Updating directory names for GNU Octave

.gitattributes

@@ -1,8 +1,8 @@
 # Auto detect text files and perform LF normalization
 * text=auto
-examples_matlab_octave/* linguist-documentation
-doc_matlab_octave/* linguist-documentation
-doc_C++/* linguist-documentation
+examples/octave/* linguist-documentation
+doc/sphinx/octave/* linguist-documentation
+doc/doxygen/cpp/* linguist-documentation
 *.html linguist-detectable=false
 *.htm linguist-detectable=false
 *.css linguist-detectable=false

.github/PULL_REQUEST_TEMPLATE.md

@@ -6,7 +6,7 @@
      - ✅ Provide tests for your changes.
      - 📝 Use descriptive commit messages.
      - 📗 Update any related documentation and include any relevant screenshots.
-     - 📝 Add license information in the appropriate place. See MATLAB or C++ code for reference.
+     - 📝 Add license information in the appropriate place. See GNU Octave or C++ code for reference.
 
           SPDX-License-Identifier: GPL-3.0-or-later
           © 2008-2024 San Diego State University Research Foundation (SDSURF).

.github/workflows/matlab-tests.yml

@@ -33,8 +33,8 @@ jobs:
         with:
           test-results-junit: test-results/results.xml
           code-coverage-cobertura: code-coverage/coverage.xml
-          source-folder: src/matlab_octave
-          select-by-folder: tests/matlab_octave
+          source-folder: src/octave
+          select-by-folder: tests/octave
           strict: false
           use-parallel: false
           generate-summary: true

.zenodo.json

@@ -157,7 +157,7 @@
             "name": "GNU General Public License v3.0", 
             "key": "gpl-3.0"
         }, 
-        "language": "MATLAB/Octave", 
+        "language": "Octave (MATLAB)", 
         "url": "https://api.github.com/repos/jcorbino/mole", 
         "subscribers_url": "https://api.github.com/repos/jcorbino/mole/subscribers", 
         "created_at": "2017-08-12T19:03:04Z", 

CMakeLists.txt

@@ -149,10 +149,10 @@ set(LINK_LIBS ${ARMADILLO_LIBRARIES}
 # Add subdirectories
 add_subdirectory(src/cpp)
 add_subdirectory(tests/cpp)
-add_subdirectory(tests/matlab_octave)
+add_subdirectory(tests/octave)
 add_subdirectory(examples/cpp)
 
 # Custom target to build everything
-add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_matlab_octave)
+add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_octave)
 
 

CONTRIBUTING.md

@@ -59,7 +59,7 @@ The MOLE library follows a consistent structure across Octave and C++ implementa
 
 #### Octave Core Functions
 
-Core functions are located in `src/matlab_octave/` and follow this pattern:
+Core functions are located in `src/octave/` and follow this pattern:
 
 ```matlab
 function OUTPUT = functionName(k, m, dx, ...)
@@ -157,7 +157,7 @@ When contributing core functionality, identify which category your contribution
 
 If adding a new operator, follow this checklist:
 
-1. **Octave Implementation** (`src/matlab_octave/newoperator.m`):
+1. **Octave Implementation** (`src/octave/newoperator.m`):
    ```matlab
    function OP = newoperator(k, m, dx)
    % Returns a new mimetic operator
@@ -195,7 +195,7 @@ Examples are organized by PDE type in the `examples/` directory:
 
 ```
 examples/
-├── matlab_octave/         # Octave examples
+├── octave/         # Octave examples
 │   ├── elliptic1D.m       # Basic examples
 │   ├── parabolic2D.m      # 2D examples
 │   └── compact_operators/ # Specialized examples
@@ -223,7 +223,7 @@ Organize your examples by PDE type:
 clc
 close all
 
-addpath('../../src/matlab_octave')  % REQUIRED: Add path to MOLE library
+addpath('../../src/octave')  % REQUIRED: Add path to MOLE library
 
 %% Problem Parameters
 % [Describe each parameter with physical meaning]
@@ -404,7 +404,7 @@ $$
 ---
 
 This example is implemented in:
-- [Octave](https://github.com/csrc-sdsu/mole/blob/main/examples/matlab_octave/example_name.m)
+- [Octave](https://github.com/csrc-sdsu/mole/blob/main/examples/octave/example_name.m)
 - [C++](https://github.com/csrc-sdsu/mole/blob/main/examples/cpp/example_name.cpp) *(if available)*
 
