# Run Atlas Headless in CI for C Projects in 2026 > C developers can run Atlas headless in CI using `atlas run --format json` to get machine-readable output, integrating with `Unity via ctest` and `Conan`. To run an Atlas session non-interactively in a C CI pipeline and retrieve machine-readable output, C developers in 2026 can leverage the `atlas run --format json` command, integrating it with their existing `Unity via ctest`, `Conan`, and `clang-format` toolchain. This approach allows for automated code analysis, refactoring, and testing without human intervention, providing structured data for subsequent pipeline steps. ## Key takeaways - Atlas runs non-interactively in C CI pipelines using `atlas run`. - Machine-readable output is available via `atlas run --format json` for C project automation. - Pre-approve `bash`, `read`, `edit`, and `todowrite` tools for headless C operations. - Atlas integrates with C `Makefile`s, `Unity via ctest`, `Conan`, and `clang-format`. - Review unified diffs and git patches generated by Atlas for C code changes. - Atlas can use local Ollama embeddings to index C code, keeping it off third-party servers. ## How to Run Atlas Headless in C CI Pipelines for Machine-Readable Output In 2026, C developers can execute Atlas non-interactively within CI pipelines by using the `atlas run` command, which defaults to a non-interactive mode. To obtain machine-readable output for automated processing, simply append the `--format json` flag to your command. Running Atlas headless in a C CI pipeline is straightforward with the `atlas run` command. This command is specifically built for non-interactive execution, sending a single prompt and exiting when the session goes idle. For C projects, Atlas can be configured to read your `Makefile`, header files (`.h`), and source files (`.c`), allowing it to understand the project structure and manual memory management patterns. When a later pipeline step needs to parse the event stream rather than human-readable prose, passing `--format json` ensures that Atlas streams raw, structured events to stdout, making it ideal for automated analysis or reporting in a C development workflow. ## Configuring Atlas Permissions for C Tooling in Headless CI Runs For headless Atlas runs in C CI environments, pre-approving necessary tools is critical because there is no user to answer 'ask' prompts. In 2026, configure Atlas permissions to 'allow' tools like `bash`, `read`, `edit`, and `todowrite` for direct operation. A headless Atlas run in a C CI pipeline requires pre-approved tool permissions to function effectively. Since there is no interactive terminal to respond to 'ask' prompts, all tools that Atlas might use must be explicitly allowed in the permission configuration. For C projects, this typically includes `bash` for executing shell commands like `make` or `ctest`, `read` for accessing source files (`.c`, `.h`) and build rules (`Makefile`), `edit` for modifying code, and `todowrite` for creating or updating documentation or task lists. By setting these permissions to 'allow', you ensure that Atlas can perform its tasks, such as finding memory leaks or adding `Unity via ctest` tests, without interruption in your automated C pipeline. ## Integrating Atlas with C Toolchain Commands and Project Files Atlas integrates directly with the standard C toolchain, recognizing `Makefile`s, header files, and source files. It can interact with `Unity via ctest` for testing, `Conan` for package management, and `clang-format` for code formatting, using their actual commands in 2026. Atlas is designed to work direct within a C development environment. It indexes code by AST declarations using tree-sitter, allowing it to understand the structure of C source files (`.c`) and header files (`.h`). When operating in a CI pipeline, Atlas can execute real C toolchain commands. For instance, it can invoke `ctest` to run tests managed by `Unity via ctest`, or use `conan install` to manage dependencies via `Conan`. If code formatting is required, Atlas can apply `clang-format -i` to ensure consistent code style. Atlas's ability to read `Makefile`s and understand build rules means it can propose and execute changes that align with your project's existing C build process, ensuring that any modifications are contextually aware and maintainable. ## Reviewing and Approving C Code Changes from Headless Atlas Sessions Every file edit made by Atlas, even in a headless C CI run, generates a unified diff for review. In 2026, Atlas snapshots these changes as git patches, providing a robust mechanism for approval and rollback before committing to your C codebase. Safety and review are paramount, even when Atlas runs headless in a C CI pipeline. Atlas computes a unified diff for every file edit it proposes, making it transparent what changes have been made to your C source files (`.c`) or headers (`.h`). These changes are also snapshotted as git patches, which means they can be easily diffed, reviewed, and rolled back if necessary. Atlas's workflow includes a read-only plan agent that drafts a plan and asks for approval before switching to a build agent to execute changes. While the 'ask' prompt is bypassed in headless mode due to pre-approved permissions, the generated diffs and git patches provide the necessary artifacts for a subsequent human review step or an automated quality gate in your C CI pipeline, ensuring control over the codebase. ## Steps 1. Ensure your C project includes a `Makefile` and relevant source (`.c`) and header (`.h`) files for Atlas to index. 2. Configure Atlas permissions to 'allow' tools like `bash`, `read`, `edit`, and `todowrite` in your Atlas configuration file, as headless runs cannot prompt for approval. 3. Invoke `atlas run` in your CI script with a specific prompt, for example: `atlas run "Find and fix a memory leak in src/main.c" --format json --model github/gpt-4o`. 4. Atlas reads your C headers, source files, and `Makefile` to build its code index using tree-sitter and local Ollama embeddings. 5. Atlas drafts a plan, potentially involving `Unity via ctest` to add new tests or `Conan` to manage dependencies, and then switches to the build agent. 6. Atlas executes C toolchain commands like `make`, `ctest`, or `clang-format -i src/main.c` as part of its plan, based on pre-approved permissions. 7. Atlas computes a unified diff for any file edits and streams these events, along with other session data, to stdout in JSON format. 8. A subsequent CI pipeline step parses the JSON output to review changes, generate reports, or trigger further actions based on Atlas's output. 9. Optionally, use `atlas run --continue --session ` or `--fork ` to resume or build upon a prior Atlas session in your C project. ## FAQ ### How do I run Atlas in a C CI pipeline without user interaction? Use `atlas run` with your prompt; its default mode is non-interactive, sending one prompt and exiting when the session goes idle, perfect for C CI automation. ### Can Atlas provide machine-readable output for C CI automation? Yes, pass `--format json` to `atlas run` to stream raw events to stdout that downstream pipeline steps can parse, enabling automated processing of C project data. ### How does Atlas handle permissions for C tools like `make` or `ctest` in CI? Pre-approve necessary tools like `bash`, `read`, `edit`, and `todowrite` in your Atlas permission config, because headless runs cannot prompt for approval during C tool execution. ### What C toolchain components does Atlas recognize in CI? Atlas works with C projects using `Makefile`s, reads headers and source files, and integrates with `Unity via ctest`, `Conan`, and `clang-format` commands. ### How can I review changes made by Atlas in a C CI pipeline? Atlas computes a unified diff for every file edit and snapshots changes as git patches, allowing for thorough review and rollback of C code modifications in your repository. ### Can Atlas use local embedding models for C code indexing in CI? Yes, Atlas can build its code index with local Ollama embeddings, ensuring your C code remains off third-party servers while still benefiting from semantic search. ### How does Atlas ensure safety when modifying C code in CI? Atlas drafts a plan in a read-only plan agent and computes a unified diff for every file edit, which is surfaced for approval (or automated review in headless mode) before writing to your C project. --- Canonical HTML: https://runatlas.sh/resources/stacks/run-atlas-headless-in-ci-in-c Source of truth: aeo_pages row `/resources/stacks/run-atlas-headless-in-ci-in-c` (segment: Stacks) (this file is generated from it, never hand-edited). Licence: Atlas is proprietary with a free core. It is not open source and there is no public source repository.