Add adaptahop dataset

css/style.css

@@ -1161,8 +1161,6 @@ label {
 	.twitter a:hover { background: url(../img/social/twitter.png) no-repeat bottom center; }
 	.vimeo a { background: url(../img/social/vimeo.png) no-repeat top center; }	
 	.vimeo a:hover { background: url(../img/social/vimeo.png) no-repeat bottom center; }
-	.google a { background: url(../img/social/google+.png) no-repeat top center; }	
-	.google a:hover { background: url(../img/social/google+.png) no-repeat bottom center; }
 	.yahoo a { background: url(../img/social/yahoo.png) no-repeat top center; }	
 	.yahoo a:hover { background: url(../img/social/yahoo.png) no-repeat bottom center; }
 

extensions.yaml

@@ -40,11 +40,9 @@
   import_as: yt.extensions.viewyt
   contact: Austin Gilbert
 - name: ytree
-  url: http://ytree.readthedocs.io
+  url: https://ytree.readthedocs.io
+  image: ytree.png
   description: |
-    A merger-tree code with yt-style syntax for loading data and field
-    access. ytree can create merger-trees from Gadget FoF/Subfind catalogs,
-    either for all or just a specific set of halos, and can load data from
-    consistent-trees and Rockstar catalogs.
+    Analyze merger tree data from multiple sources. It's yt for merger trees!
   import_as: ytree
   contact: Britton Smith

gallery.yaml

@@ -1,9 +1,39 @@
+- title: Mesh-refinement for laser-plasma interation simulations with WarpX
+  textwidth: 7
+  imagewidth: 5
+  text: >
+    Yt was used to render this multi-stage laser-plasma acceleration simulation
+    with the electromagnetic particle-in-cell code
+    <a href="https://github.com/ECP-WarpX/WarpX">WarpX</a>, see
+    <a href="https://www.sciencedirect.com/science/article/pii/S0168900218300524"> Vay et al. 2018</a>.
+    An ultrashort ultraintense laser pulse (red) propagates through a
+    low-density plasma and triggers plasma oscillations with strong electric
+    field (yellow-blue). A beam of electrons (white dots) is trapped in this
+    wake and accelerated to high energies (GeV). The horizontal lines show
+    lines of plasma particles. For higher accuracy, a refinement patch is added
+    around the electron beam (white parallelepiped).
+  images:
+    - img/gallery/warpx.png
+- title: Mixed-morphology SNR simulations with a cloudy environment
+  textwidth: 7
+  imagewidth: 5
+  text: >
+    In <a href="http://adsabs.harvard.edu/abs/2019ApJ...875...81Z">
+    Zhang et al. 2019</a>,
+    authours used yt to present the 3D simulation of
+    a mixed-morphology supernova remnant.
+    The volumetric rendering of density shows in the top panel,
+    with a density histogram (black curve)
+    and the transfer function in the bottom panel.
+    The SNR shock front is in cyan, and dense clouds are in red.
+  images:
+    - img/gallery/mmsnr_3d_rendering.png
 - title: Standing Accretion Shock Instability Spiral Wave in a Core-Collapse Supernova Simulations
   textwidth: 7
   imagewidth: 5
   text: >
     In <a href="http://adsabs.harvard.edu/abs/2018ApJ...865...81O">O'Connor
-    & Couch (2018)</a>, the authors used yt for the visualization of their data. 
+    & Couch (2018)</a>, the authors used yt for the visualization of their data.
     This figure, a volume rendering of entropy near the gain region of a
     core-collapse supernova, shows the multidimensional hydrodynamic instabilities
     at work.  Both turbulence and the standing accretion shock instability
@@ -74,7 +104,7 @@
     (2012)</a> and conducted with <a href="http://enzo-project.org">Enzo</a>.
     The bottom panels show the density, temperature, and metallicity of the
     same slice.  This figure was published in the reference above as Figure 9.
-  images: 
+  images:
     - img/gallery/wise-rp.jpg
 - title: Density and Temperature Around a Forming Star
   textwidth: 5
@@ -138,7 +168,7 @@
 - title: GMC Identification
   textwidth: 7
   imagewidth: 5
-  images: 
+  images:
     - img/gallery/benincasa.jpg
   text: >
     A slice through the z-plane of a typical cloud from <a
@@ -148,7 +178,7 @@
 - title: Velocity Structure of a Collapsing Cloud
   textwidth: 7
   imagewidth: 5
-  images: 
+  images:
     - img/gallery/Smith_2015_F10.png
   text: >
     Figure 10 from <a href="http://arxiv.org/abs/1504.07639">Smith et al.

