feat: add casing as possible setting within the c++ code

CONTRIBUTING.md

@@ -106,7 +106,7 @@ The checks we perform are the following:
 
 ### VS Code
 
-Our IDE of choice is [VS Code][vscode].  Download and install it, and then
+Our IDE of choice is [Visual Studio Code][vscode] (VS Code).  Download and install it, and then
 follow the instructions below to get it set up.
 
 [vscode]: https://code.visualstudio.com/

README.md

@@ -2,13 +2,11 @@
 [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/9399/badge)](https://www.bestpractices.dev/projects/9399)
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/sandialabs/sansmic/badge)](https://scorecard.dev/viewer/?uri=github.com/sandialabs/sansmic)
 
-![Lines of code](https://sloc.xyz/github/sandialabs/sansmic/?category=code)
 [![Test Matrix](https://github.com/sandialabs/sansmic/actions/workflows/test-matrix.yml/badge.svg?branch=main)](https://github.com/sandialabs/sansmic/actions/workflows/test-matrix.yml)
 [![codecov](https://codecov.io/github/sandialabs/sansmic/graph/badge.svg?token=oDeMIUHoqg)](https://codecov.io/github/sandialabs/sansmic)
 [![Deploy Sphinx documentation](https://github.com/sandialabs/sansmic/actions/workflows/gh-pages.yml/badge.svg?branch=main)](https://github.com/sandialabs/sansmic/actions/workflows/gh-pages.yml)
 
 [![pypi](https://img.shields.io/pypi/v/sansmic.svg?maxAge=3600)](https://pypi.org/project/sansmic/)
-[![Downloads](https://static.pepy.tech/badge/sansmic)](https://pepy.tech/project/sansmic)
 
 ## SANSMIC
 
@@ -34,7 +32,7 @@ The sansmic package requires Python 3.9 or greater and at least the
 numpy and pandas packages.
 
 Installation can be accomplished most easily by using the PyPI.
-It can also be installed by downloading a wheel from the 
+It can also be installed by downloading a wheel from the
 [releases](https://github.com/sandialabs/sansmic/releases)
 in this repository, or by cloning this repository and building it
 yourself. Finally, a standalone executable has been created that
@@ -44,12 +42,18 @@ on the right side of the page).
 
 
 #### PyPI wheels
+![PyPI - Wheel](https://img.shields.io/pypi/wheel/sansmic?logo=pypi&logoColor=white)
+
 To install a pre-compiled version of sansmic, use the pip command
 
     python -m pip install sansmic
 
 
 #### Build from source
+![Git](https://img.shields.io/badge/Git-F05032?logo=git&logoColor=fff)
+![C++](https://img.shields.io/badge/C++-%2300599C.svg?logo=c%2B%2B&logoColor=fff)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/sansmic?logo=python&logoColor=fff&label=cpython)
+
 To download and build from source, you should clone the repository
 (or, fork sansmic and clone your repository) and then install using
 the editable (``-e``) flag.
@@ -85,7 +89,9 @@ If you would like to contribute, please read the
 [guide to contributing](CONTRIBUTING.md).
 
 ### License & Copyright
-See [LICENSE](LICENSE) and [COPYRIGHT](COPYRIGHT.md).
+![License - BSD-3-Clause](https://img.shields.io/pypi/l/sansmic?label=LICENSE)
+
+See the [LICENSE](LICENSE) and [COPYRIGHT](COPYRIGHT.md) files with the code.
 
 [Sandia National Laboratories](https://www.sandia.gov)
 is a multimission laboratory managed

docs/conf.py

@@ -241,7 +241,10 @@
     "use_edit_page_button": False,
     "primary_sidebar_end": ["indices.html"],
     "show_toc_level": 2,
-    # "secondary_sidebar_items": ["page-toc"], #["page-toc", "edit-this-page", "sourcelink"],
+    "secondary_sidebar_items": {
+        "**": ["page-toc", "sourcelink"],
+        "examples/**": [],
+    },
     "navbar_start": [
         "navbar-logo",
     ],
@@ -250,3 +253,6 @@
         "navbar-icon-links",
     ],
 }
+nbsphinx_thumbnails = {
+    "basic-example/basic": "/_static/basic-thumbnail.png",
+}

