Updating directory names for GNU Octave by Tony-Drummond · Pull Request #452 · csrc-sdsu/mole

Tony-Drummond · 2026-09-04T04:07:40Z

What type of PR is this? (check all applicable)

Description

Renamed all subdirectories containing the GNU Octave scripts with the implementation of MOLE v1.2, and all tests and examples. Updated internal links to support the auto-documentation mechanisms.

Related Issues & Documents

I have created an Issue that is paired with this PR
Closes Part 2: Rename subdirectories and check all internal links #450

QA Instructions, Screenshots, Recordings

Keep-open request

I am requesting maintainer review for keep-open.

Reason:

Added/updated tests?

_We encourage you to test all code included with MOLE, including examples.

Yes. Unit tests for Octave and Documentation (Doxygen, Sphinx, and Read The Docs pages)
No, and this is why: please replace this line with details on why tests
have not been included
I need help with writing tests

Read Contributing Guide and Code of Conduct

📖 I have read the MOLE Contributing Guide: https://github.com/csrc-sdsu/mole/blob/main/CONTRIBUTING.md
📖 I have read the MOLE Code of Conduct: https://github.com/csrc-sdsu/mole/blob/main/CODE_OF_CONDUCT.md

[optional] Are there any post deployment tasks we need to perform?

[optional] What gif best describes this PR or how it makes you feel?

codecov · 2026-09-04T04:09:52Z

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

Fixed Makefile

Tony-Drummond · 2026-09-04T07:06:18Z

Hi Software Engineering Gov. Circle (@cpaolini, @jbrzensk, @valeriabarra, @joehellmers, @gpagallo) and @jcastillo001 This completes the rename of the MOLE GNU Octave subdirectory. For MOLE v.1.2 the impacted subdirectories by this PR are:
./tests/octave
./examples/octave
./doc/sphinx/source/api/octave
./doc/sphinx/octave
./src/octave

Copilot

🟡 Changes recommended

There are a couple of concrete issues in the updated wiring/utility code (notably mismatched .gitattributes paths and missing invalid-parameter handling) that should be fixed to avoid broken repo metadata and brittle runtime behavior.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR refactors the repository’s Octave-related layout by renaming the prior matlab_octave-named directories to octave and updating code/doc links and build/test wiring to match, aligning with the MOLE v1.2 Octave implementation organization.

Changes:

Renames Octave source/examples/tests directories to src/octave, examples/octave, and tests/octave, and updates addpath(...) usage accordingly.
Updates CMake/CI/docs references (README, Sphinx, Doxygen notes) to the new Octave paths.
Adds/relocates a large set of Octave .m implementation files and generated Octave API documentation assets.

File summaries

File	Description
.gitattributes	Updates linguist documentation paths (currently mismatched; needs correction).
tests/octave/CMakeLists.txt	Registers Octave `.m` tests (executed via `matlab -batch`; wording should be clarified).
tests/octave/testPoissonAccuracy.m	Adds a Poisson accuracy test (minor documentation/clarity fix suggested).
src/octave/interpolFacesToCentersG1DPeriodic.m	Adds periodic interpolator (needs explicit invalid-`k` handling).
src/octave/**	Moves/adds Octave implementation functions under the new directory name.
examples/octave/**	Updates examples to reference `src/octave` and adjusts Octave wording in comments/docs.
doc/sphinx/source/**	Updates Sphinx navigation and links to `examples/octave` and `api/octave`.
.github/workflows/matlab-tests.yml	Updates MATLAB CI test selection to `src/octave` and `tests/octave`.
README.md / CONTRIBUTING.md	Updates developer docs and commands to new Octave directory naming.

