Add lower bounds to dependencies (#1246)

* Add lower bounds to dependencies

* Add all lower bounds

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add bounds in test dependencies

* Fix Ruff error

* Add lower bound for packaging

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

pyproject.toml

@@ -37,23 +37,25 @@ classifiers = [
 keywords = ["medical", "image processing", "pytorch", "augmentation", "mri"]
 requires-python = ">=3.9,<3.13"
 dependencies = [
-    "deprecated",
-    "humanize",
-    "nibabel",
-    "numpy>=1.15",
-    "scipy",
-    "simpleitk!=2.0.*,!=2.1.1.1",
-    "torch>=1.1",
-    "tqdm",
-    "typer",
+    "deprecated>=1.2",
+    "humanize>=0.1",
+    "nibabel>=3",
+    "numpy>=1.20",
+    "packaging>=20",
+    "rich>=10",
+    "scipy>=1.7",
+    "simpleitk >=1.3, !=2.0.*, !=2.1.1.1",
+    "torch>=1.9",
+    "tqdm>=4.40",
+    "typer>=0.1",
 ]
 
 [project.optional-dependencies]
 csv = [
-    "pandas",
+    "pandas>=1",
 ]
 plot = [
-    "matplotlib",
+    "matplotlib>=3.4",
 ]
 
 [project.scripts]
@@ -74,7 +76,8 @@ dev = [
     { include-group = "maintain" },
     { include-group = "test" },
     "ipykernel",
-    "ruff",
+    "ruff>0.0.40",
+    "ipywidgets",
 ]
 doc = [
     "einops",
@@ -91,13 +94,13 @@ maintain = [
     "pre-commit-uv",
 ]
 test = [
-    "coverage",
-    "mypy",
-    "parameterized",
-    "pillow",
-    "pytest",
+    "coverage>=5",
+    "mypy>=0.800",
+    "parameterized>=0.7",
+    "pillow>=8",
+    "pytest>=5",
     "pytest-cov",
-    "pytest-sugar",
+    "pytest-sugar>=0.10",
     "tox-uv",
     "types-deprecated",
 ]

tests/data/test_io.py

@@ -159,6 +159,7 @@ def test_write_nd_with_a_read_it_with_b(save_lib, load_lib, dims):
         tensor.squeeze(),
         loaded_tensor.squeeze(),
         msg=f'Save lib: {save_lib}; load lib: {load_lib}; dims: {dims}',
+        check_stride=False,
     )
     TorchioTestCase.assert_tensor_equal(affine, loaded_affine)
 

tests/transforms/preprocessing/test_histogram_standardization.py

@@ -1,6 +1,7 @@
 import numpy as np
 import pytest
 import torch
+from packaging.version import Version
 
 from torchio import LabelMap
 from torchio import ScalarImage
@@ -80,7 +81,10 @@ def test_with_saved_dict(self):
         landmarks_dict = {'image': landmarks}
         landmarks_path = self.dir / 'landmarks_dict.pth'
         torch.save(landmarks_dict, landmarks_path)
-        landmarks_dict = torch.load(landmarks_path, weights_only=False)
+        kwargs = {}
+        if Version(torch.__version__) >= Version('1.13'):
+            kwargs['weights_only'] = False
+        landmarks_dict = torch.load(landmarks_path, **kwargs)
         transform = HistogramStandardization(landmarks_dict)
         transform(self.dataset[0])
 

tests/transforms/preprocessing/test_to_canonical.py

@@ -28,6 +28,7 @@ def test_las_to_ras(self):
         self.assert_tensor_almost_equal(
             transformed.t1.data,
             torch.from_numpy(array_flip),
+            check_stride=False,
         )
 
         fixture = np.eye(4)