Merge pull request #19 from kipoi/fix_output_schema

fix get_output_schema

Author: Avsecz

kipoiseq/dataloaders/sequence.py

@@ -247,11 +247,12 @@ def __getitem__(self, idx):
 
     @classmethod
     def get_output_schema(cls):
+        output_schema = deepcopy(cls.output_schema)
         kwargs = default_kwargs(cls)
         ignore_targets = kwargs['ignore_targets']
         if ignore_targets:
-            cls.output_schema.targets = None
-        return cls.output_schema
+            output_schema.targets = None
+        return output_schema
 
 
 # TODO - properly deal with samples outside of the genome
@@ -354,6 +355,7 @@ def __getitem__(self, idx):
     def get_output_schema(cls):
         """Get the output schema. Overrides the default `cls.output_schema`
         """
+        output_schema = deepcopy(cls.output_schema)
 
         # get the default kwargs
         kwargs = default_kwargs(cls)
@@ -366,10 +368,10 @@ def get_output_schema(cls):
         input_shape = mock_input_transform.get_output_shape(kwargs['auto_resize_len'])
 
         # modify it
-        cls.output_schema.inputs.shape = input_shape
+        output_schema.inputs.shape = input_shape
 
         # (optionally) get rid of the target shape
         if kwargs['ignore_targets']:
-            cls.output_schema.targets = None
+            output_schema.targets = None
 
-        return cls.output_schema
+        return output_schema

setup.py

@@ -4,7 +4,7 @@
 from setuptools import setup, find_packages
 
 requirements = [
-    "kipoi>=0.4.2",
+    "kipoi>=0.5.5",
     # "genomelake",
     "pybedtools",
     "pyfaidx",

tests/dataloaders/test_sequence.py

@@ -122,30 +122,34 @@ def test_examples_exist(cls):
 def test_output_schape():
     Dl = deepcopy(SeqIntervalDl)
     assert Dl.get_output_schema().inputs.shape == (None, 4)
-    override_default_kwargs(Dl, {"auto_resize_len": 100})
-    assert Dl.get_output_schema().inputs.shape == (100, 4)
-
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": 1, "alphabet_axis": 2})
-    assert Dl.get_output_schema().inputs.shape == (100, 1, 4)
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": None, "alphabet_axis": 1})  # reset
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": 2})
-    assert Dl.get_output_schema().inputs.shape == (100, 4, 1)
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": None, "alphabet_axis": 1})  # reset
-
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "alphabet": "ACGTD"})
-    assert Dl.get_output_schema().inputs.shape == (100, 5)
-    override_default_kwargs(Dl, {"auto_resize_len": 100, "alphabet": "ACGT"})  # reset
-
-    override_default_kwargs(Dl, {"auto_resize_len": 160, "dummy_axis": 2, "alphabet_axis": 0})
-    assert Dl.get_output_schema().inputs.shape == (4, 160, 1)
-
-    override_default_kwargs(Dl, {"auto_resize_len": 160, "dummy_axis": 2, "alphabet_axis": 1})
-    assert Dl.get_output_schema().inputs.shape == (160, 4, 1)
-    targets = Dl.get_output_schema().targets
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 100})
+    assert Dlc.get_output_schema().inputs.shape == (100, 4)
+
+    # original left intact
+    assert Dl.get_output_schema().inputs.shape == (None, 4)
+
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": 1, "alphabet_axis": 2})
+    assert Dlc.get_output_schema().inputs.shape == (100, 1, 4)
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 100, "dummy_axis": 2})
+    assert Dlc.get_output_schema().inputs.shape == (100, 4, 1)
+    # original left intact
+    assert Dl.get_output_schema().inputs.shape == (None, 4)
+
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 100, "alphabet": "ACGTD"})
+    assert Dlc.get_output_schema().inputs.shape == (100, 5)
+
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 160, "dummy_axis": 2, "alphabet_axis": 0})
+    assert Dlc.get_output_schema().inputs.shape == (4, 160, 1)
+
+    Dlc = override_default_kwargs(Dl, {"auto_resize_len": 160, "dummy_axis": 2, "alphabet_axis": 1})
+    assert Dlc.get_output_schema().inputs.shape == (160, 4, 1)
+    targets = Dlc.get_output_schema().targets
     assert targets.shape == (None,)
 
-    override_default_kwargs(Dl, {"ignore_targets": True})
-    assert Dl.get_output_schema().targets is None
+    Dlc = override_default_kwargs(Dl, {"ignore_targets": True})
+    assert Dlc.get_output_schema().targets is None
     # reset back
-    override_default_kwargs(Dl, {"ignore_targets": False})
-    Dl.output_schema.targets = targets
+
+    # original left intact
+    assert Dl.get_output_schema().inputs.shape == (None, 4)
+    assert Dl.get_output_schema().targets.shape == (None, )