junifer 0.0.7.dev18__py3-none-any.whl → 0.0.7.dev43__py3-none-any.whl

junifer/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.7.dev18'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev18')
+__version__ = version = '0.0.7.dev43'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev43')

junifer/api/decorators.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from ..pipeline import PipelineComponentRegistry
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 

junifer/api/functions.py

@@ -294,8 +294,7 @@ def queue(
     valid_kind = ["HTCondor", "GNUParallelLocal"]
     if kind not in valid_kind:
         raise_error(
-            f"Invalid value for `kind`: {kind}, "
-            f"must be one of {valid_kind}"
+            f"Invalid value for `kind`: {kind}, must be one of {valid_kind}"
         )
 
     # Create a folder within the CWD to store the job files / config

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -218,8 +218,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         # Copy executable if not local
         if hasattr(self, "_exec_path"):
             logger.info(
-                f"Copying {self._executable} to "
-                f"{self._exec_path.resolve()!s}"
+                f"Copying {self._executable} to {self._exec_path.resolve()!s}"
             )
             shutil.copy(
                 src=Path(__file__).parent.parent / "res" / self._executable,
@@ -235,15 +234,14 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         self._elements_file_path.write_text(textwrap.dedent(self.elements()))
         # Create pre run
         logger.info(
-            f"Writing {self._pre_run_path.name} to "
-            f"{self._job_dir.resolve()!s}"
+            f"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
         self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
         make_executable(self._pre_run_path)
         # Create run
         logger.info(
-            f"Writing {self._run_path.name} to " f"{self._job_dir.resolve()!s}"
+            f"Writing {self._run_path.name} to {self._job_dir.resolve()!s}"
         )
         self._run_path.touch()
         self._run_path.write_text(textwrap.dedent(self.run()))
@@ -258,8 +256,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         make_executable(self._pre_collect_path)
         # Create collect
         logger.info(
-            f"Writing {self._collect_path.name} to "
-            f"{self._job_dir.resolve()!s}"
+            f"Writing {self._collect_path.name} to {self._job_dir.resolve()!s}"
         )
         self._collect_path.touch()
         self._collect_path.write_text(textwrap.dedent(self.collect()))

junifer/api/queue_context/htcondor_adapter.py

@@ -264,9 +264,7 @@ class HTCondorAdapter(QueueContextAdapter):
             )
 
         junifer_collect_args = (
-            "collect "
-            f"{self._yaml_config_path.resolve()!s} "
-            f"{verbose_args}"
+            f"collect {self._yaml_config_path.resolve()!s} {verbose_args}"
         )
         log_dir_prefix = f"{self._log_dir.resolve()!s}/junifer_collect"
         fixed = (
@@ -316,7 +314,7 @@ class HTCondorAdapter(QueueContextAdapter):
                 "$DAG_STATUS\n"
             )
         elif self._collect == "on_success_only":
-            var += f"JOB collect {self._submit_collect_path}\n" "PARENT "
+            var += f"JOB collect {self._submit_collect_path}\nPARENT "
             for idx, _ in enumerate(self._elements):
                 var += f"run{idx} "
             var += "CHILD collect\n"
@@ -328,14 +326,13 @@ class HTCondorAdapter(QueueContextAdapter):
         logger.info("Creating HTCondor job")
         # Create logs
         logger.info(
-            f"Creating logs directory under " f"{self._job_dir.resolve()!s}"
+            f"Creating logs directory under {self._job_dir.resolve()!s}"
         )
         self._log_dir.mkdir(exist_ok=True, parents=True)
         # Copy executable if not local
         if hasattr(self, "_exec_path"):
             logger.info(
-                f"Copying {self._executable} to "
-                f"{self._exec_path.resolve()!s}"
+                f"Copying {self._executable} to {self._exec_path.resolve()!s}"
             )
             shutil.copy(
                 src=Path(__file__).parent.parent / "res" / self._executable,
@@ -344,8 +341,7 @@ class HTCondorAdapter(QueueContextAdapter):
             make_executable(self._exec_path)
         # Create pre run
         logger.info(
-            f"Writing {self._pre_run_path.name} to "
-            f"{self._job_dir.resolve()!s}"
+            f"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
         self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
@@ -374,7 +370,7 @@ class HTCondorAdapter(QueueContextAdapter):
         self._submit_collect_path.write_text(textwrap.dedent(self.collect()))
         # Create DAG
         logger.debug(
-            f"Writing {self._dag_path.name} to " f"{self._job_dir.resolve()!s}"
+            f"Writing {self._dag_path.name} to {self._job_dir.resolve()!s}"
         )
         self._dag_path.touch()
         self._dag_path.write_text(textwrap.dedent(self.dag()))

