refactor: move cli/runner/verification into pipeline/

README.md

@@ -93,7 +93,7 @@ mxalign slurm path/to/config.yaml --account your_account --queue your_queue --co
 You can also execute the entire configuration-driven pipeline directly from Python using the `Runner` class.
 
 ```python
-from mxalign.runner import Runner
+from mxalign.pipeline.runner import Runner
 
 # Initialize the runner with a YAML config file or a dictionary
 runner = Runner("path/to/config.yaml")

examples/advanced.ipynb

@@ -384,7 +384,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mxalign.runner import Runner\n",
+    "from mxalign.pipeline.runner import Runner\n",
     "\n",
     "runner = Runner(\"./config.yaml\")"
    ]

pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
 ]
 
 [project.scripts]
-mxalign = "mxalign.cli:main"
+mxalign = "mxalign.pipeline.cli:main"
 
 [project.optional-dependencies]
 earthkit = [

src/mxalign/__init__.py

@@ -1,5 +1,8 @@
-from .transformations.transform import transform
-from .transformations.registry import available_transformations, register_transformation
+from .pipeline.transformations.transform import transform
+from .pipeline.transformations.registry import (
+    available_transformations,
+    register_transformation,
+)
 from .alignment.interpolations.interpolate import interpolate
 from .alignment.interpolations.registry import (
     available_interpolations,
@@ -10,7 +13,7 @@
 
 from . import accessor
 from . import alignment
-from . import transformations
+from . import pipeline
 
 __all__ = [
     "transform",
@@ -23,5 +26,5 @@
     "align_space",
     "accessor",
     "alignment",
-    "transformations",
+    "pipeline",
 ]

src/mxalign/pipeline/__init__.py

@@ -0,0 +1,5 @@
+from . import transformations
+
+__all__ = [
+    "transformations",
+]

src/mxalign/runner.py → src/mxalign/pipeline/runner.py

@@ -3,11 +3,11 @@
 
 from mlwp_data_loaders import load_and_validate_dataset
 
-from .utils.config import Config
+from .config import Config
 from .transformations.transform import transform
-from .alignment.time import align_time
-from .alignment.nans import broadcast_nans
-from .utils.save import save_dataset, save_metrics
+from ..alignment.time import align_time
+from ..alignment.nans import broadcast_nans
+from .save import save_dataset, save_metrics
 from .verification import Metric
 
 

tests/test_dates.py

@@ -2,9 +2,9 @@
 
 import pytest
 
-from mxalign.utils.config import Config
-from mxalign.utils.dates import Dates
-from mxalign.utils.save import DatasetPath
+from mxalign.pipeline.config import Config
+from mxalign.pipeline.dates import Dates
+from mxalign.pipeline.save import DatasetPath
 
 # 3 reference times (daily) × 3 lead times (0, 12, 24h)
 DATES = dict(start="2020-01-01", end="2020-01-03", period="1D", range="24h", step="12h")

tests/test_runner.py

@@ -1,6 +1,6 @@
 import pytest
 
-from mxalign.runner import Runner
+from mxalign.pipeline.runner import Runner
 
 
 def _runner(datasets: dict, alignment: dict) -> Runner:

tests/test_transformations.py

@@ -1,11 +1,11 @@
 import pytest
 import xarray as xr
 
-from mxalign.transformations.registry import (
+from mxalign.pipeline.transformations.registry import (
     available_transformations,
     register_transformation,
 )
-from mxalign.transformations.transform import transform
+from mxalign.pipeline.transformations.transform import transform
 
 
 @register_transformation("_test_double")