.pre-commit-config.yaml

@@ -17,24 +17,22 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.23
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.10.0
-    hooks:
-      - id: black
-        exclude: ^(docs/|examples/|tools/)
-        args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.11.2
     hooks:
       - id: ruff
         types_or: [python, jupyter]
         exclude: ^(__init__.py)
         args: [--output-format, grouped, --show-fixes]
+      - id: ruff-format
+        types_or: [python, jupyter]
+        exclude: ^(__init__.py)
+        args: [--check, --diff]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
@@ -47,10 +45,3 @@ repos:
       - id: rst-backticks
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.19.1"
-    hooks:
-      - id: blacken-docs
-        additional_dependencies:
-          - black==24.4.2
-        args: [-l 79]

README.md

@@ -8,7 +8,6 @@
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/junifer/badges/version.svg)](https://anaconda.org/conda-forge/junifer)
 ![GitHub](https://img.shields.io/github/license/juaml/junifer?style=flat-square)
 ![Codecov](https://img.shields.io/codecov/c/github/juaml/junifer?style=flat-square)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)

conda-env.yml

@@ -1,33 +1,45 @@
 name: junifer-dev
 channels:
   - conda-forge
-  - defaults
 dependencies:
-  - python>=3.10,<=3.11
+  - python>=3.10,<=3.13
-  - click=8.1.*
+  - click>=8.1.3,<8.2
-  - numpy>=1.22,<1.27
+  - numpy>=1.26.0,<2.0.0
-  - pandas>=1.4.0,<2.2
+  - scipy>=1.10.0,<=1.15.0
-  - nibabel>=3.2.0,<5.2
+  - pandas>=2.0.0,<2.3.0
-  - nilearn>=0.9.0,<=0.10.1
+  - nibabel>=5.2.0,<5.4.0
-  - sqlalchemy>=1.4.27,<= 2.0.21
+  - nilearn>=0.10.3,<=0.10.4
-  - ruamel.yaml=0.17.*
+  - sqlalchemy>=2.0.25,<=2.1.0
-  - h5py>=3.8,<=3.9
+  - ruamel.yaml>=0.17,<0.19
-  - seaborn>=0.11,<=0.13
+  - h5py>=3.10
-  - sphinx>=5.3,<7.3
+  - tqdm>=4.66.1,<4.67.0
-  - sphinx-gallery>=0.11.0,<0.15.0
+  - templateflow>=23.0.0
-  - furo>=2022.9.29,<2023.10.0
+  - lapy>=1.0.0,<2.0.0
-  - numpydoc>=1.5.0,<1.6
+  - lazy_loader==0.4
+  - importlib_metadata
+  - looseversion==1.3.0
+  - bctpy==0.6.0
+  - neurokit2>=0.1.7
+  - seaborn>=0.13.0,<0.14.0
+  - sphinx>=7.3.0,<8.1.0
+  - sphinx-gallery>=0.17.0,<0.18.0
+  - furo>=2024.4.27,<2024.9.0
+  - numpydoc>=1.6.0,<1.9.0
   - sphinx-copybutton>=0.5.1,<0.5.3
-  - towncrier>=22.12.0,<23.7
+  - towncrier>=23.10.0,<24.7.0
   - sphinxcontrib-mermaid>=0.8.1,<0.10
+  - sphinxcontrib-towncrier==0.4.0a0
+  - setuptools-scm>=8
   - tox
+  - pre-commit
+  - ruff>=0.1.0
   - ipykernel
   - pytest-cov
   - pytest
-  - black
-  - ruff
   - codespell
+  - tomli
   - pip
   - pip:
-    - datalad>=0.15.4,<0.20
+    - datalad>=1.0.0,<1.2.0
-    - julearn==0.3.0
+    - julearn==0.3.3
+    - junifer_data==1.3.0

docs/changes/newsfragments/441.misc

@@ -0,0 +1 @@
+Regular repository maintenance by updating ``.pre-commit-config.yaml``, replacing ``black`` with ``ruff-format`` and updating tool configs by `Synchon Mandal`_

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"Invalid value for `kind`: {kind}, must be one of {valid_kind}"
-            f"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"Copying {self._executable} to {self._exec_path.resolve()!s}"
-                f"{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"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
-            f"{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"Writing {self._collect_path.name} to {self._job_dir.resolve()!s}"
-            f"{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"collect {self._yaml_config_path.resolve()!s} {verbose_args}"
-            f"{self._yaml_config_path.resolve()!s} "
-            f"{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"Copying {self._executable} to {self._exec_path.resolve()!s}"
-                f"{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"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
-            f"{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/VOIs/meta/AutobiographicalMemory_VOIs.txt

@@ -1,23 +0,0 @@
--2	-53	18	PCu-PCC_LR
--25	-26	-14	HC-PHC-AMG_L
--47	-61	26	TPJ_L
--3	47	-1	Medial-prefrontal-cortex_rACC(bilateral)_L
--56	-8	-14	STS_MTG_inferior-temporal-sulcus_L
--47	25	-5	Ventrolateral-prefrontal-cortex_temporal-pole_L
-23	-31	-12	HC-PHC_R
--3	12	57	Middle-frontal-gyrus_LR
-49	-59	27	TPJ_R
--45	3	45	Posterior-lateral-prefrontal-cortex_L
--40	47	14	Frontal-pole(lateral)_L
-23	-13	-15	HC-PHC_R
-49	-5	-13	Temporal-pole_STS_MTG_R
--37	14	-32	Temporal-pole_L
--37	-81	30	Occ_L
--46	24	21	Dorsolateral-prefrontal-cortex_L
-50	27	-5	Ventrolateral-prefrontal-cortex_R
--11	55	17	Frontal_pole(medial)_L
-3	-9	5	Thalamus_R
--5	33	22	rACC_L
--6	-37	33	PCC_L
--28	9	51	Superior-frontal-sulcus_L
-28	1	-19	AMG_R

junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt

@@ -1,19 +0,0 @@
-36.0	22.0	-4.0	RaIns
-2.0	16.0	48.0	preSMA
-48.0	12.0	30.0	rIFGp
-36.0	2.0	54.0	rdPMC
-48.0	30.0	24.0	rIFGa
--38.0	-44.0	46.0	lIPS
--24.0	-66.0	48.0	lSPL
-40.0	-46.0	46.0	rIPS
-60.0	-44.0	24.0	rIPC
-30.0	-62.0	52.0	rSPL
--44.0	10.0	30.0	lIFG
--34.0	20.0	-4.0	LaIns
--26.0	2.0	52.0	ldPMC
-6.0	-18.0	-2.0	rThal
--40.0	-66.0	-10.0	lIOG
-48.0	19.0	6.0	rIFG
-8.0	29.0	30.0	aMCC
--45.0	27.0	30.0	lIFG
-11.0	7.0	7.0	rNcaud

junifer/data/coordinates/VOIs/meta/CogAR_VOIs.txt

@@ -1,8 +0,0 @@
--40	-64	-12	Fusiform_L
-36	22	-4	Insula_R
--44	10	32	Precentral_L
-60	-44	24	Temporal_Sup_R
-0	18	48	Supp_Motor_Area_L
--36	-46	46	Parietal_Inf_L
-38	-46	44	Parietal_Inf_R
--26	0	54	Frontal_Mid_L

junifer/data/coordinates/VOIs/meta/DMNBuckner_VOIs.txt

@@ -1,6 +0,0 @@
-0	-53	26	PCC
-0	52	-6	MPFC
--48	-62	36	lAG
-46	-62	32	rAG
--24	-22	-20	lHF
-24	-22	-20	rHF

junifer/data/coordinates/VOIs/meta/Dosenbach2010_MNI_VOIs.txt

@@ -1,160 +0,0 @@
-6	64	3	vmPFC
-29	57	18	aPFC
--29	57	10	aPFC
-0	51	32	mPFC
--25	51	27	aPFC
-9	51	16	vmPFC
--6	50	-1	vmPFC
-27	49	26	aPFC
-42	48	-3	vent aPFC
--43	47	2	vent aPFC
--11	45	17	vmPFC
-39	42	16	vlPFC
-8	42	-5	vmPFC
-9	39	20	ACC
-46	39	-15	vlPFC
-40	36	29	dlPFC
-23	33	47	sup frontal
-34	32	7	vPFC
--2	30	27	ACC
--16	29	54	sup frontal
--1	28	40	ACC
-46	28	31	dlPFC
--52	28	17	vPFC
--44	27	33	dlPFC
-51	23	8	vFC
-38	21	-1	ant insula
-9	20	34	dACC
--36	18	2	ant insula
-40	17	40	dFC
--6	17	34	basal ganglia
-0	15	45	mFC
-58	11	14	frontal
--46	10	14	vFC
-44	8	34	dFC
-60	8	34	dFC
--42	7	36	dFC
--55	7	23	vFC
--20	6	7	basal ganglia
-14	6	7	basal ganglia
--48	6	1	vFC
-10	5	51	pre-SMA
-43	1	12	vFC
-0	-1	52	SMA
-37	-2	-3	mid insula
-53	-3	32	frontal
-58	-3	17	precentral gyrus
--12	-3	13	thalamus
--42	-3	11	mid insula
--44	-6	49	precentral gyrus
--26	-8	54	parietal
-46	-8	24	precentral gyrus
--54	-9	23	precentral gyrus
-44	-11	38	precentral gyrus
--47	-12	36	parietal
-33	-12	16	mid insula
--36	-12	15	mid insula
--12	-12	6	thalamus
-11	-12	6	thalamus
-32	-12	2	mid insula
-59	-13	8	temporal
--30	-14	1	mid insula
--38	-15	59	parietal
-52	-15	-13	inf temporal
--47	-18	50	parietal
-46	-20	45	parietal
--55	-22	38	parietal
--54	-22	22	precentral gyrus
--54	-22	9	temporal
-41	-23	55	parietal
-42	-24	17	post insula
-11	-24	2	basal ganglia
--59	-25	-15	inf temporal
-1	-26	31	post cingulate
-18	-27	62	parietal
--38	-27	60	parietal
--30	-28	9	post insula
--24	-30	64	parietal
-51	-30	5	temporal
--41	-31	48	post parietal
--4	-31	-4	post cingulate
-54	-31	-18	fusiform
--41	-37	16	temporal
--53	-37	13	temporal
-28	-37	-15	fusiform
--3	-38	45	precuneus
-34	-39	65	sup parietal
-8	-40	50	precuneus
--41	-40	42	IPL
-58	-41	20	parietal
--8	-41	3	post cingulate
--61	-41	-2	inf temporal
--28	-42	-11	occipital
--5	-43	25	post cingulate
-9	-43	25	precuneus
-43	-43	8	temporal
-54	-44	43	IPL
--55	-44	30	parietal
--28	-44	-25	lat cerebellum
--35	-46	48	post parietal
-42	-46	21	sup temporal
--48	-47	49	IPL
--41	-47	29	angular gyrus
--59	-47	11	temporal
--53	-50	39	IPL
-5	-50	33	precuneus
--18	-50	1	occipital
-44	-52	47	IPL
--5	-52	17	post cingulate
--24	-54	-21	lat cerebellum
--37	-54	-37	inf cerebellum
-10	-55	17	post cingulate
--6	-56	29	precuneus
--34	-57	-24	lat cerebellum
--32	-58	46	IPS
--11	-58	17	post cingulate
-32	-59	41	IPS
-51	-59	34	angular gyrus
--34	-60	-5	occipital
-36	-60	-8	occipital
--6	-60	-15	med cerebellum
--25	-60	-34	inf cerebellum
-32	-61	-31	inf cerebellum
-46	-62	5	temporal
--48	-63	35	angular gyrus
--52	-63	15	TPJ
--44	-63	-7	occipital
--16	-64	-21	med cerebellum
-21	-64	-22	lat cerebellum
-19	-66	-1	occipital
-1	-66	-24	med cerebellum
--34	-67	-29	inf cerebellum
-11	-68	42	precuneus
-17	-68	20	occipital
--36	-69	40	IPS
-39	-71	13	occipital
--9	-72	41	occipital
-45	-72	29	occipital
--11	-72	-14	med cerebellum
-29	-73	29	occipital
-33	-73	-30	inf cerebellum
--2	-75	32	occipital
--29	-75	28	occipital
-5	-75	-11	med cerebellum
-14	-75	-21	med cerebellum
--16	-76	33	occipital
--42	-76	26	occipital
-9	-76	14	occipital
-15	-77	32	occipital
-20	-78	-2	occipital
--21	-79	-33	inf cerebellum
--6	-79	-33	inf cerebellum
--5	-80	9	post occipital
-29	-81	14	post occipital
-33	-81	-2	post occipital
-18	-81	-33	inf cerebellum
--37	-83	-2	post occipital
--29	-88	8	post occipital
-13	-91	2	post occipital
-27	-91	2	post occipital
--4	-94	12	post occipital

