dcccpy 0.2.0__tar.gz → 0.3.0a1__tar.gz

{dcccpy-0.2.0/src/dcccpy.egg-info → dcccpy-0.3.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcccpy
-Version: 0.2.0
+Version: 0.3.0a1
 Summary: Python wrapper for the DCCCcore PET biomarker command-line tool
 Author: DCCCSlicer contributors
 License-Expression: CC-BY-NC-ND-4.0
@@ -138,6 +138,23 @@ dcccpy centiloid --input amyloid_pet.nii --output result.nii
 dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+The Python helper accepts the same staged exports. Pass one integer or a
+sequence; only the requested stages are saved:
+
+```python
+dcccpy.adni_pet_core(
+    "dynamic_pet.nii.gz",
+    "standardized.nii.gz",
+    tracer="fdg",
+    level=(1, 3),
+)
+```
+
+Level 1 is the motion-corrected dynamic PET, Level 2 is its 3D average, and
+Level 3 is the standardized ADNI-style image. The output argument names the
+highest selected level, while selected lower levels receive `_Coreg` or
+`_Coreg_Avg` suffixes.
+
 `adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
 `fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
 Aβ and tau retain cerebellar gray normalization.
@@ -189,7 +206,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -197,7 +214,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -215,11 +232,11 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
+The current optional runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.
 
-The plain `dcccpy` package remains slim and downloads the full matching
-`DCCCcore` release package from GitHub on first use when no installed runtime is
-available.
+The `dcccpy` 0.3 alpha package targets DCCCcore 4.5.0-alpha. Because the optional
+runtime wheels still contain DCCCcore 4.4.0, this alpha wrapper ignores those
+older runtimes and downloads the full matching GitHub release on first use.

{dcccpy-0.2.0 → dcccpy-0.3.0a1}/README.md

@@ -107,6 +107,23 @@ dcccpy centiloid --input amyloid_pet.nii --output result.nii
 dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+The Python helper accepts the same staged exports. Pass one integer or a
+sequence; only the requested stages are saved:
+
+```python
+dcccpy.adni_pet_core(
+    "dynamic_pet.nii.gz",
+    "standardized.nii.gz",
+    tracer="fdg",
+    level=(1, 3),
+)
+```
+
+Level 1 is the motion-corrected dynamic PET, Level 2 is its 3D average, and
+Level 3 is the standardized ADNI-style image. The output argument names the
+highest selected level, while selected lower levels receive `_Coreg` or
+`_Coreg_Avg` suffixes.
+
 `adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
 `fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
 Aβ and tau retain cerebellar gray normalization.
@@ -158,7 +175,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -166,7 +183,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -184,11 +201,11 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
+The current optional runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.
 
-The plain `dcccpy` package remains slim and downloads the full matching
-`DCCCcore` release package from GitHub on first use when no installed runtime is
-available.
+The `dcccpy` 0.3 alpha package targets DCCCcore 4.5.0-alpha. Because the optional
+runtime wheels still contain DCCCcore 4.4.0, this alpha wrapper ignores those
+older runtimes and downloads the full matching GitHub release on first use.

{dcccpy-0.2.0 → dcccpy-0.3.0a1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcccpy"
-version = "0.2.0"
+version = "0.3.0a1"
 description = "Python wrapper for the DCCCcore PET biomarker command-line tool"
 readme = "README.md"
 requires-python = ">=3.9"

{dcccpy-0.2.0 → dcccpy-0.3.0a1}/src/dcccpy/core.py

@@ -411,12 +411,23 @@ def adni_pet_core(
     output: str | os.PathLike[str] | None = None,
     *,
     tracer: str,
+    level: int | Sequence[int] = 3,
     **kwargs: object,
 ) -> DCCCResult:
-    """Run tracer-specific ADNI PET Core preprocessing."""
+    """Run tracer-specific ADNI PET Core preprocessing.
+
+    ``level`` accepts one level or a sequence: 1 exports Coreg, 2 exports
+    Coreg/Avg, and 3 exports the standardized image. Multiple levels produce
+    multiple files while ``output`` identifies the deepest requested level.
+    """
 
     extra_args = list(kwargs.pop("extra_args", ()))
     extra_args.extend(["--tracer", tracer])
+    levels = (level,) if isinstance(level, int) else tuple(level)
+    if not levels or any(value not in (1, 2, 3) for value in levels):
+        raise ValueError("level must contain one or more of: 1, 2, 3")
+    if levels != (3,):
+        extra_args.extend(["--level", *(str(value) for value in levels)])
     return _spatial_command("adni-pet-core", input, output, extra_args=extra_args, **kwargs)
 
