add cursor rules

Author: singlesp

.cursor/rules/pennlinc-shared.mdc

@@ -0,0 +1,47 @@
+---
+alwaysApply: true
+---
+# PennLINC BIDS App Shared Conventions
+
+This project is one of four PennLINC BIDS Apps (qsiprep, qsirecon, xcp_d, aslprep) sharing
+the same architecture and conventions. See [AGENTS.md](mdc:AGENTS.md) for full details.
+
+## Architecture
+
+- CLI in `xcp_d/cli/` (parser.py, run.py, workflow.py, version.py)
+- Singleton config in [config.py](mdc:xcp_d/config.py) with sections: environment, execution, workflow, nipype, seeds
+- Workflows in `xcp_d/workflows/` using Nipype's `pe.Workflow`, `pe.Node`, `pe.MapNode`
+- Interfaces in `xcp_d/interfaces/` following Nipype patterns
+- Tests in `xcp_d/tests/` with pytest; integration tests gated by markers
+
+## Workflow Rules
+
+- Name all workflow factory functions `init_<name>_wf`; return a Workflow object
+- Use `LiterateWorkflow` from `niworkflows.engine.workflows`
+- Define `inputnode` and `outputnode` as `niu.IdentityInterface` nodes
+- Use `workflow.connect([(src, dst, [('out', 'in')])])` syntax with `# fmt:skip` on multi-line connects
+- Read global settings from `config` module, not function parameters
+
+## Interface Rules
+
+- Use Nipype traits for input/output specs (`File`, `traits.Bool`, etc.)
+- Implement `_run_interface(self, runtime)`, return `runtime`
+- Set outputs via `self._results['field'] = value`
+
+## Code Style
+
+- Linter: `ruff check`; Formatter: `ruff format`
+- Import sorting via ruff (isort-compatible)
+- Add `# fmt:skip` after multi-line `workflow.connect()` calls
+
+## Testing
+
+- Unit tests in `test_*.py` -- no external data or network access required
+- Integration tests use `@pytest.mark.<marker>` and are excluded by default
+- Fixtures: `data_dir`, `working_dir`, `output_dir` in conftest.py
+
+## BIDS
+
+- Outputs must conform to BIDS Derivatives specification
+- Use `pybids.BIDSLayout` for input queries
+- Use `DerivativesDataSink` for writing BIDS-compliant outputs

.cursor/rules/xcp_d.mdc

@@ -0,0 +1,64 @@
+---
+globs: "*.py"
+---
+# XCP-D Project Rules
+
+## Project Identity
+
+- Package: `xcp_d` -- fMRI postprocessing BIDS App
+- Default branch: `main`
+- Entry point: [xcp_d/cli/run.py](mdc:xcp_d/cli/run.py)
+
+## Linting & Formatting
+
+- Linter/formatter: ruff ~= 0.15.0
+- Config: [pyproject.toml](mdc:pyproject.toml) under `[tool.ruff]`
+- Pre-commit: [.pre-commit-config.yaml](mdc:.pre-commit-config.yaml) with ruff v0.6.2
+- Black is disabled (`[tool.black] exclude = ".*"`)
+- **Cleanest ignore list** of all four repos: only S105, S311, S603
+
+## Version Management
+
+- Uses `__about__.py` pattern: [xcp_d/__about__.py](mdc:xcp_d/__about__.py)
+- Exports `__version__`, `__packagename__`, `__copyright__`, `__credits__`
+- `_version.py` is auto-generated by hatch-vcs; `__about__.py` imports from it
+
+## `fill_doc` Decorator
+
+Use `@fill_doc` (from `xcp_d.utils.doc`) on workflow init functions to inject shared
+parameter documentation. The decorator fills `%(parameter_name)s` placeholders in docstrings.
+
+## Config Hashing
+
+`config.hash_config()` creates unique identifiers for pipeline configurations.
+Used to detect when outputs need regeneration due to parameter changes.
+See `DEFAULT_CONFIG_HASH_FIELDS` in [xcp_d/config.py](mdc:xcp_d/config.py).
+
+## Ingression Modules
+
+`xcp_d/ingression/` adapts non-BIDS input formats:
+- `abcdbids.py`: ABCD-BIDS format
+- `hcpya.py`: HCP Young Adult format
+- `ukbiobank.py`: UK Biobank format
+When adding new input formats, create a module in this directory.
+
+## Executive Summary Reports
+
+HTML reports generated via Jinja2 templates in `xcp_d/data/executive_summary_templates/`.
+Interface: `xcp_d/interfaces/execsummary.py`; utils: `xcp_d/utils/execsummary.py`.
+
+## Key Module Paths
+
+- BOLD workflows: `xcp_d/workflows/bold/` (cifti, nifti, concatenation)
+- Anatomical workflows: `xcp_d/workflows/anatomical/` (surface, volume, parcellation)
+- Parcellation: [xcp_d/workflows/parcellation.py](mdc:xcp_d/workflows/parcellation.py)
+- Bundled atlases: `xcp_d/data/atlases/` (Glasser, Gordon, HCP, Tian, MIDB, MyersLabonte)
+- Nuisance configs: `xcp_d/data/nuisance/` (YAML strategy files)
+- Config: [xcp_d/config.py](mdc:xcp_d/config.py)
+
+## Testing
+
+- Test extras: `tests` in pyproject.toml
+- Parallel test execution supported via `pytest-xdist`
+- Integration test markers defined in `[tool.pytest.ini_options]`
+- `mock_config` context manager in `xcp_d/tests/tests.py` for workflow unit tests

.gitignore

@@ -3,7 +3,6 @@ xcp_d/tests/pytests
 xcp_d/tests/test_data
 xcp_d/tests/data/test_data
 .circleci/local_xcpd_path.txt
-.cursor
 
 # setuptools-scm
 xcp_d/_version.py