Merge branch 'support-passthrough' into 'master'

Support a pipeline with "passthrough" or None as estimator

See merge request !302

bob/bio/base/pipelines/pipelines.py

@@ -198,12 +198,16 @@ def check_valid_pipeline(pipeline_simple):
     """
 
     # CHECKING THE TRANSFORMER
-    # Checking if it's a Scikit Pipeline or a estimator
+    # Checking if it's a Scikit Pipeline or an estimator
     if isinstance(pipeline_simple.transformer, Pipeline):
 
         # Checking if all steps are wrapped as samples, if not, we should wrap them
         for p in pipeline_simple.transformer:
-            if not is_instance_nested(p, "estimator", SampleWrapper):
+            if (
+                not is_instance_nested(p, "estimator", SampleWrapper)
+                and type(p) is not str
+                and p is not None
+            ):
                 wrap(["sample"], p)
 
     # In this case it can be a simple estimator. AND

bob/bio/base/test/test_pipeline_simple.py

@@ -518,6 +518,26 @@ def test_database_full_failure():
         _run_with_failure(False, sporadic_fail=False)
 
 
+def test_pipeline_simple_passthrough():
+    """Ensure that PipelineSimple accepts a passthrough Estimator."""
+    passthrough = make_pipeline(None)
+    pipeline = PipelineSimple(passthrough, Distance())
+    assert isinstance(pipeline, PipelineSimple)
+
+    pipeline_with_passthrough = make_pipeline("passthrough")
+    pipeline = PipelineSimple(pipeline_with_passthrough, Distance())
+    assert isinstance(pipeline, PipelineSimple)
+    db = DummyDatabase()
+    scores = pipeline(
+        db.background_model_samples(), db.references(), db.probes()
+    )
+    assert len(scores) == 10
+    for sample_scores in scores:
+        assert len(sample_scores) == 10
+        for score in sample_scores:
+            assert isinstance(score.data, float)
+
+
 def _create_test_config(path):
     with open(path, "w") as f:
         f.write(