local pytest passing. osf paths updated.

flatironinstitute · Jun 20, 2024 · e13b5de · e13b5de
1 parent c567e34
commit e13b5de
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Showing 5 changed files with 12 additions and 12 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -36,10 +36,10 @@ jobs:
           pip install pytest
       - name: Get test data from OSF
         run: |
-          mkdir -p data/dataset_2_submissions tests/data/
+          mkdir -p data/dataset_2_submissions tests/data/ tests/results
           wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/dataset_2_submissions/submission_0.pt?download=true -O data/dataset_2_submissions/submission_0.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/gt_maps_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
-          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata_10.csv?download=true -O tests/data/metadata_10.csv 
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/gt_maps_flat_10.pt
+          wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/test_metadata_10.csv?download=true -O tests/data/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 
       - name: Test with pytest
         run: |

diff --git a/tests/config_files/test_config_distribution_to_distribution.yaml b/tests/config_files/test_config_distribution_to_distribution.yaml
@@ -1,7 +1,7 @@
-input_fname: results/test_map_to_map_distance_matrix_submission_0.pkl
+input_fname: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
 metrics:
   - l2
-gt_metadata_fname: data/metadata.csv
+gt_metadata_fname: tests/data/test_metadata_10.csv
 n_replicates: 3
 n_pool_microstate: 2
 replicate_fraction: 0.9

diff --git a/tests/config_files/test_config_map_to_map.yaml b/tests/config_files/test_config_map_to_map.yaml
@@ -7,8 +7,8 @@ data:
     metadata_key: populations
     label_key: id
   ground_truth:
-    volumes: tests/data/gt_maps_flat_10.pt 
-    metadata: tests/data/metadata_10.csv 
+    volumes: tests/data/test_maps_gt_flat_10.pt 
+    metadata: tests/data/test_metadata_10.csv 
   mask: 
     do: true
     volume: data/mask_dilated_wide_224x224.mrc
@@ -20,4 +20,4 @@ analysis:
   normalize:
     do: true
     method: median_zscore
-output: tests/test_map_to_map_distance_matrix_submission_0.pkl
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
diff --git a/tests/test_distribution_to_distribution.py b/tests/test_distribution_to_distribution.py
@@ -1,7 +1,7 @@
 from omegaconf import OmegaConf
 from cryo_challenge._commands import run_distribution2distribution_pipeline
 
-args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
 
-def test_run_distribution2distribution_pipeline(args):    
+def test_run_distribution2distribution_pipeline():   
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_distribution_to_distribution.yaml'})
     run_distribution2distribution_pipeline.main(args)
diff --git a/tests/test_map_to_map.py b/tests/test_map_to_map.py
@@ -1,7 +1,7 @@
 from omegaconf import OmegaConf
 from cryo_challenge._commands import run_map2map_pipeline
 
-args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map_distance_matrix.yaml'})
 
-def test_run_map2map_pipeline(args):    
+def test_run_map2map_pipeline():    
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map.yaml'})
     run_map2map_pipeline.main(args)