Merge pull request #4 from MatthewTurk/ytree

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Merge pull request #4 from MatthewTurk/ytree

Adding notes about ytree

citations.tsv

@@ -2,4 +2,5 @@ string citation standard_citation citation_id
 @doi:10.1038/nature15383 doi:10.1038/nature15383 doi:10.1038/nature15383 1CgEbr6CQ
 @doi:10.1088/0067-0049/192/1/9 doi:10.1088/0067-0049/192/1/9 doi:10.1088/0067-0049/192/1/9 1GOm01ggN
 @doi:10.3847/1538-4357/aa7e2d doi:10.3847/1538-4357/aa7e2d doi:10.3847/1538-4357/aa7e2d 1DgKJy4lE
+@doi:10.5281/zenodo.1174374 doi:10.5281/zenodo.1174374 doi:10.5281/zenodo.1174374 VB3RIyxd
 @url:https://github.com/greenelab/manubot url:https://github.com/greenelab/manubot url:https://github.com/greenelab/manubot cTN2TQIL

manuscript.html

@@ -8,7 +8,7 @@
  <meta name="author" content="Matthew Turk" />
  <meta name="author" content="Nathan J Goldbaum" />
  <meta name="author" content="Add Yourself" />
- <meta name="dcterms.date" content="2018-02-16" />
+ <meta name="dcterms.date" content="2018-02-17" />
  <meta name="keywords" content="markdown, publishing, manubot" />
  <title>Introducing yt 3.0: Analysis and Visualization of Volumetric Data</title>
  <style type="text/css">
@@ -96,7 +96,7 @@
 <header>
 <h1 class="title">Introducing yt 3.0: Analysis and Visualization of Volumetric Data</h1>
 </header>
-<p><small><em> This manuscript was automatically generated from <a href="https://github.com/yt-project/yt-3.0-paper/tree/e3fcc6a8e403a5123303c7daf027f5da9400a832">yt-project/yt-3.0-paper@e3fcc6a</a> on February 16, 2018. </em></small></p>
+<p><small><em> This manuscript was automatically generated from <a href="https://github.com/yt-project/yt-3.0-paper/tree/1ed7383a1818952b35f7b8d7ae23dcfcff7e73b0">yt-project/yt-3.0-paper@1ed7383</a> on February 17, 2018. </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
 <li><p><strong>The yt Project</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/XXXX-XXXX-XXXX-XXXX">XXXX-XXXX-XXXX-XXXX</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/yt-project">yt-project</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <a href="https://twitter.com/yt_astro">yt_astro</a><br> <small> NumFOCUS · Funded by Grant XXXXXXXX </small></p></li>
@@ -317,6 +317,8 @@ <h3 id="trident">Trident</h3>
 <h3 id="powderday">Powderday</h3>
 <p><span class="citation" data-cites="1CgEbr6CQ">[<a href="#ref-1CgEbr6CQ">4</a>]</span></p>
 <h3 id="ytree">ytree</h3>
+<p>Building on <code>yt</code> for access to halo catalogs, and implementing a similar system for derived fields as applied to graph datasets, ytree <span class="citation" data-cites="VB3RIyxd">[<a href="#ref-VB3RIyxd">5</a>]</span> is a system for analyzing merger trees from analysis of dark matter halos in cosmological simulations.</p>
+<p>ytree provides flexibility in determining the path that a given analysis takes through the graph of merger trees; for instance, it enables the user to select if they wish to follow the “most massive” progenitor halo backwards in time, or even to set their own criteria for this. Connecting this to the raw, unprocessed data from the simulation (such as the unsampled particle or cell content that comprises the halos) allows researchers to deepen and guide their analysis based on the physical characteristics of the merger history.</p>
 <h2 id="future-directions">Future Directions</h2>
 <h2 id="conclusions">Conclusions</h2>
 <h2 id="acknowledgments">Acknowledgments</h2>
@@ -345,6 +347,11 @@ <h2 id="references" class="page_break_before">References</h2>
 Desika Narayanan, Matthew Turk, Robert Feldmann, Thomas Robitaille, Philip Hopkins, Robert Thompson, Christopher Hayward, David Ball, Claude-André Faucher-Giguère, Dušan Kereš<br />
 <em>Nature</em> (2015-09) <a href="https://doi.org/10.1038/nature15383" class="uri">https://doi.org/10.1038/nature15383</a></p>
 </div>
+<div id="ref-VB3RIyxd">
+<p>5. <strong>Brittonsmith/Ytree: Ytree Version 2.0.2 Release</strong><br />
+Britton Smith<br />
+<em>Zenodo</em> (2018-02-16) <a href="https://doi.org/10.5281/zenodo.1174374" class="uri">https://doi.org/10.5281/zenodo.1174374</a></p>
+</div>
 </div>
 <script>
 // AnchorJS minified version below.