junifer/data/coordinates/VOIs/meta/Empathy_VOIs.txt

@@ -1,22 +0,0 @@
-2.0	56.0	18.0	dmPFC
--8.0	54.0	34.0	dmPFC
-36.0	22.0	-8.0	raI
--30.0	20.0	4.0	laI
-50.0	12.0	-8.0	rIFG
-54.0	16.0	20.0	rIFG/Area44
-50.0	30.0	4.0	rIFG/Area45
--44.0	24.0 	-6.0	lIFG
--4.0	18.0	50.0	SMA
--2.0	28.0	20.0	aMCC
--4.0	42.0	18.0	rACC
--2.0	-32.0	28.0	PCC
-52.0	-58.0	22.0	rTPJ
--56.0	-58.0	22.0	lTPJ
-22.0	-2.0	-16.0	rAm
-54.0	-8.0	-16.0	rMTG
-52.0	-36.0	2.0	rpSTS
--12.0	-4.0	12.0	laTh
-6.0	-32.0	2.0	rpTh
-26.0	-26.0	-12.0	rHippo
-2.0	-20.0	-12.0	Midbrain
-14.0	4.0	0.0	rGP

junifer/data/coordinates/VOIs/meta/Motor_VOIs.txt

@@ -1,10 +0,0 @@
--39.0	-21.0	54.0	lSMC*
-41.0	-16.0	57.0	rSMC*
--3.0	-2.0	54.0	SMA
--57.0	2.0	32.0	lPMCv
--53.0	-24.0	21.0	lIPC
-45.0	-38.0	48.0	rIPC
--23.0	-7.0	1.0	lBG
-25.0	-8.0	3.0	rBG
--22.0	-52.0	26.0	lCba
-18.0	-54.0	-22.0	rCba

junifer/data/coordinates/VOIs/meta/MultiTask_VOIs.txt

@@ -1,9 +0,0 @@
--34	22	-4 	leftInsula
-34	24	0	rightInsula
--26	0	52	Frontal_Mid_L
-44	38	28	Frontal_Inf_Tri_R
-46	10	28	Frontal_Inf_Oper_R
--6	18	50	Supp_Motor_Area_L
--34	-52	56	Parietal_Inf_L
-32	-52	50	Parietal_Inf_R
-32	6	58	Frontal_Mid_R

junifer/data/coordinates/VOIs/meta/PhysioStress_VOIs.txt

@@ -1,18 +0,0 @@
-38.0	18.0	0.0	rIns
-52.0	12.0	-4.0	rSTG
-60.0	6.0	2.0	rTP
-22.0	0.0	-4.0	rPall
--38.0	14.0	4.0	lIns
--58.0	0.0	6.0	lOP4
--20.0	6.0	2.0	lPut
-4.0	6.0	46.0	rSMA
-0.0	14.0	36.0	lMCC
--42.0	-18.0	18.0	lOP3
--54.0	-24.0	24.0	lSMG
--36.0	-20.0	2.0	lIns
--14.0	-12.0	10.0	lTh
-10.0	-18.0	4.0	rTh
-56.0	-24.0	24.0	lSMG
-44.0	-14.0	16.0	rOP3
-38.0	50.0	12.0	rMFG
--24.0	-66.0	-26.0	lCb

