Dev (#111)

* kill bob the builder

* pip publish without semantic release

* oops

* adding checkout to pip-squeak

* fixed main.yml

* fixed main.yml

* fixed main.yml

* skip autopipeline in pip testing

* adding code coverage

* removed pytest-xdist

* xdist removed, -n flag gone

.github/workflows/main.yml

@@ -41,9 +41,42 @@ jobs:
 
       - name: Pip install
         run: pip install .
+
       - name: Run tests
-        run: pip install pytest && pytest tests -v
+        run: |
+          pip install pytest pytest-cov
+          pytest tests -s -v --cov --cov-report xml:coverage-report/coverage.xml
+
+      - 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'
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
+
+  codecov:
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Download coverage report artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
 
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage-report/coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+          name: codecov-umbrella
+
   cd:
     permissions:
         contents: write

pyproject.toml

@@ -37,7 +37,6 @@ betapipeline = "imgtools.autopipeline_refactored:main"
 pytest = "^8.2.0"
 ruff = "^0.4.4"
 pytest-cov = ">=4.0.0"
-pytest-xdist = ">=3.5.0"
 
 [tool.poetry.extras]
 torch = ["torch", "torchio"]

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="med-imagetools",
-    version="1.2.0.2",
+    version="1.3.0.1",
     author="Sejin Kim, Michal Kazmierski, Kevin Qu, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",
@@ -28,5 +28,5 @@
         "License :: OSI Approved :: Apache Software License",
         "Development Status :: 2 - Pre-Alpha"
     ],
-    python_requires='>=3.6',
+    python_requires='>=3.7',
 )