Review details

Files reviewed: 179/347 changed files
Comments generated: 2
Review effort level: Lite

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

+examples_octave/* linguist-documentation
+doc_octave/* linguist-documentation


Tony-Drummond · 2026-09-04T22:53:05Z

+# Find all GNU Octave test files (test*.m)
 file(GLOB TEST_SOURCES test*.m)

 # Enable testing
 enable_testing()


@jbrzensk,For now it runs the Octave scripts as if they were MATLAB script, given the full compatibility. For consistency, all these tests are going to be under the same directory and reference as GNU Octave tests ONLY. @cpaolini has plans to include the GNU tests runner, and he advised to run both MATLAB test runners and the GNU test runners to demonstrate that all MOLE GNU Octave's scripts are fully compatible with MATLAB.

valeriabarra · 2026-09-04T20:48:59Z

Hi @Tony-Drummond , thank you. I think you mentioned that also some files in the julia/MOLE.jl directory needto updated, but I don't see them being included here. Thanks

Tony-Drummond · 2026-09-04T22:47:54Z

Hi @valeriabarra , this was included in the email I sent to the Software Engineering Gov. Circle (the name of the files that I identified are in bold)
./julia/MOLE.jl/docs/src/examples/index.md:
The MOLE library contains many examples written in OCTAVE/MATLAB, C++, and Julia. These examples span a broad range of partial differential equations. Below are more technical explinations of the examples included in the library.
The name for OCTAVE/MATLAB, C++, and Julia will be the same (i.e., the files elliptic1D.m, elliptic1D.cpp, and elliptic1D.jl solve the same differential equation explained here under Elliptic1D). These examples are only the ones implemented in Julia. There are many more OCTAVE/MATLAB and C++ examples, which can be found in the main MOLE documentation.
The MOLE library contains many examples written in OCTAVE/MATLAB, C++, and Julia. These examples span a broad range of partial differential equations. Below are more technical explinations of the examples included in the library.
The name for OCTAVE/MATLAB, C++, and Julia will be the same (i.e., the files elliptic1D.m, elliptic1D.cpp, and elliptic1D.jl solve the same differential equation explained here under Elliptic1D). These examples are only the ones implemented in Julia. There are many more OCTAVE/MATLAB and C++ examples, which can be found in the main MOLE documentation.
.
/julia/MOLE.jl/examples/hyperbolic/hyperbolic1D.jl:
from MATLAB MOLE example using the Leapfrog Scheme

./julia/MOLE.jl/src/BCs/scalarBC.jl:
Fields mirror the MATLAB function:
Fields mirror the MATLAB function:
1D BC applicator. Mirrors MATLAB addScalarBC1D.

# Equivalent of MATLAB: q = find(dc.^2 + nc.^2, 1)
2D BC applicator. Mirrors MATLAB addScalarBC2D.

jbrzensk · 2026-09-04T23:01:15Z

Looks like the only change is the gitattributes file, to reference the corret locations.

valeriabarra · 2026-09-04T23:08:00Z

Hi @valeriabarra , this was included in the email I sent to the Software Engineering Gov. Circle (the name of the files that I identified are in bold) ./julia/MOLE.jl/docs/src/examples/index.md: The MOLE library contains many examples written in OCTAVE/MATLAB, C++, and Julia. These examples span a broad range of partial differential equations. Below are more technical explinations of the examples included in the library. The name for OCTAVE/MATLAB, C++, and Julia will be the same (i.e., the files elliptic1D.m, elliptic1D.cpp, and elliptic1D.jl solve the same differential equation explained here under Elliptic1D). These examples are only the ones implemented in Julia. There are many more OCTAVE/MATLAB and C++ examples, which can be found in the main MOLE documentation. The MOLE library contains many examples written in OCTAVE/MATLAB, C++, and Julia. These examples span a broad range of partial differential equations. Below are more technical explinations of the examples included in the library. The name for OCTAVE/MATLAB, C++, and Julia will be the same (i.e., the files elliptic1D.m, elliptic1D.cpp, and elliptic1D.jl solve the same differential equation explained here under Elliptic1D). These examples are only the ones implemented in Julia. There are many more OCTAVE/MATLAB and C++ examples, which can be found in the main MOLE documentation. . /julia/MOLE.jl/examples/hyperbolic/hyperbolic1D.jl: from MATLAB MOLE example using the Leapfrog Scheme

