get tests to pass

eogrow/pipelines/batch_to_eopatch.py

@@ -102,7 +102,6 @@ def filter_patch_list(self, patch_list: PatchList) -> PatchList:
     def _get_output_features(self) -> list[tuple[FeatureType, str]]:
         """Lists all features that the pipeline outputs."""
         features = [feature_mapping.feature for feature_mapping in self.config.mapping]
-        features.extend(feature_mapping.feature for feature_mapping in self.config.mapping)
 
         if self.config.userdata_feature_name:
             features.append((FeatureType.META_INFO, self.config.userdata_feature_name))

eogrow/pipelines/merge_samples.py

@@ -73,6 +73,7 @@ def build_workflow(self) -> EOWorkflow:
             self.storage.get_folder(self.config.input_folder_key),
             filesystem=self.storage.filesystem,
             features=self.config.features_to_merge,
+            load_timestamps=True if self.config.include_timestamp else "auto",
         )
         output_task = OutputTask(name=self._OUTPUT_NAME)
         return EOWorkflow(linearly_connect_tasks(load_task, output_task))
@@ -101,7 +102,7 @@ def merge_and_save_features(self, patches: list[EOPatch]) -> None:
         if self.config.include_timestamp:
             arrays = []
             for patch, sample_num in zip(patches, patch_sample_nums):
-                arrays.append(np.tile(np.array(patch.timestamps), (sample_num, 1)))
+                arrays.append(np.tile(np.array(patch.get_timestamps()), (sample_num, 1)))
                 patch.timestamps = []
 
             self._save_array(np.concatenate(arrays, axis=0), "TIMESTAMPS")

eogrow/pipelines/testing.py

@@ -135,6 +135,7 @@ def build_workflow(self) -> EOWorkflow:
             self.storage.get_folder(self.config.output_folder_key),
             filesystem=self.storage.filesystem,
             overwrite_permission=OverwritePermission.OVERWRITE_FEATURES,
+            save_timestamps=self.config.timestamps is not None,
         )
         save_node = EONode(save_task, inputs=[previous_node])
 

eogrow/utils/testing.py

@@ -114,7 +114,7 @@ def _calculate_stats(self, folder: str | None = None) -> JsonDict:
             if self.filesystem.isdir(content_path):
                 fs_data_info = get_filesystem_data_info(self.filesystem, content_path)
                 if fs_data_info.bbox is not None:
-                    eopatch = EOPatch.load(content_path, filesystem=self.filesystem)
+                    eopatch = EOPatch.load(content_path, filesystem=self.filesystem, load_timestamps=True)
                     stats[content] = self._calculate_eopatch_stats(eopatch)
                 else:  # Probably it is not an EOPatch folder
                     stats[content] = self._calculate_stats(folder=content_path)

tests/pipelines/test_merge_samples.py

@@ -7,11 +7,11 @@
 
 @pytest.mark.chain()
 @pytest.mark.order(after="test_features.py::test_features_pipeline")
-@pytest.mark.parametrize(
-    ("experiment_name", "reset_folder"),
-    [("merge_features_samples", True), ("merge_reference_samples", False)],
-)
-def test_merge_samples_pipeline(config_and_stats_paths, experiment_name, reset_folder):
-    config_path, stats_path = config_and_stats_paths("merge_samples", experiment_name)
-    output_path = run_config(config_path, reset_output_folder=reset_folder)
+def test_merge_samples_pipeline(config_and_stats_paths):
+    config_path, stats_path = config_and_stats_paths("merge_samples", "merge_features_samples")
+    output_path = run_config(config_path, reset_output_folder=True)
+    compare_content(output_path, stats_path)
+
+    config_path, stats_path = config_and_stats_paths("merge_samples", "merge_reference_samples")
+    output_path = run_config(config_path, reset_output_folder=False)
     compare_content(output_path, stats_path)

tests/pipelines/test_testing.py

@@ -7,7 +7,7 @@
 
 @pytest.mark.chain()
 @pytest.mark.parametrize("experiment_name", ["testing", "timestamps_only"])
-def test_features_pipeline(config_and_stats_paths, experiment_name):
+def test_data_generating_pipeline(config_and_stats_paths, experiment_name):
     config_path, stats_path = config_and_stats_paths("testing", experiment_name)
     output_path = run_config(config_path)
     compare_content(output_path, stats_path)