[INFRA] Python test automation

.github/workflows/run_demos_python.yml

@@ -0,0 +1,42 @@
+name: run python demos
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  demos:
+    continue-on-error: true
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: ["3.7"]
+
+    steps:
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: "recursive"
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .
+          pip install -r requirements_dev.txt
+
+      - name: Display Python version and packages
+        run: |
+          python -c "import sys; print(sys.version)"
+          pip list
+
+      - name: Run tests and generate coverage report
+        run: pytest  --nbmake --nbmake-timeout=3000 "./examples"

.github/workflows/run_tests_python.yml

@@ -0,0 +1,54 @@
+name: tests and coverage with python
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  tests:
+    continue-on-error: true
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: "recursive"
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .
+          pip install -r requirements_dev.txt
+
+      - name: Display Python version and packages
+        run: | 
+          python -c "import sys; print(sys.version)"
+          pip list
+
+      - name: Prepare data
+        run: make tests/data/nsdcoreexampledataset.mat          
+
+      - name: Run tests and generate coverage report
+        run: pytest -v --cov glmsingle --cov-report xml tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: python
+          name: codecov-umbrella
+          fail_ci_if_error: true
+          verbose: true

requirements.txt

@@ -1,8 +1,8 @@
-numpy
-scipy
-sklearn
-matplotlib
-tqdm
-fracridge
-nibabel
-h5py
+fracridge>=1.4.3
+h5py>=3.1.0
+matplotlib>=3.3.4
+nibabel>=3.2.2
+numpy>=1.17.0
+scikit-learn>=0.23.2
+scipy>=1.5.4
+tqdm>=4.63.1

setup.cfg

@@ -0,0 +1,21 @@
+[flake8]
+max-line-length = 99
+
+ignore = D203, W503
+
+exclude =
+    .git,
+    docs,
+    __pycache__,
+    old,
+    build,
+    dist
+    'matlab/fracridge'
+
+max-complexity = 10
+
+[tool:pytest]
+branch = True
+source = glmsingle/*
+include = glmsingle/*
+testpaths = tests

setup.py

@@ -28,5 +28,6 @@
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,
-    install_requires=requires
+    install_requires=requires,
+    python_requires='>=3.6'
 )

tests/__init__.py

@@ -0,0 +1 @@
+"""Unit test package for glmsingle."""

tests/test_glmsingleunit.py

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+from os.path import join
+from os.path import abspath
+from os.path import dirname
+import scipy
+import scipy.io as sio
+from glmsingle.glmsingle import GLM_single
+
+test_dir = dirname(abspath(__file__))
+data_dir = join(test_dir, "data")
+data_file = join(data_dir, "nsdcoreexampledataset.mat")
+
+output_dir = join(test_dir, "outputs")
+
+
+def test_smoke_test():
+
+    X = sio.loadmat(data_file)
+
+    data = []
+    design = []
+    for r in range(3):  # range(len(X['data'][0])):
+        data.append(X["data"][0, r][50:70, 7:27, 0:1, :])
+        design.append(scipy.sparse.csr_matrix.toarray(X["design"][0, r]))
+
+    stimdur = X["stimdur"][0][0]
+    tr = X["tr"][0][0]
+
+    opt = {"wantmemoryoutputs": [1, 1, 1, 1]}
+
+    # OPTIONAL: PUT THIS IN?
+    # opt['wantlibrary'] = 0
+
+    glmsingle_obj = GLM_single(opt)
+    glmsingle_obj.fit(design, data, stimdur, tr, outputdir=join(output_dir, "python"))