Chore/pin versions

.github/workflows/unit_test.yml

@@ -23,20 +23,40 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
+          cache-dependency-path: pyproject.toml
       # You can test your matrix by printing the current Python version
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-          pip install -r requirements.txt
+          pip install torch --index-url https://download.pytorch.org/whl/cpu
+          pip install ".[test,preproc,plot]"
       - name: Install libomp (macOS)
         if: runner.os == 'macOS'
         run: brew install libomp
       - name: Test with pytest
         run: |
-          pip install pytest pytest-cov
           python -m pytest --doctest-modules --junitxml=junit/test-results.xml --cov=. --cov-report=xml --cov-report=html -r w ${{ runner.os == 'macOS' && '-k "not test_deep_learning_algorithms"' || '' }}
           python -m pytest --doctest-modules --junitxml=junit/test-results-brain.xml --cov=. --cov-report=xml --cov-report=html --dataFile tests/IVIMmodels/unit_tests/generic_brain.json -r w -k test_ivim_fit_saved
 
+  # Requirements.txt test run -> hashed pinned versions
+  lock:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
+          pip install -r requirements.txt
+      - name: Test with pytest
+        run: |
+          pip install pytest pytest-cov
+          python -m pytest --doctest-modules --junitxml=junit/test-results.xml --cov=. --cov-report=xml --cov-report=html -r w
+          python -m pytest --doctest-modules --junitxml=junit/test-results-brain.xml --cov=. --cov-report=xml --cov-report=html --dataFile tests/IVIMmodels/unit_tests/generic_brain.json -r w -k test_ivim_fit_saved

pyproject.toml

@@ -20,17 +20,17 @@ authors = [
     {name = "Oliver J. Gurney-Champion", email = "o.j.gurney-champion@amsterdamumc.nl"},
 ]
 dependencies = [
-    "numpy",
-    "scipy",
+    "numpy>=2,<3",
+    "scipy>=1.13",
     "nibabel",
-    "torch",
-    "torchio",
+    "torch>=2.2,<3",
+    "torchio>=1.2,<2",
     "joblib",
-    "dipy",
+    "dipy>=1.12.1,<2",
     "cvxpy",
     "nlopt",
     "tqdm",
-    "pandas",
+    "pandas>=2.2,<4",
     "statsmodels",
     "ivimnet",
     "super-ivim-dc>1.0.0",
@@ -40,6 +40,7 @@ dependencies = [
 [project.optional-dependencies]
 test = [
     "pytest",
+    "pytest-cov",
     "pytest-json-report",
 ]
 docs = [
@@ -50,8 +51,13 @@ plot = [
     "matplotlib",
     "scienceplots",
 ]
+preproc = [
+    "nipype",
+    "itk",
+    "pyyaml",
+]
 all = [
-    "osipi-ivim[test,docs,plot]",
+    "osipi-ivim[test,docs,plot,preproc]",
 ]
 
 [project.urls]