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Docs: Add Julia API doc and graphviz to sphinx doc
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‎doc/sphinx/source/api/julia/index.md‎

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# Julia
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This section documents the Julia implementation of the MOLE toolkit, MOLE.jl.
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The API documentation is generated automatically from the docstrings in the Julia source files located in `mole/julia/MOLE.jl/src`.
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The published MOLE.jl documentation can be found on the [MOLE.jl Documentation website](https://www.mole-ose.org/MOLE.jl-docs/dev/).
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```{eval-rst}
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.. only:: html
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The following diagram shows the key modules and functions in the MOLE.jl API and their relationships:
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.. graphviz::
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digraph mole_jl_api_structure {
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bgcolor="transparent";
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rankdir=TB; // Top to Bottom layout
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compound=true;
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node [shape=box, style=filled, fontname="Arial", fontsize=10, margin="0.3,0.1"];
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edge [fontname="Arial", fontsize=9];
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// Color definitions
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node [fillcolor="#E8F4F9"]; // Light blue for base nodes
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// Core package
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subgraph cluster_base {
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label="Core Package";
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style=filled;
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color="#F5F5F5";
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MOLE [label="MOLE.jl\n(Package)"];
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}
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// Core modules
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subgraph cluster_modules {
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label="Core Modules";
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style=filled;
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color="#F5F5F5";
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node [fillcolor="#E8F4F9"];
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Operators [label="Operators"];
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BCs [label="BCs"];
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}
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// Operators
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subgraph cluster_operators {
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label="Core Operators";
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style=filled;
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color="#F5F5F5";
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node [fillcolor="#D5E8D4"]; // Light green for operators
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Interpol [label="interpol\n(Interpolation)"];
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Gradient [label="grad\n(Gradient)"];
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Divergence [label="div\n(Divergence)"];
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Laplacian [label="lap\n(Laplacian)"];
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}
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// Boundary Conditions
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subgraph cluster_bc {
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label="Boundary Conditions";
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style=filled;
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color="#F5F5F5";
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node [fillcolor="#FFE6CC"]; // Light orange for boundary conditions
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RobinBC [label="robinBC\n(Robin/Neumann/Dirichlet)"];
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ScalarBC1D [label="ScalarBC1D"];
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ScalarBC2D [label="ScalarBC2D"];
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AddScalarBC [label="addScalarBC!\n(Apply Scalar BCs)"];
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}
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// Grid Variants
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subgraph cluster_grids {
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label="Grid and Dimension Variants";
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style=filled;
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color="#F5F5F5";
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node [fillcolor="#DAE8FC"]; // Light blue for utilities
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OneD [label="1D Operators"];
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TwoD [label="2D Operators"];
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Uniform [label="Uniform Grids"];
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NonUniform [label="Non-uniform Grids"];
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}
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// Module relationships
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edge [color="#0000AA", penwidth=1.5];
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MOLE -> {Operators BCs};
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// API ownership relationships
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edge [color="#0000AA", penwidth=1.5];
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Operators -> {Interpol Gradient Divergence Laplacian};
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BCs -> {RobinBC ScalarBC1D ScalarBC2D AddScalarBC};
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// Usage relationships
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edge [style=dashed, dir=forward, color="#006600", penwidth=1.0];
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Gradient -> Laplacian;
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Divergence -> Laplacian;
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// Grid and dimension relationships
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edge [style=dotted, dir=forward, color="#990000", penwidth=1.0];
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OneD -> {Interpol Gradient Divergence Laplacian RobinBC ScalarBC1D AddScalarBC};
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TwoD -> {Gradient Divergence Laplacian RobinBC ScalarBC2D AddScalarBC};
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Uniform -> {Interpol Gradient Divergence Laplacian};
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NonUniform -> {Gradient Divergence};
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// Boundary condition relationships
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edge [style=dashed, constraint=false, color="#AA6600", penwidth=1.0];
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RobinBC -> {Gradient Divergence Laplacian};
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ScalarBC1D -> AddScalarBC;
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ScalarBC2D -> AddScalarBC;
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AddScalarBC -> {Gradient Divergence Laplacian};
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// Add a legend
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subgraph cluster_legend {
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label="Legend";
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style=filled;
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color="#F5F5F5";
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fontsize=10;
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node [shape=none, style=none, label=""];
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edge [style=none];
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leg_title [label="Relationship Types:", shape=none, fontsize=9];
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leg_module [label="Module/API Ownership", shape=none, fontsize=9];
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leg_usage [label="Operator Usage", shape=none, fontsize=9];
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leg_grid [label="Grid/Dimension Support", shape=none, fontsize=9];
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leg_boundary [label="Boundary Modification", shape=none, fontsize=9];
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leg_title -> leg_module [style=solid, color="#0000AA", penwidth=1.5];
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leg_title -> leg_usage [style=dashed, color="#006600", penwidth=1.0];
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leg_title -> leg_grid [style=dotted, color="#990000", penwidth=1.0];
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leg_title -> leg_boundary [style=dashed, color="#AA6600", penwidth=1.0];
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}
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}
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.. only:: latex
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The MOLE.jl API consists of several key components:
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Core Package:
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* **MOLE.jl**: Julia implementation of Mimetic Operators Library Enhanced.
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Core Modules:
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* **MOLE.Operators**: Provides mimetic discrete operators.
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* **MOLE.BCs**: Provides boundary-condition utilities and scalar boundary-condition support.
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Core Operators:
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* **interpol**: Interpolation operator for grid transformations.
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* **grad**: Gradient operator with support for one- and two-dimensional grids.
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* **div**: Divergence operator with support for one- and two-dimensional grids.
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* **lap**: Laplacian operator related to gradient and divergence operators.
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Boundary Conditions:
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* **robinBC**: Constructs Robin, Neumann, and Dirichlet boundary-condition contributions.
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* **ScalarBC1D**: Scalar boundary-condition data for one-dimensional problems.
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* **ScalarBC2D**: Scalar boundary-condition data for two-dimensional problems.
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* **addScalarBC!**: Applies scalar boundary conditions to operators or systems.
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Grid and Dimension Variants:
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* **1D Operators**: One-dimensional versions of interpolation, gradient, divergence, Laplacian, and boundary-condition routines.
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* **2D Operators**: Two-dimensional versions of gradient, divergence, Laplacian, and boundary-condition routines.
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* **Uniform Grids**: Operators defined using regular grid spacing.
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* **Non-uniform Grids**: Operators defined using coordinate ticks or non-uniform grid spacing.
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Key Features:
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* MOLE.jl exposes operators through Julia modules rather than C++ classes.
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* Core operators are grouped under **MOLE.Operators**.
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* Boundary-condition tools are grouped under **MOLE.BCs**.
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* Laplacian functionality is closely related to Gradient and Divergence.
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* Boundary-condition utilities can modify operator behavior or system matrices.
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* Several operators support both uniform and non-uniform grids.
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```

‎doc/sphinx/source/index.md‎

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api/cpp/index
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api/matlab_octave/index-beta
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api/julia/index
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```
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```{toctree}

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