How does Atlas ensure my MATLAB refactor does not break existing code?

Atlas ensures safety by first mapping all public symbols and their callers using `lsp findReferences`. It then pins behavior by running `matlab.unittest (runtests)` to establish a green baseline. All structural changes are applied with `apply_patch`, which validates against the file's current state, and `matlab.unittest (runtests)` is re-run after each change to immediately detect regressions.

Can Atlas help me find all callers of a specific MATLAB function?

Yes, Atlas can precisely find all callers of a specific MATLAB function. You can use the `atlas lsp findReferences --symbol 'YourFunctionName'` command. Atlas builds an AST index of your `.m` files, allowing it to accurately identify all references across your project, even in complex codebases.

What if my MATLAB test suite is slow? Does Atlas still re-run it frequently?

Atlas's workflow emphasizes re-running `matlab.unittest (runtests)` after each small change for immediate feedback. If your full test suite is slow, consider creating a focused test file for the module being refactored, for example `tests/myModuleRefactorTests.m`, and instruct Atlas to run only that specific file using `atlas bash --command 'runtests tests/myModuleRefactorTests.m'`.

How does Atlas handle conflicts if my MATLAB file changes while Atlas is working?

Atlas's `apply_patch` tool is designed to handle this. It anchors changes on context lines and `old_lines`. If the target `.m` file has drifted or changed significantly since the patch was generated, `apply_patch` will fail with a `Failed to find context` error, preventing it from applying changes incorrectly. You would then review the drift and regenerate the patch if necessary.

Can Atlas help me maintain MATLAB code style during refactoring?

Yes, Atlas can assist with code style. After making structural changes, you can ask Atlas to apply the `MATLAB Format Code` conventions to the touched `.m` files. This ensures that your refactored code adheres to your project's formatting standards before you approve the changes.

Is my MATLAB code sent to third-party servers when using Atlas?

No, Atlas can build its code index with local Ollama embeddings, keeping your MATLAB code off third-party servers. This ensures that your proprietary `.m` files and intellectual property remain within your local environment, addressing common security and privacy concerns for enterprise MATLAB development.

Refactor a Legacy MATLAB Module with Atlas in 2026

To restructure an old MATLAB module without altering its behavior or disrupting its callers, Atlas provides a robust workflow that integrates directly with your existing `matlab.unittest (runtests)` test suite and `MATLAB Format Code` conventions. This ensures that every change is verified against a green baseline, preventing silent breakage and maintaining code integrity throughout the refactoring process.

How Atlas Maps MATLAB Module Public Surfaces

In 2026, understanding a legacy MATLAB module's external dependencies is the critical first step in any refactor. Atlas achieves this by leveraging its lsp tool's `documentSymbol` operation, which precisely identifies all public functions, classes, and properties within your `.m` files. This initial mapping provides a comprehensive overview of the module's exposed interface.

Atlas begins a MATLAB refactor by building an Abstract Syntax Tree (AST) index of your codebase using tree-sitter, which allows it to understand the structural declarations within your `.m` files. The `lsp` tool then performs a `documentSymbol` operation to enumerate every function signature, `classdef` block, and public method. Following this, Atlas executes `findReferences` on each identified symbol. For instance, running `atlas lsp findReferences --symbol 'myPublicFunction'` will list every callsite across your project where `myPublicFunction` is invoked. This exhaustive enumeration of callers is crucial for tracking all dependencies and ensuring no callsite is overlooked during the restructuring, preventing silent breakage that often plagues manual refactoring efforts in complex MATLAB projects.

Pinning MATLAB Module Behavior with Tests

Before any structural changes are applied to a legacy MATLAB module, Atlas ensures its current behavior is immutably pinned by running existing `matlab.unittest (runtests)` test suites. This establishes a 'green baseline' in 2026, against which all subsequent modifications will be validated. A successful test run confirms the module's current functionality before refactoring begins.

The core principle of safe refactoring with Atlas in MATLAB is to prove behavior before and after changes. Atlas uses its `bash` tool to execute your existing `matlab.unittest (runtests)` commands. For example, `atlas bash --command 'runtests tests/myModuleTests.m'` will run the specified test file. Atlas records the output, establishing a 'green baseline' of passing tests. This baseline is paramount: if the tests pass before refactoring, any subsequent failure indicates a behavioral change introduced by the refactor, which Atlas will immediately flag. This iterative testing approach, re-running tests after each small change, is far more effective than a single, large test run at the end, providing immediate feedback and pinpointing regressions precisely.

Applying Structural Changes to MATLAB Code with Atlas

Restructuring a MATLAB module with Atlas involves precise, context-aware edits applied through the `apply_patch` tool, ensuring changes are anchored to specific lines and refuse to apply if the file has drifted. This method minimizes the risk of introducing errors during the refactor, a common challenge in 2026 when dealing with evolving codebases. Atlas drafts a plan in a read-only agent before any edits.

Once the public surface is mapped and behavior is pinned, Atlas proceeds with structural changes using its `apply_patch` tool. This tool is designed for robustness: it seeks each hunk's context and `old_lines` within the target `.m` file. If the file has drifted or the context lines do not match, `apply_patch` will fail with a `Failed to find context` error, preventing unintended modifications to an outdated file. For instance, if Atlas proposes moving a function within `myLegacyModule.m`, the patch will include surrounding lines to ensure the edit lands exactly where intended. Atlas drafts a detailed plan in a read-only plan agent, outlining every proposed change before switching to a build agent to execute `apply_patch`, providing a critical layer of review and safety.