junifer/cli/tests/test_parser.py

@@ -18,6 +18,23 @@ def test_parse_yaml_failure() -> None:
         parse_yaml("foo.yaml")
 
 
+def test_parse_yaml_empty_elements_failure(tmp_path: Path) -> None:
+    """Test YAML parsing with empty elements failure.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    # Write test file
+    fname = tmp_path / "test_parse_yaml_empty_elements_failure.yaml"
+    fname.write_text("elements:")
+    # Check test file
+    with pytest.raises(ValueError, match="elements key was defined"):
+        parse_yaml(fname)
+
+
 def test_parse_yaml_success(tmp_path: Path) -> None:
     """Test YAML parsing success.
 
@@ -159,6 +176,41 @@ def test_parse_yaml_absolute_path(tmp_path: Path) -> None:
     parse_yaml(yaml_fname)
 
 
+def test_parse_yaml_multi_module_deps(tmp_path: Path) -> None:
+    """Test YAML parsing with multi-module import with deps.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    t_tmp_path = tmp_path / "test_with_multi_module"
+
+    # Write .py to include
+    py_path = t_tmp_path / "external"
+    py_path.mkdir(exist_ok=True, parents=True)
+    py_fname_1 = py_path / "first.py"
+    py_fname_1.write_text(
+        "import numpy as np\nfrom second import hej\n"
+        "def junifer_module_deps(): return ['second.py']\n"
+    )
+    py_fname_2 = py_path / "second.py"
+    py_fname_2.write_text("def hej(): print('hej')\n")
+
+    # Write yaml
+    yaml_path = t_tmp_path / "yamls"
+    yaml_path.mkdir(exist_ok=True, parents=True)
+    yaml_fname = yaml_path / "test_parse_yaml_multi_module.yaml"
+
+    yaml_fname.write_text(
+        "foo: bar\nwith:\n  - ../external/first.py\n  - scipy\n"
+    )
+
+    # Check test file
+    parse_yaml(yaml_fname)
+
+
 def test_parse_storage_uri_relative(tmp_path: Path) -> None:
     """Test YAML parsing with storage and relative URI.
 
@@ -212,3 +264,17 @@ def test_parse_storage_uri_relative(tmp_path: Path) -> None:
     assert "foo" in contents
     assert contents["foo"] == "bar"
     assert "storage" in contents
+
+
+def test_parse_yaml_queue_venv_relative(tmp_path: Path) -> None:
+    """Test YAML parsing with relative venv queue.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    fname = tmp_path / "test_parse_yaml_queue_venv_relative.yaml"
+    fname.write_text("queue:\n  env:\n    kind: venv\n    name: .venv\n")
+    _ = parse_yaml(fname)

junifer/data/_dispatch.py

@@ -95,7 +95,7 @@ def get_data(
             target_data=target_data,
             extra_input=extra_input,
         )
-    else:
+    else:  # pragma: no cover
         raise_error(f"Unknown data kind: {kind}")
 
 
@@ -125,7 +125,7 @@ def list_data(kind: str) -> list[str]:
         return ParcellationRegistry().list
     elif kind == "mask":
         return MaskRegistry().list
-    else:
+    else:  # pragma: no cover
         raise_error(f"Unknown data kind: {kind}")
 
