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enh: initial commit to begin with some unit tests
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Sets up a barebones infrastructure for testing, hopefully to give a
kickstart to the work on #40.

cc/ @celprov, @sebastientourbier


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oesteban committed Nov 9, 2021
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68 changes: 68 additions & 0 deletions eddymotion/conftest.py
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# 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
Empty file.
23 changes: 23 additions & 0 deletions eddymotion/tests/test_dmri.py
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# 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."""
23 changes: 23 additions & 0 deletions eddymotion/tests/test_estimator.py
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# 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."""
23 changes: 23 additions & 0 deletions eddymotion/tests/test_integration.py
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# 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."""
42 changes: 42 additions & 0 deletions eddymotion/tests/test_model.py
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# 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)))
64 changes: 64 additions & 0 deletions eddymotion/tests/test_version.py
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# 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"

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