Add images from COMETS simulations

docs/build/_sources/index.rst.txt

@@ -3,30 +3,31 @@
    You can adapt this file completely to your liking, but it should at
    least contain the root `toctree` directive.
 
-.. image:: images/cometspy_logo.png
-  :width: 800
-  :alt: COMETSpy logo
-
 COMETS is a software platform for performing **computer simulations of
 metabolism in spatially structured microbial communities**. It is based on
 stoichiometric modeling of the genome-scale metabolic network of
 individual microbial species (using dynamic flux balance analysis), and
 on a discrete approximation of convection-diffusion equations.
 
-.. TODO: Insert images from COMETS imulations here, i.e. colony morpologies from Ilija's presentation
+.. Images from COMETS imulations here, i.e. colony morpologies
+.. image:: images/comets_results.png
+  :width: 800
+  :alt: Results from COMETS simulations
 
 COMETSpy is a Python package that provides a user-friendly interface to
 COMETS. It allows users to easily set up and run simulations, and to
 analyze the results. COMETSpy is designed to be used in conjunction with
 COMETS. It is not a standalone package, and requires COMETS to be
 installed on the user's computer.
 
+.. TODO: Insert a graphic here showing the relationship between COMETS and COMETSpy
+
 This documentation is meant to aide users in installing COMETSpy and
 using COMETSpy to run simulations and analyze the results. If you need
 help and do not easily find an answer in this documentation, ask your question
 in a `new issue on GitHub <https://github.com/segrelab/cometspy/issues/new>`_.
-Any question that you have likely indicates a shortcoming in the documentation,
-which we will want to fix!
+**Any question that you have likely indicates a shortcoming in the documentation,
+which we will want to fix!**
 
 The newest version of COMETS, which was developed as a partnership between
 researchers at `Boston University <https://www.bu.edu/segrelab/>`_,

docs/build/index.html

@@ -29,12 +29,12 @@
 
           <div class="body" role="main">
 
-  <a class="reference internal image-reference" href="_images/cometspy_logo.png"><img alt="COMETSpy logo" src="_images/cometspy_logo.png" style="width: 800px;" /></a>
-<p>COMETS is a software platform for performing <strong>computer simulations of
+  <p>COMETS is a software platform for performing <strong>computer simulations of
 metabolism in spatially structured microbial communities</strong>. It is based on
 stoichiometric modeling of the genome-scale metabolic network of
 individual microbial species (using dynamic flux balance analysis), and
 on a discrete approximation of convection-diffusion equations.</p>
+<a class="reference internal image-reference" href="_images/comets_results.png"><img alt="Results from COMETS simulations" src="_images/comets_results.png" style="width: 800px;" /></a>
 <p>COMETSpy is a Python package that provides a user-friendly interface to
 COMETS. It allows users to easily set up and run simulations, and to
 analyze the results. COMETSpy is designed to be used in conjunction with
@@ -44,8 +44,8 @@
 using COMETSpy to run simulations and analyze the results. If you need
 help and do not easily find an answer in this documentation, ask your question
 in a <a class="reference external" href="https://github.com/segrelab/cometspy/issues/new">new issue on GitHub</a>.
-Any question that you have likely indicates a shortcoming in the documentation,
-which we will want to fix!</p>
+<strong>Any question that you have likely indicates a shortcoming in the documentation,
+which we will want to fix!</strong></p>
 <p>The newest version of COMETS, which was developed as a partnership between
 researchers at <a class="reference external" href="https://www.bu.edu/segrelab/">Boston University</a>,
 <a class="reference external" href="https://eeb.yale.edu/people/alvaro-sanchez">Yale University</a> and the

docs/source/index.rst

@@ -3,30 +3,31 @@
    You can adapt this file completely to your liking, but it should at
    least contain the root `toctree` directive.
 
-.. image:: images/cometspy_logo.png
-  :width: 800
-  :alt: COMETSpy logo
-
 COMETS is a software platform for performing **computer simulations of
 metabolism in spatially structured microbial communities**. It is based on
 stoichiometric modeling of the genome-scale metabolic network of
 individual microbial species (using dynamic flux balance analysis), and
 on a discrete approximation of convection-diffusion equations.
 
-.. TODO: Insert images from COMETS imulations here, i.e. colony morpologies from Ilija's presentation
+.. Images from COMETS imulations here, i.e. colony morpologies
+.. image:: images/comets_results.png
+  :width: 800
+  :alt: Results from COMETS simulations
 
 COMETSpy is a Python package that provides a user-friendly interface to
 COMETS. It allows users to easily set up and run simulations, and to
 analyze the results. COMETSpy is designed to be used in conjunction with
 COMETS. It is not a standalone package, and requires COMETS to be
 installed on the user's computer.
 
+.. TODO: Insert a graphic here showing the relationship between COMETS and COMETSpy
+
 This documentation is meant to aide users in installing COMETSpy and
 using COMETSpy to run simulations and analyze the results. If you need
 help and do not easily find an answer in this documentation, ask your question
 in a `new issue on GitHub <https://github.com/segrelab/cometspy/issues/new>`_.
-Any question that you have likely indicates a shortcoming in the documentation,
-which we will want to fix!
+**Any question that you have likely indicates a shortcoming in the documentation,
+which we will want to fix!**
 
 The newest version of COMETS, which was developed as a partnership between
 researchers at `Boston University <https://www.bu.edu/segrelab/>`_,