Enable with syntax using the new MetopReader.dataset method. (#17)

Author: lupemba

README.md

@@ -59,8 +59,8 @@ reduced_data_folder = Path(reduced_data_folder)
 reduced_data_files = [f for f in reduced_data_folder.iterdir() if f.is_file()]
 
 test_file_name = next((s for s in reduced_data_files if s.name.startswith("ASCA_SZO")))
-test_file_path = reduced_data_folder / test_file_name
-ds = metop_reader.open_dataset(file_path=str(test_file_path), maskingvalue = float("nan"))
+test_file_path = str(reduced_data_folder / test_file_name)
+ds = metop_reader.open_dataset(file_path=test_file_path, maskingvalue = float("nan"))
 ```
 
 2. Check keys
@@ -175,6 +175,26 @@ print(longitude_slice_np)
 metop_reader.close_dataset(ds)
 ```
 
+8. It is recommended to use the `with` syntax to automaticlly close the file
+
+```python
+latitude = None
+
+with metop_reader.dataset(test_file_path, maskingvalue = float("nan")) as ds:
+  latitude = metop_reader.as_array(ds['latitude'])
+  latitude = np.array(latitude, copy = None)
+
+print(latitude.shape)
+```
+<details>
+
+<summary>Output of the print </summary>
+
+```
+(42, 10)
+```
+
+</details>
 ## Development
 
 Pre-requisite: Install podman or docker in your machine.

metoppy/__init__.py

@@ -11,7 +11,7 @@
 """Metoppy package initialization."""
 
 # Optional: version info
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 # Import main classes/functions
 from .metopreader import MetopReader

metoppy/metopreader.py

@@ -12,7 +12,7 @@
 """MetopDatasets.jl Python wrapper class: MetopReader."""
 
 from juliacall import Main
-
+from contextlib import contextmanager
 
 class MetopReader:
     """Python wrapper class for MetopDatasets.jl Julia package."""
@@ -129,3 +129,23 @@ def get_test_data_artifact(self):
             A MetopDataset object containing test data for validation or demo purposes.
         """
         return self._get_test_data_artifact()
+    
+    @contextmanager
+    def dataset(self, file_path: str, **kwargs):
+        """
+        Open a dataset using the python `with` syntax. The method opens the file using `open_dataset()` and
+        then finally closes the file using `close_dataset()` once the excution of the `with` block is completed.
+        
+        Example
+        ----------
+        :: 
+            metop_reader = MetopReader()
+            with metop_reader.dataset("path to a file") as ds:
+                # read some data
+            
+        """
+        ds = self.open_dataset(file_path, **kwargs)
+        try:
+            yield ds
+        finally:
+            self.close_dataset(ds)

metoppy/tests/test_basic_interface.py

@@ -36,7 +36,7 @@ def test_file(request, metop_reader):
     test_file_name = next((f for f in reduced_data_files if f.name.startswith(product_type)), None)
     test_file_path = reduced_data_folder / test_file_name
 
-    return test_file_path
+    return str(test_file_path)
 
 
 @pytest.mark.parametrize("test_file", ["ASCA_SZO"], indirect=True)
@@ -45,7 +45,7 @@ def test_get_keys(metop_reader, test_file):
     Simple test for metop_reader.get_key
     """
     # arrange
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # act
     keys = metop_reader.get_keys(ds)
@@ -69,7 +69,7 @@ def test_close_dataset(metop_reader, test_file):
     """
     # arrange
     import juliacall
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # act
     metop_reader.close_dataset(ds)
@@ -85,7 +85,7 @@ def test_shape(metop_reader, test_file):
     Simple test for metop_reader.shape.
     """
     # arrange
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # act
     latitude = ds['latitude']
@@ -110,7 +110,7 @@ def test_read_single_value(metop_reader, test_file):
     """
     # arrange
     import datetime
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # act
     CO2_radiance = ds["gs1cspect"][91, 0, 0, 0]
@@ -137,7 +137,7 @@ def test_read_array(metop_reader, test_file):
     """
     # arrange
     import numpy as np
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # act
     latitude_julia = metop_reader.as_array(ds['latitude'])
@@ -165,7 +165,7 @@ def test_type_stable_array(metop_reader, test_file):
     """
     # arrange
     import numpy as np
-    ds = metop_reader.open_dataset(file_path=str(test_file), maskingvalue = float("nan"))
+    ds = metop_reader.open_dataset(test_file, maskingvalue = float("nan"))
 
     # act
     latitude = np.array(metop_reader.as_array(ds['latitude']), copy = None)
@@ -186,7 +186,7 @@ def test_different_file_types(metop_reader, test_file):
     Test that different types of test files can be opened.
     """
     # act
-    ds = metop_reader.open_dataset(file_path=str(test_file))
+    ds = metop_reader.open_dataset(test_file)
 
     # assert
     assert ds is not None
@@ -204,7 +204,7 @@ def test_no_auto_convert(metop_reader, test_file):
     """
     # arrange
     from juliacall import Main as jl
-    ds = metop_reader.open_dataset(file_path=str(test_file), auto_convert=False)
+    ds = metop_reader.open_dataset(test_file, auto_convert=False)
 
     # act
     start_time = ds["record_start_time"][2]
@@ -216,4 +216,29 @@ def test_no_auto_convert(metop_reader, test_file):
     assert start_time.millisecond == 73275381
 
     # clean 
-    metop_reader.close_dataset(ds)
+    metop_reader.close_dataset(ds)
+
+
+@pytest.mark.parametrize("test_file", ["ASCA_SZO"], indirect=True)
+def test_with_dataset(metop_reader, test_file):
+    """
+    Test using `with` syntax to read data from a data set.
+    """
+    # arrange
+    import numpy as np
+    import juliacall
+    ds_place_holder = None
+    latitude = None
+
+    # act
+    with metop_reader.dataset(test_file, maskingvalue = float("nan")) as ds:
+        latitude_julia = metop_reader.as_array(ds['latitude'])
+        latitude = np.array(latitude_julia, copy = None)
+        ds_place_holder = ds
+
+    # assert
+    assert np.all((-90 < latitude)&(latitude < 90)) # check values
+    assert latitude.shape == (42,10) # check size
+    with pytest.raises(juliacall.JuliaError): # check that file is closed.
+        ds_place_holder['longitude'][0,0]
+ 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "metoppy"
-version = "0.1.0"
+version = "0.1.1"
 description = "Python package wrapper of MetopDatasets.jl Julia package for reading products from the METOP satellites."
 authors = [
     { name = "Simon Kok Lupemba", email = "simon.koklupemba@eumetsat.int" },