Cleanup (#55)

Code cleanup: Harmonized imports across the package, replaced NamedTuple and SimpleNamespace usage, and enforced
consistent naming conventions.
Refactored utilities: Renamed utils.py to fileops.py to better reflect its scope; extracted NIfTI helpers into a
dedicated nifti.py module.
Improved project config: Expanded Ruff lint rules, added norecursedirs for test data.
Docstring improvements: Added and expanded docstrings throughout core modules.

Author: nx10

.github/workflows/test.yaml

@@ -11,11 +11,6 @@ on:
   pull_request:
   workflow_dispatch:
     inputs:
-      slow:
-        description: Run slow tests
-        required: false
-        default: false
-        type: boolean
       e2e:
         description: Run end-to-end tests
         required: false
@@ -58,18 +53,6 @@ jobs:
           --log-level=DEBUG \
           --verbose
 
-    - name: Run slow tests
-      if: matrix.os == 'ubuntu-latest' && github.event_name == 'workflow_dispatch' && inputs.slow == true
-      shell: bash
-      run: >
-        uv run pytest \
-          -m "slow" \
-          --runner=docker \
-          --junitxml=pytest-slow.xml \
-          --cov=src tests \
-          --cov-append \
-          --verbose
-
     - name: Run full pipeline tests
       if: matrix.os == 'ubuntu-latest' && github.event_name == 'workflow_dispatch' && inputs.e2e == true
       shell: bash
@@ -102,6 +85,17 @@ jobs:
         pytest-xml-coverage-path: ./coverage.xml
         junitxml-path: ./pytest.xml
 
+  codegen:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - name: Setup venv
+      uses: ./.github/actions/setup-venv
+    - name: Check generated files are up-to-date
+      run: |
+        uv run scripts/generate_bids_tools.py
+        git diff --exit-code || (echo "Generated files are out of date. Run: uv run scripts/generate_bids_tools.py" && exit 1)
+
   ruff:
     runs-on: ubuntu-latest
     steps:

.gitignore

@@ -164,3 +164,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+
+.claude
+/nul

README.md

@@ -43,13 +43,13 @@ The pipeline requires the following neuroimaging tools:
 from rbc.workflows import anatomical, functional
 
 # Anatomical preprocessing
-anatomical.single_session(
+anatomical.single_session_preprocess(
     in_t1w="sub-01_T1w.nii.gz",
     output_dir="derivatives/rbc"
 )
 
 # Functional preprocessing (in development)
-functional.single_session(
+functional.single_session_preprocess(
     in_bold="sub-01_task-rest_bold.nii.gz",
     in_t1w="sub-01_T1w.nii.gz",
     output_dir="derivatives/rbc"

pyproject.toml

@@ -7,10 +7,8 @@ license = "MIT"
 readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
-  "bids2table>=2.1.2",
   "nibabel>=5.3.3",
-  "niwrap>=0.8.3",
-  "niwrap-helper>=0.7.0",
+  "niwrap>=0.8.3"
 ]
 
 [dependency-groups]
@@ -27,11 +25,14 @@ docs = ["pdoc>=15.0.0"]
 [tool.pytest.ini_options]
 pythonpath = ["src"]
 testpaths = ["tests"]
+norecursedirs = [
+  "tests/data"
+]
 markers = [
   "unit: Fast (<1s) unit tests (e.g. utilities, BIDS parsing, file operations)",
-  "integration: Medium (1-5 min) integration tests with small/downsampled data",
-  "slow: Long (30+ min) tests; skip on CI",
-  "full_pipeline: End-to-end workflow tests; skip on CI"
+  "integration: Integration tests with real data",
+  "slow: Long-running tests (manual marker on individual tests)",
+  "full_pipeline: End-to-end workflow tests"
 ]
 
 [tool.coverage.report]
@@ -50,39 +51,45 @@ extend-exclude = ["src/rbc/core/bids.py", "tests/unit/test_bids.py"]
 