generate.py

@@ -1,7 +1,9 @@
 from __future__ import print_function
+import git
 import yaml
 import os
 import sys
+import tempfile
 from jinja2 import Environment, FileSystemLoader
 
 PATH = os.path.dirname(os.path.abspath(__file__))
@@ -34,12 +36,12 @@ def _page(func):
 
 @page('index')
 def index():
-    examples = yaml.load(open("examples.yaml", "r"))
+    examples = yaml.load(open("examples.yaml", "r"), Loader=yaml.SafeLoader)
     return {'title': 'Home', 'examples': examples}
 
 @page('gallery')
 def gallery():
-    entries = yaml.load(open("gallery.yaml", "r"))
+    entries = yaml.load(open("gallery.yaml", "r"), Loader=yaml.SafeLoader)
     return {'entries': entries}
 
 name_ignores = ["convert-repo"]
@@ -52,28 +54,26 @@ def about():
     # Uncomment for rapid dev
     if "--fast" in sys.argv:
         return {'developers': []}
-    import git
     if yt_path:
         repo = git.Repo(yt_path)
     else:
-        import tempfile
-        repo_path = tempfile.mkdtemp()
-        repo = git.Repo.clone_from(
-            'https://github.com/yt-project/yt', repo_path)
-    shortlog = repo.git.shortlog('-ns').split('\n')
-    repo.close()
-    devs = set([sl.split('\t')[1] for sl in shortlog])
+        with tempfile.TemporaryDirectory() as repo_path:
+            with git.Repo.clone_from(
+                "https://github.com/yt-project/yt", repo_path
+            ) as repo:
+                shortlog = repo.git.shortlog(["-ns", "HEAD"]).split("\n")
+    devs = set([sl.split("\t")[1] for sl in shortlog])
     for name in name_ignores:
         devs.discard(name)
-    return {'developers': sorted(devs, key=lastname_sort)}
+    return {"developers": sorted(devs, key=lastname_sort)}
 
 @page('community')
 def community():
     return {}
 
 @page('members')
 def members():
-    members = yaml.load(open("members.yaml", "r"))
+    members = yaml.load(open("members.yaml", "r"), Loader=yaml.SafeLoader)
     members.sort(key = lambda a: lastname_sort(a['name']))
     return {'members': members}
 
@@ -91,7 +91,7 @@ def data():
 
 @page('extensions')
 def extensions():
-    extensions = yaml.load(open("extensions.yaml", "r"))
+    extensions = yaml.load(open("extensions.yaml", "r"), Loader=yaml.SafeLoader)
     return {'extensions': extensions}
 
 @page('slack')

members.yaml

@@ -10,6 +10,10 @@
   content: >
     Corentin has been a yt project developer since 2017. He has been involved in
     maintaining and improving RAMSES' frontend.
+- name: Niels Claes
+  since: 2019
+- name: Jared Coughlin
+  since: 2020
 - name: Brian Crosby
   since: 2016
 - name: Bili Dong
@@ -26,6 +30,8 @@
     Nathan has been involved in yt development since 2011. He has been involved
     in writing and maintaining yt's plotting functionality, the FLASH, Enzo,
     and SPH frontends, and yt's unit system.
+- name: Chris Havlin
+  since: 2021
 - name: Cameron Hummels
   since: 2014
   content: >
@@ -100,6 +106,15 @@
   since: 2014
 - name: Brian O'Shea
   since: 2014
+- name: Clément Robert
+  since: 2019
+  content:
+    Clément has been using multiple hydro-simulation codes and got frustrated
+    with the wheel-reinventing that was too often required to read and analyze
+    code specific data formats. In 2018, he fell in love with yt's philosophy
+    for building and sharing one flexible tool with a community of users and
+    developers and started working on a frontend for MPI-AMRVAC, which came to
+    life in 2019.
 - name: Douglas Rudd
   since: 2014
   content: >

requirements.txt

@@ -1,3 +1,5 @@
 pyyaml>=4.2b1
-GitPython==2.1.3
+GitPython==2.1.15
+gitdb2==2.0.6
+gitdb==0.6.4
 Jinja2>=2.10.1

templates/about.html

@@ -23,7 +23,7 @@ <h1>Mission Statement</h1>
       </div>
 
       <div class="text-center">
-          <iframe src="http://www.ohloh.net/p/129183/widgets/project_factoids_stats.html" scrolling="no" marginHeight=0 marginWidth=0 style="height: 250px; width: 370px; border: none; background: white;"></iframe>
+          <script type='text/javascript' src='https://www.openhub.net/p/yt_amr/widgets/project_factoids_stats?format=js'></script>
       </div>
 
