Merge pull request #42 from jjjermiah/39-add-code-coverage-to-gha

build: Update Codecov action and add coverage badge

.github/workflows/main.yml

@@ -27,16 +27,20 @@ jobs:
       - name: Install poetry
         uses: snok/install-poetry@v1
 
-      - name: Install package
-        run: poetry install
-
       - name: Test with pytest
-        run: poetry run pytest
+        run: |
+          pip install -r requirements.txt
+          poetry install
+          pytest --cov --cov-report=xml
 
       - name: Use Codecov to track coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
-          file: ./coverage.xml
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)
+          name: codecov-umbrella
 
       - name: Build documentation
         run: poetry run make html --directory docs/

README.md

@@ -1,5 +1,7 @@
 [![PyTests](https://github.com/jjjermiah/NBIA-toolkit/actions/workflows/main.yml/badge.svg)](https://github.com/jjjermiah/NBIA-toolkit/actions/workflows/main.yml)
 [![Documentation Status](https://readthedocs.org/projects/nbia-toolkit/badge/?version=latest)](https://nbia-toolkit.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/jjjermiah/NBIA-toolkit/graph/badge.svg?token=JKREY71D0R)](https://codecov.io/gh/jjjermiah/NBIA-toolkit)
+
 
 # NBIA Toolkit 
 A python package that provides programmatic access to query and download images from the National Biomedical Imaging Archive (**NBIA**) and The Cancer Imaging Archive (**TCIA**) databases.

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]

requirements.txt

@@ -4,3 +4,5 @@ pytest-cov==4.0.0
 ruff==v0.0.260
 coverage-badge~=1.1.0
 requests==2.31.0
+pydicom==2.4.3
+tqdm==4.66.1

src/nbiatoolkit/nbia.py

@@ -1,8 +1,8 @@
-from nbiatoolkit.auth import OAuth2
-from nbiatoolkit.utils.nbia_endpoints import NBIA_ENDPOINTS
-from nbiatoolkit.logger.logger import setup_logger
-from nbiatoolkit.utils.md5 import validateMD5
-from nbiatoolkit.dicomsort import DICOMSorter
+from .auth import OAuth2
+from .utils.nbia_endpoints import NBIA_ENDPOINTS
+from .logger.logger import setup_logger
+from .utils.md5 import validateMD5
+from .dicomsort import DICOMSorter
 
 import requests
 from requests.exceptions import JSONDecodeError as JSONDecodeError

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