 #### Variants

README.md

@@ -126,7 +126,7 @@ make run_tests
 Octave equivalent of the C++ test suite. We recommend running these tests before using MOLE to ensure proper setup.
 
 ```matlab
-make run_matlab_octave_tests
+make run_octave_tests
 ```
 
 ## Examples

doc/sphinx/Makefile

@@ -44,6 +44,7 @@ help:
 # Doxygen documentation
 doc-doxygen:
 	@echo "Generating Doxygen documentation..."
+	@mkdir -p $(DOXYDIR)
 	@cd ../.. && doxygen Doxyfile
 	@if [ ! -d "$(DOXYXML)" ]; then \
 		echo "Error: Doxygen XML output directory not found at $(DOXYXML)"; \

doc/sphinx/octave/README.md

@@ -0,0 +1 @@
+This folder contains **generated** documentation of *MOLE's* Octave version via a tool called [M2HTML](https://www.gllmflndn.com/software/matlab/m2html). Please note that we do not regularly update this documentation.

doc/doxygen/matlab_octave/index.html → doc/sphinx/octave/index.html

@@ -5,19 +5,19 @@
   <link rel="shortcut icon" href="../logo.png" type="image/x-icon">
   <title>MOLE's Documentation</title>
   <meta name="keywords" content="matlab, octave, m2html, documentation">
-  <meta name="description" content="MATLAB/Octave Documentation by M2HTML">
+  <meta name="description" content="Octave Documentation by M2HTML (MATLAB)">
   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
   <meta name="generator" content="m2html &copy; 2005 Guillaume Flandin">
   <meta name="robots" content="index, follow">
   <link type="text/css" rel="stylesheet" href="m2html.css">
 </head>
 <frameset cols="20%, 80%">
-  <frame scrolling="yes" name="menu" src="mole_MATLAB/menu.html"></frame>
+  <frame scrolling="yes" name="menu" src="mole_Octave/menu.html"></frame>
   <frame scrolling="yes" name="function" src="about:blank"></frame>
 </frameset>
 <noframe>
-This is a MATLAB/Octave Documentation by M2HTML.<br>
+This is a Octave Documentation by M2HTML (Compatible with MATLAB).<br>
 Go to <a href="menu.html">menu.html</a> for the documentation of all
-the MATLAB/Octave functions.
+the Octave functions.
 </noframe>
 </html>

doc/doxygen/matlab_octave/menu.html → doc/sphinx/octave/menu.html

@@ -2,21 +2,21 @@
                 "http://www.w3.org/TR/REC-html40/loose.dtd">
 <html>
 <head>
-  <title>MATLAB/Octave Index</title>
-  <meta name="keywords" content="mole_MATLAB">
-  <meta name="description" content="mole_MATLAB">
+  <title>Octave Index (compatible with MATLAB)</title>
+  <meta name="keywords" content="mole_Octave">
+  <meta name="description" content="mole_Octave">
   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
   <meta name="generator" content="m2html &copy; 2005 Guillaume Flandin">
   <meta name="robots" content="index, follow">
   <link type="text/css" rel="stylesheet" href="./m2html.css">
 </head>
 <body>
 <a name="_top"></a>
-<h1>MATLAB/Octave Index</h1>
-<h2>MATLAB/Octave Directories</h2>
+<h1>Octave Index</h1>
+<h2>Octave Directories</h2>
 <ul style="list-style-image:url(./matlabicon.gif)">
-<li><a href="mole_MATLAB/menu.html" target="menu">mole_MATLAB</a></li></ul>
-<!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- -->
+<li><a href="mole_Octave/menu.html" target="menu">mole_Octave</a></li></ul>
+<!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --><!-- --"><!-- --"><!-- --"><!-- --"><!-- --"><!-- --"><!-- --"><!-- --><!-- --><!-- --"><!-- --"><!-- -->
 
