Merge pull request #9 from natashabatalha/dev

Dev
natashabatalha · Apr 21, 2020 · cf073d3 · cf073d3
2 parents e808fcf + 34b3a5f
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -0,0 +1,30 @@
+.. :changelog:
+
+History
+-------
+
+2.0 (2020-04-21)
+~~~~~~~~~~~~~~~~~~
+
+* Explicit Brown Dwarf tutorials 
+* Coupling to brand new python cloud code `Virga`!!
+* Ability to specify wave range in `opannection` and ability to resample (consult your local theorist before doing this)
+* Added "Opacity Factor" so that users can easiy query opacity data without going through SQL 
+* Removed opacity from git-lfs (was a bad system and users were having trouble)
+* Fixed critical spherical integration bug and added more robust steps for 1d vs. 3d. Also added full tutorial to explain differences here. 
+* Added notebook for surface reflectivity
+
+1.0 (2020-2-7)
+~~~~~~~~~~~~~~
+
+* Thermal emission added 
+* Changed the way the code output is returned to single dictionary. 
+* Tutorials to map 3D input onto Gauss/Chebysev Angles 
+
+0.0 (2019-4-19)
+~~~~~~~~~~~~~~~
+
+* Reflected light component only 
+* added git-lfs opacity database from only 0.3-1 micron 
+* made opacity database sqlite to speed up queries 
+* tutorials added for initial setup, adding clouds, visualizations, analyzing approximations, and opacity queries
diff --git a/README.rst b/README.rst
@@ -7,7 +7,7 @@
    </div>
    <br/><br/>
 
-Reflected light spectroscopy for planetary atmospheres.
+Spectroscopy for planetary atmospheres.
 
 Docs 
 ----

diff --git a/docs/conf.py b/docs/conf.py
@@ -58,17 +58,16 @@
 
 # General information about the project.
 project = 'picaso'
-copyright = '2018, Natasha E. Batalha'
 author = 'Natasha E. Batalha'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = '2.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -126,8 +125,8 @@
 #    This notebook can be downloaded at : https://github.com/natashabatalha/picaso/tree/master/docs/notebooks/{{ docname }}
 #
 
-def setup(app):
-    app.add_stylesheet('https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css')
-    app.add_javascript('https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js')
-    app.add_javascript('https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js')
+#def setup(app):
+#    app.add_stylesheet('https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css')
+#    app.add_javascript('https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js')
+#    app.add_javascript('https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js')
 
diff --git a/docs/index.rst b/docs/index.rst
@@ -19,69 +19,44 @@ Use Cases
 
 .. raw:: html 
 
-	 <div class="row">
-	  <div class="col-md-6">
-	    <div class="thumbnail">
-	      <a href="_images/planettype.png">
-	        <img src="_images/planettype.png" alt="Planet Type" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	  <div class="col-md-6">
-	    <div class="thumbnail">
-	      <a href="_images/refem.png">
-	        <img src="_images/refem.png" alt="Geometry" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	  </div>
-	  <div class="row">
-	  <div class="col-md-12">
-	    <div class="thumbnail">
-	      <a href="_images/multiphase.png">
-	        <img src="_images/multiphase.png" alt="Multi Phases" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	</div>
-	</div>
+   <div align="center">
+   <img src="_images/planettype.png" width="300px">
+   </img>
+   <img src="_images/refem.png" width="300px">
+   </img>
+   <br/>
+   </div>
+   <br/><br/>
+
+   <div align="center">
+   <img src="_images/multiphase.png" width="600px">
+   </img>
+   <br/>
+   </div>
+   <br/><br/>
+
 
 Resources
 =========
 
 .. raw:: html 
 
-	 <div class="row">
-	  <div class="col-md-3">
-	    <div class="thumbnail">
-	      <a href="installation.html">
-	        <img src="_images/installation.png" alt="installation" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	  <div class="col-md-3">
-	    <div class="thumbnail">
-	      <a href="tutorials.html">
-	        <img src="_images/tutorials.png" alt="tutorials" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	  <div class="col-md-3">
-	    <div class="thumbnail">
-	      <a href="https://natashabatalha.github.io/picaso_dev">
-	        <img src="_images/derivations.png" alt="derivations" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	  <div class="col-md-3">
-	    <div class="thumbnail">
-	      <a href="picaso.html">
-	        <img src="_images/picaso.png" alt="code" style="width:100%">
-	      </a>
-	    </div>
-	  </div>
-	</div>
-	</div>
+   <div align="center">
+   <a href="installation.html">
+   <img src="_images/installation.png" width="150px">
+   </img></a>
+   <a href="tutorials.html">
+   <img src="_images/tutorials.png" width="150px">
+   </img></a>
+   <a href="https://natashabatalha.github.io/picaso_dev">
+   <img src="_images/derivations.png" width="150px">
+   </img></a>
+   <a href="picaso.html">
+   <img src="_images/picaso.png" width="150px">
+   </img></a>      
+   <br/>
+   </div>
+   <br/><br/>
 
 
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -21,9 +21,11 @@ Install with Git
 Download and Link Reference Documentation
 -----------------------------------------
 
-1) If you did not download the github repository, make sure you pull the `Reference Folder <https://github.com/natashabatalha/picaso/tree/master/reference>`_.  
+1) Download the `Reference Folder from Github <https://github.com/natashabatalha/picaso/tree/master/reference>`_. You may have this already if you did a Git clone.
 
-2) Now you can create an environment variable:
+2) Download the `Resampled Opacity File from Zenodo <https://doi.org/10.5281/zenodo.3759675>`_. Unzip and place in the `Reference Folder you downloaded from Github <https://github.com/natashabatalha/picaso/tree/master/reference>`_.
+
+3) Now you can create an environment variable:
 
 
 .. code-block:: bash
@@ -44,6 +46,8 @@ Should look something like this
 	ls
 	base_cases	config.json	opacities
 
+Your opacities folder shown above should include the unzipped `opacity.db` `file downloaded from zenodo <https://doi.org/10.5281/zenodo.3759675>`_. This is mostly a matter of preference, as PICASO allows you to point to an opacity directory. Personally, I like to store something with the reference data so that I don't have to constantly specify a folder path when running the code. 
+
 Download and Link Pysynphot Stellar Data
 ----------------------------------------
 

diff --git a/docs/notebooks/6_BrownDwarfs.ipynb b/docs/notebooks/6_BrownDwarfs.ipynb
@@ -11,7 +11,7 @@
     "In this tutorial you will learn:\n",
     "\n",
     "1. How to turn that feature off \n",
-    "2. Query a profile from the Sonora Grid (not you will need to download and untar this to provide a filepath.) \n",
+    "2. Query a profile from the [Sonora Grid](https://zenodo.org/record/1309035#.Xo5GbZNKjGJ). Note, this is note necessary -- just convenient! \n",
     "3. Create a Brown Dwarf Spectrum "
    ]
   },

diff --git a/setup.py b/setup.py
@@ -41,7 +41,7 @@
 # to this sample package.
 setup(
     name='picaso', 
-    version = '1.0',
+    version = '2.0',
     description = 'planetary intesity code for atmospheric scattering observations',
     long_description = 'README.rst',
     author = 'Natasha E. Batalha',
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,7 +7,7 @@ @@
        </div>
        <br/><br/>
-    Reflected light spectroscopy for planetary atmospheres.
+    Spectroscopy for planetary atmospheres.
     Docs
     ----
@@ Expand Down @@