Merge branch 'create_python_module' into 'main'

Create python module

See merge request !5

README.md

@@ -14,7 +14,16 @@ pip install (--user) https://gitlab.dkrz.de/ch1187/rechunk-data/-/archive/2206.0
 User the `--user` flag if you do not have super user rights and are not using `anaconda`, `pipenv` or `virtual env`
 
 ## Usage
-Basic usage:
+### Using the python module
+
+```python
+from rechunk_data import rechunk_dataset
+import xarray as xr
+dset = xr.open_mfdataset("/data/*", parallel=True, combine="by_coords")
+new_data = rechunk_dataset(dset)
+```
+
+### Using the command line interface:
 
 ```bash
 rechunk-data --help

src/rechunk_data/__init__.py

@@ -6,13 +6,11 @@ from pathlib import Path
 from typing import List, Optional
 from ._rechunk import (
     rechunk_netcdf_file,
-    _search_for_nc_files,
-    _save_dataset,
-    _rechunk_dataset,
+    rechunk_dataset,
     logger,
 )
 
-__version__ = "2206.0.2"
+__version__ = "2206.0.3"
 PROGRAM_NAME = "rechunk-data"
 
 

src/rechunk_data/__init__.pyi

@@ -11,6 +11,7 @@ def _save_dataset(
     dset: xr.Dataset, file_name: Path, encoding: Dict[str, Any], engine: str
 ) -> None: ...
 def _rechunk_dataset(dset: xr.Dataset) -> Tuple[xr.Dataset, Dict[str, Any]]: ...
+def rechunk_dataset(dset: xr.Dataset) -> xr.Dataset: ...
 def rechunk_netcdf_file(
     input_path: os.PathLike,
     output_path: Optional[os.PathLike] = ...,

src/rechunk_data/_rechunk.py

@@ -90,6 +90,22 @@ def _rechunk_dataset(dset: xr.Dataset) -> Tuple[xr.Dataset, Dict[str, Any]]:
     return dset, encoding
 
 
+def rechunk_dataset(dset: xr.Dataset) -> xr.Dataset:
+    """Rechunk a xarray dataset.
+
+    Parameters
+    ----------
+    dset: xarray.Dataset
+        Input dataset that is going to be rechunked
+
+    Returns
+    -------
+    xarray.Dataset: rechunked dataset
+    """
+    data, _ = _rechunk_dataset(dset)
+    return data
+
+
 def rechunk_netcdf_file(
     input_path: os.PathLike,
     output_path: Optional[os.PathLike] = None,

src/rechunk_data/tests/test_rechunk_netcdf.py

@@ -4,7 +4,8 @@ from tempfile import NamedTemporaryFile, TemporaryDirectory
 from pathlib import Path
 
 import dask
-from rechunk_data import rechunk_netcdf_file, _save_dataset
+from rechunk_data import rechunk_netcdf_file, rechunk_dataset
+from rechunk_data._rechunk import _save_dataset
 
 
 def test_rechunk_data_dir_with_overwrite(data_dir: Path) -> None:
@@ -38,6 +39,13 @@ def test_rechunk_single_data_file(data_file: Path) -> None:
             assert Path(temp_file.name).exists()
 
 
+def test_rechunk_dataset(small_chunk_data) -> None:
+    """Test rechunking an xarray dataset."""
+    with dask.config.set({"array.chunk-size": "1MiB"}):
+        new_data = rechunk_dataset(small_chunk_data)
+        assert list(new_data.data_vars) == list(small_chunk_data.data_vars)
+
+
 def test_wrong_or_format(small_chunk_data, caplog) -> None:
     """Testing wrong file format."""
     caplog.clear()

src/rechunk_data/tests/test_rechunking.py

@@ -2,7 +2,7 @@
 
 import xarray as xr
 
-from rechunk_data import _rechunk_dataset
+from rechunk_data._rechunk import _rechunk_dataset
 
 
 def test_rechunking_small_data(

src/rechunk_data/tests/test_search_files.py

 """Unit tests for searching for files."""
 from pathlib import Path
 
-from rechunk_data import _search_for_nc_files
+from rechunk_data._rechunk import _search_for_nc_files
 
 
 def test_search_directory(data_dir: Path) -> None: