junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/cli/tests/test_cli_utils.py

@@ -3,8 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import importlib
 import platform as pl
-import sys
 
 import pytest
 
@@ -32,8 +32,8 @@ def test_get_python_information() -> None:
 
 def test_get_dependency_information_short() -> None:
     """Test short version of _get_dependency_information()."""
-    dependency_information = _get_dependency_information(long_=False)
     dependency_list = [
+        "aenum",
         "click",
         "numpy",
         "scipy",
@@ -46,14 +46,20 @@ def test_get_dependency_information_short() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "h5py",
+        "h5io",
         "lazy_loader",
         "looseversion",
         "junifer_data",
         "structlog",
+        "pydantic",
+        "typing_extensions",
     ]
 
-    if sys.version_info < (3, 11):
-        dependency_list.append("importlib_metadata")
+    # Import dependencies as only loaded modules are reported
+    for module in dependency_list:
+        importlib.import_module(module)
+    dependency_information = _get_dependency_information(long_=False)
 
     assert frozenset(dependency_information.keys()) == frozenset(
         dependency_list
@@ -62,9 +68,8 @@ def test_get_dependency_information_short() -> None:
 
 def test_get_dependency_information_long() -> None:
     """Test long version of _get_dependency_information()."""
-    dependency_information = _get_dependency_information(long_=True)
-    dependency_information_keys = list(dependency_information.keys())
     dependency_list = [
+        "aenum",
         "click",
         "numpy",
         "scipy",
@@ -77,8 +82,20 @@ def test_get_dependency_information_long() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "h5py",
+        "h5io",
         "lazy_loader",
+        "looseversion",
+        "junifer_data",
+        "structlog",
+        "pydantic",
+        "typing_extensions",
     ]
+    # Import dependencies as only loaded modules are reported
+    for module in dependency_list:
+        importlib.import_module(module)
+    dependency_information = _get_dependency_information(long_=True)
+    dependency_information_keys = list(dependency_information.keys())
     for key in dependency_list:
         assert key in dependency_information_keys
 

junifer/cli/utils.py

@@ -70,18 +70,23 @@ def _get_dependency_information(long_: bool) -> dict[str, str]:
         # Get dependencies for junifer
         dist = distribution("junifer")
         # Compile regex pattern
-        re_pattern = re.compile("[a-z-_.]+")
-
-        for pkg_with_version in dist.requires:  # type: ignore
-            # Perform regex search
-            matches = re.findall(pattern=re_pattern, string=pkg_with_version)
+        re_pattern = re.compile(r"^\s*([A-Za-z0-9][A-Za-z0-9._-]*)")
+
+        for requirement in dist.requires:  # type: ignore
+            # Split requirement and environment marker
+            pkg_with_version, _, marker = requirement.partition(";")
+            # Skip optional dependencies
+            if "extra" in marker:
+                continue
             # Extract package name
-            key = matches[0]
+            match = re_pattern.match(pkg_with_version)
+            if match is None:
+                continue
+            # Convert distribution name to module name
+            key = match.group(1).replace("-", "_")
 
             if key in dependency_versions.keys():
-                # Check if pkg part of optional dependencies
-                if "extra" not in matches:
-                    pruned_dependency_versions[key] = dependency_versions[key]
+                pruned_dependency_versions[key] = dependency_versions[key]
 
     return pruned_dependency_versions
 

junifer/configs/__init__.py

@@ -2,3 +2,8 @@
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/configs/juseless/datagrabbers/__init__.pyi

@@ -2,12 +2,14 @@ __all__ = [
     "JuselessDataladAOMICID1000VBM",
     "JuselessDataladCamCANVBM",
     "JuselessDataladIXIVBM",
+    "IXISite",
     "JuselessUCLA",
+    "UCLATask",
     "JuselessDataladUKBVBM",
 ]
 
 from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM
 from .camcan_vbm import JuselessDataladCamCANVBM
-from .ixi_vbm import JuselessDataladIXIVBM
-from .ucla import JuselessUCLA
+from .ixi_vbm import JuselessDataladIXIVBM, IXISite
+from .ucla import JuselessUCLA, UCLATask
 from .ukb_vbm import JuselessDataladUKBVBM

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -4,11 +4,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from pathlib import Path
-from typing import Union
+from typing import Literal
+
+from pydantic import AnyUrl
 
 from ....api.decorators import register_datagrabber
-from ....datagrabber import PatternDataladDataGrabber
+from ....datagrabber import DataType, PatternDataladDataGrabber
+from ....typing import DataGrabberPatterns
 
 
 __all__ = ["JuselessDataladAOMICID1000VBM"]
@@ -22,27 +24,19 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
 
     Parameters
     ----------
-    datadir : str or pathlib.Path or None, optional
-        The directory where the datalad dataset will be cloned. If None,
-        the datalad dataset will be cloned into a temporary directory
-        (default None).
+    datadir : pathlib.Path, optional
+        That path where the datalad dataset will be cloned.
+        If not specified, the datalad dataset will be cloned into a temporary
+        directory.
 
     """
 
-    def __init__(self, datadir: Union[str, Path, None] = None) -> None:
-        uri = "https://gin.g-node.org/felixh/ds003097_ReproVBM"
-        types = ["VBM_GM"]
-        replacements = ["subject"]
-        patterns = {
-            "VBM_GM": {
-                "pattern": ("{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"),
-                "space": "IXI549Space",
-            },
-        }
-        super().__init__(
-            types=types,
-            datadir=datadir,
-            uri=uri,
-            replacements=replacements,
-            patterns=patterns,
-        )
+    uri: AnyUrl = AnyUrl("https://gin.g-node.org/felixh/ds003097_ReproVBM")
+    types: list[Literal[DataType.VBM_GM]] = [DataType.VBM_GM]  # noqa: RUF012
+    patterns: DataGrabberPatterns = {  # noqa: RUF012
+        "VBM_GM": {
+            "pattern": ("{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"),
+            "space": "IXI549Space",
+        },
+    }
+    replacements: list[str] = ["subject"]  # noqa: RUF012

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -5,11 +5,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from pathlib import Path
-from typing import Union
+from typing import Literal
+
+from pydantic import AnyUrl
 
 from ....api.decorators import register_datagrabber
-from ....datagrabber import PatternDataladDataGrabber
+from ....datagrabber import DataType, PatternDataladDataGrabber
+from ....typing import DataGrabberPatterns
 
 
 __all__ = ["JuselessDataladCamCANVBM"]
@@ -23,30 +25,21 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
 
     Parameters
     ----------
-    datadir : str or pathlib.Path or None, optional
-        The directory where the datalad dataset will be cloned. If None,
-        the datalad dataset will be cloned into a temporary directory
-        (default None).
+    datadir : pathlib.Path, optional
+        That path where the datalad dataset will be cloned.
+        If not specified, the datalad dataset will be cloned into a temporary
+        directory.
 
     """
 
-    def __init__(self, datadir: Union[str, Path, None] = None) -> None:
-        uri = (
-            "ria+http://cat_12.5.ds.inm7.de"
-            "#a139b26a-8406-11ea-8f94-a0369f287950"
-        )
-        types = ["VBM_GM"]
-        replacements = ["subject"]
-        patterns = {
-            "VBM_GM": {
-                "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
-                "space": "IXI549Space",
-            },
-        }
-        super().__init__(
-            types=types,
-            datadir=datadir,
-            uri=uri,
-            replacements=replacements,
-            patterns=patterns,
-        )
+    uri: AnyUrl = AnyUrl(
+        "ria+http://cat_12.5.ds.inm7.de#a139b26a-8406-11ea-8f94-a0369f287950"
+    )
+    types: list[Literal[DataType.VBM_GM]] = [DataType.VBM_GM]  # noqa: RUF012
+    patterns: DataGrabberPatterns = {  # noqa: RUF012
+        "VBM_GM": {
+            "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
+            "space": "IXI549Space",
+        },
+    }
+    replacements: list[str] = ["subject"]  # noqa: RUF012

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -5,15 +5,29 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from pathlib import Path
-from typing import Union
+from enum import StrEnum
+from typing import Annotated, ClassVar, Literal
+
+from pydantic import AnyUrl, BeforeValidator
 
 from ....api.decorators import register_datagrabber
-from ....datagrabber import PatternDataladDataGrabber
-from ....utils import raise_error
+from ....datagrabber import DataType, PatternDataladDataGrabber
+from ....typing import DataGrabberPatterns
+from ....utils import ensure_list
+
+
+__all__ = ["IXISite", "JuselessDataladIXIVBM"]
+
+
+class IXISite(StrEnum):
+    """Accepted IXI sites."""
+
+    Guys = "Guys"
+    HH = "HH"
+    IOP = "IOP"
 
 
-__all__ = ["JuselessDataladIXIVBM"]
+_sites = Literal[IXISite.Guys, IXISite.HH, IXISite.IOP]
 
 
 @register_datagrabber
@@ -24,53 +38,31 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
 
     Parameters
     ----------
-    datadir : str or pathlib.Path or None, optional
-        The directory where the datalad dataset will be cloned. If None,
-        the datalad dataset will be cloned into a temporary directory
-        (default None).
-    sites : {"Guys", "HH", "IOP"} or list of the options or None, optional
-        Which sites to access data from. If None, all available sites are
-        selected (default None).
+    datadir : pathlib.Path, optional
+        That path where the datalad dataset will be cloned.
+        If not specified, the datalad dataset will be cloned into a temporary
+        directory.
+    sites : {"Guys", "HH", "IOP"} or list of the options, optional
+        IXI sites.
+        By default, all available sites are selected.
 
