Add CLAUDE.md with codebase guidance for Claude Code

CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Framework: Viash + Nextflow
+
+This is a [Viash](https://viash.io)-based benchmarking task for spatial transcriptomics cell segmentation, part of the [OpenProblems](https://openproblems.bio) initiative. Every executable is a **Viash component** — a self-contained unit pairing a `config.vsh.yaml` (metadata, arguments, Docker setup) with a `script.py` or `script.R`. Nextflow workflows orchestrate multi-component pipelines.
+
+## Common Commands
+
+```bash
+# Sync test resources from S3 (required before testing)
+scripts/sync_resources.sh
+
+# Build all components (Docker-cached)
+viash ns build --parallel --setup cachedbuild
+
+# Build all Docker containers (run before local benchmark)
+scripts/project/build_all_docker_containers.sh
+
+# Test a single component
+viash test src/methods/cellpose/config.vsh.yaml
+
+# Test all components in parallel
+viash ns test --parallel
+
+# Run benchmark locally (test scale)
+scripts/run_benchmark/run_test_local.sh
+
+# Run full local benchmark
+scripts/run_benchmark/run_full_local.sh
+
+# Create a new method or metric from template
+common/scripts/create_component
+
+# Inspect the Docker image ID and Dockerfile for a built component
+target/executable/<name>/<name> ---docker_image_id
+target/executable/<name>/<name> ---dockerfile
+
+# Run a single built component directly
+target/executable/<name>/<name> --input <input> --output <output>
+
+# Run a built component as a Nextflow workflow
+nextflow run target/nextflow/<name> -profile docker --id <id> --input <input> --publish_dir out/
+```
+
+## Architecture
+
+The task follows a fixed pipeline defined by the API specs in `src/api/`:
+
+```
+Raw spatial data
+    → [data_processor] process_dataset    → unlabelled + solution files
+    → [method / control_method]           → prediction file
+    → [data_processor] process_prediction → formatted prediction
+    → [metric] ari                        → score file
+```
+
+**Component types** (each defined in `src/api/comp_*.yaml`):
+- `control_method` — baseline segmentations (random Voronoi, true labels, empty labels)
+- `method` — segmentation algorithms under evaluation (currently: Cellpose)
+- `data_processor` — preprocessing and postprocessing steps
+- `metric` — evaluation metrics (currently: ARI)
+- `workflow` — Nextflow pipelines in `src/workflows/`
+
+**File format contracts** are defined in `src/api/file_*.yaml`. All component I/O must conform to these schemas. The `common/component_tests/run_and_check_output.py` helper enforces them during tests.
+
+## Component Structure
+
+Each component under `src/` follows this pattern:
+```
+src/<type>/<name>/
+├── config.vsh.yaml   # arguments, Docker image, test resources, test defaults
+└── script.py         # or script.R
+```
+
+Test resources and default parameters for `viash test` are declared inside `config.vsh.yaml` under `info.test_resources` and `info.test_default`.
+
+## Data Formats
+
+- **Spatial data**: Zarr-based `SpatialData` objects (`.zarr/`)
+- **Single-cell data**: AnnData HDF5 files (`.h5ad`)
+- Additional sources of ground truth will include spatial proteomics or annotated histology
+- Test datasets live in `resources_test/` (downloaded via `scripts/sync_resources.sh` from S3)
+
+## Important Notes
+
+- The `common/` directory is a **git submodule** — clone with `git clone --recursive` or run `git submodule update --init` after cloning.
+- `README.md` is **auto-generated** from the YAML API specs; do not edit it directly.
+- All components run inside Docker containers by default. Use `--platform docker` / `--engine docker` flags with Viash when needed.
+- `_viash.yaml` is the project-level Viash config (project name, organization, package registry, test resource S3 paths).
+- Don't commit to main, always create a new branch
+- Fill in the summary for a src/methods/<component>/config.vsh.yaml. Write a one sentence summary and a one paragraph summary of how this method works based on documentation and references.
+- always use viash test to test new components