Merge branch 'main' into add-harmonypy

openproblems-bio · Dec 4, 2024 · 5387cb6 · 5387cb6
2 parents 2f05980 + b7efc89
commit 5387cb6
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Showing 6 changed files with 25 additions and 22 deletions.
diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh
@@ -110,5 +110,6 @@ viash run src/data_processors/process_dataset/config.vsh.yaml -- \
 
 # # only run this if you have access to the openproblems-data bucket
 aws s3 sync --profile op \
-  "$DATASET_DIR" s3://openproblems-data/resources_test/task_cyto_batch_integration \
+  resources_test/task_cyto_batch_integration/starter_file \
+  s3://openproblems-data/resources_test/task_cyto_batch_integration/starter_file \
   --delete --dryrun
diff --git a/src/api/comp_control_method.yaml b/src/api/comp_control_method.yaml
@@ -24,10 +24,10 @@ arguments:
     __merge__: file_integrated.yaml
     required: true
     direction: output
-# test_resources:
-#   - type: python_script
-#     path: /common/component_tests/run_and_check_output.py
-#   - type: python_script
-#     path: /common/component_tests/check_config.py
-#   - path: /resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
-#     dest: resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - type: python_script
+    path: /common/component_tests/check_config.py
+  - path: /resources_test/task_cyto_batch_integration/starter_file
+    dest: resources_test/task_cyto_batch_integration/starter_file
diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml
@@ -23,9 +23,9 @@ arguments:
     __merge__: file_validation.yaml
     direction: output
     required: true
-# test_resources:
-#   - path: /resources_test/common/cxg_mouse_pancreas_atlas
-#     dest: resources_test/common/cxg_mouse_pancreas_atlas
-#   - type: python_script
-#     path: /common/component_tests/run_and_check_output.py
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - path: /resources_test/task_cyto_batch_integration/starter_file
+    dest: resources_test/task_cyto_batch_integration/starter_file
 
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
@@ -3,9 +3,9 @@ info:
   type: method
   type_info:
     label: Method
-    summary: A method.
+    summary: A method for integrating batch effects in cytometry data.
     description: |
-      A method to predict the task effects.
+      A method for integrating batch effects in cytometry data.
 arguments:
   - name: --input
     __merge__: file_unintegrated_censored.yaml

diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
@@ -23,10 +23,10 @@ arguments:
     __merge__: file_score.yaml
     direction: output
     required: true
-# test_resources:
-#   - type: python_script
-#     path: /common/component_tests/run_and_check_output.py
-#   - type: python_script
-#     path: /common/component_tests/check_config.py
-#   - path: /resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
-#     dest: resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
+test_resources:
+  - type: python_script
+    path: /common/component_tests/run_and_check_output.py
+  - type: python_script
+    path: /common/component_tests/check_config.py
+  - path: /resources_test/task_cyto_batch_integration/starter_file
+    dest: resources_test/task_cyto_batch_integration/starter_file
diff --git a/src/metrics/accuracy/config.vsh.yaml b/src/metrics/accuracy/config.vsh.yaml
@@ -10,6 +10,8 @@ __merge__: ../../api/comp_metric.yaml
 # Can contain only lowercase letters or underscores.
 name: accuracy
 
+status: disabled
+
 # Metadata for your component
 info:
   metrics: