add tests

.github/workflows/test.yml

@@ -4,8 +4,41 @@ on:
   pull_request:
   schedule: [{cron: '4 3 1 * *'}]  # M H d m w (monthly at 3:04)
 jobs:
+  test:
+    if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
+    strategy:
+      matrix:
+        python: [3.8, 3.14]
+        os: [ubuntu]
+        include: [{os: macos, python: 3.14}, {os: windows, python: 3.14}]
+    runs-on: ${{ matrix.os }}-latest
+    timeout-minutes: 5
+    defaults: {run: {shell: bash}}
+    steps:
+    - uses: actions/checkout@v7
+      with: {fetch-depth: 0}
+    - uses: actions/setup-python@v7
+      with:
+        python-version: ${{ matrix.python }}
+    - run: pip install -e .[full,dev]
+    - run: pytest --cov=brainweb --cov-fail-under=50 --cov-report=xml --cov-report=term-missing
+    - name: codacy
+      run: |
+        bash <(curl -fsL https://coverage.codacy.com/get.sh) report -l Python -r coverage.xml --partial || :
+      env:
+        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+  finish:
+    continue-on-error: ${{ github.event_name != 'push' }}
+    needs: test
+    runs-on: ubuntu-slim
+    steps:
+    - name: codacy
+      run: |
+        bash <(curl -fsL https://coverage.codacy.com/get.sh) final || :
+      env:
+        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
   deploy:
-    name: PyPI Deploy
+    needs: test
     runs-on: ubuntu-latest
     environment: pypi
     permissions: {contents: write, id-token: write, packages: write}

.gitignore

@@ -6,3 +6,6 @@ __pycache__/
 /*.egg*/
 /build/
 /dist/
+
+/.coverage*
+/coverage.xml

.pre-commit-config.yaml

@@ -26,6 +26,24 @@ repos:
     args: [-i]
     types: [text]
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
+  - id: pytest
+    name: pytest
+    language: python
+    entry: env PYTHONPATH=. pytest
+    args: [--cov=brainweb, -vv, -k=quick]
+    types: [python]
+    pass_filenames: false
+    additional_dependencies:
+    - pytest-cov
+    - numpy
+    - requests
+    - scikit-image
+    - tqdm>=4.42.0
+- repo: https://github.com/PyCQA/bandit
+  rev: 1.9.4
+  hooks:
+  - id: bandit
+    args: [-c, pyproject.toml]
 - repo: https://github.com/PyCQA/flake8
   rev: 7.3.0
   hooks:
@@ -53,3 +71,6 @@ repos:
   rev: 9.0.0b1
   hooks:
   - id: isort
+ci:
+  autoupdate_schedule: monthly
+  skip: [pytest]

README.ipynb

@@ -37,8 +37,8 @@
     "[PyPI-target]: https://pypi.org/project/brainweb\n",
     "[CI]: https://img.shields.io/github/actions/workflow/status/casperdcl/brainweb/test.yml?branch=main&label=brainweb&logo=GitHub\n",
     "[CI-target]: https://github.com/casperdcl/brainweb/actions/workflows/test.yml\n",
-    "[Quality]: https://api.codacy.com/project/badge/Grade/cdad13693b0141199c31d5b44c7ab185\n",
-    "[Quality-target]: https://www.codacy.com/app/casper-dcl/brainweb\n",
+    "[Quality]: https://app.codacy.com/project/badge/Grade/cdad13693b0141199c31d5b44c7ab185\n",
+    "[Quality-target]: https://app.codacy.com/gh/casperdcl/brainweb\n",
     "[DOI]: https://img.shields.io/badge/DOI-10.5281/zenodo.3269888-blue.svg\n",
     "[DOI-target]: https://doi.org/10.5281/zenodo.3269888\n",
     "[LICENCE]: https://img.shields.io/pypi/l/brainweb.svg?label=licence\n",

README.md

@@ -18,7 +18,7 @@ coregistration.
 
 [![PyPI](https://img.shields.io/pypi/v/brainweb.svg)](https://pypi.org/project/brainweb)
 [![CI](https://img.shields.io/github/actions/workflow/status/casperdcl/brainweb/test.yml?branch=main&label=brainweb&logo=GitHub)](https://github.com/casperdcl/brainweb/actions/workflows/test.yml)
-[![Quality](https://api.codacy.com/project/badge/Grade/cdad13693b0141199c31d5b44c7ab185)](https://www.codacy.com/app/casper-dcl/brainweb)
+[![Quality](https://app.codacy.com/project/badge/Grade/cdad13693b0141199c31d5b44c7ab185)](https://app.codacy.com/gh/casperdcl/brainweb)
 [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3269888-blue.svg)](https://doi.org/10.5281/zenodo.3269888)
 [![LICENCE](https://img.shields.io/pypi/l/brainweb.svg?label=licence)](https://www.mozilla.org/MPL/2.0)
 

brainweb/utils.py

@@ -10,7 +10,12 @@
 import numpy as np
 import requests
 from numpy.random import seed
-from scipy.ndimage.filters import gaussian_filter
+
+try:
+    from scipy.ndimage import gaussian_filter
+except ImportError: # scikit-image<2
+    from scipy.ndimage.filters import gaussian_filter
+
 from skimage.transform import resize
 from tqdm.auto import tqdm, trange
 from tqdm.contrib import tenumerate
@@ -169,7 +174,8 @@ def get_file(fname, origin, cache_dir=None, chunk_size=None):
         except Exception:
             log.warning("cannot create:" + cache_dir)
     if not os.access(cache_dir, os.W_OK):
-        cache_dir = path.join('/tmp', '.brainweb')
+        from tempfile import gettempdir
+        cache_dir = path.join(gettempdir(), '.brainweb')
         if not path.exists(cache_dir):
             os.makedirs(cache_dir)
 