 
@@ -172,7 +172,7 @@ def load_data(
         return ParcellationRegistry().load(name=name, **kwargs)
     elif kind == "mask":
         return MaskRegistry().load(name=name, **kwargs)
-    else:
+    else:  # pragma: no cover
         raise_error(f"Unknown data kind: {kind}")
 
 
@@ -217,7 +217,7 @@ def register_data(
         return MaskRegistry().register(
             name=name, space=space, overwrite=overwrite, **kwargs
         )
-    else:
+    else:  # pragma: no cover
         raise_error(f"Unknown data kind: {kind}")
 
 
@@ -244,5 +244,5 @@ def deregister_data(kind: str, name: str) -> None:
         return ParcellationRegistry().deregister(name=name)
     elif kind == "mask":
         return MaskRegistry().deregister(name=name)
-    else:
+    else:  # pragma: no cover
         raise_error(f"Unknown data kind: {kind}")

junifer/data/coordinates/_ants_coordinates_warper.py

@@ -27,7 +27,7 @@ class ANTsCoordinatesWarper:
         seeds: ArrayLike,
         target_data: dict[str, Any],
         warp_data: dict[str, Any],
-    ) -> ArrayLike:
+    ) -> ArrayLike:  # pragma: no cover
         """Warp ``seeds`` to correct space.
 
         Parameters

junifer/data/coordinates/_coordinates.py

@@ -339,7 +339,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         seeds, labels, _ = self.load(name=coords)
 
         # Transform coordinate if target data is native
-        if target_data["space"] == "native":
+        if target_data["space"] == "native":  # pragma: no cover
             # Check for extra inputs
             if extra_input is None:
                 raise_error(

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -27,7 +27,7 @@ class FSLCoordinatesWarper:
         seeds: ArrayLike,
         target_data: dict[str, Any],
         warp_data: dict[str, Any],
-    ) -> ArrayLike:
+    ) -> ArrayLike:  # pragma: no cover
         """Warp ``seeds`` to correct space.
 
         Parameters

junifer/data/coordinates/tests/test_coordinates.py

@@ -8,7 +8,13 @@ import numpy as np
 import pytest
 from numpy.testing import assert_array_equal
 
-from junifer.data import CoordinatesRegistry
+from junifer.data import (
+    deregister_data,
+    get_data,
+    list_data,
+    load_data,
+    register_data,
+)
 from junifer.datareader import DefaultDataReader
 from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
 
@@ -16,7 +22,8 @@ from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
 def test_register_built_in_check() -> None:
     """Test coordinates registration check for built-in coordinates."""
     with pytest.raises(ValueError, match=r"built-in"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="DMNBuckner",
             coordinates=np.zeros(2),
             voi_names=["1", "2"],
@@ -26,14 +33,16 @@ def test_register_built_in_check() -> None:
 
 def test_register_overwrite() -> None:
     """Test coordinates registration check for overwriting."""
-    CoordinatesRegistry().register(
+    register_data(
+        kind="coordinates",
         name="MyList",
         coordinates=np.zeros((2, 3)),
         voi_names=["roi1", "roi2"],
         space="MNI",
     )
     with pytest.raises(ValueError, match=r"already registered"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="MyList",
             coordinates=np.ones((2, 3)),
             voi_names=["roi2", "roi3"],
@@ -41,7 +50,8 @@ def test_register_overwrite() -> None:
             overwrite=False,
         )
 
-    CoordinatesRegistry().register(
+    register_data(
+        kind="coordinates",
         name="MyList",
         coordinates=np.ones((2, 3)),
         voi_names=["roi2", "roi3"],
@@ -49,7 +59,7 @@ def test_register_overwrite() -> None:
         overwrite=True,
     )
 
