feat: benchmark 8 spec

_data/benchmarks.yaml

@@ -428,11 +428,20 @@
       mode: lines
       variations: [b, c]
 
-- title: Nucleation
-  description: Nucleation benchmark
+- title: Homogeneous Nucleation
+  description: Homogeneous nucleation benchmark
   image: https://user-images.githubusercontent.com/1986844/66938477-396aff80-f00f-11e9-8c21-b59356a3b0e0.png
   num: 8
   revisions:
+    - version: 1
+      variations: [a, b, c]
+      event:
+        name: Hackathon 5
+        url: "benchmarks/benchmark8.ipynb"
+      url: "benchmarks/benchmark8.ipynb"
+      commit:
+        sha: "e19007361211"
+        url: "benchmarks/benchmark8.ipynb"
     - version: 0
       variations: [a, b, c, d]
       event:

_includes/head.html

@@ -102,6 +102,7 @@
 <script type="text/x-mathjax-config">
   MathJax.Hub.Config({
     <!-- extensions: ["tex2jax.js"], -->
+    TeX: { equationNumbers: {autoNumber: "AMS"}},
     jax: ["input/TeX", "output/HTML-CSS"],
     tex2jax: {
       inlineMath: [ ['$','$'], ["\\(","\\)"] ],

_nix/env.nix

@@ -16,5 +16,25 @@ nixpkgs.stdenv.mkDerivation rec {
     pip install jupyter_contrib_nbextensions --user > /dev/null 2>&1
     jupyter contrib nbextension install --user > /dev/null 2>&1
     jupyter nbextension enable spellchecker/main > /dev/null 2>&1
+    jupyter nbextension enable equation-numbering/main > /dev/null 2>&1
+
+    # Bibliography tools
+    # see https://jupyter.brynmawr.edu/services/public/dblank/jupyter.cs/Examples/Calico%20Document%20Tools%20and%20Bibtex.ipynb
+    # also see
+    # https://jupyter.brynmawr.edu/services/public/dblank/Jupyter%20Notebook%20Users%20Manual.ipynb#5.-Bibliographic-Support
+
+    CURDIR=$(pwd)
+    MYTMPDIR=$(mktemp -d)
+    cd $MYTMPDIR
+    # This is my own version as notebook-extensions needed modifications
+    # Orignal repo is
+    # https://github.com/Calysto/notebook-extensions
+    git clone https://github.com/wd15/notebook-extensions.git
+    cd notebook-extensions
+    jupyter nbextension install calysto --user
+    jupyter nbextension enable calysto/document-tools/main --user
+    cd $CURDIR
+    rm -rf $MYTMPDIR
+
   '';
 }

benchmarks/benchmark8a.1.ipynb.md

@@ -0,0 +1,4 @@
+---
+layout: redirected
+redirect_to: ../../benchmarks/benchmark8.ipynb/
+---

benchmarks/benchmark8b.1.ipynb.md

@@ -0,0 +1,4 @@
+---
+layout: redirected
+redirect_to: ../../benchmarks/benchmark8.ipynb/
+---

benchmarks/benchmark8c.1.ipynb.md

@@ -0,0 +1,4 @@
+---
+layout: redirected
+redirect_to: ../../benchmarks/benchmark8.ipynb/
+---

index.html

@@ -11,10 +11,6 @@
   {% include wiki-nav.html %}
 </div>
 
-<div id="twitter-right">
-  {% include twitter.html %}
-</div>
-
 <div id="sponsor-logos-container">
   <div class="col s0 m0 l0 xl12" id="sponsor-logos">
     {% include logos.html %}

simulations/8a.1.html

@@ -0,0 +1,6 @@
+---
+layout: default
+---
+
+{% assign benchmark_id = page.url | remove: '/simulations/' | remove: '/' %}
+{% include result_comparison.html benchmark_id=benchmark_id %}

simulations/8b.1.html

@@ -0,0 +1,6 @@
+---
+layout: default
+---
+
+{% assign benchmark_id = page.url | remove: '/simulations/' | remove: '/' %}
+{% include result_comparison.html benchmark_id=benchmark_id %}

simulations/8c.1.html

@@ -0,0 +1,6 @@
+---
+layout: default
+---
+
+{% assign benchmark_id = page.url | remove: '/simulations/' | remove: '/' %}
+{% include result_comparison.html benchmark_id=benchmark_id %}

simulations/upload.md

@@ -16,14 +16,14 @@ feel free to upload benchmark results via pull requests on
 GitHub. More benchmark results will greatly improve the utility of the
 website and encourage community collaboration.
 
-Each benchmark result is stored in a [YAML
-file][YAML] called
-`meta.yaml` in a separate directory in
-[_data/simulations]({{ site.links.github }}/tree/master/_data/simulations).
-A [YAML file][YAML] is a
-minimal, human readable syntax for structured data. The `meta.yaml`
-file stores the meta data for only one benchmark result and a new
-directory is required for each new benchmark result.
+
+Each benchmark result is stored in a [YAML file][YAML] called
+`meta.yaml` in a separate directory in [_data/simulations]({{
+site.links.github }}/tree/master/_data/simulations).  A [YAML file][YAML]
+is a minimal, human readable syntax for structured
+data. The `meta.yaml` file stores the meta data for only one benchmark
+result and a new directory is required for each new benchmark result.
+
 
 <h4> How to Upload </h4>
 
@@ -69,10 +69,8 @@ The following is the minimal description of a benchmark result with
 relevant comments. The definitive archetype resides at
 [`_data/simulations/example/example.yaml`]({{ site.links.simmeta
 }}/example/meta.yaml). To understand the YAML syntax consult either
-the [Ansible
-documentation][YAML] for a
-simple overview or the [YAML site](http://www.yaml.org/) for a more in
-depth description.
+the [Ansible documentation][YAML] for a simple overview or the [YAML
+site](http://www.yaml.org/) for a more in depth description.
 
 ```
 ---