Iterative Verification and Call Site Migration in MATLAB

After each structural change lands in a MATLAB module, Atlas immediately re-runs the `matlab.unittest (runtests)` suite to verify behavior, preventing regressions from accumulating. In 2026, Atlas also tracks remaining call sites with a `todowrite` list, ensuring a partially migrated module is never mistaken for a finished one, providing clear progress visibility.

The refactoring workflow with Atlas is inherently iterative. After each successful `apply_patch` operation, Atlas automatically re-runs the `matlab.unittest (runtests)` suite using its `bash` tool. This immediate feedback loop is vital for catching regressions early. If tests fail, Atlas can help diagnose the issue or roll back the change using its git patch snapshots. Concurrently, Atlas maintains a `todowrite` list to track all identified call sites that still need migration. As each call site is updated, it is removed from the list. This ensures that even complex refactors involving hundreds of `.m` files and numerous callers remain manageable, providing a clear, actionable list of remaining work and preventing premature completion of the refactor.

Ensuring Safety and Review in MATLAB Refactoring with Atlas

Atlas prioritizes safety and developer review throughout the MATLAB refactoring process, offering multiple checkpoints before any code is written. Every Atlas tool call is permission-gated, and a unified diff is computed for every file edit, surfaced for approval before writing, ensuring transparency and control in 2026.

Atlas integrates several layers of safety and review into its refactoring workflow for MATLAB. First, every Atlas tool call, including `lsp`, `apply_patch`, and `bash`, is permission-gated against `allow`, `ask`, and `deny` rules, giving developers granular control over agent actions. Second, Atlas drafts a comprehensive plan in a read-only plan agent, detailing all proposed steps before any modifications are attempted. Third, for every file edit, Atlas computes a unified diff and surfaces it for explicit approval before writing changes to disk. This allows MATLAB developers to review exactly what Atlas intends to change in their `.m` files, `buildfile.m`, or `tests/` directories. Atlas also reads `git` branches, status, and diffs, and can stage and create commits on your behalf, further streamlining the review and version control process, and can snapshot file changes as `git` patches for easy rollback.

Step by step

01Initialize Atlas in your MATLAB project directory containing `.m` files and `buildfile.m`.
02Map the module's public surface: Run `atlas lsp documentSymbol` to list all exported functions and classes, then `atlas lsp findReferences --symbol 'YourFunctionName'` for each to enumerate all callers.
03Pin existing behavior: Execute `atlas bash --command 'runtests tests/YourModuleTests.m'` to run your `matlab.unittest (runtests)` suite and record a green baseline.
04Draft a refactoring plan: Ask Atlas to draft a plan for restructuring a specific part of your module, reviewing the read-only plan agent's output.
05Apply structural changes iteratively: Use `atlas apply_patch --file 'path/to/your/module.m' --patch 'your_hunk_content'` for each small, isolated change, reviewing the unified diff before approval.
06Verify behavior after each change: Immediately re-run `atlas bash --command 'runtests tests/YourModuleTests.m'` to ensure the `matlab.unittest (runtests)` suite remains green.
07Track remaining call sites: Use `atlas todowrite add 'Migrate callsite for oldFunction in callerFile.m'` to manage the list of callers needing updates, removing entries as they are migrated.
08Format touched files: Before committing, ask Atlas to apply `MATLAB Format Code` conventions to the modified `.m` files for consistency.

Frequently asked questions

How does Atlas ensure my MATLAB refactor does not break existing code?: Atlas ensures safety by first mapping all public symbols and their callers using `lsp findReferences`. It then pins behavior by running `matlab.unittest (runtests)` to establish a green baseline. All structural changes are applied with `apply_patch`, which validates against the file's current state, and `matlab.unittest (runtests)` is re-run after each change to immediately detect regressions.
Can Atlas help me find all callers of a specific MATLAB function?: Yes, Atlas can precisely find all callers of a specific MATLAB function. You can use the `atlas lsp findReferences --symbol 'YourFunctionName'` command. Atlas builds an AST index of your `.m` files, allowing it to accurately identify all references across your project, even in complex codebases.
What if my MATLAB test suite is slow? Does Atlas still re-run it frequently?: Atlas's workflow emphasizes re-running `matlab.unittest (runtests)` after each small change for immediate feedback. If your full test suite is slow, consider creating a focused test file for the module being refactored, for example `tests/myModuleRefactorTests.m`, and instruct Atlas to run only that specific file using `atlas bash --command 'runtests tests/myModuleRefactorTests.m'`.
How does Atlas handle conflicts if my MATLAB file changes while Atlas is working?: Atlas's `apply_patch` tool is designed to handle this. It anchors changes on context lines and `old_lines`. If the target `.m` file has drifted or changed significantly since the patch was generated, `apply_patch` will fail with a `Failed to find context` error, preventing it from applying changes incorrectly. You would then review the drift and regenerate the patch if necessary.
Can Atlas help me maintain MATLAB code style during refactoring?: Yes, Atlas can assist with code style. After making structural changes, you can ask Atlas to apply the `MATLAB Format Code` conventions to the touched `.m` files. This ensures that your refactored code adheres to your project's formatting standards before you approve the changes.
Is my MATLAB code sent to third-party servers when using Atlas?: No, Atlas can build its code index with local Ollama embeddings, keeping your MATLAB code off third-party servers. This ensures that your proprietary `.m` files and intellectual property remain within your local environment, addressing common security and privacy concerns for enterprise MATLAB development.

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