 

{dcccpy-0.2.0 → dcccpy-0.3.0a1}/src/dcccpy/runtime.py

@@ -12,7 +12,10 @@ from pathlib import Path
 from typing import Iterable
 
 
-DCCCCORE_VERSION = "4.4.0"
+DCCCCORE_VERSION = "4.5.0-alpha"
+# The optional runtime wheels currently contain the last stable native core.
+# Do not let an installed older runtime shadow the release selected above.
+RUNTIME_PACKAGE_DCCCCORE_VERSION = "4.4.0"
 RELEASE_REPO = "tctco/DCCCSlicer"
 
 
@@ -99,7 +102,10 @@ def _main_package_vendor_dirs() -> list[Path]:
     return [vendor_root / key, vendor_root]
 
 
-def _runtime_package_dirs() -> list[Path]:
+def _runtime_package_dirs(version: str = DCCCCORE_VERSION) -> list[Path]:
+    if version != RUNTIME_PACKAGE_DCCCCORE_VERSION:
+        return []
+
     roots: list[Path] = []
     try:
         import dcccpy_linux_runtime
@@ -141,7 +147,7 @@ def find_existing_dccccore(version: str = DCCCCORE_VERSION) -> Path | None:
         if candidate.exists():
             return candidate
 
-    for candidate in candidate_executables(_runtime_package_dirs()):
+    for candidate in candidate_executables(_runtime_package_dirs(version)):
         if candidate.exists():
             return candidate
 

{dcccpy-0.2.0 → dcccpy-0.3.0a1/src/dcccpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcccpy
-Version: 0.2.0
+Version: 0.3.0a1
 Summary: Python wrapper for the DCCCcore PET biomarker command-line tool
 Author: DCCCSlicer contributors
 License-Expression: CC-BY-NC-ND-4.0
@@ -138,6 +138,23 @@ dcccpy centiloid --input amyloid_pet.nii --output result.nii
 dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+The Python helper accepts the same staged exports. Pass one integer or a
+sequence; only the requested stages are saved:
+
+```python
+dcccpy.adni_pet_core(
+    "dynamic_pet.nii.gz",
+    "standardized.nii.gz",
+    tracer="fdg",
+    level=(1, 3),
+)
+```
+
+Level 1 is the motion-corrected dynamic PET, Level 2 is its 3D average, and
+Level 3 is the standardized ADNI-style image. The output argument names the
+highest selected level, while selected lower levels receive `_Coreg` or
+`_Coreg_Avg` suffixes.
+
 `adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
 `fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
 Aβ and tau retain cerebellar gray normalization.
@@ -189,7 +206,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -197,7 +214,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.5.0-alpha --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -215,11 +232,11 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
+The current optional runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.
 
-The plain `dcccpy` package remains slim and downloads the full matching
-`DCCCcore` release package from GitHub on first use when no installed runtime is
-available.
+The `dcccpy` 0.3 alpha package targets DCCCcore 4.5.0-alpha. Because the optional
+runtime wheels still contain DCCCcore 4.4.0, this alpha wrapper ignores those
+older runtimes and downloads the full matching GitHub release on first use.

{dcccpy-0.2.0 → dcccpy-0.3.0a1}/tests/test_core.py

@@ -142,7 +142,7 @@ def test_dccccore_path_can_disable_auto_download(tmp_path: Path, monkeypatch: py
 
 
 def test_dccccore_path_auto_downloads_to_cache(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
-    asset_root = tmp_path / "asset" / "DCCCcore-4.4.0-ubuntu-latest-x64"
+    asset_root = tmp_path / "asset" / "DCCCcore-4.5.0-alpha-ubuntu-latest-x64"
     asset_root.mkdir(parents=True)
     exe = asset_root / "DCCCcore"
     exe.write_text("#!/usr/bin/env sh\nprintf 'fake dccccore\\n'\n")
@@ -150,7 +150,7 @@ def test_dccccore_path_auto_downloads_to_cache(tmp_path: Path, monkeypatch: pyte
 
