incorporate pytest in github workflows

.github/workflows/testing.yml

@@ -0,0 +1,53 @@
+# GHA workflow for running tests.
+#
+# Largely taken from
+# https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+# Please check the link for more detailed instructions
+
+name: Run tests
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache dependencies and test data
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pip
+            tests/data
+            data
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml', '**/tests/scripts/fetch_test_data.sh') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - 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.outputs.cache-hit != 'true'
+        run: |
+          sh tests/scripts/fetch_test_data.sh
+
+      - name: Test with pytest
+        run: |
+          pytest tests/test_map_to_map.py
+          pytest tests/test_distribution_to_distribution.py

pyproject.toml

@@ -58,7 +58,8 @@ dev = [
   "pytest",
   "mypy",
   "pre-commit",
-  "ruff"
+  "ruff",
+  "omegaconf"
 ]
 
 [project.urls]

tests/config_files/test_config_distribution_to_distribution.yaml

@@ -0,0 +1,12 @@
+input_fname: tests/results/test_map_to_map_distance_matrix_submission_0.pkl
+metrics:
+  - l2
+gt_metadata_fname: tests/data/test_metadata_10.csv
+n_replicates: 3
+n_pool_microstate: 2
+replicate_fraction: 0.9
+cvxpy_solver: ECOS
+optimal_q_kl:
+  n_iter: 100000
+  break_atol: 0.0001
+output_fname: results/test_distribution_to_distribution_submission_0.pkl

tests/config_files/test_config_map_to_map.yaml

@@ -0,0 +1,23 @@
+data:
+  n_pix: 224
+  psize: 2.146 
+  submission:
+    fname: tests/data/dataset_2_submissions/test_submission_0_n8.pt
+    volume_key: volumes
+    metadata_key: populations
+    label_key: id
+  ground_truth:
+    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
+analysis:
+  metrics:
+    - l2
+  chunk_size_submission: 80
+  chunk_size_gt: 190
+  normalize:
+    do: true
+    method: median_zscore
+output: tests/results/test_map_to_map_distance_matrix_submission_0.pkl

tests/data/test_metadata_2.csv

@@ -0,0 +1,3 @@
+index,volumes,populations_count,pc1,populations
+3238,13396.mrc,1,-231.62100638454024,2.9636654614427123e-05
+3789,30099.mrc,2,243.32448171011487,5.927330922885425e-05

tests/scripts/fetch_test_data.sh

@@ -0,0 +1,5 @@
+mkdir -p data/dataset_2_submissions tests/data/dataset_2_submissions tests/results
+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 

tests/test_distribution_to_distribution.py

@@ -0,0 +1,7 @@
+from omegaconf import OmegaConf
+from cryo_challenge._commands import run_distribution2distribution_pipeline
+
+
+def test_run_distribution2distribution_pipeline():   
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_distribution_to_distribution.yaml'})
+    run_distribution2distribution_pipeline.main(args)

tests/test_map_to_map.py

@@ -0,0 +1,7 @@
+from omegaconf import OmegaConf
+from cryo_challenge._commands import run_map2map_pipeline
+
+
+def test_run_map2map_pipeline():    
+    args = OmegaConf.create({'config': 'tests/config_files/test_config_map_to_map.yaml'})
+    run_map2map_pipeline.main(args)