REF: cleaner code.

.importlinter

@@ -1,4 +1,4 @@
-# Import Linter configuration for ADAPT
+# Import Linter configuration for Adapt
 #
 # Purpose:
 # Enforce architectural boundaries so the codebase stays modular,
@@ -19,22 +19,14 @@ root_packages =
 include_external_packages = False
 
 # ==========================================================
-# 1. Scientific modules must remain independent
+# 1. Scientific module independence — enforced by pytest
 # ==========================================================
 #
-# No module may import from any other module — directly or
-# transitively. Shared types belong in adapt.contracts.
+# Inter-module imports and upward imports from modules/ are
+# caught by tests/test_architecture.py, which auto-discovers
+# subpackages at runtime. No explicit module list needed there.
+# Run: pytest tests/test_architecture.py
 
-[importlinter:contract:independent_modules]
-name = Adapt modules remain independent
-type = independence
-modules =
-    adapt.modules.acquisition
-    adapt.modules.analysis
-    adapt.modules.detection
-    adapt.modules.ingest
-    adapt.modules.projection
-    adapt.modules.tracking
 
 # ==========================================================
 # 2. Modules do not depend on runtime orchestration
@@ -68,12 +60,39 @@ type = forbidden
 source_modules =
     adapt.modules
 forbidden_modules =
+    adapt.execution
     adapt.persistence
     adapt.api
     adapt.gui
     adapt.visualization
     adapt.configuration
 
+# ==========================================================
+# 3b. Utils package imports no adapt internals
+# ==========================================================
+#
+# adapt.utils contains pure stdlib functions shared across
+# the codebase. It must not depend on any adapt layer or
+# it creates import cycles and loses its zero-dependency value.
+
+[importlinter:contract:utils_are_pure]
+name = Utils package imports no adapt internals
+type = forbidden
+source_modules =
+    adapt.utils
+forbidden_modules =
+    adapt.modules
+    adapt.contracts
+    adapt.execution
+    adapt.runtime
+    adapt.persistence
+    adapt.configuration
+    adapt.api
+    adapt.gui
+    adapt.visualization
+    adapt.cli
+    adapt.extensions
+
 # ==========================================================
 # 4. Persistence is infrastructure — no science, no orchestration
 # ==========================================================

README.md

@@ -4,17 +4,13 @@
 [![CI](https://github.com/ARM-DOE/Adapt/actions/workflows/ci.yml/badge.svg)](https://github.com/ARM-DOE/Adapt/actions?query=workflow%3ACI)
 [![Codecov](https://img.shields.io/codecov/c/github/ARM-DOE/Adapt.svg?logo=codecov)](https://codecov.io/gh/ARM-DOE/Adapt)
 [![CodeFactor](https://www.codefactor.io/repository/github/arm-doe/adapt/badge)](https://www.codefactor.io/repository/github/arm-doe/adapt)
+[![Security](https://github.com/ARM-DOE/Adapt/actions/workflows/security-analysis.yml/badge.svg)](https://arm-doe.github.io/Adapt/)
+[![Virus](https://github.com/ARM-DOE/Adapt/actions/workflows/virus.yml/badge.svg)](https://arm-doe.github.io/Adapt/)
 
 
 [![Docs](https://github.com/ARM-DOE/Adapt/actions/workflows/docs.yml/badge.svg)](https://arm-doe.github.io/Adapt/)
 [![PyPi release](https://github.com/ARM-DOE/Adapt/actions/workflows/pypi-release.yml/badge.svg)](https://arm-doe.github.io/Adapt/) 
-[![PyPI - Version](https://img.shields.io/pypi/v/arm-adapt)](https://pypi.org/project/arm-adapt/)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/arm-adapt?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pypi.org/project/arm-adapt/)
-
-[![Security](https://github.com/ARM-DOE/Adapt/actions/workflows/security-analysis.yml/badge.svg)](https://arm-doe.github.io/Adapt/)
-[![Virus](https://github.com/ARM-DOE/Adapt/actions/workflows/virus.yml/badge.svg)](https://arm-doe.github.io/Adapt/)
-
-
 [![PyPI - License](https://img.shields.io/pypi/l/arm-adapt)](https://github.com/ARM-DOE/Adapt?tab=License-1-ov-file#)
 [![ARM](https://img.shields.io/badge/Sponsor-ARM-blue.svg?colorA=00c1de&colorB=00539c)](https://www.arm.gov/)
 

