maybe it's poetry?

bhklab · May 17, 2024 · c725ca3 · c725ca3
1 parent 0b754ca
commit c725ca3
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Showing 3 changed files with 16 additions and 8 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -43,14 +43,17 @@ jobs:
         uses: abatilo/actions-poetry@v2
         with:
           poetry-version: 1.8.2
-      - name: Install the project dependencies
-        run: poetry install --with dev
-
-      - name: Test with pytest
-        run: |
-          # Github action runners now have 4 cores
-          poetry run pytest tests -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml
-
+      # - name: Install the project dependencies
+      #   run: poetry install --with dev
+      # - name: Test with pytest
+      #   run: |
+      #     # Github action runners now have 4 cores
+      #     poetry run pytest tests -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml
+      - name: Pip install
+        run: pip install .
+      - name: Run tests
+        run: pip install pytest && pytest tests -v
+
       - name: Upload coverage report artifact to be used by Codecov
         # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'

diff --git a/src/imgtools/io/loaders.py b/src/imgtools/io/loaders.py
@@ -101,6 +101,7 @@ def read_dicom_auto(path, series=None, file_names=None):
         dcms = [path]
     else:
         dcms = glob.glob(pathlib.Path(path, "*.dcm").as_posix())
+
     for dcm in dcms:
         meta = dcmread(dcm)
         if meta.SeriesInstanceUID != series and series is not None:

diff --git a/tests/test_modalities.py b/tests/test_modalities.py
@@ -16,13 +16,17 @@
 @pytest.fixture
 def modalities_path():
     curr_path = pathlib.Path(__file__).parent.parent.resolve()
+    print(os.listdir(curr_path))
+
     # qc_path = pathlib.Path(os.path.join(curr_path, "data", "Head-Neck-PET-CT", "HN-CHUS-082"))
     # path = {}
     # path["CT"] = os.path.join(qc_path, "08-27-1885-CA ORL FDG TEP-06980/3.000000-Merged-05195")
     # path["RTSTRUCT"] = os.path.join(qc_path, "08-27-1885-06980/Pinnacle POI-67882")
     # path["RTDOSE"] = os.path.join(qc_path, "08-27-1885-06980/89632")
     # path["PT"] = os.path.join(qc_path, "08-27-1885-TEP cancerologique TEP-06980/552650.000000-LOR-RAMLA-72508")
     qc_path = pathlib.Path(curr_path, "data", "Head-Neck-PET-CT", "HN-CHUS-052").as_posix()
+    assert os.path.exists(qc_path), "Dataset not found"
+
     path = {}
     path["CT"] = pathlib.Path(qc_path, "08-27-1885-CA ORL FDG TEP POS TX-94629/3.000000-Merged-06362").as_posix()
     path["RTSTRUCT"] = pathlib.Path(qc_path, "08-27-1885-OrophCB.0OrophCBTRTID derived StudyInstanceUID.-94629/Pinnacle POI-41418").as_posix()