enh: initial commit to begin with some unit tests

Sets up a barebones infrastructure for testing, hopefully to give a
kickstart to the work on #40.

cc/ @celprov, @sebastientourbier


Former-commit-id: 805760b [formerly 152e0d4]
Former-commit-id: 723b8b0
Former-commit-id: 2be92b3

eddymotion/conftest.py

@@ -0,0 +1,68 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""py.test configuration."""
+import os
+from pathlib import Path
+import numpy
+import nibabel
+import pytest
+
+test_data_env = os.getenv("TEST_DATA_HOME", str(Path.home() / "eddy-tests"))
+test_output_dir = os.getenv("TEST_OUTPUT_DIR")
+test_workdir = os.getenv("TEST_WORK_DIR")
+data_dir = Path(__file__).parent / "tests" / "data"
+
+
+def pytest_report_header(config):
+    return f"""\
+TEST_DATA_HOME={test_data_env}s
+TEST_OUTPUT_DIR={test_output_dir or '<unset> (output files will be discarded)'}.
+TEST_WORK_DIR={test_workdir or '<unset> (intermediate files will be discarded)'}.
+"""
+
+
+@pytest.fixture(autouse=True)
+def doctest_imports(doctest_namespace):
+    """Populates doctests with some conveniency imports."""
+    doctest_namespace["np"] = numpy
+    doctest_namespace["nb"] = nibabel
+    doctest_namespace["os"] = os
+    doctest_namespace["Path"] = Path
+
+
+@pytest.fixture
+def outdir():
+    """Determine if test artifacts should be stored somewhere or deleted."""
+    return None if test_output_dir is None else Path(test_output_dir)
+
+
+@pytest.fixture
+def datadir():
+    """Return a data path outside the package's structure (i.e., large datasets)."""
+    return Path(test_data_env)
+
+
+@pytest.fixture
+def pkg_datadir():
+    """Return a data path inside the package's structure (i.e., small, empty files)."""
+    return data_dir

eddymotion/tests/test_dmri.py

@@ -0,0 +1,23 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Unit tests exercising the dMRI data structure."""

eddymotion/tests/test_estimator.py

@@ -0,0 +1,23 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Unit tests exercising the estimator."""

eddymotion/tests/test_integration.py

@@ -0,0 +1,23 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Integration tests."""

eddymotion/tests/test_model.py

@@ -0,0 +1,42 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Unit tests exercising models."""
+import pytest
+import numpy as np
+from eddymotion import model
+
+
+def test_trivial_model():
+    """Check the implementation of the trivial B0 model."""
+
+    # Should not allow initialization without a B0
+    with pytest.raises(ValueError):
+        model.TrivialB0Model(gtab=np.eye(4))
+
+    _S0 = np.random.normal(size=(10, 10, 10))
+
+    tmodel = model.TrivialB0Model(gtab=np.eye(4), S0=_S0)
+
+    assert tmodel.fit() is None
+
+    assert np.all(_S0 == tmodel.predict((1, 0, 0)))

eddymotion/tests/test_version.py

@@ -0,0 +1,64 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Test _version.py."""
+import sys
+from collections import namedtuple
+from pkg_resources import DistributionNotFound
+from importlib import reload
+import eddymotion
+
+
+def test_version_scm0(monkeypatch):
+    """Retrieve the version via setuptools_scm."""
+
+    class _version:
+        __version__ = "10.0.0"
+
+    monkeypatch.setitem(sys.modules, "eddymotion._version", _version)
+    reload(eddymotion)
+    assert eddymotion.__version__ == "10.0.0"
+
+
+def test_version_scm1(monkeypatch):
+    """Retrieve the version via pkg_resources."""
+    monkeypatch.setitem(sys.modules, "eddymotion._version", None)
+
+    def _dist(name):
+        Distribution = namedtuple("Distribution", ["name", "version"])
+        return Distribution(name, "success")
+
+    monkeypatch.setattr("pkg_resources.get_distribution", _dist)
+    reload(eddymotion)
+    assert eddymotion.__version__ == "success"
+
+
+def test_version_scm2(monkeypatch):
+    """Check version could not be interpolated."""
+    monkeypatch.setitem(sys.modules, "eddymotion._version", None)
+
+    def _raise(name):
+        raise DistributionNotFound("No get_distribution mock")
+
+    monkeypatch.setattr("pkg_resources.get_distribution", _raise)
+    reload(eddymotion)
+    assert eddymotion.__version__ == "unknown"