junifer/data/coordinates/VOIs/meta/Power2011_MNI_VOIs.txt

@@ -1,264 +0,0 @@
--25	-98	-12	1
-27	-97	-13	2
-24	32	-18	3
--56	-45	-24	4
-8	41	-24	5
--21	-22	-20	6
-17	-28	-17	7
--37	-29	-26	8
-65	-24	-19	9
-52	-34	-27	10
-55	-31	-17	11
-34	38	-12	12
--7	-52	61	13
--14	-18	40	14
-0	-15	47	15
-10	-2	45	16
--7	-21	65	17
--7	-33	72	18
-13	-33	75	19
--54	-23	43	20
-29	-17	71	21
-10	-46	73	22
--23	-30	72	23
--40	-19	54	24
-29	-39	59	25
-50	-20	42	26
--38	-27	69	27
-20	-29	60	28
-44	-8	57	29
--29	-43	61	30
-10	-17	74	31
-22	-42	69	32
--45	-32	47	33
--21	-31	61	34
--13	-17	75	35
-42	-20	55	36
--38	-15	69	37
--16	-46	73	38
-2	-28	60	39
-3	-17	58	40
-38	-17	45	41
--49	-11	35	42
-36	-9	14	43
-51	-6	32	44
--53	-10	24	45
-66	-8	25	46
--3	2	53	47
-54	-28	34	48
-19	-8	64	49
--16	-5	71	50
--10	-2	42	51
-37	1	-4	52
-13	-1	70	53
-7	8	51	54
--45	0	9	55
-49	8	-1	56
--34	3	4	57
--51	8	-2	58
--5	18	34	59
-36	10	1	60
-32	-26	13	61
-65	-33	20	62
-58	-16	7	63
--38	-33	17	64
--60	-25	14	65
--49	-26	5	66
-43	-23	20	67
--50	-34	26	68
--53	-22	23	69
--55	-9	12	70
-56	-5	13	71
-59	-17	29	72
--30	-27	12	73
--41	-75	26	74
-6	67	-4	75
-8	48	-15	76
--13	-40	1	77
--18	63	-9	78
--46	-61	21	79
-43	-72	28	80
--44	12	-34	81
-46	16	-30	82
--68	-23	-16	83
--58	-26	-15	84
-27	16	-17	85
--44	-65	35	86
--39	-75	44	87
--7	-55	27	88
-6	-59	35	89
--11	-56	16	90
--3	-49	13	91
-8	-48	31	92
-15	-63	26	93
--2	-37	44	94
-11	-54	17	95
-52	-59	36	96
-23	33	48	97
--10	39	52	98
--16	29	53	99
--35	20	51	100
-22	39	39	101
-13	55	38	102
--10	55	39	103
--20	45	39	104
-6	54	16	105
-6	64	22	106
--7	51	-1	107
-9	54	3	108
--3	44	-9	109
-8	42	-5	110
--11	45	8	111
--2	38	36	112
--3	42	16	113
--20	64	19	114
--8	48	23	115
-65	-12	-19	116
--56	-13	-10	117
--58	-30	-4	118
-65	-31	-9	119
--68	-41	-5	120
-13	30	59	121
-12	36	20	122
-52	-2	-16	123
--26	-40	-8	124
-27	-37	-13	125
--34	-38	-16	126
-28	-77	-32	127
-52	7	-30	128
--53	3	-27	129
-47	-50	29	130
--49	-42	1	131
--31	19	-19	132
--2	-35	31	133
--7	-71	42	134
-11	-66	42	135
-4	-48	51	136
--46	31	-13	137
--10	11	67	138
-49	35	-12	139
-8	-91	-7	140
-17	-91	-14	141
--12	-95	-13	142
-18	-47	-10	143
-40	-72	14	144
-8	-72	11	145
--8	-81	7	146
--28	-79	19	147
-20	-66	2	148
--24	-91	19	149
-27	-59	-9	150
--15	-72	-8	151
--18	-68	5	152
-43	-78	-12	153
--47	-76	-10	154
--14	-91	31	155
-15	-87	37	156
-29	-77	25	157
-20	-86	-2	158
-15	-77	31	159
--16	-52	-1	160
-42	-66	-8	161
-24	-87	24	162
-6	-72	24	163
--42	-74	0	164
-26	-79	-16	165
--16	-77	34	166
--3	-81	21	167
--40	-88	-6	168
-37	-84	13	169
-6	-81	6	170
--26	-90	3	171
--33	-79	-13	172
-37	-81	1	173
--44	2	46	174
-48	25	27	175
--47	11	23	176
--53	-49	43	177
--23	11	64	178
-58	-53	-14	179
-24	45	-15	180
-34	54	-13	181
--21	41	-20	182
--18	-76	-24	183
-17	-80	-34	184
-35	-67	-34	185
-47	10	33	186
--41	6	33	187
--42	38	21	188
-38	43	15	189
-49	-42	45	190
--28	-58	48	191
-44	-53	47	192
-32	14	56	193
-37	-65	40	194
--42	-55	45	195
-40	18	40	196
--34	55	4	197
--42	45	-2	198
-33	-53	44	199
-43	49	-2	200
--42	25	30	201
--3	26	44	202
-11	-39	50	203
-55	-45	37	204
-42	-0	47	205
-31	33	26	206
-48	22	10	207
--35	20	0	208
-36	22	3	209
-37	32	-2	210
-34	16	-8	211
--11	26	25	212
--1	15	44	213
--28	52	21	214
--0	30	27	215
-5	23	37	216
-10	22	27	217
-31	56	14	218
-26	50	27	219
--39	51	17	220
-2	-24	30	221
-6	-24	-0	222
--2	-13	12	223
--10	-18	7	224
-12	-17	8	225
--5	-28	-4	226
--22	7	-5	227
--15	4	8	228
-31	-14	2	229
-23	10	1	230
-29	1	4	231
--31	-11	-0	232
-15	5	7	233
-9	-4	6	234
-54	-43	22	235
--56	-50	10	236
--55	-40	14	237
-52	-33	8	238
-51	-29	-4	239
-56	-46	11	240
-53	33	1	241
--49	25	-1	242
--16	-65	-20	243
--32	-55	-25	244
-22	-58	-23	245
-1	-62	-18	246
-33	-12	-34	247
--31	-10	-36	248
-49	-3	-38	249
--50	-7	-39	250
-10	-62	61	251
--52	-63	5	252
--47	-51	-21	253
-46	-47	-17	254
-47	-30	49	255
-22	-65	48	256
-46	-59	4	257
-25	-58	60	258
--33	-46	47	259
--27	-71	37	260
--32	-1	54	261
--42	-60	-9	262
--17	-59	64	263
-29	-5	54	264

junifer/data/coordinates/VOIs/meta/Power2013_MNI_VOIs.tsv

@@ -1,264 +0,0 @@
-22	-65	48	1
-25	-58	60	2
--35	20	0	3
-12	36	20	4
-40	18	40	5
-54	-28	34	6
-36	22	3	7
-59	-17	29	8
--45	0	9	9
-46	-59	4	10
--32	-1	54	11
-32	14	56	12
--42	-60	-9	13
--34	3	4	14
-37	1	-4	15
-29	-5	54	16
-11	-39	50	17
-37	-65	40	18
--34	-38	-16	19
--52	-63	5	20
--10	11	67	21
--44	2	46	22
--3	26	44	23
-49	8	-1	24
--33	-46	47	25
--27	-71	37	26
-55	-45	37	27
-7	8	51	28
-36	10	1	29
--39	51	17	30
-10	-62	61	31
--16	-5	71	32
-43	49	-2	33
-37	32	-2	34
-10	-2	45	35
-47	-30	49	36
-36	-9	14	37
--3	2	53	38
--51	8	-2	39
--1	15	44	40
-31	-14	2	41
-19	-8	64	42
--10	-2	42	43
-65	-33	20	44
--30	-27	12	45
-6	-72	24	46
--7	-52	61	47
--49	-42	1	48
--49	25	-1	49
--5	18	34	50
--23	11	64	51
-31	33	26	52
--0	30	27	53
--53	-22	23	54
--42	-55	45	55
--50	-34	26	56
-48	22	10	57
-31	56	14	58
-44	-8	57	59
-49	35	-12	60
--56	-50	10	61
-2	-24	30	62
-29	-39	59	63
--42	-74	0	64
--34	55	4	65
-13	-1	70	66
-42	-0	47	67
--3	42	16	68
-5	23	37	69
-51	-29	-4	70
-0	-15	47	71
-52	-33	8	72
-34	16	-8	73
--7	-71	42	74
--29	-43	61	75
-33	-53	44	76
--55	-40	14	77
--17	-59	64	78
-56	-5	13	79
-46	-47	-17	80
--11	26	25	81
-22	-42	69	82
--13	-40	1	83
-43	-23	20	84
--53	-49	43	85
--47	11	23	86
-54	-43	22	87
-53	33	1	88
-10	22	27	89
--55	-9	12	90
--58	-30	-4	91
--42	45	-2	92
-56	-46	11	93
--45	-32	47	94
-11	-66	42	95
--28	-79	19	96
--47	-76	-10	97
--2	38	36	98
--54	-23	43	99
--28	52	21	100
-47	-50	29	101
--2	-35	31	102
-50	-20	42	103
--42	38	21	104
-26	50	27	105
-58	-53	-14	106
-47	10	33	107
-32	-26	13	108
--46	31	-13	109
-10	-46	73	110
-27	-37	-13	111
-43	-72	28	112
-52	-2	-16	113
--2	-37	44	114
-38	43	15	115
--60	-25	14	116
--41	6	33	117
--2	-13	12	118
-42	-66	-8	119
-9	-4	6	120
-29	1	4	121
-15	5	7	122
--42	25	30	123
--26	-40	-8	124
-65	-31	-9	125
-44	-53	47	126
--18	-76	-24	127
--35	20	51	128
--28	-58	48	129
--49	-26	5	130
--53	-10	24	131
--47	-51	-21	132
-58	-16	7	133
-49	-42	45	134
-40	-72	14	135
--32	-55	-25	136
--14	-18	40	137
--41	-75	26	138
--16	-77	34	139
-4	-48	51	140
--68	-41	-5	141
-35	-67	-34	142
-22	39	39	143
--56	-13	-10	144
-15	-63	26	145
--15	4	8	146
-29	-77	25	147
-38	-17	45	148
-23	10	1	149
-66	-8	25	150
-51	-6	32	151
--39	-75	44	152
--11	45	8	153
-52	7	-30	154
--21	41	-20	155
--12	-95	-13	156
-8	42	-5	157
-34	38	-12	158
--16	-46	73	159
-37	-84	13	160
-18	-47	-10	161
--11	-56	16	162
-48	25	27	163
--53	3	-27	164
-46	16	-30	165
--31	19	-19	166
-37	-81	1	167
-52	-59	36	168
-27	16	-17	169
-24	45	-15	170
--44	12	-34	171
--46	-61	21	172
--49	-11	35	173
--25	-98	-12	174
--33	-79	-13	175
-11	-54	17	176
-23	33	48	177
--3	-49	13	178
-12	-17	8	179
--38	-33	17	180
-8	48	-15	181
--10	39	52	182
-43	-78	-12	183
-20	-29	60	184
--40	-19	54	185
--20	45	39	186
-13	30	59	187
--24	-91	19	188
--16	29	53	189
-8	-91	-7	190
--21	-31	61	191
-6	67	-4	192
-17	-80	-34	193
--23	-30	72	194
-2	-28	60	195
-15	-77	31	196
-3	-17	58	197
-55	-31	-17	198
--31	-10	-36	199
--40	-88	-6	200
--18	63	-9	201
-27	-59	-9	202
-49	-3	-38	203
--31	-11	-0	204
-65	-24	-19	205
-17	-28	-17	206
--7	51	-1	207
-24	32	-18	208
-9	54	3	209
--7	-55	27	210
--21	-22	-20	211
-34	54	-13	212
--38	-15	69	213
--38	-27	69	214
-65	-12	-19	215
--16	-52	-1	216
--8	48	23	217
--3	44	-9	218
--37	-29	-26	219
-27	-97	-13	220
-17	-91	-14	221
-6	54	16	222
-8	41	-24	223
-8	-48	31	224
-24	-87	24	225
--58	-26	-15	226
-29	-17	71	227
--68	-23	-16	228
--10	-18	7	229
--13	-17	75	230
--7	-33	72	231
-15	-87	37	232
--20	64	19	233
-42	-20	55	234
-26	-79	-16	235
--10	55	39	236
-13	-33	75	237
-33	-12	-34	238
--26	-90	3	239
--7	-21	65	240
-10	-17	74	241
--44	-65	35	242
-6	-59	35	243
-6	64	22	244
--18	-68	5	245
--16	-65	-20	246
-8	-72	11	247
-13	55	38	248
--14	-91	31	249
--3	-81	21	250
-20	-86	-2	251
--50	-7	-39	252
--56	-45	-24	253
--8	-81	7	254
-20	-66	2	255
-6	-81	6	256
-52	-34	-27	257
--15	-72	-8	258
-6	-24	-0	259
-28	-77	-32	260
-22	-58	-23	261
-1	-62	-18	262
--22	7	-5	263
--5	-28	-4	264

