Small edits across docs and tutorials

docs/src/CheatSheet.md

@@ -5,7 +5,7 @@ of the interactive construction of boundary curves, background grid, etc.
 When possible, the commands presented below give
 generic versions of the function calls, e.g., for creating a new curve or
 adding the curve to a boundary chain. The script
-`interactive_outer_boundary_generic.jl` in the `examples` folder
+`interactive_outer_boundary_generic.jl` in the `examples/` folder
 constructs an identical example mesh as shown in the [Guided tour](@ref)
 using generic function calls.
 
@@ -36,11 +36,11 @@ The `options` are any sum of `MODEL`, `GRID`, `REFINEMENTS`, and `MESH`.
 ## Curves
 
 ```
-   c = new(name, startLocation [x,y,z],endLocation [x,y,z])  *Straight Line*
-   c = new(name,center [x,y,z],radius, startAngle, endAngle) *Circular Arc*
-   c = new(name, xEqn, yEqn, zEqn)                           *Parametric equation*
-   c = new(name, dataFile)                                   *Spline with data from a file*
-   c = new(name, nKnots, knotsMatrix)                        *Spline with given knot values*
+   c = new(name, startLocation [x,y,z], endLocation [x,y,z])   *Straight Line*
+   c = new(name, center [x,y,z], radius, startAngle, endAngle) *Circular Arc*
+   c = new(name, xEqn, yEqn, zEqn)                             *Parametric equation*
+   c = new(name, dataFile)                                     *Spline with data from a file*
+   c = new(name, nKnots, knotsMatrix)                          *Spline with given knot values*
 ```
 
 Shown here is the use of the function `new`, which is a shortcut to the full functions, e.g. `newCircularArcCurve`, etc. which have the same arguments.
@@ -55,9 +55,9 @@ Shown here is the use of the function `new`, which is a shortcut to the full fun
 ## Adding to a Project
 
 ```
-   add!(p, c)                        *Add outer boundary curve*
-   add!(p, c, <InnerBoundaryName>)   *Add curve to an inner boundary*
-   add!(p, r)                        *Add refinement region*
+   add!(p, c)                      *Add outer boundary curve*
+   add!(p, c, <InnerBoundaryName>) *Add curve to an inner boundary*
+   add!(p, r)                      *Add refinement region*
 
    addBackgroundGrid!(p, [top, left, bottom, right], [nX, nY, nZ]) *No outer boundary*
    addBackgroundGrid!(p, [dx, dy, dz])                             *If an outer boundary is present*
@@ -76,7 +76,7 @@ Shown here is the use of the function `add!`, which is a shortcut to the full fu
 ## Removing from Project
 
 ```
-   removeOuterboundary!(p)                    *Entire outer boundary curve*
+   removeOuterBoundary!(p)                    *Entire outer boundary curve*
    removeInnerBoundary!(p, innerBoundaryName) *Entire inner boundary curve*
    remove!(p, name)                           *Curve in outer boundary*
    remove!(p, name, innerBoundaryName)        *Curve in inner boundary*

docs/src/development.md

@@ -32,7 +32,8 @@ are available for almost any operating system. They also are preinstalled on
 virtually all Unix-like systems.  However, Vim and Emacs come with their own,
 steep learning curve if they have never been used before. Therefore, if in doubt, it
 is probably easier to get started with a classic GUI-based text editor (like
-Juno). If you decide to use Vim or Emacs, make sure that you install the
+VS Code with the [Julia extension](https://code.visualstudio.com/docs/languages/julia)).
+If you decide to use Vim or Emacs, make sure that you install the
 corresponding Vim plugin
 [julia-vim](https://github.com/JuliaEditorSupport/julia-vim) or Emacs major
 mode [julia-emacs](https://github.com/JuliaEditorSupport/julia-emacs).

docs/src/github-git.md

@@ -193,7 +193,7 @@ the following steps need to be taken (as documented for GitLab in issue
      java -jar bfg-1.13.0.jar --strip-blobs-bigger-than 10M HOHQMesh.jl.git
 
      # Enter repo
-     cd Trixi.jl.git
+     cd HOHQMesh.jl.git
 
      # Clean up reflog and force aggressive garbage collection
      git reflog expire --expire=now --all && git gc --prune=now --aggressive

docs/src/guided-tour.md

@@ -1,6 +1,6 @@
 # Guided tour
 
-In this brief overview, we highlight two scripts from the `examples` folder
+In this brief overview, we highlight two scripts from the `examples/` folder
 that demonstrate the interactive mesh functionality of HOHQMesh.jl. In depth
 explanations of the functionality are provided in the [Tutorials](@ref).
 
