test: Update pytest coverage command in GitHub workflow

Add source directory for coverage in pyproject.toml

Fix import statements in test files

.github/workflows/main.yml

@@ -34,7 +34,7 @@ jobs:
         run: |
           pip install pytest
           pip install pytest-cov
-          poetry run pytest --cov=./ --cov-report=xml
+          poetry run pytest --cov --cov-report=xml
 
       - name: Use Codecov to track coverage
         uses: codecov/codecov-action@v3

pyproject.toml

@@ -26,6 +26,8 @@ python-semantic-release = "^8.5.1"
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
+# [tool.coverage]
+# source = "src/nbiatoolkit"
 
 # https://python-semantic-release.readthedocs.io/en/latest/configuration.html
 [tool.semantic_release]

tests/test_auth.py

@@ -4,7 +4,7 @@
 # pytest -v -s 
 
 import pytest
-from nbiatoolkit import OAuth2
+from src.nbiatoolkit import OAuth2
 import time 
 import requests
 

tests/test_dicom_helpers.py

@@ -1,4 +1,4 @@
-from nbiatoolkit.dicomsort.helper_functions import parseDICOMKeysFromFormat,sanitizeFileName,truncateUID
+from src.nbiatoolkit.dicomsort.helper_functions import parseDICOMKeysFromFormat,sanitizeFileName,truncateUID
 import pytest
 ###############################################################################
 # parseDICOMKeysFromFormat

tests/test_md5.py

@@ -1,6 +1,6 @@
 import os
-from nbiatoolkit.utils.md5 import validateMD5, calculateMD5, MD5HashMismatchError
-from nbiatoolkit.utils.nbia_endpoints import NBIA_ENDPOINTS
+from src.nbiatoolkit.utils.md5 import validateMD5, calculateMD5, MD5HashMismatchError
+from src.nbiatoolkit.utils.nbia_endpoints import NBIA_ENDPOINTS
 import requests
 import pytest
 from tempfile import TemporaryDirectory

tests/test_nbia.py

@@ -5,7 +5,7 @@
 # pytest -v -n 8 tests/test_nbia.py::test_getCollections
 
 import pytest
-from nbiatoolkit import NBIAClient
+from src.nbiatoolkit import NBIAClient
 from tempfile import TemporaryDirectory
 import os