Merge branch 'source' into conda-numbering

source/arche/tutorial_py/setup.rst

@@ -60,7 +60,6 @@ root tutorial directory. Create one that looks like:
         setup(
             name='tut',
             packages=['tut'],
-            scripts=['xo'],
             **setup_kwargs
             )
 
@@ -70,7 +69,7 @@ Now we can install the tutorial project via,
 .. code-block:: console
 
     ~ $ cd tutorial
-    ~/tutorial $ python setup.py install --user
+    ~/tutorial $ python -m pip install .
 
 
 Let's now make an example input file in a special ``input`` directory:
@@ -81,7 +80,7 @@ Let's now make an example input file in a special ``input`` directory:
     ~/tutorial $ mkdir -p input
     ~/tutorial $ touch input/storage.py
 
-Now open up the ``input/storage.`` input file and edit it to look like:
+Now open up the ``input/storage.py`` input file and edit it to look like:
 
 .. code-block:: python
 

source/basics/acknowledgements.rst

@@ -21,6 +21,10 @@ by a number of programs and agencies.
 
    * Lab-grad program
 
+* National Nuclear Security Administration
+
+  * NNIS Fellowship
+
 The |Cyclus| project benefits greatly from the computational resources of the
 University of Wisconsin-Madison's `Center for High Throughput Computing
 <http://chtc.cs.wisc.edu>`_ and it's `BaTLab <http://www.batlab.org>`_ build

source/basics/projects.rst

@@ -13,7 +13,17 @@ Consortium for Verification Technology
     :width: 100
 
 As part of the `Consortium for Verification Technology (CVT)
-<http://cvt.engin.umich.edu/>`_, |Cyclus| is being used to study issues in
-nuclear security and non-proliferation. Research areas include the
+<http://cvt.engin.umich.edu/>`_, |Cyclus| was used to study issues in
+nuclear security and non-proliferation. Research areas included the
 incorporation of social-behavioral models to agent interactions, nuclear
 material tracking and forensics, and detector sensitivity estimation.
+
+Systems Analysis & Integration Campaign
+---------------------------------------
+
+As part of the `Systems Analysis & Integration Campaign (SA&I) 
+<https://fuelcycleoptions.inl.gov/SitePages/Home.aspx>`_, |Cyclus| is 
+used for modeling fuel cycles to understand potential future fuel 
+cycle needs and the economics of those fuel cycles. 
+
+

source/cep/cep6.rst

@@ -3,7 +3,7 @@ CEP 6 - |Cyclus| Pull Request Style Guide
 
 :CEP: 6
 :Title: |Cyclus| Pull Request Style Guide 
-:Last-Modified: 2015-05-08
+:Last-Modified: 2024-04-11
 :Author: Matthew Gidden
 :Status: Draft
 :Type: Process
@@ -84,7 +84,7 @@ Automation
 
 Using the Github `API <https://developer.github.com/v3/>`_ either directly or
 through a module like `github3.py
-<https://github3py.readthedocs.org/en/master/>`_ in conjunction with a standard
+<https://github3.readthedocs.io/en/latest/>`_ in conjunction with a standard
 style can allow for the automation of otherwise repetitive and time consuming
 tasks. A chief use case is the generation of release notes. Specifically, if
 every PR that enables a major and minor feature can be identified and

source/index.rst

@@ -30,32 +30,11 @@ The |Cyclus| project repository is located at http://github.com/cyclus/cyclus
 
 Quick Start
 -----------
-:doc:`Get started with Cyclus <user/install>`
-
-News
-----
-
-**June 1st, 2018:** :doc:`Cyclus Newsletter Spring 2018! <newsletters/may2018>`
-
-**October 6th, 2017:** :doc:`Cyclus Newsletter Fall 2017! <newsletters/oct2017>`
-
-**December 13, 2016:** :doc:`Cyclus v1.5.0 is released <previous/v1.5>`
-
-**July 6-8, 2016:** Technical workshop on Dynamic Fuel Cycle in Paris, France
-
-**August 13, 2015:** :doc:`Cyclus included in FY2016 workscopes for the NEUP program <news/fy16neup>`
-
-**July 21-24, 2015:** Joint workshop with CLASS_ project held in Madison, WI
-
-**June 10, 2015:** First Cyclus :doc:`user tutorial <user/tutorial/index>` and :doc:`developer tutorial <arche/tutorial/index>` are held at the 2015 ANS Annual Meeting in San Antonio, TX
-
-**June 7, 2015:** :doc:`Cyclus v1.3.1 is released <previous/v1.3>`
 