./julia/MOLE.jl/src/BCs/scalarBC.jl: Fields mirror the MATLAB function: Fields mirror the MATLAB function: 1D BC applicator. Mirrors MATLAB addScalarBC1D.
# Equivalent of MATLAB: q = find(dc.^2 + nc.^2, 1)
2D BC applicator. Mirrors MATLAB addScalarBC2D.

Hi, yes, I saw that, but I do not see those references being changed in this PR. Are you considering adding them here or you prefer a separate PR? Thanks

Tony-Drummond · 2026-09-04T23:49:09Z

@valeriabarra, I updated the MOLE.jl related files. I just didn't want to interfere with anything else happening inside the MOLE.jl development.

Updating directory names for GNU Octave

9169ed2

Updating directory names for GNU Octave

51c40f3

Fixed Makefile

Tony-Drummond force-pushed the subdir_rename/GNU_Octave branch from 9906502 to 51c40f3 Compare September 4, 2026 06:41

Tony-Drummond requested review from cpaolini, jbrzensk and jcastillo001 September 4, 2026 07:08

jbrzensk requested a lite review from Copilot September 4, 2026 18:51

Merge branch 'main' into subdir_rename/GNU_Octave

b999507

Copilot started reviewing on behalf of jbrzensk September 4, 2026 18:52 View session

Copilot AI reviewed Sep 4, 2026

View reviewed changes

Tony-Drummond added 2 commits September 4, 2026 16:36

fixes to .gitattributes

7512112

Changing files from the MOLE.jl implamentation

0a951e6

jbrzensk approved these changes Sep 5, 2026

View reviewed changes

Navigation Menu

Uh oh!

Updating directory names for GNU Octave - #452

Updating directory names for GNU Octave#452
Tony-Drummond wants to merge 5 commits into
mainfrom
subdir_rename/GNU_Octave

Tony-Drummond commented Sep 4, 2026

Uh oh!

codecov Bot commented Sep 4, 2026 •

edited

Loading

Uh oh!

Tony-Drummond commented Sep 4, 2026 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Tony-Drummond Sep 4, 2026

Uh oh!

valeriabarra commented Sep 4, 2026

Uh oh!

Tony-Drummond commented Sep 4, 2026

Uh oh!

jbrzensk commented Sep 4, 2026

Uh oh!

valeriabarra commented Sep 4, 2026

Uh oh!

Tony-Drummond commented Sep 4, 2026 •

edited

Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

		examples_octave/* linguist-documentation
		doc_octave/* linguist-documentation

Uh oh!

Conversation

Tony-Drummond commented Sep 4, 2026

What type of PR is this? (check all applicable)

Description

Related Issues & Documents

QA Instructions, Screenshots, Recordings

Keep-open request

Added/updated tests?

Read Contributing Guide and Code of Conduct

[optional] Are there any post deployment tasks we need to perform?

[optional] What gif best describes this PR or how it makes you feel?

Uh oh!

codecov Bot commented Sep 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Tony-Drummond commented Sep 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

🟡 Changes recommended

Uh oh!

Tony-Drummond Sep 4, 2026

Choose a reason for hiding this comment

Uh oh!

valeriabarra commented Sep 4, 2026

Uh oh!

Tony-Drummond commented Sep 4, 2026

Uh oh!

jbrzensk commented Sep 4, 2026

Uh oh!

valeriabarra commented Sep 4, 2026

Uh oh!

Tony-Drummond commented Sep 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

codecov Bot commented Sep 4, 2026 •

edited

Loading

Tony-Drummond commented Sep 4, 2026 •

edited

Loading

Tony-Drummond commented Sep 4, 2026 •

edited

Loading