-    coord, names, space = CoordinatesRegistry().load("MyList")
+    coord, names, space = load_data(kind="coordinates", name="MyList")
     assert_array_equal(coord, np.ones((2, 3)))
     assert names == ["roi2", "roi3"]
     assert space == "MNI"
@@ -58,7 +68,8 @@ def test_register_overwrite() -> None:
 def test_register_valid_input() -> None:
     """Test coordinates registration check for valid input."""
     with pytest.raises(TypeError, match=r"numpy.ndarray"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="MyList",
             coordinates=[1, 2],
             voi_names=["roi1", "roi2"],
@@ -66,7 +77,8 @@ def test_register_valid_input() -> None:
             overwrite=True,
         )
     with pytest.raises(ValueError, match=r"2D array"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="MyList",
             coordinates=np.zeros((2, 3, 4)),
             voi_names=["roi1", "roi2"],
@@ -75,7 +87,8 @@ def test_register_valid_input() -> None:
         )
 
     with pytest.raises(ValueError, match=r"3 values"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="MyList",
             coordinates=np.zeros((2, 4)),
             voi_names=["roi1", "roi2"],
@@ -83,7 +96,8 @@ def test_register_valid_input() -> None:
             overwrite=True,
         )
     with pytest.raises(ValueError, match=r"voi_names"):
-        CoordinatesRegistry().register(
+        register_data(
+            kind="coordinates",
             name="MyList",
             coordinates=np.zeros((2, 3)),
             voi_names=["roi1", "roi2", "roi3"],
@@ -95,13 +109,13 @@ def test_register_valid_input() -> None:
 def test_list() -> None:
     """Test listing of available coordinates."""
     assert {"DMNBuckner", "MultiTask", "VigAtt", "WM"}.issubset(
-        set(CoordinatesRegistry().list)
+        set(list_data(kind="coordinates"))
     )
 
 
 def test_load() -> None:
     """Test loading coordinates from file."""
-    coord, names, space = CoordinatesRegistry().load("DMNBuckner")
+    coord, names, space = load_data(kind="coordinates", name="DMNBuckner")
     assert coord.shape == (6, 3)  # type: ignore
     assert names == ["PCC", "MPFC", "lAG", "rAG", "lHF", "rHF"]
     assert space == "MNI"
@@ -110,7 +124,7 @@ def test_load() -> None:
 def test_load_nonexisting() -> None:
     """Test loading coordinates that not exist."""
     with pytest.raises(ValueError, match=r"not found"):
-        CoordinatesRegistry().load("NonExisting")
+        load_data(kind="coordinates", name="NonExisting")
 
 
 def test_get() -> None:
@@ -121,11 +135,19 @@ def test_get() -> None:
         element_data = reader.fit_transform(element)
         vbm_gm = element_data["VBM_GM"]
         # Get tailored coordinates
-        tailored_coords, tailored_labels = CoordinatesRegistry().get(
-            coords="DMNBuckner", target_data=vbm_gm
+        tailored_coords, tailored_labels = get_data(
+            kind="coordinates", names="DMNBuckner", target_data=vbm_gm
         )
         # Get raw coordinates
-        raw_coords, raw_labels, _ = CoordinatesRegistry().load("DMNBuckner")
+        raw_coords, raw_labels, _ = load_data(
+            kind="coordinates", name="DMNBuckner"
+        )
         # Both tailored and raw should be same for now
         assert_array_equal(tailored_coords, raw_coords)
         assert tailored_labels == raw_labels
+
+
+def test_deregister() -> None:
+    """Test coordinates deregistration."""
+    deregister_data(kind="coordinates", name="MyList")
+    assert "MyList" not in list_data(kind="coordinates")

junifer/data/masks/_ants_mask_warper.py

@@ -56,7 +56,7 @@ class ANTsMaskWarper:
         dst: str,
         target_data: dict[str, Any],
         warp_data: Optional[dict[str, Any]],
-    ) -> "Nifti1Image":
+    ) -> "Nifti1Image":  # pragma: no cover
         """Warp ``mask_img`` to correct space.
 
         Parameters

junifer/data/masks/_fsl_mask_warper.py

@@ -53,7 +53,7 @@ class FSLMaskWarper:
         mask_img: "Nifti1Image",
         target_data: dict[str, Any],
         warp_data: dict[str, Any],
-    ) -> "Nifti1Image":
+    ) -> "Nifti1Image":  # pragma: no cover
         """Warp ``mask_img`` to correct space.
 
         Parameters