fix tests for pipelines to take in slp paths

tests/test_trait_pipelines.py

@@ -15,10 +15,27 @@
 )
 
 
-def test_dicot_pipeline(canola_h5, soy_h5):
+def test_dicot_pipeline(
+    canola_h5,
+    soy_h5,
+    canola_primary_slp,
+    canola_lateral_slp,
+    soy_primary_slp,
+    soy_lateral_slp,
+):
     # Load the data
-    canola = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
-    soy = Series.load(soy_h5, primary_name="primary", lateral_name="lateral")
+    canola = Series.load(
+        series_name="canola",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
+    soy = Series.load(
+        series_name="soy",
+        h5_path=soy_h5,
+        primary_path=soy_primary_slp,
+        lateral_path=soy_lateral_slp,
+    )
 
     pipeline = DicotPipeline()
     canola_traits = pipeline.compute_plant_traits(canola)
@@ -30,26 +47,36 @@ def test_dicot_pipeline(canola_h5, soy_h5):
     assert all_traits.shape == (2, 1036)
 
 
-def test_OlderMonocot_pipeline(rice_main_10do_h5):
-    rice = Series.load(rice_main_10do_h5, crown_name="crown")
+def test_OlderMonocot_pipeline(rice_main_10do_h5, rice_main_10do_slp):
+    rice = Series.load(
+        series_name="rice_10do",
+        h5_path=rice_main_10do_h5,
+        crown_path=rice_main_10do_slp,
+    )
 
     pipeline = OlderMonocotPipeline()
     rice_10dag_traits = pipeline.compute_plant_traits(rice)
 
     assert rice_10dag_traits.shape == (72, 102)
 
 
-def test_younger_monocot_pipeline(rice_h5, rice_folder):
-    rice = Series.load(rice_h5, primary_name="primary", crown_name="crown")
-    rice_series_all = find_all_series(rice_folder)
-    series_all = [
-        Series.load(series, primary_name="primary", crown_name="crown")
-        for series in rice_series_all
-    ]
-
+def test_younger_monocot_pipeline(rice_pipeline_output_folder):
+    # Find slp paths in folder
+    slp_paths = find_all_slp_paths(rice_pipeline_output_folder)
+    assert len(slp_paths) == 4
+    # Load series from slps
+    rice_series_all = load_series_from_slps(
+        slp_paths=slp_paths, h5s=False, csv_path=None
+    )
+    assert len(rice_series_all) == 2
+    # Get first series
+    rice_series = rice_series_all[0]
+    # Initialize pipeline for younger monocot
     pipeline = YoungerMonocotPipeline()
-    rice_traits = pipeline.compute_plant_traits(rice)
-    all_traits = pipeline.compute_batch_traits(series_all)
+    # Get traits for the first series using the pipeline
+    rice_traits = pipeline.compute_plant_traits(rice_series)
+    # Get all traits for all series using the pipeline
+    all_traits = pipeline.compute_batch_traits(rice_series_all)
 
     # Dataframe shape assertions
     assert rice_traits.shape == (72, 104)
@@ -96,14 +123,22 @@ def test_younger_monocot_pipeline(rice_h5, rice_folder):
     ).all(), "angle_column in all_traits contains values out of range [0, 180]"
 
 
-def test_older_monocot_pipeline(rice_main_10do_h5, rice_10do_folder):
-    rice = Series.load(rice_main_10do_h5, crown_name="crown")
-    rice_series_all = find_all_series(rice_10do_folder)
-    series_all = [Series.load(series, crown_name="crown") for series in rice_series_all]
+def test_older_monocot_pipeline(rice_10do_pipeline_output_folder):
+    # Find slp paths in folder
+    slp_paths = find_all_slp_paths(rice_10do_pipeline_output_folder)
+    assert len(slp_paths) == 1
+    # Load series from slps
+    rice_series_all = load_series_from_slps(
+        slp_paths=slp_paths, h5s=False, csv_path=None
+    )
+    assert len(rice_series_all) == 1
+    # Get first series
+    rice_series = rice_series_all[0]
+    assert rice_series.series_name == "scan0K9E8BI"
 
     pipeline = OlderMonocotPipeline()
-    rice_traits = pipeline.compute_plant_traits(rice)
-    all_traits = pipeline.compute_batch_traits(series_all)
+    all_traits = pipeline.compute_batch_traits(rice_series_all)
+    rice_traits = pipeline.compute_plant_traits(rice_series)
 
     # Dataframe shape assertions
     assert rice_traits.shape == (72, 102)
@@ -148,27 +183,26 @@ def test_multiple_dicot_pipeline(
     multiple_arabidopsis_11do_h5,
     multiple_arabidopsis_11do_folder,
     multiple_arabidopsis_11do_csv,
+    multiple_arabidopsis_11do_primary_slp,
+    multiple_arabidopsis_11do_lateral_slp,
 ):
     arabidopsis = Series.load(
-        multiple_arabidopsis_11do_h5,
-        primary_name="primary",
-        lateral_name="lateral",
+        series_name="997_1",
+        h5_path=multiple_arabidopsis_11do_h5,
+        primary_path=multiple_arabidopsis_11do_primary_slp,
+        lateral_path=multiple_arabidopsis_11do_lateral_slp,
+        csv_path=multiple_arabidopsis_11do_csv,
+    )
+    arabidopsis_slp_paths = find_all_slp_paths(multiple_arabidopsis_11do_folder)
+    arabidopsis_series_all = load_series_from_slps(
+        slp_paths=arabidopsis_slp_paths,
+        h5s=True,
         csv_path=multiple_arabidopsis_11do_csv,
     )
-    arabidopsis_series_all = find_all_series(multiple_arabidopsis_11do_folder)
-    series_all = [
-        Series.load(
-            series,
-            primary_name="primary",
-            lateral_name="lateral",
-            csv_path=multiple_arabidopsis_11do_csv,
-        )
-        for series in arabidopsis_series_all
-    ]
 
     pipeline = MultipleDicotPipeline()
     arabidopsis_traits = pipeline.compute_multiple_dicots_traits(arabidopsis)
-    all_traits = pipeline.compute_batch_multiple_dicots_traits(series_all)
+    all_traits = pipeline.compute_batch_multiple_dicots_traits(arabidopsis_series_all)
 
     # Dataframe shape assertions
     assert pd.DataFrame([arabidopsis_traits["summary_stats"]]).shape == (1, 315)