junifer/data/coordinates/VOIs/meta/Rew_VOIs.txt

@@ -1,25 +0,0 @@
-12.0	10.0	-6.0	rNAc
--10.0	8.0	-4.0	lPall
-36.0	20.0	-6.0	rIns
--32.0	20.0	-4.0	lIns
-0.0	24.0	40.0	dmPFC
-0.0	54.0	-8.0	medOFC
-24.0	-2.0	-16.0	rAm
-6.0	-14.0	8.0	rTh
--6.0	-16.0	8.0	lTh
-0.0	8.0	48.0	SMA
-8.0	-18.0	-10.0	rBrainStem
--6.0	-18.0	-10.0	lBrainStem
-2.0	44.0	20.0	ACC
--24.0	2.0	52.0	lMFG
--38.0	-4.0	6.0	lIns(Id3)
-24.0	40.0	-14.0	rMidOFC(Fo3)
--16.0	42.0	-14.0	lMidOFC(Fo3)
-40.0	32.0	32.0	raMFG
--28.0	-56.0	48.0	lIPL(IPS)
-28.0	-58.0	50.0	rAG
-0.0	-32.0	32.0	PCC
--36.0	50.0	10.0	lFP
--46.0	42.0	-4.0	lLOFC
-30.0	4.0	50.0	rpMFG
--22.0	30.0	48.0	lSFG

junifer/data/coordinates/VOIs/meta/Somatosensory_VOIs.txt

@@ -1,10 +0,0 @@
--48.0	-20.0	20.0	S1_L
--54.0	-20.0	48.0	postcentralG_S1_L
--44.0	-26.0	58.0	postcentralG_S1_L
--38.0	-12.0	4.0	Ins_claustrum_L
--40.0	4.0	10.0	pars_opercularis_Ins_L
-56.0	-22.0	20.0	SMG_R
-56.0	-34.0	18.0	pSTG_R
-56.0	-38.0	28.0	IPL_SMG_R
-60.0	-20.0	32.0	postcentralG_R
--4.0	14.0	36.0	MCC_L

junifer/data/coordinates/VOIs/meta/ToM_VOIs.txt

@@ -1,15 +0,0 @@
-0.0	52.0	-12.0	vmPFC
-2.0	58.0	12.0	FP
--8.0	56.0	30.0	dmPFC
-2.0	-56.0	30.0	Prc
-56.0	-50.0	18.0	rTPJ
--48.0	-56.0	24.0	lTPJ
-54.0	-2.0	-20.0	rTP
--54.0	-2.0	-24.0	lTP
-52.0	-18.0	-12.0	rMTG
--54.0	-28.0	-4.0	lMTG
-50.0	-34.0	0.0	rpSTS
--58.0	-44.0	4.0	lpSTS
-54.0	28.0	6.0	rIFG
--48.0	30.0	-12.0	lIFG
-48.0	-72.0	8.0	rV5

junifer/data/coordinates/VOIs/meta/VigAtt_VOIs.txt

@@ -1,16 +0,0 @@
--2.0	8.0	50.0	aParacentralL
-8.0	32.0	46.0	rmpSFG
-0.0	26.0	34.0	dMCC
-50.0	8.0	32.0	rIFJ
-40.0	22.0	-4.0	raI
-46.0	36.0	20.0	rIFS
--40.0	-12.0	60.0	lPrecentralG
--46.0	-68.0	-6.0	lIOG
--48.0	8.0	30.0	lIFJ
-62.0	-38.0	17.0	rTPJ
-8.0	-12.0	6.0	rTh
-32.0	-90.0	4.0	rMOG
--42.0	12.0	-2.0	laI
--10.0	-14.0	6.0	lTh
-6.0	-58.0	-18.0	Cb
-44.0	-44.0	46.0	rIPL

junifer/data/coordinates/VOIs/meta/WM_VOIs.txt

@@ -1,23 +0,0 @@
--32.0	22.0	-2.0	aIns_l
--48.0	10.0	26.0	IFG_l
--46.0	26.0	24.0	lPFCc_l
--38.0	50.0	10.0	lPFCr_l
-36.0	22.0	-6.0	aIns_r
-50.0	14.0	24.0	IFG_r
-44.0	34.0	32.0	lPFCc_r
-38.0	54.0	6.0	lPFCr_l
-2.0	18.0	48.0	pmFC
--28.0	0.0	56.0	psFC
-30.0	2.0	56.0	psFC
--42.0	-42.0	46.0	IPS_l
--34.0	-52.0	48.0	SPL_l
--24.0	-66.0	54.0	SPLp_l
-42.0	-44.0	44.0	IPSa_r
-32.0	-58.0	48.0	IPSp_r
-16.0	-66.0	56.0	SPLp_r
--12.0	-12.0	12.0	Thal_l
--16.0	2.0	14.0	Ncaud_l
--16.0	0.0	2.0	GP_l
-12.0	-10.0	10.0	Thal_r
--34.0	-66.0	-20.0	Cb_FG_l
-32.0	-64.0	-18.0	Cb_FG_r

