Raise test coverage: Full test suit, contract wrappers, execution, separation

src/adapt/contracts/time.py

@@ -10,6 +10,8 @@
 returning a dataset to the context.
 """
 
+import contextlib
+
 import numpy as np
 import xarray as xr
 
@@ -41,10 +43,8 @@ def assert_time_normalized(ds: xr.Dataset) -> None:
         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:
+            with contextlib.suppress(Exception):
                 tv = tv.item()
-            except Exception:
-                pass
         module = getattr(type(tv), "__module__", "")
         require(
             not module.startswith("cftime"),

src/adapt/utils/time.py

@@ -0,0 +1,33 @@
+"""Time normalization helpers shared across ADAPT modules."""
+
+import contextlib
+from datetime import UTC, datetime
+
+import numpy as np
+
+
+def normalize_time_scalar(time_val):
+    """Normalize xarray/cftime/numpy time representations to a scalar."""
+    tv = time_val
+    while isinstance(tv, np.ndarray) and tv.size == 1:
+        tv = tv.reshape(-1)[0]
+    if isinstance(tv, np.ndarray):
+        tv = tv.reshape(-1)[0]
+
+    if hasattr(tv, "item"):
+        with contextlib.suppress(TypeError, ValueError):
+            tv = tv.item()
+
+    if getattr(type(tv), "__module__", "").startswith("cftime"):
+        tv = datetime(
+            int(tv.year),
+            int(tv.month),
+            int(tv.day),
+            int(tv.hour),
+            int(tv.minute),
+            int(tv.second),
+            int(getattr(tv, "microsecond", 0) or 0),
+            tzinfo=UTC,
+        )
+
+    return tv

tests/cli/test_config_command.py

@@ -0,0 +1,49 @@
+import os
+import shutil
+from argparse import Namespace
+from pathlib import Path
+
+from adapt.cli import _config_cmd
+
+
+def test_adapt_config_handles_deleted_cwd(tmp_path, monkeypatch):
+    # Create and chdir into a temp directory, then delete it to simulate stale cwd.
+    cwd = tmp_path / "gone"
+    cwd.mkdir()
+    os.chdir(cwd)
+    shutil.rmtree(cwd)
+
+    home = tmp_path / "home"
+    home.mkdir()
+    monkeypatch.setenv("HOME", str(home))
+
+    # No output arg: must fail loudly (cannot resolve ./config.yaml).
+    args = Namespace(output=None)
+    try:
+        _config_cmd(args)
+    except FileNotFoundError as e:
+        assert "Current working directory no longer exists" in str(e)
+    else:
+        raise AssertionError(
+            "Expected FileNotFoundError when cwd is missing and no output is provided"
+        )
+
+    # Absolute output path should still work even when cwd is missing.
+    os.chdir(home)
+    out = Path(home) / "config.yaml"
+    args2 = Namespace(output=str(out))
+    _config_cmd(args2)
+    assert out.exists()
+    text = out.read_text()
+    assert f'base_dir: "{str(home)}"' in text
+
+
+def test_adapt_config_sets_base_dir_to_output_parent(tmp_path):
+    out_dir = tmp_path / "nested"
+    out_path = out_dir / "my_config.yaml"
+    args = Namespace(output=str(out_path))
+    _config_cmd(args)
+
+    assert out_path.exists()
+    text = out_path.read_text()
+    assert f'base_dir: "{str(out_dir)}"' in text