pyproject.toml

@@ -58,6 +58,7 @@ adapt = "adapt.cli:main"
 dev = [
     "pytest>=7.0",
     "pytest-cov",
+    "import-linter>=2.0",
 ]
 docs = [
     "sphinx>=7.0",

src/adapt/cli.py

@@ -19,7 +19,7 @@
 """
 
 import argparse
-import contextlib
+import logging
 import os
 import signal
 import sys
@@ -33,6 +33,8 @@
 # Single-instance enforcement
 # ---------------------------------------------------------------------------
 
+logger = logging.getLogger(__name__)
+
 _PID_FILE = Path.home() / '.adapt' / 'pipeline.pid'
 
 
@@ -58,8 +60,10 @@ def _write_pid() -> None:
 
 
 def _remove_pid() -> None:
-    with contextlib.suppress(Exception):
+    try:
         _PID_FILE.unlink(missing_ok=True)
+    except OSError as exc:
+        logger.warning("Could not remove PID file %s: %s", _PID_FILE, exc)
 
 
 # ---------------------------------------------------------------------------
@@ -82,8 +86,8 @@ def _build_run_nexrad_parser(sub: argparse.ArgumentParser) -> None:
         help='Processing mode',
     )
     sub.add_argument('--start-time', dest='start_time', help='Start time (ISO 8601)')
-    sub.add_argument('--end-time',   dest='end_time',   help='End time (ISO 8601)')
-    sub.add_argument('--base-dir',   dest='base_dir',   help='Repository output directory')
+    sub.add_argument('--end-time', dest='end_time', help='End time (ISO 8601)')
+    sub.add_argument('--base-dir', dest='base_dir', help='Repository output directory')
     sub.add_argument(
         '--run-id',
         dest='run_id',

src/adapt/configuration/defaults.yaml

@@ -6,8 +6,8 @@
 
 pipeline:
   modules:
-    - adapt.modules.ingest.module
-    - adapt.modules.detection.module
-    - adapt.modules.projection.module
-    - adapt.modules.analysis.module
-    - adapt.modules.tracking.module
+    - adapt.execution.nodes.ingest
+    - adapt.execution.nodes.detection
+    - adapt.execution.nodes.projection
+    - adapt.execution.nodes.analysis
+    - adapt.execution.nodes.tracking

src/adapt/contracts/__init__.py

@@ -5,16 +5,35 @@
 
 All pipeline stage validators and the ContractViolation exception live here.
 Import from this package — never from individual contract submodules.
+
+Naming convention
+-----------------
+assert_*  : primitive validators that may take extra arguments (e.g. variable
+            names). Call these from other validators or tests.
+check_*   : bound, zero-extra-arg wrappers. Register these directly in a
+            module's ``input_contracts`` or ``output_contracts`` dict.
 """
 
-from adapt.contracts.analysis import assert_analysis_output, assert_cell_adjacency
-from adapt.contracts.grid import assert_gridded
+from adapt.contracts.analysis import (
+    assert_analysis_output,
+    assert_cell_adjacency,
+    check_cell_adjacency,
+    check_cell_stats,
+)
+from adapt.contracts.grid import assert_gridded, check_grid_ds_2d
 from adapt.contracts.pipeline import ContractViolation, require
-from adapt.contracts.projection import assert_projected
-from adapt.contracts.segmentation import assert_segmented
-from adapt.contracts.tracking import assert_cell_events, assert_tracked_cells
+from adapt.contracts.projection import assert_projected, check_projected_ds
+from adapt.contracts.segmentation import assert_segmented, check_segmented_ds
+from adapt.contracts.time import assert_time_normalized, check_time_normalized
+from adapt.contracts.tracking import (
+    assert_cell_events,
+    assert_tracked_cells,
+    check_cell_events,
+    check_tracked_cells,
+)
 