junifer/data/coordinates/VOIs/meta/eMDN_VOIs.txt

@@ -1,17 +0,0 @@
--46.0	6.0	30.0	IFG_l
-50.0	12.0	28.0	IFG_r
--32.0	20.0	2.0	aIns_l
-36.0	22.0	0.0	aIns_r
--4.0	14.0	44.0	SMA_l
-6.0	18.0	46.0	SMA_r
--32.0	-52.0	46.0	IPS_l
-32.0	-58.0	48.0	IPS_r
-44.0	36.0	20.0	MFG_r
--28.0	-4.0	52.0	dPMC_l
--44.0	32.0	22.0	MFG_l
-32.0	0.0	52.0	dPMC_r
--20.0	6.0	4.0	Put_l
-10.0	-12.0	8.0	Thal_r
--46.0	-60.0	-10.0	ITG_l
-22.0	6.0	4.0	Put_r
--10.0	-16.0	6.0	Thal_l

junifer/data/coordinates/VOIs/meta/eSAD_VOIs.txt

@@ -1,12 +0,0 @@
-0.0	38.0	10.0	ACC
--24.0	-10.0	-20.0	AmyHipp_L
-24.0	-8.0	-22.0	AmyHipp_R
--2.0	-52.0	26.0	PrC
--2.0	32.0	-8.0	SGC
--46.0	-66.0	18.0	TPJ_L
-50.0	-60.0	18.0	TPJ_R
--2.0	52.0	14.0	dmPFC
--6.0	10.0	-8.0	vBG_L
-6.0	10.0	-8.0	vBG_R
--2.0	50.0	-10.0	vmPFC
--54.0	-10.0	-20.0	aMTS/aMTG

junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt

@@ -1,16 +0,0 @@
-0	-53	6	PCC
-0	52	-6	MPFC
--48	-62	36	lAG
-46	-62	32	rAG
--24	-22	-20	lHF
-24	-22	-20	rHF
-10	-22	42	Middlecingulate
--48	-20	38	lIPG
-0	-48	-30	cerebellum
-34	-80	-34	rCerebellum
-56	30	8	rdlPFC
--42	-82	10	lateraloccipital
--54	24	10	rdrPFC
-22	34	54	RSFG
--50	14	-40	lTempP
--38	14	54	leftmiddlefrontalgyrus(BA6)

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(
+        tailored_coords, tailored_labels = get_data(
-            coords="DMNBuckner", target_data=vbm_gm
+            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

junifer/data/masks/tests/test_masks.py

@@ -20,7 +20,14 @@ from nilearn.masking import (
 )
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
-from junifer.data import MaskRegistry
+from junifer.data import (
+    MaskRegistry,
+    deregister_data,
+    get_data,
+    list_data,
+    load_data,
+    register_data,
+)
 from junifer.data.masks import compute_brain_mask
 from junifer.data.masks._masks import (
     _load_ukb_mask,
@@ -112,7 +119,8 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
 def test_register_built_in_check() -> None:
     """Test mask registration check for built-in masks."""
     with pytest.raises(ValueError, match=r"built-in mask"):
-        MaskRegistry().register(
+        register_data(
+            kind="mask",
             name="GM_prob0.2",
             mask_path="testmask.nii.gz",
             space="MNI",
@@ -122,36 +130,39 @@ def test_register_built_in_check() -> None:
 
 def test_list_incorrect() -> None:
     """Test incorrect information check for list masks."""
-    assert "testmask" not in MaskRegistry().list
+    assert "testmask" not in list_data(kind="mask")
 
 
 def test_register_already_registered() -> None:
     """Test mask registration check for already registered."""
     # Register custom mask
-    MaskRegistry().register(
+    register_data(
+        kind="mask",
         name="testmask",
         mask_path="testmask.nii.gz",
         space="MNI",
     )
-    out = MaskRegistry().load("testmask", path_only=True)
+    out = load_data(kind="mask", name="testmask", path_only=True)
     assert out[1] is not None
     assert out[1].name == "testmask.nii.gz"
 
     # Try registering again
     with pytest.raises(ValueError, match=r"already registered."):
-        MaskRegistry().register(
+        register_data(
+            kind="mask",
             name="testmask",
             mask_path="testmask.nii.gz",
             space="MNI",
         )
-    MaskRegistry().register(
+    register_data(
+        kind="mask",
         name="testmask",
         mask_path="testmask2.nii.gz",
         space="MNI",
         overwrite=True,
     )
 
-    out = MaskRegistry().load("testmask", path_only=True)
+    out = load_data(kind="mask", name="testmask", path_only=True)
     assert out[1] is not None
     assert out[1].name == "testmask2.nii.gz"
 
@@ -185,16 +196,17 @@ def test_register(
 
     """
     # Register custom mask
-    MaskRegistry().register(
+    register_data(
+        kind="mask",
         name=name,
         mask_path=mask_path,
         space=space,
         overwrite=overwrite,
     )
     # List available mask and check registration
-    assert name in MaskRegistry().list
+    assert name in list_data(kind="mask")
     # Load registered mask
-    _, fname, mask_space = MaskRegistry().load(name=name, path_only=True)
+    _, fname, mask_space = load_data(kind="mask", name=name, path_only=True)
     # Check values for registered mask
     assert fname is not None
     assert fname.name == f"{name}.nii.gz"
@@ -218,7 +230,7 @@ def test_list_correct(mask_name: str) -> None:
         The parametrized mask name.
 
     """
-    assert mask_name in MaskRegistry().list
+    assert mask_name in list_data(kind="mask")
 
 
 def test_load_incorrect() -> None:
@@ -270,9 +282,12 @@ def test_vickery_patil(
         The parametrized name of the mask file.
 
