test: reorganize suite by module under test and remove duplicates

.github/workflows/konfai_ci.yml

@@ -59,7 +59,7 @@ jobs:
         run: pip install ruff==0.15.2
 
       - name: Run ruff lint
-        run: ruff check konfai konfai-apps/konfai_apps
+        run: ruff check konfai konfai-apps/konfai_apps tests
 
   format:
     runs-on: ubuntu-latest
@@ -75,7 +75,7 @@ jobs:
         run: pip install ruff==0.15.2
 
       - name: Check formatting
-        run: ruff format --check konfai konfai-apps/konfai_apps
+        run: ruff format --check konfai konfai-apps/konfai_apps tests
 
   build:
     runs-on: ubuntu-latest

pyproject.toml

@@ -163,9 +163,9 @@ scikit-image = "*"
 test = { cmd = "pytest -q tests/", description = "Run the test suite" }
 test-apps = { cmd = "pytest -q konfai-apps/tests", description = "Run the konfai-apps test suite" }
 test-cov = { cmd = "pytest --cov=konfai --cov-report=term-missing tests/", description = "Run tests with coverage" }
-lint = { cmd = "ruff check konfai konfai-apps/konfai_apps", description = "Lint source code" }
-format = { cmd = "ruff format konfai konfai-apps/konfai_apps", description = "Format source code" }
-format-check = { cmd = "ruff format --check konfai konfai-apps/konfai_apps", description = "Check formatting without modifying files" }
+lint = { cmd = "ruff check konfai konfai-apps/konfai_apps tests", description = "Lint source code" }
+format = { cmd = "ruff format konfai konfai-apps/konfai_apps tests", description = "Format source code" }
+format-check = { cmd = "ruff format --check konfai konfai-apps/konfai_apps tests", description = "Check formatting without modifying files" }
 typecheck = { cmd = "python -m mypy konfai --ignore-missing-imports --no-site-packages", description = "Type-check the konfai package" }
 build = { cmd = "python -m build", description = "Build sdist and wheel" }
 check = { depends-on = ["lint", "format-check", "test", "test-apps"], description = "Run all quality checks" }
@@ -181,9 +181,9 @@ ruff = "==0.15.2"
 pre-commit = "*"
 
 [tool.pixi.feature.lint.tasks]
-lint = { cmd = "ruff check konfai konfai-apps/konfai_apps", description = "Lint source code" }
-format = { cmd = "ruff format konfai konfai-apps/konfai_apps", description = "Format source code" }
-format-check = { cmd = "ruff format --check konfai konfai-apps/konfai_apps", description = "Check formatting without modifying files" }
+lint = { cmd = "ruff check konfai konfai-apps/konfai_apps tests", description = "Lint source code" }
+format = { cmd = "ruff format konfai konfai-apps/konfai_apps tests", description = "Format source code" }
+format-check = { cmd = "ruff format --check konfai konfai-apps/konfai_apps tests", description = "Check formatting without modifying files" }
 pre-commit-install = { cmd = "pre-commit install --hook-type pre-commit --hook-type commit-msg", description = "Install pre-commit and commit-msg hooks" }
 pre-commit-run = { cmd = "pre-commit run --all-files", description = "Run pre-commit hooks on all repository files" }
 

tests/assets/Workflows/TinySynth.py

@@ -1,5 +1,4 @@
 import torch
-
 from konfai.network import network
 
 

tests/conftest.py

@@ -0,0 +1,63 @@
+# Copyright (c) 2025 Valentin Boussot
+#
+# 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.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+"""Shared fixtures for the KonfAI test suite."""
+
+from collections.abc import Callable
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def _konfai_env(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Harmless per-test defaults for the mandatory KONFAI environment variables.
+
+    ``Config()`` requires ``KONFAI_config_file`` and ``KONFAI_CONFIG_MODE`` (AGENTS.md §7).
+    Tests that exercise the config engine override these with ``monkeypatch.setenv``.
+    """
+    monkeypatch.setenv("KONFAI_config_file", "/tmp/konfai-none.yml")
+    monkeypatch.setenv("KONFAI_CONFIG_MODE", "Done")
+
+
+@pytest.fixture
+def write_config(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> Callable[..., Path]:
+    """Write a YAML config to ``tmp_path`` and point the KONFAI env vars at it."""
+
+    def write(content: str, *, mode: str = "Done", name: str = "config.yml") -> Path:
+        config_path = tmp_path / name
+        config_path.write_text(content, encoding="utf-8")
+        monkeypatch.setenv("KONFAI_config_file", str(config_path))
+        monkeypatch.setenv("KONFAI_CONFIG_MODE", mode)
+        return config_path
+
+    return write
+
+
+@pytest.fixture
+def image_attributes():
+    """Factory for an ``Attribute`` carrying Origin/Spacing/Direction geometry."""
+    from konfai.utils.dataset import Attribute
+
+    def make(origin: list[float], spacing: list[float]) -> Attribute:
+        attributes = Attribute()
+        attributes["Origin"] = np.asarray(origin, dtype=np.float64)
+        attributes["Spacing"] = np.asarray(spacing, dtype=np.float64)
+        attributes["Direction"] = np.eye(len(origin), dtype=np.float64).reshape(-1)
+        return attributes
+
+    return make

tests/integration/test_konfai_core_workflows.py

@@ -9,11 +9,12 @@
 
 import numpy as np
 import pytest
-
 from konfai.evaluator import build_evaluate
 from konfai.predictor import build_predict
 from konfai.trainer import build_train
 
+pytestmark = pytest.mark.integration
+
 ASSETS_DIR = Path(__file__).resolve().parents[1] / "assets" / "Workflows"
 REPO_ROOT = Path(__file__).resolve().parents[2]
 SimpleITK = pytest.importorskip("SimpleITK")
@@ -219,9 +220,7 @@ def main() -> None:
 
             if __name__ == "__main__":
                 main()
-            """.replace(
-                "__TRAIN_NAME__", train_name
-            )
+            """.replace("__TRAIN_NAME__", train_name)
         ),
         encoding="utf-8",
     )