     """
 
-    def __init__(
-        self,
-        datadir: Union[str, Path, None] = None,
-        sites: Union[str, list[str], None] = None,
-    ) -> None:
-        uri = (
-            "ria+http://cat_12.5.ds.inm7.de"
-            "#b7107c52-8408-11ea-89c6-a0369f287950"
-        )
-        types = ["VBM_GM"]
-        replacements = ["site", "subject"]
-        patterns = {
-            "VBM_GM": {
-                "pattern": ("{site}/{subject}/mri/m0wp1{subject}.nii.gz"),
-                "space": "IXI549Space",
-            },
-        }
-
-        # validate and/or transform 'site' input
-        all_sites = ["HH", "Guys", "IOP"]
-        if sites is None:
-            sites = all_sites
-
-        if isinstance(sites, str):
-            sites = [sites]
-
-        for s in sites:
-            if s not in all_sites:
-                raise_error(
-                    f"{s} not a valid site in IXI VBM dataset!"
-                    f"Available sites are {all_sites}"
-                )
-        self.sites = sites
-        super().__init__(
-            types=types,
-            datadir=datadir,
-            uri=uri,
-            replacements=replacements,
-            patterns=patterns,
-        )
+    uri: AnyUrl = AnyUrl(
+        "ria+http://cat_12.5.ds.inm7.de#b7107c52-8408-11ea-89c6-a0369f287950"
+    )
+    types: list[Literal[DataType.VBM_GM]] = [DataType.VBM_GM]  # noqa: RUF012
+    sites: ClassVar[
+        Annotated[IXISite | list[IXISite], BeforeValidator(ensure_list)]
+    ] = [
+        IXISite.Guys,
+        IXISite.HH,
+        IXISite.IOP,
+    ]
+    patterns: DataGrabberPatterns = {  # noqa: RUF012
+        "VBM_GM": {
+            "pattern": ("{site}/{subject}/mri/m0wp1{subject}.nii.gz"),
+            "space": "IXI549Space",
+        },
+    }
+    replacements: list[str] = ["site", "subject"]  # noqa: RUF012

junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py

@@ -31,10 +31,3 @@ def test_JuselessDataladIXIVBM() -> None:
             out["VBM_GM"]["path"].name == f"m0wp1sub-{test_element[1]}.nii.gz"
         )
         assert out["VBM_GM"]["path"].exists()
-
-
-def test_JuselessDataladIXIVBM_invalid_site() -> None:
-    """Test JuselessDataladIXIVBM with invalid site."""
-    with pytest.raises(ValueError, match="notavalidsite not a valid site"):
-        with JuselessDataladIXIVBM(sites="notavalidsite"):
-            pass

junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 import socket
-from typing import Optional, Union
 
 import pytest
 
@@ -53,7 +52,7 @@ def test_JuselessUCLA() -> None:
     ],
 )
 def test_JuselessUCLA_partial_data_access(
-    types: Union[str, list[str]],
+    types: str | list[str],
 ) -> None:
     """Test JuselessUCLA DataGrabber partial data access.
 
@@ -80,19 +79,11 @@ def test_JuselessUCLA_partial_data_access(
             assert types in out
 
 
-def test_JuselessUCLA_incorrect_data_type() -> None:
-    """Test JuselessUCLA DataGrabber incorrect data type."""
-    with pytest.raises(
-        ValueError, match="`patterns` must contain all `types`"
-    ):
-        _ = JuselessUCLA(types="Eunomia")
-
-
 @pytest.mark.parametrize(
     "tasks",
     [None, "rest", ["rest", "stopsignal"]],
 )
-def test_JuselessUCLA_task_params(tasks: Optional[str]) -> None:
+def test_JuselessUCLA_task_params(tasks: str | None) -> None:
     """Test JuselessUCLA with different task parameters.
 
     Parameters
@@ -125,11 +116,3 @@ def test_JuselessUCLA_task_params(tasks: Optional[str]) -> None:
         else:
             for el in all_elements:
                 assert el[1] in ["rest", "stopsignal"]
-
-
-def test_JuselessUCLA_invalid_tasks() -> None:
-    """Test JuselessUCLA with invalid task parameters."""
-    with pytest.raises(
-        ValueError, match="invalid is not a valid task in the UCLA"
-    ):
-        JuselessUCLA(tasks="invalid")