diff --git a/.gitattributes b/.gitattributes index ea8de3ecd..2709c11b2 100644 --- a/.gitattributes +++ b/.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 diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 05ab21a5b..ad98f9cc6 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.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). diff --git a/.github/workflows/matlab-tests.yml b/.github/workflows/matlab-tests.yml index 72d2a4511..82578468f 100644 --- a/.github/workflows/matlab-tests.yml +++ b/.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 diff --git a/.zenodo.json b/.zenodo.json index cb26ba44f..99f74a6de 100644 --- a/.zenodo.json +++ b/.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", diff --git a/CMakeLists.txt b/CMakeLists.txt index 2a900e579..29380576c 100644 --- a/CMakeLists.txt +++ b/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) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 84d58b65d..7df2cde0e 100644 --- a/CONTRIBUTING.md +++ b/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 diff --git a/README.md b/README.md index 46b81d176..cfbe80b3e 100644 --- a/README.md +++ b/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 diff --git a/doc/doxygen/matlab_octave/README.md b/doc/doxygen/matlab_octave/README.md deleted file mode 100644 index 596e8f112..000000000 --- a/doc/doxygen/matlab_octave/README.md +++ /dev/null @@ -1 +0,0 @@ -This folder contains **generated** documentation of *MOLE's* MATLAB/Octave version via a tool called [M2HTML](https://www.gllmflndn.com/software/matlab/m2html). Please note that we do not regularly update this documentation. diff --git a/doc/sphinx/Makefile b/doc/sphinx/Makefile index d00af8b62..303d509df 100644 --- a/doc/sphinx/Makefile +++ b/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)"; \ diff --git a/doc/sphinx/octave/README.md b/doc/sphinx/octave/README.md new file mode 100644 index 000000000..e5b3f95f7 --- /dev/null +++ b/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. diff --git a/doc/doxygen/matlab_octave/alpha.png b/doc/sphinx/octave/alpha.png similarity index 100% rename from doc/doxygen/matlab_octave/alpha.png rename to doc/sphinx/octave/alpha.png diff --git a/doc/doxygen/matlab_octave/c++.png b/doc/sphinx/octave/c++.png similarity index 100% rename from doc/doxygen/matlab_octave/c++.png rename to doc/sphinx/octave/c++.png diff --git a/doc/doxygen/matlab_octave/c.png b/doc/sphinx/octave/c.png similarity index 100% rename from doc/doxygen/matlab_octave/c.png rename to doc/sphinx/octave/c.png diff --git a/doc/doxygen/matlab_octave/demoicon.gif b/doc/sphinx/octave/demoicon.gif similarity index 100% rename from doc/doxygen/matlab_octave/demoicon.gif rename to doc/sphinx/octave/demoicon.gif diff --git a/doc/doxygen/matlab_octave/down.png b/doc/sphinx/octave/down.png similarity index 100% rename from doc/doxygen/matlab_octave/down.png rename to doc/sphinx/octave/down.png diff --git a/doc/doxygen/matlab_octave/doxysearch.php b/doc/sphinx/octave/doxysearch.php similarity index 100% rename from doc/doxygen/matlab_octave/doxysearch.php rename to doc/sphinx/octave/doxysearch.php diff --git a/doc/doxygen/matlab_octave/fortran.png b/doc/sphinx/octave/fortran.png similarity index 100% rename from doc/doxygen/matlab_octave/fortran.png rename to doc/sphinx/octave/fortran.png diff --git a/doc/doxygen/matlab_octave/hp.png b/doc/sphinx/octave/hp.png similarity index 100% rename from doc/doxygen/matlab_octave/hp.png rename to doc/sphinx/octave/hp.png diff --git a/doc/doxygen/matlab_octave/index.html b/doc/sphinx/octave/index.html similarity index 77% rename from doc/doxygen/matlab_octave/index.html rename to doc/sphinx/octave/index.html index 1226961cc..7775bab6d 100644 --- a/doc/doxygen/matlab_octave/index.html +++ b/doc/sphinx/octave/index.html @@ -5,19 +5,19 @@