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" target="_parent">m2html</a></strong> &copy; 2005</address>
 </body>

doc/doxygen/matlab_octave/mole_MATLAB/DI2.html → doc/sphinx/octave/mole_Octave/DI2.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>DI2
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/DI3.html → doc/sphinx/octave/mole_Octave/DI3.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>DI3
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/GI1.html → doc/sphinx/octave/mole_Octave/GI1.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>GI1
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/GI13.html → doc/sphinx/octave/mole_Octave/GI13.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>GI13
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/GI2.html → doc/sphinx/octave/mole_Octave/GI2.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>GI2
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/curl2D.html → doc/sphinx/octave/mole_Octave/curl2D.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>curl2D
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div.html → doc/sphinx/octave/mole_Octave/div.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div2D.html → doc/sphinx/octave/mole_Octave/div2D.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div2D
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div2DCurv.html → doc/sphinx/octave/mole_Octave/div2DCurv.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div2DCurv
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div2DNonUniform.html → doc/sphinx/octave/mole_Octave/div2DNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div2DNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div3D.html → doc/sphinx/octave/mole_Octave/div3D.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div3D
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div3DCurv.html → doc/sphinx/octave/mole_Octave/div3DCurv.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div3DCurv
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/div3DNonUniform.html → doc/sphinx/octave/mole_Octave/div3DNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>div3DNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/divNonUniform.html → doc/sphinx/octave/mole_Octave/divNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>divNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad.html → doc/sphinx/octave/mole_Octave/grad.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad2D.html → doc/sphinx/octave/mole_Octave/grad2D.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad2D
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad2DCurv.html → doc/sphinx/octave/mole_Octave/grad2DCurv.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad2DCurv
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad2DNonUniform.html → doc/sphinx/octave/mole_Octave/grad2DNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad2DNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad3D.html → doc/sphinx/octave/mole_Octave/grad3D.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad3D
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad3DCurv.html → doc/sphinx/octave/mole_Octave/grad3DCurv.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad3DCurv
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/grad3DNonUniform.html → doc/sphinx/octave/mole_Octave/grad3DNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>grad3DNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/gradNonUniform.html → doc/sphinx/octave/mole_Octave/gradNonUniform.html

@@ -15,7 +15,7 @@
 </head>
 <body>
 <a name="_top"></a>
-<!-- menu.html mole_MATLAB -->
+<!-- menu.html mole_Octave -->
 <h1>gradNonUniform
 </h1>
 

doc/doxygen/matlab_octave/mole_MATLAB/graph.html → doc/sphinx/octave/mole_Octave/graph.html

@@ -2,20 +2,20 @@
                 "http://www.w3.org/TR/REC-html40/loose.dtd">
 <html>
 <head>
-  <title>Dependency Graph for mole_MATLAB</title>
-  <meta name="keywords" content="dependency, graph, dependence, mole_MATLAB">
-  <meta name="description" content="Dependency graph for mole_MATLAB">
+  <title>Dependency Graph for mole_Octave</title>
+  <meta name="keywords" content="dependency, graph, dependence, mole_Octave">
+  <meta name="description" content="Dependency graph for mole_Octave">
   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
   <meta name="generator" content="m2html &copy; 2005 Guillaume Flandin">
   <meta name="robots" content="index, follow">
   <link type="text/css" rel="stylesheet" href="../m2html.css">
 </head>
 <body>
 <a name="_top"></a>
-<h1>Dependency Graph for mole_MATLAB</h1>
+<h1>Dependency Graph for mole_Octave</h1>
 
 <center>
-<img src="graph.png" usemap="#mainmap" alt="Dependency Graph for mole_MATLAB" border="2" style="color:#000;">  
+<img src="graph.png" usemap="#mainmap" alt="Dependency Graph for mole_Octave" border="2" style="color:#000;">  
 <map name="mainmap">
 <area shape="poly" id="node1" href="curl2D.html" title="curl2D" alt="" coords="731,29,728,22,720,15,707,10,692,7,674,5,657,7,641,10,629,15,621,22,618,29,621,37,629,43,641,49,657,52,674,53,692,52,707,49,720,43,728,37">
 <area shape="poly" id="node2" href="div2D.html" title="div2D" alt="" coords="779,125,776,118,769,111,758,106,743,103,728,101,712,103,697,106,686,111,679,118,676,125,679,133,686,139,697,145,712,148,728,149,743,148,758,145,769,139,776,133">