some fixes for docs

Author: zingale

docs/source/conf.py

@@ -137,6 +137,9 @@
     ]
 }
 
+linkcheck_ignore = [r"https://ascelibrary.org",
+                    r"https://doi.org/10.1061/(ASCE)0733-9429(1999)125:11(1210)"]
+
 
 # -- Options for HTMLHelp output ------------------------------------------
 

docs/source/index.rst

@@ -63,7 +63,7 @@ pyro: a python hydro code
 .. toctree::
    :caption: Bibliography
 
-   references
+   zreferences
 
 
 Indices and tables

docs/source/mesh_basics.rst

@@ -100,7 +100,7 @@ Jupyter notebook
 ----------------
 
 A Jupyter notebook that illustrates some of the basics of working with
-the grid is provided as `mesh-examples.ipynb <https://github.com/python-hydro/pyro2/blob/main/mesh/mesh-examples.ipynb>`_. This will
+the grid is provided as `mesh-examples.ipynb <https://github.com/python-hydro/pyro2/blob/main/pyro/mesh/mesh-examples.ipynb>`_. This will
 demonstrate, for example, how to use the :func:`ArrayIndexer <pyro.mesh.array_indexer.ArrayIndexer>` methods to
 construct differences.
 

docs/source/refs.bib

@@ -35,4 +35,26 @@ @article{ZALESAK1979335
 url = "http://www.sciencedirect.com/science/article/pii/0021999179900512",
 author = "Steven T Zalesak",
 abstract = "The theory of flux-corrected transport (FCT) developed by Boris and Book [J. Comput. Phys. 11 (1973) 38; 18 (1975) 248; 20 (1976) 397] is placed in a simple, generalized format, and a new algorithm for implementing the critical flux limiting stage' in multidimensions without resort to time splitting is presented. The new flux limiting algorithm allows the use of FCT techniques in multidimensional fluid problems for which time splitting would produce unacceptable numerical results, such as those involving incompressible or nearly incompressible flow fields. The “clipping” problem associated with the original one dimensional flux limiter is also eliminated or alleviated. Test results and applications to a two dimensional fluid plasma problem are presented."
-}
+}
+
+
+@article{stoker:1958,
+  author = {Stoker,J. J.  and Lindsay,R. Bruce },
+  title = {Water Waves},
+  journal = {Physics Today},
+  volume = {11},
+  number = {8},
+  pages = {28-30},
+  year = {1958},
+  URL = {https://doi.org/10.1063/1.3062689}
+}
+
+@article{chao:1999,
+  author = {Chao Wu  and Guofu Huang  and Yonghong Zheng },
+  title = {Theoretical Solution of Dam-Break Shock Wave},
+  journal = {Journal of Hydraulic Engineering},
+  volume = {125},
+  number = {11},
+  pages = {1210-1215},
+  year = {1999}
+}

docs/source/swe_basics.rst

@@ -42,12 +42,11 @@ y-directions. It can be run as:
    pyro_sim.py swe dam inputs.dam.x
    pyro_sim.py swe dam inputs.dam.y
 
-A simple script, ``dam_compare.py`` in ``analysis/`` will read a pyro output
-file and plot the solution over the exact dam break solution (as given by
-`Stoker (1958) <https://doi.org/10.1063/1.3062689>`_ and
-`Wu, Huang & Zheng (1999) <https://doi.org/10.1061/(ASCE)0733-9429(1999)125:11(1210)>`_). Below we see
-the result for a dam break run with 128 points in the x-direction, and run
-until t = 0.3 s.
+A simple script, ``dam_compare.py`` in ``analysis/`` will read a pyro
+output file and plot the solution over the exact dam break solution
+(as given by :cite:`stoker:1958` and :cite:`chao:1999`.  Below we see
+the result for a dam break run with 128 points in the x-direction, and
+run until t = 0.3 s.
 
 .. image:: dam_compare.png
    :align: center