diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index b348ec5..e7e472d 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -22,6 +22,13 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} + - name: Cache pip wheels + uses: actions/cache@v3 + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }} + restore-keys: | + ${{ runner.os }}-pip- - name: Install dependencies run: | python -m pip install --upgrade pip @@ -29,10 +36,11 @@ jobs: pip install pytest - name: Get test data from OSF run: | + mkdir data/dataset_2_submissions 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_float16.pt?download=true -O tests/data/gt_maps_flat_10.pt - wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O tests/data/metadat_10a.csv - wget https://files.osf.io/v1/resources/8h6fz/providers/dropbox/Ground_truth/metadata.csv?download=true -O data/mask_dilated_wide_224x224.mrc + 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/mask_dilated_wide_224x224.mrc?download=true -O data/mask_dilated_wide_224x224.mrc - name: Test with pytest run: | pytest tests/ diff --git a/config_files/test_config_map_to_map_distance_matrix.yaml b/config_files/test_config_map_to_map_distance_matrix.yaml deleted file mode 100644 index 0398065..0000000 --- a/config_files/test_config_map_to_map_distance_matrix.yaml +++ /dev/null @@ -1,26 +0,0 @@ -data: - n_pix: 224 - psize: 2.146 - submission: - fname: data/submission_0.pt - volume_key: volumes - metadata_key: populations - label_key: id - ground_truth: - volumes: data/test_maps_gt_flat.pt - metadata: data/test_metadata.csv - mask: - do: true - volume: data/mask_dilated_wide_224x224.mrc -analysis: - metrics: - - l2 - # - corr - # - bioem - # - fsc - chunk_size_submission: 80 - chunk_size_gt: 190 - normalize: - do: true - method: median_zscore -output: results/test_map_to_map_distance_matrix_submission_0.pkl \ No newline at end of file