Z

@tkphd, could you take a look at this again. Also, feel free to say "no" to this if you can't face looking at this problem again. Thanks.

tkphd · 2021-03-24T16:46:03Z

It's a great problem! Happy to look!

Twitter # link is a bit stupid and useless.

Htmlproofer doesn't work with Twitter links don't work on the CI

pfhub · 2021-03-24T22:06:24Z

The new PFHub live website is ready for review.

tkphd · 2021-03-25T13:12:32Z

Is a new reference available? The link labeled "Phase Field Benchmark Problems for Nucleation" goes to the dendritic growth paper.

wd15 · 2021-03-25T13:22:34Z

Is a new reference available? The link labeled "Phase Field Benchmark Problems for Nucleation" goes to the dendritic growth paper.

I noted above. Maybe mark it in your review. It would be nice if there were better review mechanisms on github for notebooks. The PR renders the notebook and reviewer would mark directly at the side of the notebook.

wd15 · 2021-03-25T13:23:27Z

https://www.reviewnb.com/

wd15 · 2021-03-25T13:24:02Z

I'll try and get that setup or look into how to use it. It's on my list of things.

wd15 · 2021-03-26T14:49:36Z

@tkphd, can you see this? https://app.reviewnb.com/wd15/pfhub/blob/issue1208-bm8/benchmarks%2Fbenchmark8.ipynb

I have no idea if you can.

This is the "pull request" view: https://app.reviewnb.com/usnistgov/pfhub/pull/1230/. It only seems to show the diff not the section for reviewing the notebook.

tkphd · 2021-03-26T21:33:16Z

Yep! I can see it, and got notified. Cool!

wd15 · 2021-03-27T12:00:23Z

Yep! I can see it, and got notified. Cool!

It's a vast improvement. Opens reviews up to more people.

wd15 · 2021-03-27T12:05:33Z

Yep! I can see it, and got notified. Cool!

I have no idea who has permissions to comment on that notebook.

wd15 · 2021-03-27T12:06:29Z

@wuwenkun, can you see this and comment to test it? https://app.reviewnb.com/wd15/pfhub/blob/issue1208-bm8/benchmarks%2Fbenchmark8.ipynb

wuwenkun · 2021-03-30T21:09:13Z

@wuwenkun, can you see this and comment to test it? https://app.reviewnb.com/wd15/pfhub/blob/issue1208-bm8/benchmarks%2Fbenchmark8.ipynb

Hi Daniel, I have added my comments to the review notebook. Could you see my comments there?

wd15 · 2021-03-31T13:35:07Z

Hi Daniel, I have added my comments to the review notebook. Could you see my comments there?

Yes, all good. Thanks!

Make simulations 4 and 5 optional in BM8a

pfhub · 2021-03-31T15:51:23Z

The new PFHub live website is ready for review.

pfhub · 2021-04-01T14:42:17Z

The new PFHub live website is ready for review.

tkphd · 2021-04-15T18:15:25Z

Very minor changes requested on reviewnb. Looks pretty good!

Use wd15's version of notebook-extensions not Calysto's, which does not have the correct modifications.

Update benchmark8 after tkphd's review - Use Y instead of X for the solid fraction - More explicit that data can be stored externally to the website and also on the website's own storage - Don't spedify the ordering of the \Delta x's. Hopefully, the website will be able to figure this out - Fix grammer - Fix broken URLs for references.

Code for particle counts was not previously shown unless the code toggle button was pressed on the website. Now the code is in a markdown cell so will always be on the website.

review-notebook-app · 2021-04-16T14:15:39Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

pfhub · 2021-04-16T14:20:26Z

The new PFHub live website is ready for review.

wd15 · 2021-04-16T14:31:07Z

@tkphd: made modifications suggested.

Note that Reviewnb is now posting a link into this PR to their version of the PR and allowing comments in the version of the notebook rendered on their PR site, which is really nice. Reviewnb is getting better.

tkphd · 2021-04-16T15:17:59Z

Yeah! They were very responsive to a spellcheck issue I opened, looks like an active project. Very cool.

tkphd

Looks good to me!
Suggestion for @wuwenkun: if you create an arXiv record for the preprint, we can link to that until it clears peer review & publication.

Link to nucleation paper was broken.

wd15 · 2021-04-16T19:18:37Z

Looks good to me!
Suggestion for @wuwenkun: if you create an arXiv record for the preprint, we can link to that until it clears peer review & publication.

It's already out. I fixed the link to it in the notebook.

pfhub · 2021-04-16T19:22:13Z

The new PFHub live website is ready for review.

wd15 added 2 commits November 17, 2020 19:58

docs: new benchmark 8 spec

d78ebe0

build(nix): notebook extension with bibtex

4c70e71

Allow equation numbering and bibtex citations in noteobok

wd15 force-pushed the issue1208-bm8 branch from 6b33621 to 4c70e71 Compare November 18, 2020 00:59

wd15 marked this pull request as ready for review November 18, 2020 01:03

fix for htmlproofer

6dfddb7

wd15 requested a review from tkphd November 19, 2020 00:43

wd15 added the enhancement label Nov 19, 2020

wd15 added this to the April 2021 Meeting 1 milestone Nov 19, 2020

ci: update surge token

57dc220

wd15 requested a review from wuwenkun March 24, 2021 16:01

wd15 added 6 commits March 24, 2021 17:44

fix: broken link to yaml info

d477760

fix: remove twitter from the frontpage

0f023f0

Twitter # link is a bit stupid and useless.

test: switch off htmlproofer for twitter links

e909924

Htmlproofer doesn't work with Twitter links don't work on the CI

docs(notebooks): change wording

5ef24aa

Merge branch 'master' into issue1208-bm8

7182e65

Merge branch 'master' into issue1208-bm8

638b2ac

fix: update for wenkun review

52ffb10

Make simulations 4 and 5 optional in BM8a

wd15 added 3 commits April 16, 2021 10:02

build: use correct version of notebook-exenstions

6a68835

Use wd15's version of notebook-extensions not Calysto's, which does not have the correct modifications.

fix: add particle count code correctly

a97879e

Code for particle counts was not previously shown unless the code toggle button was pressed on the website. Now the code is in a markdown cell so will always be on the website.

tkphd approved these changes Apr 16, 2021

View reviewed changes

fix: link to nucleation paper

65ccdc2

Link to nucleation paper was broken.

wd15 merged commit 48969f0 into usnistgov:master Apr 16, 2021

wd15 deleted the issue1208-bm8 branch October 7, 2021 18:14

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feat: benchmark 8 spec #1230

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feat: benchmark 8 spec #1230

feat: benchmark 8 spec #1230

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TODO

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Code Refactoring

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