docs/um/outputs.rst

@@ -0,0 +1,157 @@
+Outputs
+=======
+
+
+
+
+Files created
+-------------------
+
+
+
+
+
+
+File formats
+------------
+
+
+HDF5-formatted files
+~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Notation and naming
+
+``\-- item``
+    an item is either a group (folder) or a data object (array)
+``@-- attribute``
+    an attribute is metadata associated with an item
+``\-- data: <type>[dim1][dim2]``
+    data is a an N-D array of type ``<type>`` (usually string, float, or integer)
+    with ``dim1`` rows and, optionally, ``dim2`` columns.
+``(identifier)``
+    an identifier surrounded by ``( )`` indicates that a group or data is optional
+``<identifier>``
+    an identifier surrounded by ``< >`` indicates that the group is indexed, e.g., 1, 2, ...
+
+
+.. rubric:: General organization
+
+
+.. rubric:: Spatially referenced data
+
+
+.. rubric:: Time dependent data
+
+
+
+.. rubric:: File layout
+
+
+.. plantuml::
+
+    root level
+    \-- sansmic
+    \-- cavern
+    \-- scenario
+        \-- <id>
+            \-- config
+            \-- simulation
+
+.. verbatim::
+
+    sansmic
+     @-- version: Integer[2]
+     \-- author
+     |   @-- name: String[]
+     |   @-- (email: String[])
+     \-- creator
+         @-- name: String[]
+         @-- version: String[]
+
+    cavern
+     @-- name: String[]
+     @-- wells: String[variable]
+     \-- (depthzero)
+     |    @-- crs: String[]
+     |    \-- elev: Float[]
+     \-- (centerline)
+     |    @-- crs: String[]
+     |    @-- axis: String[2]
+     |    \-- coords: Float[2]
+     \-- geometry: Float[variable][by-format]
+     |    @-- format: String[]
+     |    @-- num-cells: Integer[]
+     |    @-- depth-range: Float[2]
+
+    config
+     @-- title: String[]
+     @-- comments: String[]
+     @-- units: String[]
+     \-- casings
+     |    \-- <id:Integer>: Float[2]
+     \-- solver
+     |    @-- timestep: Float[]
+     |    @-- save-frequency: Integer[]
+     |    @-- absolue-error: Float[]
+     |    @-- relative-error: Float[]
+     |    ...
+     \-- stages
+         \-- <id:Integer>
+             @-- title: String[]
+
+    simulation
+     \-- node_depth:       Float[nn]
+     \-- node_height:      Float[nn]
+     \-- node_radius0:     Float[nn]
+     \-- time_hours:       Float[ns]
+     \-- time_days:        Float[ns]
+     \-- state
+     |    \-- step_id:         Integer[ns]
+     |    \-- stage_id:        Integer[ns]
+     |    \-- run_mode:        Integer[ns]
+     |    \-- inj_phase:       Integer[ns]
+     |    \-- inj_cell:        Integer[ns]
+     |    \-- prod_cell:       Integer[ns]
+     |    \-- plume_cell:      Integer[ns]
+     |    \-- obi_cell:        Integer[ns]
+     |    \-- convergence:     Float[ns]
+     |    \-- stepsize:        Float[ns]
+     \-- instantaneous
+     |    \-- inj_depth:       Float[ns]
+     |    \-- prod_depth:      Float[ns]
+     |    \-- plume_depth:     Float[ns]
+     |    \-- obi_depth:       Float[ns]
+     |    \-- flow_out:        Float[ns]
+     |    \-- flow_in:         Float[ns]
+     |    \-- jet_length:      Float[ns]
+     |    \-- jet_velocity:    Float[ns]
+     |    \-- jet_radius:      Float[ns]
+     |    \-- inj_sg:          Float[ns]
+     |    \-- prod_sg:         Float[ns]
+     |    \-- cavern_sg:       Float[ns]
+     |    \-- cavern_volume:   Float[ns]
+     \-- cumulative
+     |    \-- insol_top_depth: Float[ns]
+     |    \-- insol_height:    Float[ns]
+     |    \-- inj_volume:      Float[ns]
+     |    \-- prod_volume:     Float[ns]
+     |    \-- fill_volume:     Float[ns]
+     |    \-- insol_volume:    Float[ns]
+     |    \-- vented_volume:   Float[ns]
+     \-- nodes
+          \-- radius:          Float[ns][nn]
+          \-- dr0:             Float[ns][nn]
+          \-- dr_dt:           Float[ns][nn]
+          \-- theta:           Float[ns][nn]
+          \-- xincl:           Float[ns][nn]
+          \-- volume:          Float[ns][nn]
+          \-- density:         Float[ns][nn]
+          \-- dC_dt:           Float[ns][nn]
+          \-- dC_dz:           Float[ns][nn]
+          \-- dis_flag:        Integer[ns][nn]
+          \-- dis_factor:      Float[ns][nn]
+          \-- diff_coeff:      Float[ns][nn]
+          \-- plume_radius:    Float[ns][nn]
+          \-- plume_velocity:  Float[ns][nn]
+          \-- plume_density:   Float[ns][nn]
+          \-- inflow:          Float[ns][nn]

docs/um/scenarios.rst

@@ -457,7 +457,7 @@ number of stages. A stage **requires** a title key.
         way as an hour is for 'hourly'. *This is the recommended option
         for most simulations.*
 
-    "bystage"
+    "stage"
         Only save results at the end of each injection and each rest
         period. This is the most efficient method in terms of storage
         and processing time, but provides little data for debugging or

docs/userman.rst

@@ -3,7 +3,6 @@ User Guide
 
 .. toctree::
     :maxdepth: 1
-    :hidden:
 
     um/intro
     um/getting-started