 __all__ = [
+    # primitives
     "ContractViolation",
     "require",
     "assert_gridded",
@@ -24,4 +43,14 @@
     "assert_cell_adjacency",
     "assert_tracked_cells",
     "assert_cell_events",
+    "assert_time_normalized",
+    # bound checks — register these in input_contracts / output_contracts
+    "check_grid_ds_2d",
+    "check_segmented_ds",
+    "check_projected_ds",
+    "check_cell_stats",
+    "check_cell_adjacency",
+    "check_tracked_cells",
+    "check_cell_events",
+    "check_time_normalized",
 ]

src/adapt/contracts/analysis.py

@@ -94,3 +94,13 @@ def assert_cell_adjacency(df: pd.DataFrame) -> None:
         (df["touching_boundary_pixels"] >= 1).all(),
         "Cell adjacency contract violated: touching_boundary_pixels must be >= 1",
     )
+
+
+def check_cell_stats(df: pd.DataFrame) -> None:
+    """Bound contract for cell statistics DataFrame."""
+    assert_analysis_output(df)
+
+
+def check_cell_adjacency(df: pd.DataFrame) -> None:
+    """Bound contract for cell adjacency DataFrame."""
+    assert_cell_adjacency(df)

src/adapt/contracts/grid.py

@@ -38,3 +38,8 @@ def assert_gridded(ds: xr.Dataset, reflectivity_var: str) -> None:
         refl.ndim == 2,
         f"Grid contract violated: '{reflectivity_var}' has {refl.ndim} dims, expected 2",
     )
+
+
+def check_grid_ds_2d(ds: xr.Dataset) -> None:
+    """Bound contract for the standard 2D grid output (reflectivity variable name fixed)."""
+    assert_gridded(ds, "reflectivity")

src/adapt/contracts/projection.py

@@ -46,3 +46,8 @@ def assert_projected(ds: xr.Dataset, max_steps: int = 5) -> None:
             f"Projection contract violated: found {num_steps} steps, expected {expected_steps} "
             f"(1 registration + {max_steps_actual} projections from config)",
         )
+
+
+def check_projected_ds(ds: xr.Dataset) -> None:
+    """Bound contract for the standard projected dataset."""
+    assert_projected(ds)

src/adapt/contracts/segmentation.py

@@ -48,3 +48,8 @@ def assert_segmented(ds: xr.Dataset, labels_name: str) -> None:
         labels.ndim == 2,
         f"Segmentation contract violated: '{labels_name}' has {labels.ndim} dims, expected 2",
     )
+
+
+def check_segmented_ds(ds: xr.Dataset) -> None:
+    """Bound contract for the standard segmented dataset (cell_labels variable name fixed)."""
+    assert_segmented(ds, "cell_labels")

src/adapt/contracts/time.py

@@ -0,0 +1,59 @@
+# Copyright © 2026, UChicago Argonne, LLC
+# See LICENSE for terms and disclaimer.
+
+"""Time coordinate contract.
+
+Enforces that datasets crossing module boundaries carry a normalized time
+coordinate — numpy datetime64, not cftime — so no module needs its own
+conversion logic. Modules that read raw radar data (e.g. ingest) are
+responsible for calling adapt.utils.time.normalize_time_scalar before
+returning a dataset to the context.
+"""
+
+import numpy as np
+import xarray as xr
+
+from adapt.contracts.pipeline import require
+
+
+def assert_time_normalized(ds: xr.Dataset) -> None:
+    """Enforce that the dataset time coordinate is numpy-compatible, not cftime.
+
+    Parameters
+    ----------
+    ds : xr.Dataset
+        Dataset crossing a module boundary.
+
+    Raises
+    ------
+    ContractViolation
+        If the dataset has no time coordinate, or if the time coordinate
+        uses cftime objects instead of numpy datetime64.
+    """
+    require(
+        "time" in ds.coords or hasattr(ds, "attrs") and "time" in ds.attrs,
+        "Time contract violated: dataset has no 'time' coordinate or attribute. "
+        "Every dataset crossing a module boundary must carry a time stamp.",
+    )
+
+    if "time" in ds.coords:
+        raw = ds.coords["time"].values
+        tv = raw.flat[0] if isinstance(raw, np.ndarray) and raw.ndim > 0 else raw
+        # unwrap numpy scalar wrapper if needed
+        if hasattr(tv, "item"):
+            try:
+                tv = tv.item()
+            except Exception:
+                pass
+        module = getattr(type(tv), "__module__", "")
+        require(
+            not module.startswith("cftime"),
+            f"Time contract violated: time coordinate is cftime ({type(tv).__name__}). "
+            "Normalize with adapt.utils.time.normalize_time_scalar before returning "
+            "the dataset from the ingest or any adapter layer.",
+        )
+
+
+def check_time_normalized(ds: xr.Dataset) -> None:
+    """Bound contract for time normalization — use in module input_contracts."""
+    assert_time_normalized(ds)