@@ -178,7 +184,7 @@ def get_file(fname, origin, cache_dir=None, chunk_size=None):
     if not path.exists(fpath):
         log.debug(f"Downloading {fpath} from {origin}")
         try:
-            d = requests.get(origin, stream=True)
+            d = requests.get(origin, stream=True, timeout=(10, None))
             with tqdm(total=float(d.headers.get('Content-length') or 0), desc=fname, unit="B", unit_scale=True,
                       unit_divisor=1024, leave=False) as fprog:
                 with open(fpath, 'wb') as fo:
@@ -583,12 +589,16 @@ def register(src, target=None, ROI=None, target_shape=Shape.mMR, src_resolution=
     """
     from dipy.align.imaffine import AffineMap, transform_centers_of_mass
 
-    assert src.ndim == 3
+    def assert3D(ndim, name):
+        if ndim != 3:
+            raise ValueError(f"{name} must be 3D, got {ndim}D")
+
+    assert3D(src.ndim, "src")
     if target is not None:
-        assert target.ndim == 3
-    assert len(target_shape) == 3
-    assert len(src_resolution) == 3
-    assert len(target_resolution) == 3
+        assert3D(target.ndim, "target")
+    assert3D(len(target_shape), "target_shape")
+    assert3D(len(src_resolution), "src_resolution")
+    assert3D(len(target_resolution), "target_resolution")
 
     if ROI is None:
         ROI = ((0, None),)
@@ -605,7 +615,9 @@ def register(src, target=None, ROI=None, target_shape=Shape.mMR, src_resolution=
     affine_init[:3, -1] -= moving.shape * src_resolution / target_resolution
     affine_init[:3, -1] /= 2
     affine_init[:3, -1] += src_offset
-    affine_map = AffineMap(np.eye(4), target_shape, np.eye(4), moving.shape, affine_init) # unmoved target
+    # unmoved target
+    affine_map = AffineMap(np.eye(4), domain_grid_shape=target_shape, domain_grid2world=np.eye(4),
+                           codomain_grid_shape=moving.shape, codomain_grid2world=affine_init)
     src = affine_map.transform(moving)
 
     if target is not None:

pyproject.toml

@@ -27,15 +27,19 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3"]
 dependencies = [
-    "tqdm>=4.42.0",
     "numpy",
     "requests",
-    "scikit-image"]
+    "scikit-image",
+    "tqdm>=4.42.0"]
 [project.optional-dependencies]
+dev = ["pytest>=6", "pytest-cov"]
 plot = ["matplotlib"]
 register = ["dipy"]
 full = ["matplotlib", "dipy"]
 
+[tool.bandit]
+exclude_dirs = ["tests"]
+
 [tool.flake8]
 max_line_length = 120
 extend_ignore = ["E261"]
@@ -55,4 +59,15 @@ blank_line_before_nested_class_or_def = false
 
 [tool.isort]
 line_length = 120
-known_first_party = ["brainweb"]
+known_first_party = ["brainweb", "tests"]
+
+[tool.pytest.ini_options]
+log_level = "INFO"
+testpaths = ["tests"]
+markers = ["quick"]
+addopts = "-v --tb=short -rxs -W=error --durations=0 --durations-min=0.1"
+
+[tool.coverage.run]
+branch = true
+[tool.coverage.report]
+show_missing = true

tests/test_brainweb.py

@@ -0,0 +1,45 @@
+import pytest
+
+import brainweb as bw
+
+
+@pytest.mark.quick
+def test_import():
+    assert bw.__version__
+
+
+@pytest.fixture(scope="session")
+def subject_file(tmp_path_factory):
+    f, url = next(iter(bw.LINKS.items()))
+    return bw.get_file(f, url, cache_dir=tmp_path_factory.mktemp("brainweb"))
+
+
+def test_download(subject_file):
+    from pathlib import Path
+    assert Path(subject_file).exists()
+
+
+def test_load(subject_file):
+    data = bw.load_file(subject_file)
+    assert data.shape == (362, 434, 362)
+
+
+def test_mMR(subject_file):
+    vol = bw.get_mmr_fromfile(subject_file)
+    assert not {'T1', 'T2', 'uMap', 'PET'} - set(vol.keys())
+    assert vol['PET'].shape == (127, 344, 344)
+
+
+def test_lesions(subject_file):
+    vol = bw.get_mmr_fromfile(subject_file)
+    im3d = bw.add_lesions(vol['PET'])
+    assert im3d.shape == vol['PET'].shape
+    assert (im3d != vol['PET']).any()
+
+
+def test_registration(subject_file):
+    pytest.importorskip("dipy")
+    data = bw.load_file(subject_file)
+    vol = bw.get_mmr_fromfile(subject_file)
+    reg = bw.register(data[:, ::-1], target=vol['PET'], src_resolution=bw.Res.brainweb, target_resolution=bw.Res.mMR)
+    assert reg.shape == vol['PET'].shape