Merge b93c9bb into 9973d7e

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on: [push]
+
+jobs:
+  Build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Clone the repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Upgrade pip
+      run: python -m pip install --upgrade pip
+
+    - name: Install dependencies
+      run: pip install tox pre-commit flake8
+
+    - name: Run lint
+      run: tox -e lint

.github/workflows/tests.yml

@@ -0,0 +1,66 @@
+name: Tests
+
+on:
+  push:
+  schedule:
+    - cron: "0 4 * * *"
+
+jobs:
+  unit:
+    strategy:
+      matrix:
+        # TODO: add windows-latest
+        os: [ubuntu-latest, macos-latest]
+        python: ['3.6', '3.7', '3.8', '3.9']
+
+    runs-on: ${{ matrix.os }}
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - name: Set up python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Install dev requirements
+        run: pip install -r requirements-dev.txt
+
+      - name: Run unit tests
+        run: tox -e py
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v1.0.7
+        with:
+          env_vars: OS,PYTHON
+
+  cli:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set up python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Install project
+        run: pip install .
+
+      - name: Test CLI
+        run: |
+          tiotr --help
+          tiohd --help

.pre-commit-config.yaml

@@ -43,7 +43,7 @@ repos:
           pep8-naming,              # check PEP-8 naming conventions
         ]
         args: [
-          '--ignore=N813,E123,W503',  # import SimpleITK as sitk, brackets indentation, line break before binary operator
+          '--ignore=N813,E123,W503,B902',  # import SimpleITK as sitk, brackets indentation, line break before binary operator
         ]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.6.0  # Use the ref you want to point at

README.md

@@ -43,6 +43,9 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
             <a href="https://codecov.io/github/fepegar/torchio">
                 <img src="https://codecov.io/gh/fepegar/torchio/branch/master/graphs/badge.svg" alt="Coverage status">
             </a>
+            <a href="https://github.com/fepegar/torchio/actions/workflows/lint.yml">
+                <img src="https://github.com/fepegar/torchio/actions/workflows/lint.yml/badge.svg" alt="Linting status">
+            </a>
         </td>
     </tr>
     <tr>

docs/source/README.rst

@@ -3,7 +3,7 @@ TorchIO
 #######
 
 |PyPI-downloads| |PyPI-version| |Conda-version| |Google-Colab-notebook| |Docs-status|
-|Build-status| |Coverage-codecov| |Code-Quality|
+|Lint-status| |Build-status| |Coverage-codecov| |Code-Quality|
 |Code-Maintainability| |pre-commit| |Slack|
 
 
@@ -124,6 +124,10 @@ which is no longer maintained.
    :target: https://travis-ci.com/fepegar/torchio
    :alt: Build status
 
+.. |Lint-status| image:: https://github.com/fepegar/torchio/actions/workflows/lint.yml/badge.svg
+   :target: https://github.com/fepegar/torchio/actions/workflows/lint.yml
+   :alt: Build status
+
 .. |Coverage-codecov| image:: https://codecov.io/gh/fepegar/torchio/branch/master/graphs/badge.svg
    :target: https://codecov.io/github/fepegar/torchio
    :alt: Coverage status

tests/data/test_subjects_dataset.py

@@ -6,7 +6,7 @@
 
 
 class TestSubjectsDataset(TorchioTestCase):
-    
+
     def test_indexing_nonint(self):
         dset = SubjectsDataset(self.subjects_list)
         dset[torch.tensor(0)]

tests/transforms/test_transforms.py

@@ -1,7 +1,6 @@
 import copy
 import torch
 import numpy as np
-import nibabel as nib
 import torchio as tio
 import SimpleITK as sitk
 from ..utils import TorchioTestCase
@@ -100,15 +99,6 @@ def test_transforms_sitk(self):
         transformed = transform(image)
         self.assertIsInstance(transformed, sitk.Image)
 
-    def test_transforms_nib(self):
-        data = torch.rand(1, 4, 5, 8).numpy()
-        affine = np.diag((1, -2, 3, 1))
-        image = nib.Nifti1Image(data, affine)
-        transform = self.get_transform(
-            channels=('default_image_name',), labels=False)
-        transformed = transform(image)
-        self.assertIsInstance(transformed, nib.Nifti1Image)
-
     def test_transforms_subject_3d(self):
         transform = self.get_transform(channels=('t1', 't2'), is_3d=True)
         transformed = transform(self.sample_subject)

torchio/data/dataset.py

@@ -76,8 +76,12 @@ def __getitem__(self, index: int) -> Subject:
         try:
             index = int(index)
         except (RuntimeError, TypeError):
-            raise ValueError(f'Index "{index}" must be int or compatible dtype, not {type(index)}')
-
+            message = (
+                f'Index "{index}" must be int or compatible dtype,'
+                f' but an object of type "{type(index)}" was passed'
+            )
+            raise ValueError(message)
+
         subject = self._subjects[index]
         subject = copy.deepcopy(subject)  # cheap since images not loaded yet
         if self.load_getitem:

torchio/transforms/augmentation/intensity/random_ghosting.py

@@ -216,7 +216,7 @@ def add_artifact(
 def _parse_restore(restore):
     try:
         restore = float(restore)
-    except Exception as e:
+    except ValueError as e:
         raise TypeError(f'Restore must be a float, not "{restore}"') from e
     if not 0 <= restore <= 1:
         message = (

torchio/visualization.py

@@ -155,7 +155,7 @@ def plot_subject(
         fig.savefig(output_path)
     if show:
         plt.show()
-    plt.close(fig) 
+    plt.close(fig)
 
 
 def color_labels(arrays, cmap_dict):

tox.ini

@@ -12,6 +12,7 @@ passenv =
     CI
     TRAVIS
     TRAVIS_*
+    GITHUB_*
 setenv =
     PYTHONPATH = {toxinidir}
 
@@ -31,11 +32,9 @@ requires =
     pre-commit
 deps =
     flake8 >= 3.8
-    mypy
 commands =
     pre-commit run --all-files
     flake8
-    mypy
 
 
 [flake8]