purge git lfs from repo

.github/workflows/testing.yml

@@ -26,22 +26,30 @@ 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: Cache test data
+        id: cache_test_data
+        uses: actions/cache@v3
+        with:
+          path: |
+            tests/data
+            data
+          key: venv-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/tests/scripts/fetch_test_data.sh') }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
           pip install pytest omegaconf
-
+          
+      - name: Get test data from OSF
+        if: ${{ steps.cache_test_data.outputs.cache-hit != 'true' }}
+        run: |
+          sh tests/scripts/fetch_test_data.sh
+          
       - name: Test with pytest
         run: |
           pytest tests/test_preprocessing.py
           pytest tests/test_svd.py
           pytest tests/test_map_to_map.py
           pytest tests/test_distribution_to_distribution.py
+          

.gitignore

@@ -4,6 +4,9 @@ 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/
 
 

.pre-commit-config.yaml

@@ -10,7 +10,6 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
-    -   id: check-added-large-files
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.3.4

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

tutorials/1_tutorial_preprocessing.ipynb

@@ -242,7 +242,7 @@
     "# Select path to Config file\n",
     "# An example of this file is available in the path ../config_files/config_preproc.yaml\n",
     "config_preproc_path = FileChooser(os.path.expanduser(\"~\"))\n",
-    "config_preproc_path.filter_pattern = \"*.yaml\"\n",
+    "config_preproc_path.filter_pattern = '*.yaml'\n",
     "display(config_preproc_path)"
    ]
   },
@@ -265,7 +265,7 @@
     "if os.path.isabs(output_path):\n",
     "    full_output_path = output_path\n",
     "else:\n",
-    "    full_output_path = os.path.join(os.getcwd(), \"..\", output_path)"
+    "    full_output_path = os.path.join(os.getcwd(), '..', output_path)"
    ]
   },
   {