tests/configuration/test_cli_config.py

@@ -0,0 +1,115 @@
+"""Tests for CLIConfig schema and conversion to internal overrides."""
+
+from adapt.configuration.schemas.cli import CLIConfig
+
+
+def test_cli_to_internal_overrides_with_mode():
+    """Test CLI config conversion with mode override."""
+    cli = CLIConfig(mode="historical")
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "historical"
+
+
+def test_cli_to_internal_overrides_with_realtime_mode():
+    """Test CLI config conversion with realtime mode."""
+    cli = CLIConfig(mode="realtime")
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "realtime"
+
+
+def test_cli_to_internal_overrides_with_radar_id():
+    """Test CLI config conversion with radar_id override."""
+    cli = CLIConfig(radar="KMOB")
+    overrides = cli.to_internal_overrides()
+    assert overrides["downloader"]["radar"] == "KMOB"
+
+
+def test_cli_to_internal_overrides_with_log_level():
+    """Test CLI config conversion with log_level override."""
+    cli = CLIConfig(log_level="DEBUG")
+    overrides = cli.to_internal_overrides()
+    assert overrides["logging"]["level"] == "DEBUG"
+
+
+def test_cli_to_internal_overrides_with_multiple_fields():
+    """Test CLI config conversion with multiple overrides."""
+    cli = CLIConfig(mode="historical", radar="KHTX", log_level="INFO")
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "historical"
+    assert overrides["downloader"]["radar"] == "KHTX"
+    assert overrides["logging"]["level"] == "INFO"
+
+
+def test_cli_to_internal_overrides_empty():
+    """Test CLI config conversion with no overrides."""
+    cli = CLIConfig()
+    overrides = cli.to_internal_overrides()
+    assert overrides == {}
+
+
+def test_cli_config_accepts_base_dir():
+        """Test that base_dir is accepted and in overrides."""
+        cli = CLIConfig(base_dir="/path/to/output")
+        assert cli.base_dir == "/path/to/output"
+        overrides = cli.to_internal_overrides()
+        assert overrides["base_dir"] == "/path/to/output"
+
+def test_cli_config_all_log_levels():
+    """Test all valid log levels."""
+    for level in ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]:
+        cli = CLIConfig(log_level=level)
+        overrides = cli.to_internal_overrides()
+        assert overrides["logging"]["level"] == level
+
+
+def test_cli_infers_historical_mode_from_start_time():
+    """CLI automatically sets mode=historical if start_time provided without explicit mode."""
+    cli = CLIConfig(start_time="2024-01-01T00:00:00Z")
+    assert cli.mode == "historical"
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "historical"
+
+
+def test_cli_infers_historical_mode_from_end_time():
+    """CLI automatically sets mode=historical if end_time provided without explicit mode."""
+    cli = CLIConfig(end_time="2024-01-01T23:59:59Z")
+    assert cli.mode == "historical"
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "historical"
+
+
+def test_cli_infers_historical_mode_from_both_times():
+    """CLI automatically sets mode=historical if both times provided without explicit mode."""
+    cli = CLIConfig(
+        start_time="2024-01-01T00:00:00Z",
+        end_time="2024-01-01T23:59:59Z"
+    )
+    assert cli.mode == "historical"
+    overrides = cli.to_internal_overrides()
+    assert overrides["mode"] == "historical"
+    assert overrides["downloader"]["start_time"] == "2024-01-01T00:00:00Z"
+    assert overrides["downloader"]["end_time"] == "2024-01-01T23:59:59Z"
+
+
+def test_cli_explicit_mode_overrides_time_inference():
+    """Explicit mode in CLI is not overridden by time inference."""
+    cli = CLIConfig(
+        mode="realtime",
+        start_time="2024-01-01T00:00:00Z"
+    )
+    # Explicit mode should be respected
+    assert cli.mode == "realtime"
+
+
+def test_cli_time_fields_in_overrides():
+    """Test that start_time and end_time are included in overrides."""
+    cli = CLIConfig(
+        start_time="2024-01-01T00:00:00Z",
+        end_time="2024-01-01T23:59:59Z",
+        radar="KMOB"
+    )
+    overrides = cli.to_internal_overrides()
+    assert overrides["downloader"]["start_time"] == "2024-01-01T00:00:00Z"
+    assert overrides["downloader"]["end_time"] == "2024-01-01T23:59:59Z"
+    assert overrides["downloader"]["radar"] == "KMOB"
+

tests/configuration/test_cli_precedence.py

@@ -0,0 +1,78 @@
+from adapt.configuration.schemas.cli import CLIConfig
+from adapt.configuration.schemas.param import ParamConfig
+from adapt.configuration.schemas.resolve import resolve_config
+from adapt.configuration.schemas.user import UserConfig
+
+
+def test_cli_overrides_do_not_mutate_user():
+    user = UserConfig.model_validate({"RADAR_ID": "KABC", "MODE": "realtime", "BASE_DIR": "/tmp"})
+
+    cli = CLIConfig.model_validate({"radar": "KHTX"})
+
+    internal = resolve_config(ParamConfig(), user, cli)
+
+    # CLI should take precedence
+    assert internal.downloader.radar == "KHTX"
+
+    # But the original user model should remain unchanged
+    assert user.radar == "KABC"
+
+
+def test_cli_minimal_overrides_radar_id():
+    """CLI radar_id override should work correctly."""
+    user = UserConfig(base_dir="/tmp", radar="KABC")
+    cli = CLIConfig(radar="KHTX")
+
+    config = resolve_config(ParamConfig(), user, cli)
+
+    assert config.downloader.radar == "KHTX"  # CLI wins
+    assert config.base_dir == "/tmp"  # User value preserved
+
+
+def test_cli_minimal_overrides_mode():
+    """CLI mode override should work correctly.""" 
+    user = UserConfig(
+        base_dir="/tmp", 
+        radar="KABC", 
+        mode="realtime",
+        start_time="2024-01-01T00:00:00Z",
+        end_time="2024-01-01T12:00:00Z"
+    )
+    cli = CLIConfig(mode="historical")
+
+    config = resolve_config(ParamConfig(), user, cli)
+
+    assert config.mode == "historical"  # CLI wins
+    assert config.downloader.radar == "KABC"  # User value preserved
+    # Historical mode validation should pass since start/end times provided
+
+
+def test_cli_precedence_no_user_config():
+    """CLI should work even without UserConfig."""
+    cli = CLIConfig(radar="KHTX", mode="realtime")
+
+    # This will need minimal UserConfig for required fields
+    user = UserConfig(base_dir="/tmp")
+    config = resolve_config(ParamConfig(), user, cli)
+
+    assert config.downloader.radar == "KHTX"
+    assert config.mode == "realtime"
+
+
+def test_cli_only_overrides_specified_fields():
+    """CLI should only override fields that are explicitly set."""
+    user = UserConfig(
+        base_dir="/tmp",
+        radar="KABC", 
+        mode="realtime",
+        threshold=35
+    )
+
+    # CLI only sets radar_id
+    cli = CLIConfig(radar="KHTX")
+
+    config = resolve_config(ParamConfig(), user, cli)
+
+    assert config.downloader.radar == "KHTX"  # CLI override
+    assert config.mode == "realtime"  # User value preserved
+    assert config.segmenter.threshold == 35.0  # User value preserved