Merge branch 'nipreps:main' into documentation

.github/workflows/pypi-package.yml

@@ -0,0 +1,56 @@
+---
+name: Build and upload package
+
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build-package:
+    name: Build & verify package
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  auto-release-test-pypi:
+    runs-on: ubuntu-latest
+    needs: [build-package]
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    permissions:
+      id-token: write
+    steps:
+      - name: Download packages built by build-and-inspect-python-package
+        uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  auto-release-pypi:
+    runs-on: ubuntu-latest
+    environment: "Release"
+    needs: [build-package]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    permissions:
+      id-token: write
+    steps:
+      - name: Download packages built by build-and-inspect-python-package
+        uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

pyproject.toml

@@ -103,7 +103,11 @@ packages = ["src/eddymotion"]
 [tool.hatch.version]
 validate-bump = true
 source = "vcs"
-raw-options = { version_scheme = "nipreps-calver" }
+
+[tool.hatch.version.raw-options]
+version_scheme = "nipreps-calver"
+local_scheme = "no-local-version"
+
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/eddymotion/_version.py"

src/eddymotion/model/base.py

@@ -45,7 +45,7 @@ class ModelFactory:
     @staticmethod
     def init(model="DTI", **kwargs):
         """
-        Instatiate a diffusion model.
+        Instantiate a diffusion model.
 
         Parameters
         ----------

test/test_parser.py

@@ -0,0 +1,83 @@
+# 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/
+#
+
+"""Test parser."""
+
+import pytest
+
+from eddymotion.cli.parser import _build_parser
+
+MIN_ARGS = ["data/dwi.h5"]
+
+
+@pytest.mark.parametrize(
+    ("args", "code"),
+    [
+        ([], 2),
+    ],
+)
+def test_parser_errors(args, code):
+    """Check behavior of the parser."""
+    with pytest.raises(SystemExit) as error:
+        _build_parser().parse_args(args)
+
+    assert error.value.code == code
+
+
+@pytest.mark.parametrize(
+    "args",
+    [
+        MIN_ARGS,
+    ],
+)
+def test_parser_valid(tmp_path, args):
+    """Check valid arguments."""
+    datapath = tmp_path / "data"
+    datapath.mkdir(exist_ok=True)
+    args[0] = str(datapath)
+
+    opts = _build_parser().parse_args(args)
+
+    assert opts.input_file == datapath
+    assert opts.models == ["b0"]
+
+
+@pytest.mark.parametrize(
+    ("argval", "_models"),
+    [
+        ("b0", "b0"),
+        ("s0", "s0"),
+        ("avg", "avg"),
+        ("average", "average"),
+        ("mean", "mean"),
+    ],
+)
+def test_models_arg(tmp_path, argval, _models):
+    """Check the correct parsing of the models argument."""
+    datapath = tmp_path / "data"
+    datapath.mkdir(exist_ok=True)
+
+    args = [str(datapath)] + ["--models", argval]
+    opts = _build_parser().parse_args(args)
+
+    assert opts.models == [_models]