src/adapt/contracts/tracking.py

@@ -92,3 +92,15 @@ def assert_cell_events(df: pd.DataFrame) -> None:
         f"Cell events contract violated: invalid event_type present "
         f"(valid={sorted(_VALID_EVENT_TYPES)})",
     )
+
+
+def check_tracked_cells(df: pd.DataFrame) -> None:
+    """Bound contract for tracked cells DataFrame (skips validation on empty frame)."""
+    if not df.empty:
+        assert_tracked_cells(df)
+
+
+def check_cell_events(df: pd.DataFrame) -> None:
+    """Bound contract for cell events DataFrame (skips validation on empty frame)."""
+    if not df.empty:
+        assert_cell_events(df)

src/adapt/execution/graph/executor.py

@@ -69,7 +69,7 @@ def run(self, context: dict) -> dict:
 
         while len(completed) < len(self.nodes):
             iteration += 1
-            if iteration > max_iterations:
+            if iteration > max_iterations:  # pragma: no cover — preempted by no-progress check
                 pending = [n.name for n in self.nodes if n.name not in completed]
                 raise RuntimeError(
                     f"Execution graph appears to contain a cycle or unresolvable "

src/adapt/execution/nodes/__init__.py

@@ -0,0 +1,2 @@
+# Copyright © 2026, UChicago Argonne, LLC
+# See LICENSE for terms and disclaimer.

src/adapt/execution/nodes/analysis.py

@@ -0,0 +1,55 @@
+# Copyright © 2026, UChicago Argonne, LLC
+# See LICENSE for terms and disclaimer.
+
+from adapt.contracts import check_cell_adjacency, check_cell_stats
+from adapt.execution.module_registry import registry
+from adapt.modules.analysis.module import RadarCellAnalyzer
+from adapt.modules.base import BaseModule
+
+
+class AnalysisModule(BaseModule):
+    """BaseModule wrapper for RadarCellAnalyzer.
+
+    Extracts per-cell statistics (area, reflectivity, motion, centroids)
+    from a segmented/projected 2D dataset. Pure compute — no I/O.
+    Persistence is the processor's responsibility.
+
+    Context inputs
+    --------------
+    projected_ds : xr.Dataset
+        2D dataset with projections (output of ProjectionModule).
+    config : InternalConfig
+        Runtime configuration.
+    scan_time : datetime
+        Radar scan timestamp (from LoadModule).
+
+    Context outputs
+    ---------------
+    cell_stats : pd.DataFrame
+        Per-cell statistics DataFrame.
+    cell_adjacency : pd.DataFrame
+        Touching-cell pairs DataFrame.
+    """
+
+    name = "analysis"
+    inputs = ["projected_ds", "analysis_config", "scan_time"]
+    outputs = ["cell_stats", "cell_adjacency"]
+    output_contracts = {"cell_stats": check_cell_stats, "cell_adjacency": check_cell_adjacency}
+
+    def __init__(self) -> None:
+        self._analyzer = None
+
+    def run(self, context: dict) -> dict:
+        config = context["analysis_config"]
+        ds_2d = context["projected_ds"]
+
+        if self._analyzer is None:
+            self._analyzer = RadarCellAnalyzer(config)
+
+        df_cells = self._analyzer.extract(ds_2d, z_level=config.z_level)
+        df_adjacency = self._analyzer.extract_adjacency(ds_2d)
+
+        return {"cell_stats": df_cells, "cell_adjacency": df_adjacency}
+
+
+registry.register(AnalysisModule)