@@ -82,7 +82,7 @@ if isdefined(Main, :Makie)
     @info "To visualize the project (boundary curves, background grid, mesh, etc.), include `GLMakie` and run again."
  end
 
-# Generate the mesh. This produces the mesh and TecPlot files `AllFeatures.mesh` and `AllFeatures.tec`
+# Generate the mesh. This produces the mesh and TecPlot files `IceCreamCone.mesh` and `IceCreamCone.tec`
 # and save them to the `out` folder. Also, if there is an active plot in the project `p` it is
 # updated with the mesh that was generated.
 
@@ -112,16 +112,16 @@ circular arc. Again, they are defined counter-clockwise.
 
 For convenience, `newProject` will generate default run parameters used by HOHQMesh, like the plot file format
 and the smoother. The parameters can be edited with setter commands. For example, the script
-sets the polynomial order (default = 5) and the plot file format (default = "skeleton").
+resets the polynomial order (default = 5) and the plot file format (default = "skeleton").
 
 One run parameter that must be set manually is the background grid. Since there is an outer
-boundary, that determines the extent of the domain to be meshed, so only the mesh size needs
+boundary, that determines the extent of the domain to be meshed, only the mesh size needs
 to be specified using
 ```
 addBackgroundGrid!(proj::Project, bgSize::Array{Float64})
 ```
 
-The example sets the background mesh size to be 0.1 in the x and y directions.
+The example sets the background mesh size to be 0.5 in the x and y directions.
 The z component is ignored.
 
 The script finishes by generating the quad mesh and plotting the results, as shown below
@@ -132,9 +132,10 @@ Finally, the script returns the project so that it can be edited further, if des
 
 To save a control file for HOHQMesh, simply invoke
 ```
-saveProject(proj::Project, outFile::String)
+saveProject(proj::Project)
 ```
-where `outFile` is the name of the control file (traditionally with a .control extension).
+where the name of the control file (traditionally with a `.control` extension) matches the
+name of the project `proj`.
 `saveProject` is automatically called when a mesh is generated.
 
 Note, a third example script `interactive_outer_boundary_generic.jl` is identical to that

docs/src/index.md

@@ -5,11 +5,21 @@ This package is a Julia frontend to the Fortran-based *High Order Hex-Quad Meshe
 [David A. Kopriva](https://www.math.fsu.edu/~kopriva/). It augments HOHQMesh with
 [interactive functionality](@ref InteractiveTool) that gives a user the ability to create, visualize,
 and generate high-order meshes.
-It further allows one to seamlessly integrate meshes generated by HOHQMesh into a Julia-based simulation workflow.
-For example, running a simulation on an unstructured quadrilateral mesh
-with [Trixi.jl](https://trixi-framework.github.io/Trixi.jl/stable/tutorials/hohqmesh_tutorial/).
 HOHQMesh.jl is available on Linux, MacOS, and Windows.
 
+Further, one can seamlessly integrate meshes generated by HOHQMesh into a Julia-based simulation workflow.
+The presentation [From Mesh Generation to Adaptive Simulation: A Journey in Julia](https://youtu.be/_N4ozHr-t9E),
+originally given as part of JuliaCon 2022, outlines how to use HOHQMesh.jl together
+with [Trixi.jl](https://github.com/trixi-framework/Trixi.jl) for an adaptive simulation
+in two spatial dimensions on a complex domain.
+More details as well as code to run the simulation presented can be found at the
+[reproducibility repository](https://github.com/trixi-framework/talk-2022-juliacon_toolchain)
+for the presentation.
+An additional resource is a
+[tutorial](https://trixi-framework.github.io/Trixi.jl/stable/tutorials/hohqmesh_tutorial/)
+available in the Trixi.jl documentation that describes how to run a simulation
+on an unstructured quadrilateral mesh.
+
 ## Installation
 If you have not yet installed Julia, please [follow the instructions for your
 operating system](https://julialang.org/downloads/platform/). HOHQMesh.jl works

docs/src/interactive-api.md

@@ -6,19 +6,20 @@
 ```
    [Return:Project] proj = newProject(name::String, folder::String)
 ```
-The supplied name will be the default name of the mesh and plot files generated by HOHQMesh. The folder is
+The supplied name will be the default name of the control, mesh, and plot files
+generated by HOHQMesh. The folder is
 the directory in which those files will be placed. The empty project will include default `RunParameters`
-and a default `SpringSmoother`, both of which can be modified later, if desired. The only thing required to
-add is the background grid.
+and a default `SpringSmoother`, both of which can be modified later, if desired.
+The only thing required to add is the background grid.
 