 .. toctree::
     :maxdepth: 1
-
-    news/fy16neup
-    newsletters/oct2017
+
+    user/install
 
 
 Learn More
@@ -73,6 +52,26 @@ Learn More
     previous/index
     cite/index
 
+
+News
+----
+
+**June 1st, 2018:** :doc:`Cyclus Newsletter Spring 2018 <newsletters/may2018>`
+
+**October 6th, 2017:** :doc:`Cyclus Newsletter Fall 2017! <newsletters/oct2017>`
+
+**December 13, 2016:** :doc:`Cyclus v1.5.0 is released <previous/v1.5>`
+
+**July 6-8, 2016:** Technical workshop on Dynamic Fuel Cycle in Paris, France
+
+**August 13, 2015:** :doc:`Cyclus included in FY2016 workscopes for the NEUP program <news/fy16neup>`
+
+**July 21-24, 2015:** Joint workshop with CLASS_ project held in Madison, WI
+
+**June 10, 2015:** First Cyclus :doc:`user tutorial <user/tutorial/index>` and :doc:`developer tutorial <arche/tutorial_cpp/index>` are held at the 2015 ANS Annual Meeting in San Antonio, TX
+
+**June 7, 2015:** :doc:`Cyclus v1.3.1 is released <previous/v1.3>`
+
 .. _try-it:
 
 Try It -- Out-of-Service
@@ -96,6 +95,7 @@ Contributors
 ------------
 
 You can find our amazing contributors through their GitHub contributions for each of the projects:
+
 * `Cyclus Contributors <https://github.com/cyclus/cyclus/graphs/contributors>`_
 
 * `Cycamore Contributors <https://github.com/cyclus/cycamore/graphs/contributors>`_

source/numpydoc/numpydoc.py

@@ -12,7 +12,7 @@
 - Renumber references.
 - Extract the signature from the docstring, if it can't be determined otherwise.
 
-.. [1] https://github.com/numpy/numpy/blob/main/doc/HOWTO_DOCUMENT.rst.txt
+.. [1] https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard
 
 """
 from __future__ import division, absolute_import, print_function

source/user/install.rst

@@ -40,21 +40,17 @@ will identify the best approach for you.
   - **Recommended** for developers or users who **require the bleeding edge version** of |Cyclus|
   - **Required** for developers who wish to **contribute to kernel development** of |Cyclus|
 
+* :doc:`Install from Docker <install_docker>`:
 
-.. toctree::
-    :maxdepth: 1
-
-    install_binary
-    install_docker
-    install_custom
-    install_from_git
-    install_from_tarball
+  - *Requires Docker install on machine and familiarity with Docker*
 
 
 2. Run Cyclus with a Sample XML File
 -------------------------------------
 
-Try running |Cyclus| for yourself. The result will be a :doc:`database <dbdoc>` named cyclus.sqlite.  Use the drop down menu to load the sqlite file into Cyclist for data visualization, or use your favorite sqlite browser to peruse.
+Try running |Cyclus| for yourself. The result will be a :doc:`database <dbdoc>` named cyclus.sqlite.  
+Use your favorite sqlite browser to peruse, or explore the data using 
+`Cymetric <https://github.com/cyclus/cymetric>`_.
 
 .. code-block:: bash
 

source/user/tutorial/add_sep.rst

@@ -32,7 +32,7 @@ The following is the input template for ``Cycamore::Separations`` archetype:
                  <item>
                    <comp>_______</comp>
                    <eff>_______</eff>
-                 </item              
+                 </item>              
                </efficiencies>
              </info>
            </item>
@@ -47,7 +47,7 @@ The following is the input template for ``Cycamore::Separations`` archetype:
    * Used-MOX-Fuel
 * The maximum feed inventory is the most feed material that we'll have on
   hand: 1000 tonnes.
-* The maxium separations throughout is the size of our plant: 80 tonnes/timestep
+* The maximum separations throughout is the size of our plant: 80 tonnes/timestep
 * This simple scenario will have a single output stream: Separated-Fissile
     * we will hold no more than 5 tonnes of separated material on hand at any time
     * 99% of all Pu (94000) will go into that stream
@@ -82,7 +82,7 @@ Filling in the template, the input block looks like:
                  <item>
                    <comp>94000</comp>
                    <eff>0.99</eff>
-                 </item              
+                 </item>              
                </efficiencies>
              </info>
            </item>