BM8 comparison page using Jupyter #1314

wd15 · 2021-10-30T19:57:43Z

Start the switch to using Jupyter notebooks for comparison pages

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

This change is

Using plotly.express to plot the data. Everything needs to be a dataframe to use express.

Make nbextension addons for Jupyter install correctly.

Insert raw tags on notebooks for now to overcome issues with plotly and liquid syntax. Include require.js in header as now required by plotly, but not actually imported by plotly.js In addition, Clean up main.py to be more functional. Add levelset contour plot and data table Add level contour plot and data table to results notebook order of accuracy plot is implemented Finished order of accuracy plot Include more data Finish frist draft of 8a.1 comparison page Remove ipynb temp files Reduce size of notebook

…ook-comparison-page

…k-comparison-page

commit-lint · 2021-10-30T19:57:47Z

Features

ensure plotly notebooks display on site (5242e8e)

Build System

nix: improve build (d82777b)
nix: add nbval (d38fcb8)

Bug Fixes

bug fixes, small improvements (12d00ca)

Tests

make sure notebooks are tested (b8f0b3d)
make nbval lax on github actions (cef4544)
add linters to github testing (c9e043b)

Styles

clean up for linters (3f61bd6)

Contributors

wd15

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review-notebook-app · 2021-10-30T19:57:48Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

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pfhub · 2021-10-30T20:02:24Z

The new PFHub live website is ready for review.

pfhub · 2021-10-30T20:05:47Z

The new PFHub live website is ready for review.

pfhub · 2021-10-30T21:34:09Z

The new PFHub live website is ready for review.

pfhub · 2021-10-30T21:38:32Z

The new PFHub live website is ready for review.

pfhub · 2021-10-30T21:41:12Z

The new PFHub live website is ready for review.

pfhub · 2021-10-30T21:42:05Z

The new PFHub live website is ready for review.

pfhub · 2021-11-04T16:03:14Z

The new PFHub live website is ready for review.

wd15 · 2022-02-16T14:35:22Z

@tkphd: I want to switch off the commit linter, but I can't figure it out. Any ideas?

tkphd · 2022-02-16T15:26:06Z

I don't have access, but in the Repository Settings you should be able to remove the webhook.

Previoulsy all notebooks were translated into HTML with raw tags. This was because plotly breaks Jekyll without the raw tags. However, most of the notebooks don't use plotly and use Jekyll tags so should not have raw tags. Raw tags are only added to notebooks in the result/ directory that uses plotly. In future a more sophisticated method might be required for dealing with Plotly and Jekyll clashes.

htmlproofer breaks locally when the locale isn't defined.

Blacklist broken surveymonkey link for htmlproofer.

Switch off the fancy datatables rendering in the notebook version of the results comparison page for BM8.a as this does not render properly when converted to HTML.

pfhub · 2022-03-01T19:17:17Z

The new PFHub live website is ready for review.

pfhub · 2022-03-02T00:59:29Z

The new PFHub live website is ready for review.

pfhub · 2022-03-02T01:13:10Z

The new PFHub live website is ready for review.

pfhub · 2022-03-02T01:22:03Z

The new PFHub live website is ready for review.

Correct metadata for python-pfhub

wd15 · 2022-03-10T21:55:31Z

@tkphd: please take another look. Thanks!

pfhub · 2022-03-10T21:56:34Z

The new PFHub live website is ready for review.

wd15 · 2022-03-30T15:54:51Z

@tkphd: could you approve this one if it's acceptable? Thanks!

tkphd

Just a few more minor changes.

tkphd · 2022-03-30T17:19:11Z

Makefile

@@ -17,6 +17,11 @@ $(HEXBIN_OUT): $(HEXBIN_IN)

 %.ipynb.raw.html: %.ipynb
 	jupyter-nbconvert $< --output $(notdir $@) --to html --template basic
+	if [ "results/"  = "$(dir $@)" ]; then \
+	  echo 'got here'; \


If this is meant to stay, please replace "got here" with a meaningful message, perhaps including the calling process and the filename.