 ### Opening an existing project file
 
 A project can be created from an existing HOHQMesh control file with
 ```
    [Return:Project] proj = openProject(fileName::String, folder::String)
 ```
-The supplied `fileName` will be the name of the project and the generated mesh and plot files will be placed
-in the supplied `folder`.
+The supplied `fileName` will be the name of the project and the generated mesh and
+plot files will be placed in the supplied `folder`.
 
 ### Saving a `Project`
 ```
@@ -106,10 +107,12 @@ By default, the mesh, plot and stats files will be written with the name and pat
 
 ### Smoothing operations
 
-A default smoother is created when `newProject` is called, which sets the status to `ON`, type to
-`LinearAndCrossbarSpring`, and number of iterations = 25. These are generally good enough for most purposes.
-The most likely parameter to change is the number of iterations. Further details on the smoothing strategy
-and how it works are available [here](https://trixi-framework.github.io/HOHQMesh/the-control-input/#the-smoother).
+A default smoother is created when `newProject` is called, which sets the status to `ON`,
+type to `LinearAndCrossbarSpring`, and number of iterations = 25.
+These are generally good enough for most purposes.
+The most likely parameter to change is the number of iterations.
+Further details on the smoothing strategy and how it works are available
+[in the documentation](https://trixi-framework.github.io/HOHQMesh/the-control-input/#the-smoother).
 
 To change the defaults, the smoother parameters can be set/enquired with the functions
 ```
@@ -130,7 +133,7 @@ To remove the smoother altogether, use
 ### Adding the background grid
 
 There are three forms for the background grid definition, one for when there is an outer boundary,
-and two for when there is not. One form of background grid **must** to be specified
+and two for when there is not. One form of background grid **must** be specified
 after a new project has been created.
 ```
    [Return:nothing] addBackgroundGrid!(proj::Project,
@@ -165,7 +168,7 @@ If a plot is present it will be updated automatically.
 Refinement can be specified either at a point, using the `RefinementCenter`, or along a line,
 using a `RefinementLine`. You can have as many of these refinement regions as you want.
 They are useful if you know regions of the solution where refinement is needed
-(e.g. a wake) or in problematic areas of the geometry (e.g a sharp corner).
+(e.g. a wake) or in problematic areas of the geometry (e.g. a sharp corner).
 
 To create a `RefinementCenter`,
 ```
@@ -202,7 +205,7 @@ To get a reference to a refinement region with a given name, use
 
 Finally, to get a list of all the refinement regions,
 ```
-    [Return:Array{Dict{String,Any}}] array = allRefinementRegions(proj::Project)
+   [Return:Array{Dict{String,Any}}] array = allRefinementRegions(proj::Project)
 ```
 
 A refinement region can be edited by using the following:

docs/src/interactive_overview.md

@@ -5,7 +5,7 @@ mesh using Julia.
 It serves as a front end to the HOHQMesh program, and is designed to let one build a
 meshing project interactively while graphically displaying the results.
 
-Several scripts are available in the `examples` folder
+Several scripts are available in the `examples/` folder
 to get you started. These example scripts follow the naming convention of `interactive_*` where
 the phrase interactive indicates their association with this API and then trailing information
 will indicate what that script demonstrates. For instance, the file `interactive_spline_curves.jl`

docs/src/testing.md

@@ -9,7 +9,7 @@ functionality or add other errors. In the main
 which allows to run tests automatically upon certain events. When, how, and what
 is tested by GitHub Actions is controlled by the workflow file
 [`.github/workflows/ci.yml`](https://github.com/trixi-framework/HOHQMesh.jl/blob/main/.github/workflows/ci.yml).
-In Trixi and its related repositories, tests are triggered by
+In HOHQMesh and its related repositories, tests are triggered by
 * each `git push` to `main` and
 * each `git push` to any pull request.
 Besides checking functionality, we also analyze the [Test coverage](@ref) to

docs/src/tutorials/create_edit_curves.md

@@ -243,21 +243,21 @@ generate_mesh(sandbox_project)
  *******************
  2D Mesh Statistics:
  *******************
-    Total time             =    8.7928000000000006E-002
-    Number of nodes        =          513
+    Total time             =    7.5414000000000009E-002
+    Number of nodes        =          511
     Number of Edges        =          933
     Number of Elements     =          422
     Number of Subdivisions =            7
 
