configs, test data

.github/workflows/testing.yml

@@ -55,5 +55,7 @@ jobs:
           
       - name: Test with pytest
         run: |
+          pytest tests/test_preprocess.py
           pytest tests/test_map_to_map.py
           pytest tests/test_distribution_to_distribution.py
+          

tests/config_files/test_config_preproc.yaml

@@ -0,0 +1,8 @@
+submission_config_file: tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json
+seed_flavor_assignment: 0
+thresh_percentile: 93.0
+BOT_box_size: 32
+BOT_loss: wemd
+BOT_iter: 200
+BOT_refine: True
+output_path: tests/results/preproccessed_submission_x/

tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json

@@ -0,0 +1,16 @@
+{
+    "gt": {
+        "name": "gt",
+        "path": "tests/data/unprocessed_dataset_2_submissions/submission_x",
+        "box_size": 224,
+        "pixel_size": 2.146,
+        "ref_align_fname": "1.mrc"
+    },
+    "0": {
+        "name": "raw_submission_in_testdata",
+        "align": 1,
+        "box_size": 244,
+        "pixel_size": 2.146,
+        "path": "tests/data/unprocessed_dataset_2_submissions/submission_x"
+    }
+}

tests/scripts/fetch_test_data.sh

@@ -1,5 +1,8 @@
-mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
+mkdir -p data/dataset_2_submissions tests/results tests/data/unprocessed_dataset_2_submissions/submission_x
 wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
 wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/test_maps_gt_flat_10.pt
 wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/test_metadata_10.csv 
-wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc 
+for FILE in 1.mrc 2.mrc 3.mrc 4.mrc populations.txt
+do
+    wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/unprocessed_dataset_2_submissions/submission_x/${FILE}?download=true -O tests/data/unprocessed_dataset_2_submissions/submission_x/${FILE}
+done

tests/test_preprocessing.py

@@ -0,0 +1,7 @@
+from omegaconf import OmegaConf
+from cryo_challenge._commands import run_preprocessing
+
+
+def test_run_preprocessing():    
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_preproc.yaml'})
+    run_preprocessing.main(args)