     archive = tmp_path / "DCCCcore.zip"
     with zipfile.ZipFile(archive, "w") as zf:
-        zf.write(exe, "DCCCcore-4.4.0-ubuntu-latest-x64/DCCCcore")
+        zf.write(exe, "DCCCcore-4.5.0-alpha-ubuntu-latest-x64/DCCCcore")
 
     monkeypatch.delenv("DCCCPY_DCCCCORE", raising=False)
     monkeypatch.setenv("DCCCPY_AUTO_DOWNLOAD", "1")
@@ -179,20 +179,37 @@ def test_find_existing_dccccore_checks_macos_runtime_package(
     monkeypatch.setitem(sys.modules, "dcccpy_macos_runtime", module)
     monkeypatch.setenv("PATH", str(tmp_path / "empty-path"))
 
-    assert find_existing_dccccore() == exe
+    assert find_existing_dccccore("4.4.0") == exe
 
 
 def test_linux_arm64_release_platform() -> None:
     assert release_platform("linux-arm64") == "ubuntu-latest-arm64"
 
 
-def test_default_release_targets_dccccore_440() -> None:
-    assert DCCCCORE_VERSION == "4.4.0"
+def test_default_release_targets_dccccore_450_alpha() -> None:
+    assert DCCCCORE_VERSION == "4.5.0-alpha"
     assert release_url(platform_name="ubuntu-latest-x64").endswith(
-        "/releases/download/v4.4.0/DCCCcore-4.4.0-ubuntu-latest-x64.zip"
+        "/releases/download/v4.5.0-alpha/DCCCcore-4.5.0-alpha-ubuntu-latest-x64.zip"
     )
 
 
+def test_alpha_ignores_incompatible_stable_runtime_package(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    root = tmp_path / "stable-runtime"
+    root.mkdir()
+    exe = root / "DCCCcore"
+    exe.write_text("#!/usr/bin/env sh\n")
+    exe.chmod(0o755)
+
+    module = types.SimpleNamespace(dccccore_root=lambda: root)
+    monkeypatch.setitem(sys.modules, "dcccpy_linux_runtime", module)
+    monkeypatch.setenv("PATH", str(tmp_path / "empty-path"))
+
+    assert find_existing_dccccore() is None
+
+
 def test_find_existing_dccccore_checks_linux_arm64_runtime_package(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
@@ -207,7 +224,7 @@ def test_find_existing_dccccore_checks_linux_arm64_runtime_package(
     monkeypatch.setitem(sys.modules, "dcccpy_linux_arm64_runtime", module)
     monkeypatch.setenv("PATH", str(tmp_path / "empty-path"))
 
-    assert find_existing_dccccore() == exe
+    assert find_existing_dccccore("4.4.0") == exe
 
 
 def test_cli_forwards_raw_args(tmp_path: Path, monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str]) -> None:
@@ -293,6 +310,43 @@ def test_adni_pet_core_python_api_has_no_default_tracer() -> None:
         dcccpy.adni_pet_core("pet.nii")
 
 
+def test_adni_pet_core_forwards_combined_export_levels(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    fake_args = tmp_path / "args.txt"
+    fake_exe = make_fake_dccccore(tmp_path)
+    input_path = tmp_path / "pet.nii"
+    output_path = tmp_path / "adni.nii"
+    input_path.write_text("fake PET")
+    monkeypatch.setenv("DCCCPY_DCCCCORE", str(fake_exe))
+    monkeypatch.setenv("DCCCPY_FAKE_ARGS", str(fake_args))
+
+    result = dcccpy.adni_pet_core(
+        input_path, output_path, tracer="fdg", level=(1, 2)
+    )
+
+    assert result.returncode == 0
+    assert fake_args.read_text().splitlines() == [
+        "adni-pet-core",
+        "--input",
+        str(input_path),
+        "--output",
+        str(output_path),
+        "--tracer",
+        "fdg",
+        "--level",
+        "1",
+        "2",
+    ]
+
+
+@pytest.mark.parametrize("level", [(), 0, 4, (1, 4)])
+def test_adni_pet_core_rejects_invalid_export_levels(level: object) -> None:
+    with pytest.raises(ValueError, match="level must contain"):
+        dcccpy.adni_pet_core("pet.nii", tracer="fdg", level=level)  # type: ignore[arg-type]
+
+
 def test_run_adds_macos_security_hint_for_blocked_runtime(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,