Merge pull request #184 from jhlegarreta/AddCLIEntryPointTest

ENH: Add CLI entry point test

src/eddymotion/cli/run.py

@@ -29,15 +29,15 @@
 from eddymotion.estimator import EddyMotionEstimator
 
 
-def main() -> None:
+def main(argv=None) -> None:
     """
     Entry point.
 
     Returns
     -------
     None
     """
-    args = parse_args()
+    args = parse_args(argv)
 
     # Open the data with the given file path
     dwi_dataset: DWI = DWI.from_filename(args.input_file)

src/eddymotion/estimator.py

@@ -220,8 +220,8 @@ def _advanced_clip(data, p_min=35, p_max=99.98, nonnegative=True, dtype="int16",
     # Calculate stats on denoised version, to preempt outliers from biasing
     denoised = ndimage.median_filter(data, footprint=ball(3))
 
-    a_min = np.percentile(denoised[denoised > 0] if nonnegative else denoised, p_min)
-    a_max = np.percentile(denoised[denoised > 0] if nonnegative else denoised, p_max)
+    a_min = np.percentile(denoised[denoised >= 0] if nonnegative else denoised, p_min)
+    a_max = np.percentile(denoised[denoised >= 0] if nonnegative else denoised, p_max)
 
     # Clip and cast
     data = np.clip(data, a_min=a_min, a_max=a_max)

test/test_main.py

@@ -0,0 +1,69 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 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/
+#
+
+import sys
+
+import pytest
+
+from eddymotion.__main__ import main
+
+
+@pytest.fixture(autouse=True)
+def set_command(monkeypatch):
+    with monkeypatch.context() as m:
+        m.setattr(sys, "argv", ["eddymotion"])
+        yield
+
+
+def test_help(capsys):
+    with pytest.raises(SystemExit):
+        main(["--help"])
+    captured = capsys.readouterr()
+    assert captured.out.startswith("usage: eddymotion [-h]")
+
+
+def test_main(tmp_path, datadir):
+    input_file = datadir / "dwi.h5"
+
+    with pytest.raises(SystemExit):
+        main([str(input_file), str(tmp_path)])
+
+    with pytest.raises(SystemExit):
+        main(
+            [
+                str(input_file),
+                "--models",
+                "b0",
+                "--omp_nthreads",
+                "1",
+                "--n_jobs",
+                "1",
+                "--seed",
+                "1234",
+                "--output_dir",
+                str(tmp_path),
+            ]
+        )
+    # assert Path(output_dir).joinpath("dwi.h5").exists()  # Empty
+
+    # Also, call python -m eddymotion or eddymotion from CircleCI ??