Inplace (#47)

* Remove inplace from packaging.  Currently failing tests.

* Remove obsolete inplace argument.

* test_reset_index is failing with "KeyError: 'up'", which I think means there's a bug in DataArray.reset_index, because it's supposed to be able to take MultiIndex level names.

* Moved some stuff to base.

* Remove places where we rewrap DataAssemblies as DataArrays, because reset_index works on DataAssembly since the inplace argument removal changes.

brainio_collection/packaging.py

@@ -5,9 +5,9 @@
 
 import boto3
 from tqdm import tqdm
-from xarray import DataArray
 
 import brainio_base.assemblies
+from brainio_base.assemblies import get_levels
 from brainio_collection import lookup, list_stimulus_sets
 from brainio_collection.lookup import TYPE_ASSEMBLY, TYPE_STIMULUS_SET, sha1_hash
 
@@ -111,9 +111,7 @@ def package_stimulus_set(proto_stimulus_set, stimulus_set_identifier, bucket_nam
 
 def write_netcdf(assembly, target_netcdf_file):
     _logger.debug(f"Writing assembly to {target_netcdf_file}")
-    assembly = DataArray(assembly)  # if we're passed a BrainIO DataAssembly, it will automatically re-index otherwise
-    for index in assembly.indexes.keys():
-        assembly.reset_index(index, inplace=True)
+    assembly = assembly.reset_index(list(assembly.indexes))
     assembly.to_netcdf(target_netcdf_file)
     sha1 = sha1_hash(target_netcdf_file)
     return sha1

tests/test_assemblies.py

@@ -239,6 +239,13 @@ def test_aperture(self, identifier, image_id, expected_amount_gray, ratio_gray):
         assert amount_gray == expected_amount_gray
 
 
+def test_inplace():
+    d = xr.DataArray(0, None, None, None, None, None, False)
+    with pytest.raises(TypeError) as te:
+        d = d.reset_index(None, inplace=True)
+    assert "inplace" in str(te.value)
+
+
 class TestSeibert:
     @pytest.mark.private_access
     def test_dims(self):

tests/test_packaging.py

@@ -0,0 +1,57 @@
+import pytest
+from pathlib import Path
+
+from brainio_base.assemblies import DataAssembly, get_levels
+from brainio_collection.packaging import write_netcdf
+
+
+def test_write_netcdf():
+    assy = DataAssembly(
+        data=[[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12], [13, 14, 15], [16, 17, 18]],
+        coords={
+            'up': ("a", ['alpha', 'alpha', 'beta', 'beta', 'beta', 'beta']),
+            'down': ("a", [1, 1, 1, 1, 2, 2]),
+            'sideways': ('b', ['x', 'y', 'z'])
+        },
+        dims=['a', 'b']
+    )
+    netcdf_path = Path("test.nc")
+    netcdf_sha1 = write_netcdf(assy, str(netcdf_path))
+    assert netcdf_path.exists()
+
+
+def test_reset_index():
+    assy = DataAssembly(
+        data=[[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12], [13, 14, 15], [16, 17, 18]],
+        coords={
+            'up': ("a", ['alpha', 'alpha', 'beta', 'beta', 'beta', 'beta']),
+            'down': ("a", [1, 1, 1, 1, 2, 2]),
+            'sideways': ('b', ['x', 'y', 'z'])
+        },
+        dims=['a', 'b']
+    )
+    assert assy["a"].variable.level_names == ["up", "down"]
+    assert list(assy.indexes) == ["a", "b"]
+    assy = assy.reset_index(list(assy.indexes))
+    assert assy["a"].variable.level_names is None
+    assert get_levels(assy) == []
+    assert list(assy.indexes) == []
+
+
+
+def test_reset_index_levels():
+    assy = DataAssembly(
+        data=[[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12], [13, 14, 15], [16, 17, 18]],
+        coords={
+            'up': ("a", ['alpha', 'alpha', 'beta', 'beta', 'beta', 'beta']),
+            'down': ("a", [1, 1, 1, 1, 2, 2]),
+            'sideways': ('b', ['x', 'y', 'z'])
+        },
+        dims=['a', 'b']
+    )
+    assert assy["a"].variable.level_names == ["up", "down"]
+    assy = assy.reset_index(["up", "down"])
+    assert get_levels(assy) == []
+
+
+