 [tool.ruff.lint]
 select = [
-    "ANN",  # flake8-annotations
-    "ARG",  # flake8-unused-arguments
-    "B",    # flake8-bugbear
-    "C4",   # flake8-comprehensions
-    "C90",  # mccabe
-    "D",    # pydocstyle
-    "E",    # pycodestyle errors
-    "ERA",  # eradicate
-    "F",    # Pyflakes
-    "FA",   # flake8-future-annotations
-    "FBT",  # flake8-boolean-trap
-    "FURB", # refurb
-    "I",    # isort
-    "N",    # pep8-naming
-    "NPY",  # NumPy-specific rules
-    "PD",   # pandas-vet
-    "PERF", # Perflint
-    "PIE",  # flake8-pie
-    "PT",   # flake8-pytest-style
-    "PTH",  # flake8-use-pathlib
-    "Q",    # flake8-quotes
-    "RET",  # flake8-return
-    "RUF",  # Ruff-specific rules
-    "S",    # flake8-bandit
-    "SIM",  # flake8-simplify
-    "T20",  # flake8-print
-    "TCH",  # flake8-type-checking
-    "UP",   # pyupgrade
+  "ANN",  # flake8-annotations
+  "ARG",  # flake8-unused-arguments
+  "B",  # flake8-bugbear
+  "C4",  # flake8-comprehensions
+  "C90",  # mccabe
+  "D",  # pydocstyle
+  "E",  # pycodestyle errors
+  "ERA",  # eradicate
+  "F",  # Pyflakes
+  "FA",  # flake8-future-annotations
+  "FBT",  # flake8-boolean-trap
+  "FURB",  # refurb
+  "I",  # isort
+  "N",  # pep8-naming
+  "NPY",  # NumPy-specific rules
+  "PD",  # pandas-vet
+  "PERF",  # Perflint
+  "PIE",  # flake8-pie
+  "PT",  # flake8-pytest-style
+  "PTH",  # flake8-use-pathlib
+  "Q",  # flake8-quotes
+  "RET",  # flake8-return
+  "RUF",  # Ruff-specific rules
+  "S",  # flake8-bandit
+  "SIM",  # flake8-simplify
+  "T20",  # flake8-print
+  "TID",  # flake8-tidy-imports
+  "TCH",  # flake8-type-checking
+  "UP"  # pyupgrade
 ]
 ignore = []
 fixable = ["ALL"]
 unfixable = []
 
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"bids2table.format_bids_path".msg = "Prefer rbc.core.bids.bids_path / rbc.core.bids.bids_name"
+"bids2table.parse_bids_entities".msg = "Prefer rbc.core.bids.parse_bids_name"
+"types.SimpleNamespace".msg = "Prefer NamedTuple"
+
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 

scripts/generate_bids_tools.py

@@ -419,7 +419,6 @@ def w(s: str = "") -> None:
     w()
 
     # ---- TestBidsName ----
-    w("@pytest.mark.unit")
     w("class TestBidsName:")
     w('    """Tests for bids_name."""')
     w()
@@ -593,7 +592,6 @@ def w(s: str = "") -> None:
     w()
 
     # ---- TestBidsPath ----
-    w("@pytest.mark.unit")
     w("class TestBidsPath:")
     w('    """Tests for bids_path."""')
     w()
@@ -641,7 +639,6 @@ def w(s: str = "") -> None:
     w()
 
     # ---- TestParseBidsName ----
-    w("@pytest.mark.unit")
     w("class TestParseBidsName:")
     w('    """Tests for parse_bids_name."""')
     w()
@@ -724,7 +721,6 @@ def w(s: str = "") -> None:
     w()
 
     # ---- TestConstants ----
-    w("@pytest.mark.unit")
     w("class TestConstants:")
     w('    """Tests for namespace constant classes."""')
     w()

src/rbc/__init__.py

@@ -1 +1,3 @@
 """.. include:: ../../README.md"""  # noqa: D415
+
+from __future__ import annotations

src/rbc/cli/__init__.py

@@ -1,7 +1,9 @@
-"""Command line interface.
+"""Command-line interface for the RBC pipeline.
 
-This module handles CLI entry points for the RBC pipeline.
-
-Parses arguments, validates BIDS inputs, and dispatches to workflow modules.
-Subcommands are defined in rbc.cli.* modules.
+Entry point that parses arguments, validates BIDS inputs, and dispatches to
+the appropriate workflow. Each subcommand (``anatomical``, ``functional``,
+``derivatives``, ``longitudinal``, ``qc``) is defined in its own submodule
+under ``rbc.cli``.
 """
+
+from __future__ import annotations

src/rbc/cli/anatomical.py

@@ -1,5 +1,3 @@
-"""Anatomical preprocessing CLI.
+"""CLI subcommand for anatomical processing."""
 
-Command-line interface for anatomical preprocessing workflows.
-Calls into rbc.workflows.anatomical.
-"""
+from __future__ import annotations

src/rbc/cli/derivatives.py

@@ -1,5 +1,8 @@
-"""Derivative computations CLI.
+"""CLI subcommand for derivative computation.
 
-Command-line interface for computing derivatives (ALFF/fALFF, ReHo, network
-centrality, atlas-based timeseries) from preprocessed data.
+Runs post-preprocessing analyses on cleaned BOLD data: ALFF/fALFF (amplitude
+of low-frequency fluctuations), ReHo (regional homogeneity), network
+centrality, and atlas-based timeseries extraction.
 """
+
+from __future__ import annotations

src/rbc/cli/functional.py

@@ -1,5 +1,10 @@
-"""Functional preprocessing CLI.
+"""CLI subcommand for functional processing.
 
-Command-line interface for functional preprocessing workflows.
-Requires anatomical preprocessing to have been run first.
+Parses subject/session/task arguments and delegates to
+``rbc.workflows.functional.single_session_preprocess``, which runs the functional
+stream (reorientation -> TR truncation -> motion correction). Anatomical
+preprocessing must be completed first since coregistration and template
+warping depend on the anatomical outputs.
 """
+
+from __future__ import annotations