Removed it.

tkphd · 2022-03-30T17:22:37Z

_data/python-pfhub/README.md

@@ -0,0 +1,22 @@
+# Nix


Please include a one-line summary of what python-pfhub is meant to accomplish, at least, insert a top-level # PFHub Python Package, and increase the existing headings by a level (e.g., # Nix -> ## Nix).

Included short description

tkphd · 2022-03-30T17:24:00Z

_data/python-pfhub/pfhub/__init__.py

+def test(*args):
+    r"""Run all the module tests.
+
+    Equivalent to running ``py.test pymks`` in the base of


Removed references to PyMKS

tkphd

Used ReviewNB to check notebooks -- looks good!

tkphd · 2022-03-30T17:36:32Z

Rendered web page also looks good. Almost there!

- Remove references to PyMKS - Short description of Python-PFhub in README.md - Remove debug statement in Makefile

pfhub · 2022-04-04T17:56:53Z

The new PFHub live website is ready for review.

tkphd

LGTM. Nice work!

wd15 added 9 commits October 7, 2021 21:16

Testing plotly

9e527e7

Implement code to exract yaml data as daraframe

f83a5c1

Using plotly.express to plot the data. Everything needs to be a dataframe to use express.

build(nix):

fe110da

Make nbextension addons for Jupyter install correctly.

update notebooks

6387bb7

trying out github actions

c5d4632

update BM8a comparison page

35d61d5

Merge remote-tracking branch 'upstream/github-actions' into bm8-noteb…

64d6ea1

…ook-comparison-page

Merge remote-tracking branch 'origin/github-actions' into bm8-noteboo…

75ca469

…k-comparison-page

Merge branch 'master' into bm8-notebook-comparison-page

216de02

wd15 marked this pull request as ready for review October 30, 2021 20:05

wd15 added 2 commits October 30, 2021 17:28

try and trigger github actions

bd9716e

testing github actions

05dd048

wd15 added 2 commits October 30, 2021 17:36

test github actions

ca222d5

testing github actions

3f16a70

wd15 marked this pull request as draft October 31, 2021 21:25

wd15 added the enhancement label Nov 3, 2021

wd15 self-assigned this Nov 3, 2021

wd15 added this to the November 2021 Meeting milestone Nov 3, 2021

testing github actions with nix

4fe5514

fix

eb71db8

wd15 added 5 commits February 23, 2022 14:57

build(nix): explicitly define the locale

8f857d9

htmlproofer breaks locally when the locale isn't defined.

fix: blacklist broken surveymonkey link

0100c74

Blacklist broken surveymonkey link for htmlproofer.

fix: switch off datatables in jupyter notebook

c36114e

Switch off the fancy datatables rendering in the notebook version of the results comparison page for BM8.a as this does not render properly when converted to HTML.

fix: revert hackathon3 as previously fixed

0904c36

wd15 added 3 commits March 1, 2022 15:41

test: ensure new results/ notebooks are tested

3f7b26c

fix: move _data/pfhub -> _data/python-pfhub

babe28a

build(nix): rename working directory

a4f6381

test(actions): use default working directory

fd82e6b

tests(actions): fix broken yaml file

9138cb8

fix: correct metadata in python-pfhub

ab0072d

Correct metadata for python-pfhub

wd15 requested a review from tkphd March 10, 2022 21:55

tkphd requested changes Mar 30, 2022

View reviewed changes

tkphd reviewed Mar 30, 2022

View reviewed changes

docs: clean up for tkphd review

2038996

- Remove references to PyMKS - Short description of Python-PFhub in README.md - Remove debug statement in Makefile

wd15 requested a review from tkphd April 4, 2022 17:52

tkphd approved these changes Apr 8, 2022

View reviewed changes

tkphd merged commit c7f28fd into usnistgov:master Apr 8, 2022

wd15 deleted the bm8-notebook-comparison-page branch July 20, 2022 21:48

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BM8 comparison page using Jupyter #1314

BM8 comparison page using Jupyter #1314

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BM8 comparison page using Jupyter #1314

BM8 comparison page using Jupyter #1314

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wd15 commented Oct 30, 2021 • edited Loading

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Contributors

review-notebook-app bot commented Oct 30, 2021

pfhub commented Oct 30, 2021

pfhub commented Oct 30, 2021

pfhub commented Oct 30, 2021

pfhub commented Oct 30, 2021

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