Some quick fixes to migration breaks

nadeemlab · Sep 20, 2024 · d951969 · d951969
1 parent 26de250
commit d951969
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/data_curation/datasets/moldoveanu/_cell_measurement_aggregation.py b/data_curation/datasets/moldoveanu/_cell_measurement_aggregation.py
@@ -1,5 +1,6 @@
 """Merge TIFF channel file data and aggregate over cell segments."""
 
+import sys
 import warnings
 
 from pandas import DataFrame
@@ -9,7 +10,9 @@
 from numpy import isnan
 
 from _extraction_formats import create_sparse_dataframe  # pylint: disable=E0611
-from ...convenience_scripts.bimodality_assessor import BimodalityAssessor
+
+sys.path.append('../../convenience_scripts')
+from bimodality_assessor import create_bimodal_vector
 
 def aggregate_cell(group: DataFrame, channel_name: str) -> float:
     with warnings.catch_warnings():

diff --git a/data_curation/datasets/moldoveanu/extract.sh b/data_curation/datasets/moldoveanu/extract.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+mkdir -p generated_artifacts/
+
 if [[ ! -d CP_output_tiff ]];
 then
     filebase="Moldoveanu2022-cytof-RAW"