       <div class="row yt-package">

templates/base.html

@@ -6,7 +6,6 @@
     <meta name="description" content="">
     <meta name="author" content="">
     <link rel="shortcut icon" href="favicon.png" />
-    <link href="https://plus.google.com/107728486871834552760" rel="publisher" />
 
     <title>The yt Project: {{title | capitalize}}</title>
 
@@ -77,7 +76,7 @@
                     <li><a href="https://blog.yt-project.org/">yt Blog</a></li>
                     <li><a href="https://yt-project.org/doc/quickstart/index.html">Quick Start</a></li>
                     <li><a href="https://yt-project.org/doc/">Documentation</a></li>
-                    <li><a href="https://adsabs.harvard.edu/abs/2011ApJS..192....9T">ApJS paper</a>
+                    <li><a href="https://ui.adsabs.harvard.edu/abs/2011ApJS..192....9T">ApJS paper</a>
                     <li class="divider"></li>
                     <li class="dropdown-header">Help!</li>
                     <li><a href="https://mail.python.org/mm3/mailman3/lists/yt-users.python.org/">Mailing List</a></li>

templates/community.html

@@ -113,12 +113,9 @@ <h1>Sharing Scripts, Projects and Notebooks</h1>
           <h1>Social Networking</h1>
           <p>
             yt has a presence on <a href="https://twitter.com/yt_astro">twitter</a>,
-            where occasional updates are posted.  Other places for short-form
-            updates include the
-            <a href="https://www.facebook.com/ytproject">facebook page</a>,
-            and the
-            <a href="https://plus.google.com/107728486871834552760">Google+ page</a>, where occasionally 
-            hangouts, videos and live office hours are held.
+            where occasional updates are posted.  Another place for short-form
+            updates is the
+            <a href="https://www.facebook.com/ytproject">facebook page</a>.
           </p>
           <p>
             yt also has a <a href="https://blog.yt-project.org/">blog</a>, where longer-form

templates/data/index.html

@@ -61,6 +61,15 @@
         <tr><th>Auxiliary Data Files</th><th>Size (mb)</th><th>Description</th><th>Link</th></tr>
       </thead>
       <tbody>
+        <tr><td>apec_emissivity (v. 3)</td>
+          <td>243 KB</td>
+          <td>X-ray emissivity tables created
+          with <a href="http://www.atomdb.org/">AtomDB v3.0.9</a>
+          (for a collisionally ionized plasma), used for creating X-ray
+          fields. This needs to be multiplied by ne*nH instead of nH**2 (which
+          was the case in v. 2). Used in yt 4.0 and later.</td>
+          <td><a href="http://yt-project.org/data/apec_emissivity_v3.h5">download</a></td>
+        </tr>
         <tr><td>cloudy_emissivity (v. 2)</td>
             <td>2.1 MB</td>
             <td>X-ray emissivity tables created

templates/development.html

@@ -30,12 +30,7 @@ <h1>Development</h1>
           </p>
         </div>
         <div class="col-md-5">
-          <iframe src="https://www.ohloh.net/p/129183/widgets/project_basic_stats.html"
-            scrolling="no" marginheight="0" marginwidth="0"
-            style="margin-top:70px; height: 192px; background: white; 
-                   width: 334px; border: none; border-radius: 12px; 
-                   -webkit-border-radius: 12px; margin-left: auto;
-                   margin-right: auto; display: block"></iframe>
+          <script type='text/javascript' src='https://www.openhub.net/p/yt_amr/widgets/project_basic_stats?format=js'></script>
 
             <div class="slack_signup_container">
               <button type="button" class="btn btn btn-large btn-primary" id="slackSign">Join us @ Slack!</button>

templates/index.html

@@ -209,7 +209,7 @@ <h1>Get yt:<span class="text-muted"> all-in-one script.</h1>
           </p>
           <p class="lead">
             If you use yt in a publication, we request that you please consider
-            citing <a href="https://adsabs.harvard.edu/abs/2011ApJS..192....9T">our method paper</a>
+            citing <a href="https://ui.adsabs.harvard.edu/abs/2011ApJS..192....9T">our method paper</a>
             (<a href="https://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2011ApJS..192....9T&data_type=BIBTEX&db_key=AST&nocookieset=1">BibTeX</a>).
           </p>
           <p class="lead">