ci: fix missed testing with oldest (#2803)

Author: Borda

.github/workflows/ci-integrate.yml

@@ -53,6 +53,8 @@ jobs:
 
       - name: source cashing
         uses: ./.github/actions/pull-caches
+        with:
+          requires: ${{ matrix.requires }}
       - name: set oldest if/only for integrations
         if: matrix.requires == 'oldest'
         run: python .github/assistant.py set-oldest-versions --req_files='["requirements/_integrate.txt"]'

.github/workflows/ci-tests.yml

@@ -31,8 +31,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-20.04"]
-        python-version: ["3.9"]
+        os: ["ubuntu-22.04"]
+        python-version: ["3.10"]
         pytorch-version:
           - "2.0.1"
           - "2.1.2"
@@ -42,9 +42,8 @@ jobs:
           - "2.5.0"
         include:
           # cover additional python and PT combinations
-          - { os: "ubuntu-22.04", python-version: "3.10", pytorch-version: "2.0.1" }
-          - { os: "ubuntu-22.04", python-version: "3.10", pytorch-version: "2.2.2" }
-          - { os: "ubuntu-22.04", python-version: "3.11", pytorch-version: "2.3.1" }
+          - { os: "ubuntu-20.04", python-version: "3.8", pytorch-version: "2.0.1", requires: "oldest" }
+          - { os: "ubuntu-22.04", python-version: "3.11", pytorch-version: "2.4.1" }
           - { os: "ubuntu-22.04", python-version: "3.12", pytorch-version: "2.5.0" }
           # standard mac machine, not the M1
           - { os: "macOS-13", python-version: "3.10", pytorch-version: "2.0.1" }

.github/workflows/docs-build.yml

@@ -44,7 +44,6 @@ jobs:
       - name: source cashing
         uses: ./.github/actions/pull-caches
         with:
-          requires: ${{ matrix.requires }}
           pytorch-version: ${{ matrix.pytorch-version }}
           pypi-dir: ${{ env.PYPI_CACHE }}
 

requirements/segmentation_test.txt

@@ -2,4 +2,5 @@
 #  in case you want to preserve/enforce restrictions on the latest compatible version, add "strict" as an in-line comment
 
 scipy >1.0.0, <1.15.0
-monai ==1.4.0
+monai ==1.3.2 ; python_version < "3.9"
+monai ==1.4.0 ; python_version > "3.8"

setup.py

@@ -245,5 +245,6 @@ def _prepare_extras(skip_pattern: str = "^_", skip_files: Tuple[str] = ("base.tx
             "Programming Language :: Python :: 3.9",
             "Programming Language :: Python :: 3.10",
             "Programming Language :: Python :: 3.11",
+            "Programming Language :: Python :: 3.12",
         ],
     )

src/conftest.py

@@ -36,5 +36,5 @@ def collect(self) -> GeneratorExit:
     def pytest_collect_file(parent: Path, path: Path) -> Optional[DoctestModule]:
         """Collect doctests and add the reset_random_seed fixture."""
         if path.ext == ".py":
-            return DoctestModule.from_parent(parent, fspath=path)
+            return DoctestModule.from_parent(parent, path=Path(path))
         return None

src/torchmetrics/collections.py

@@ -31,6 +31,30 @@
     __doctest_skip__ = ["MetricCollection.plot", "MetricCollection.plot_all"]
 
 
+def _remove_prefix(string: str, prefix: str) -> str:
+    """Patch for older version with missing method `removeprefix`.
+
+    >>> _remove_prefix("prefix_string", "prefix_")
+    'string'
+    >>> _remove_prefix("not_prefix_string", "prefix_")
+    'not_prefix_string'
+
+    """
+    return string[len(prefix) :] if string.startswith(prefix) else string
+
+
+def _remove_suffix(string: str, suffix: str) -> str:
+    """Patch for older version with missing method `removesuffix`.
+
+    >>> _remove_suffix("string_suffix", "_suffix")
+    'string'
+    >>> _remove_suffix("string_suffix_missing", "_suffix")
+    'string_suffix_missing'
+
+    """
+    return string[: -len(suffix)] if string.endswith(suffix) else string
+
+
 class MetricCollection(ModuleDict):
     """MetricCollection class can be used to chain metrics that have the same call pattern into one single class.
 
@@ -558,9 +582,9 @@ def __getitem__(self, key: str, copy_state: bool = True) -> Metric:
         """
         self._compute_groups_create_state_ref(copy_state)
         if self.prefix:
-            key = key.removeprefix(self.prefix)
+            key = _remove_prefix(key, self.prefix)
         if self.postfix:
-            key = key.removesuffix(self.postfix)
+            key = _remove_suffix(key, self.postfix)
         return self._modules[key]
 
     @staticmethod

tests/unittests/segmentation/test_generalized_dice_score.py

@@ -16,6 +16,7 @@
 
 import pytest
 import torch
+from lightning_utilities.core.imports import RequirementCache
 from monai.metrics.generalized_dice import compute_generalized_dice
 from torchmetrics.functional.segmentation.generalized_dice import generalized_dice_score
 from torchmetrics.segmentation.generalized_dice import GeneralizedDiceScore
@@ -51,7 +52,8 @@ def _reference_generalized_dice(
     if input_format == "index":
         preds = torch.nn.functional.one_hot(preds, num_classes=NUM_CLASSES).movedim(-1, 1)
         target = torch.nn.functional.one_hot(target, num_classes=NUM_CLASSES).movedim(-1, 1)
-    val = compute_generalized_dice(preds, target, include_background=include_background, sum_over_classes=True)
+    monai_extra_arg = {"sum_over_classes": True} if RequirementCache("monai>=1.4.0") else {}
+    val = compute_generalized_dice(preds, target, include_background=include_background, **monai_extra_arg)
     if reduce:
         val = val.mean()
     return val.squeeze()