manuscript.md

@@ -4,7 +4,7 @@ author-meta:
 - Matthew Turk
 - Nathan J Goldbaum
 - Add Yourself
-date-meta: '2018-02-16'
+date-meta: '2018-02-17'
 keywords:
 - markdown
 - publishing
@@ -20,8 +20,8 @@ title: 'Introducing yt 3.0: Analysis and Visualization of Volumetric Data'
 
 <small><em>
 This manuscript was automatically generated
-from [yt-project/yt-3.0-paper@e3fcc6a](https://github.com/yt-project/yt-3.0-paper/tree/e3fcc6a8e403a5123303c7daf027f5da9400a832)
-on February 16, 2018.
+from [yt-project/yt-3.0-paper@1ed7383](https://github.com/yt-project/yt-3.0-paper/tree/1ed7383a1818952b35f7b8d7ae23dcfcff7e73b0)
+on February 17, 2018.
 </em></small>
 
 ## Authors
@@ -869,7 +869,18 @@ processing and analyzing that data.
 
 ### ytree
 
-
+Building on `yt` for access to halo catalogs, and implementing a similar system
+for derived fields as applied to graph datasets, ytree
+[@VB3RIyxd] is a system for analyzing merger trees from
+analysis of dark matter halos in cosmological simulations.
+
+ytree provides flexibility in determining the path that a given analysis takes
+through the graph of merger trees; for instance, it enables the user to select
+if they wish to follow the "most massive" progenitor halo backwards in time, or
+even to set their own criteria for this. Connecting this to the raw,
+unprocessed data from the simulation (such as the unsampled particle or cell
+content that comprises the halos) allows researchers to deepen and guide their
+analysis based on the physical characteristics of the merger history.
 
 
 ## Future Directions

references.json

@@ -536,6 +536,33 @@
  "short_url": "https://doi.org/gcx4th",
  "id": "1DgKJy4lE"
  },
+ {
+ "type": "article",
+ "id": "VB3RIyxd",
+ "author": [
+ {
+ "family": "Smith",
+ "given": "Britton"
+ }
+ ],
+ "issued": {
+ "date-parts": [
+ [
+ 2018,
+ 2,
+ 16
+ ]
+ ]
+ },
+ "abstract": "This release contains significant file i/o optimizations for the ytree frontend.",
+ "DOI": "10.5281/zenodo.1174374",
+ "page": "-",
+ "publisher": "Zenodo",
+ "title": "Brittonsmith/Ytree: Ytree Version 2.0.2 Release",
+ "URL": "https://doi.org/10.5281/zenodo.1174374",
+ "version": "ytree-2.0.2",
+ "short_url": "https://doi.org/gcx4x2"
+ },
  {
  "URL": "https://github.com/greenelab/manubot",
  "title": "greenelab/manubot",

variables.json

@@ -1,5 +1,5 @@
 {
- "date": "February 16, 2018",
+ "date": "February 17, 2018",
  "authors": [
  {
  "github": "yt-project",
@@ -94,14 +94,14 @@
  "repo_slug": "yt-project/yt-3.0-paper",
  "repo_owner": "yt-project",
  "repo_name": "yt-3.0-paper",
- "commit": "e3fcc6a8e403a5123303c7daf027f5da9400a832"
+ "commit": "1ed7383a1818952b35f7b8d7ae23dcfcff7e73b0"
  },
  "manuscript_stats": {
  "reference_counts": {
- "doi": 3,
+ "doi": 4,
  "url": 1,
- "total": 4
+ "total": 5
  },
- "word_count": 5639
+ "word_count": 5765
  }
 }