purge git lfs from repo

.github/workflows/testing.yml

@@ -26,19 +26,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: 'pip' # caching pip dependencies
 
-      - name: Install Git LFS
-        run: |
-          sudo apt-get update
-          sudo apt-get install git-lfs
-          git lfs install
-      - name: Pull LFS Files
-        run: git lfs pull
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
           pip install pytest omegaconf
 
+      - name: Get test data from OSF
+        run: |
+          sh tests/scripts/fetch_test_data.sh
       - name: Test with pytest
         run: |
           pytest tests/test_preprocessing.py

.gitignore

@@ -4,9 +4,11 @@ data/dataset_1_submissions
 data/dataset_2_ground_truth
 
 # data for testing and resulting outputs
+tests/data/Ground_truth
+tests/data/dataset_2_submissions/
+tests/data/unprocessed_dataset_2_submissions/submission_x/
 tests/results/
 
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

tests/scripts/fetch_test_data.sh

@@ -0,0 +1,12 @@
+mkdir -p tests/data/dataset_2_submissions tests/data/dataset_2_submissions tests/results tests/data/unprocessed_dataset_2_submissions/submission_x tests/data/Ground_truth/ tests/data/Ground_truth
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/dataset_2_submissions/test_submission_0_n8.pt?download=true -O tests/data/dataset_2_submissions/test_submission_0_n8.pt
+ADIR=$(pwd)
+ln -s $ADIR/tests/data/dataset_2_submissions/test_submission_0_n8.pt $ADIR/tests/data/dataset_2_submissions/submission_0.pt # symlink for svd which needs submission_0.pt for filename
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/test_maps_gt_flat_10.pt?download=true -O tests/data/Ground_truth/test_maps_gt_flat_10.pt
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/test_metadata_10.csv?download=true -O tests/data/Ground_truth/test_metadata_10.csv
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/Ground_truth/1.mrc?download=true -O tests/data/Ground_truth/1.mrc
+wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/mask_dilated_wide_224x224.mrc?download=true -O tests/data/Ground_truth/mask_dilated_wide_224x224.mrc
+for FILE in 1.mrc 2.mrc 3.mrc 4.mrc populations.txt
+do
+    wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/tests/unprocessed_dataset_2_submissions/submission_x/${FILE}?download=true -O tests/data/unprocessed_dataset_2_submissions/submission_x/${FILE}
+done