  Mesh Quality:
          Measure         Minimum         Maximum         Average  Acceptable Low Acceptable High       Reference
-     Signed Area      0.00003020      1.17336756      0.18813064      0.00000000    999.99900000      1.00000000
-    Aspect Ratio      1.00984888      2.32321419      1.31488869      1.00000000    999.99900000      1.00000000
-       Condition      1.00041121      2.42894151      1.21101797      1.00000000      4.00000000      1.00000000
-      Edge Ratio      1.01674110      3.74861238      1.59495734      1.00000000      4.00000000      1.00000000
-        Jacobian      0.00001734      1.13821390      0.14136293      0.00000000    999.99900000      1.00000000
-   Minimum Angle     32.20087774     89.35157729     68.75755243     40.00000000     90.00000000     90.00000000
-   Maximum Angle     90.60787193    152.53515465    113.36966060     90.00000000    135.00000000     90.00000000
+     Signed Area      0.00002932      1.17335568      0.18813138      0.00000000    999.99900000      1.00000000
+    Aspect Ratio      1.00953438      2.30790024      1.31439620      1.00000000    999.99900000      1.00000000
+       Condition      1.00041663      2.41773865      1.21024584      1.00000000      4.00000000      1.00000000
+      Edge Ratio      1.01673809      3.68828437      1.59413340      1.00000000      4.00000000      1.00000000
+        Jacobian      0.00001750      1.13820387      0.14143901      0.00000000    999.99900000      1.00000000
+   Minimum Angle     32.22733574     89.35690571     68.75321248     40.00000000     90.00000000     90.00000000
+   Maximum Angle     90.61089476    152.37947944    113.36221513     90.00000000    135.00000000     90.00000000
        Area Sign      1.00000000      1.00000000      1.00000000      1.00000000      1.00000000      1.00000000
 ```
 The call to `generate_mesh` also prints mesh quality statistics to the screen
@@ -413,21 +413,21 @@ generate_mesh(sandbox_project)
  *******************
  2D Mesh Statistics:
  *******************
-    Total time             =   0.13299600000000000
-    Number of nodes        =          714
+    Total time             =   0.11353599999999998
+    Number of nodes        =          712
     Number of Edges        =         1308
     Number of Elements     =          596
     Number of Subdivisions =            7
 
  Mesh Quality:
          Measure         Minimum         Maximum         Average  Acceptable Low Acceptable High       Reference
-     Signed Area      0.00003020      1.15662678      0.12823840      0.00000000    999.99900000      1.00000000
-    Aspect Ratio      1.01082600      3.14765817      1.34292128      1.00000000    999.99900000      1.00000000
-       Condition      1.00037252      2.59936116      1.22903490      1.00000000      4.00000000      1.00000000
-      Edge Ratio      1.02724726      3.74861238      1.64807401      1.00000000      4.00000000      1.00000000
-        Jacobian      0.00001734      1.13150266      0.09438571      0.00000000    999.99900000      1.00000000
-   Minimum Angle     31.88018513     89.33451932     67.86550651     40.00000000     90.00000000     90.00000000
-   Maximum Angle     90.43850948    157.31718198    114.36070355     90.00000000    135.00000000     90.00000000
+     Signed Area      0.00002932      1.15661960      0.12823902      0.00000000    999.99900000      1.00000000
+    Aspect Ratio      1.01050856      3.14732001      1.34260027      1.00000000    999.99900000      1.00000000
+       Condition      1.00037771      2.59434067      1.22850175      1.00000000      4.00000000      1.00000000
+      Edge Ratio      1.02744717      3.68828437      1.64751502      1.00000000      4.00000000      1.00000000
+        Jacobian      0.00001750      1.13149451      0.09443920      0.00000000    999.99900000      1.00000000
+   Minimum Angle     31.87236189     89.33988565     67.86178629     40.00000000     90.00000000     90.00000000
+   Maximum Angle     90.44177106    157.27121105    114.35699650     90.00000000    135.00000000     90.00000000
        Area Sign      1.00000000      1.00000000      1.00000000      1.00000000      1.00000000      1.00000000
 ```
 The visualization updates automatically and the background grid is *removed* after when the mesh is generated.