[valeriabarra]

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

• Refactor
• Feature
• Bug Fix
• Optimization
• Example
• Documentation

Description

This PR adds a Grids module for the MOLE.jl Julia implementation. This contains new functions, tests, and documentation. A follow-up PR will be created to make the Operators compatible (and retro-compatible) with the new Grid module.

Related Issues & Documents

• I have created an Issue that is paired with this PR
• Closes MOLE.jl: Add new Grids module #409

Added/updated tests?

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

• Yes
• 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

[codecov]

Codecov Report

❌ Patch coverage is 95.76923% with 11 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
julia/MOLE.jl/src/Grids/validate_grid.jl	94.58%	11 Missing ⚠️

📢 Thoughts on this report? Let us know!

[valeriabarra]

@Tony-Drummond and @joehellmers , can you still review this PR? Thank you

[valeriabarra]

@joehellmers , @Tony-Drummond , are you still able to review this PR?
The Julia formatter action that is failing is a fluke. Locally for me the formatter passes. Thanks

[github-actions]

This pull request has had no activity for 14 days. It will be marked stale in 14 days if there is no further activity.

[Copilot]

Pull request overview

Adds a Julia Grids module for constructing and validating computational grids.

Changes:

• Adds grid types, coordinate generation, validation, and constructors.
• Supports uniform grids, boundary metadata, and 2D curvilinear grids.
• Adds documentation and automated tests.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
docs/src/index.md	Documents the Grids API.
src/MOLE.jl	Loads the new module.
src/Grids/Grids.jl	Defines module exports and includes.
src/Grids/coordinates.jl	Generates grid coordinates.
src/Grids/make_grid.jl	Adds grid constructors.
src/Grids/topologies.jl	Defines grid data structures.
src/Grids/validate_grid.jl	Implements validation and normalization.
test/runtests.jl	Registers grid tests.
test/Grids/make_grid.jl	Tests grid construction.
test/Grids/validate_grid.jl	Tests validation and edge cases.

Suppressed comments (3)

julia/MOLE.jl/src/Grids/validate_grid.jl:257

• The 2D partial fallback drops all valid supplied values (m, n, and any available spacing or boundary data), leaving only dim and topology. Preserve and validate the fields that are present so the returned object can actually be completed incrementally.

    return Grid{Float64}(dim = 2, topology = topology)

julia/MOLE.jl/src/Grids/validate_grid.jl:314

• The 3D partial fallback discards m, n, o, and any supplied spacing or boundary values. A partial grid should retain and validate its present fields rather than returning an empty shell, otherwise subsequent makeGrid(grid) calls cannot recover the user's definition.

    return Grid{Float64}(dim = 3, topology = topology)

julia/MOLE.jl/src/Grids/validate_grid.jl:209

• If either m or n is absent, this partial-grid branch calls the parametric Grid{T} constructor without a type-bearing value from which T can be inferred. Thus validateGrid(Dict(:dim=>2, :topology=>:curvilinear); allowPartial=true) throws instead of returning a partial grid. Specify an element type here (consistent with the other partial branches), while separately retaining any supplied fields.

        return Grid(dim = 2, topology = :curvilinear)

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[github-actions]

This pull request has had no activity for 14 days. It will be marked stale in 14 days if there is no further activity.

[valeriabarra]

I am working to address the review. However, other work has taken precedence (see PR #460 )

[joehellmers]

@valeriabarra I'd like to add some tests for MOLE.jl. Should I add to this branch directly or via a fork?

[valeriabarra]

@valeriabarra I'd like to add some tests for MOLE.jl. Should I add to this branch directly or via a fork?

Hi @joehellmers thank you for considering contributing. Please use a separate fork and describe your intended contribution idea in an Issue first. Thank you!

[github-actions]

This pull request has had no activity for 14 days. It will be marked stale in 14 days if there is no further activity.

[valeriabarra]

Hi, I'm planning to work on this next week!

[valeriabarra]

Hi @joehellmers , this PR is ready to be merged and has been reviewed by me.

We need at least one approval from a reviewer to be able to merge the PR. Please approve or provide additional feedback if you wish. Thank you!

[valeriabarra]

Hi @joehellmers and @Tony-Drummond , This PR is ready. Please approve or provide additional feedback if you wish. We need at least one approving review to be able to merge and I can't be it. Please approve/review as soon as possible as we need to merge this ASAP. Thank you!

[Tony-Drummond]

Hi @valeriabarra, I can start looking at this next week after Tuesday. I can't work on it now.

[valeriabarra]

Hi @valeriabarra, I can start looking at this next week after Tuesday. I can't work on it now.

Thank you @Tony-Drummond , are you able to review and approve? Thanks