     """
-    mask, mask_fname, space = MaskRegistry().load(name, resolution=resolution)
+    mask, mask_fname, space = load_data(
+        kind="mask", name=name, resolution=resolution
+    )
     assert_array_almost_equal(
-        mask.header["pixdim"][1:4], pixdim  # type: ignore
+        mask.header["pixdim"][1:4],
+        pixdim,  # type: ignore
     )
     assert space == "IXI549Space"
     assert mask_fname is not None
@@ -287,7 +302,9 @@ def test_vickery_patil_error() -> None:
 
 def test_ukb() -> None:
     """Test UKB mask."""
-    mask, mask_fname, space = MaskRegistry().load("UKB_15K_GM", resolution=2.0)
+    mask, mask_fname, space = load_data(
+        kind="mask", name="UKB_15K_GM", resolution=2.0
+    )
     assert_array_almost_equal(mask.header["pixdim"][1:4], 2.0)  # type: ignore
     assert space == "MNI152NLin6Asym"
     assert mask_fname is not None
@@ -306,8 +323,8 @@ def test_get() -> None:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         vbm_gm = element_data["VBM_GM"]
         vbm_gm_img = vbm_gm["data"]
-        mask = MaskRegistry().get(
+        mask = get_data(
-            masks="compute_brain_mask", target_data=vbm_gm
+            kind="mask", names="compute_brain_mask", target_data=vbm_gm
         )
 
         assert mask.shape == vbm_gm_img.shape
@@ -355,28 +372,33 @@ def test_get_errors() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Test wrong masks definitions (more than one key per dict)
         with pytest.raises(ValueError, match=r"only one key"):
-            MaskRegistry().get(
+            get_data(
-                masks={"GM_prob0.2": {}, "Other": {}}, target_data=vbm_gm
+                kind="mask",
+                names={"GM_prob0.2": {}, "Other": {}},
+                target_data=vbm_gm,
             )
 
         # Test wrong masks definitions (pass paramaeters to non-callable mask)
         with pytest.raises(ValueError, match=r"callable params"):
-            MaskRegistry().get(
+            get_data(
-                masks={"GM_prob0.2": {"param": 1}}, target_data=vbm_gm
+                kind="mask",
+                names={"GM_prob0.2": {"param": 1}},
+                target_data=vbm_gm,
             )
 
         # Pass only parameters to the intersection function
         with pytest.raises(
             ValueError, match=r" At least one mask is required."
         ):
-            MaskRegistry().get(masks={"threshold": 1}, target_data=vbm_gm)
+            get_data(kind="mask", names={"threshold": 1}, target_data=vbm_gm)
 
         # Pass parameters to the intersection function when only one mask
         with pytest.raises(
             ValueError, match=r"parameters to the intersection"
         ):
-            MaskRegistry().get(
+            get_data(
-                masks=["compute_brain_mask", {"threshold": 1}],
+                kind="mask",
+                names=["compute_brain_mask", {"threshold": 1}],
                 target_data=vbm_gm,
             )
 
@@ -423,7 +445,7 @@ def test_nilearn_compute_masks(
         else:
             mask_spec = {mask_name: params}
 
-        mask = MaskRegistry().get(masks=mask_spec, target_data=bold)
+        mask = get_data(kind="mask", names=mask_spec, target_data=bold)
 
         assert_array_equal(mask.affine, bold_img.affine)
 
@@ -449,8 +471,9 @@ def test_get_inherit() -> None:
         gm_mask = compute_brain_mask(element_data["BOLD"], threshold=0.2)
 
         # Get mask using the compute_brain_mask function
-        mask1 = MaskRegistry().get(
+        mask1 = get_data(
-            masks={"compute_brain_mask": {"threshold": 0.2}},
+            kind="mask",
+            names={"compute_brain_mask": {"threshold": 0.2}},
             target_data=element_data["BOLD"],
         )
 
@@ -461,8 +484,9 @@ def test_get_inherit() -> None:
             "data": gm_mask,
             "space": element_data["BOLD"]["space"],
         }
-        mask2 = MaskRegistry().get(
+        mask2 = get_data(
-            masks="inherit",
+            kind="mask",
+            names="inherit",
             target_data=bold_dict,
         )
 
@@ -503,8 +527,8 @@ def test_get_multiple(
         target_img = element_data["BOLD"]["data"]
         resolution = np.min(target_img.header.get_zooms()[:3])
 
-        computed = MaskRegistry().get(
+        computed = get_data(
-            masks=junifer_masks, target_data=element_data["BOLD"]
+            kind="mask", names=junifer_masks, target_data=element_data["BOLD"]
         )
 
         masks_names = [
@@ -523,8 +547,11 @@ def test_get_multiple(
         ]
 
         mask_imgs = [
-            MaskRegistry().load(
+            load_data(
-                t_mask, path_only=False, resolution=resolution
+                kind="mask",
+                name=t_mask,
+                path_only=False,
+                resolution=resolution,
             )[0]
             for t_mask in mask_files
         ]
@@ -554,3 +581,9 @@ def test_get_multiple(
 
         expected = intersect_masks(mask_imgs, **params)
         assert_array_equal(computed.get_fdata(), expected.get_fdata())
+
+
+def test_deregister() -> None:
+    """Test mask deregistration."""
+    deregister_data(kind="mask", name="testmask")
+    assert "testmask" not in list_data(kind="mask")

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -84,7 +84,7 @@ class ANTsParcellationWarper:
         )
 
         # Native space warping
-        if dst == "native":
+        if dst == "native":  # pragma: no cover
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -32,7 +32,7 @@ class FSLParcellationWarper:
         parcellation_img: "Nifti1Image",
         target_data: dict[str, Any],
         warp_data: dict[str, Any],
-    ) -> "Nifti1Image":
+    ) -> "Nifti1Image":  # pragma: no cover
         """Warp ``parcellation_img`` to correct space.
 
         Parameters

junifer/data/parcellations/_parcellations.py

@@ -1035,17 +1035,17 @@ def _retrieve_shen(
         )
     if n_rois in (268, 368) and year == 2013:
         raise_error(
-            f"The parameter combination `resolution = {resolution}` and "
+            f"The parameter combination `n_rois = {n_rois}` and "
             "`year = 2013` is invalid"
         )
     if n_rois in (50, 100, 150) and year in (2015, 2019):
         raise_error(
-            f"The parameter combination `resolution = {resolution}` and "
+            f"The parameter combination `n_rois = {n_rois}` and "
             f"`year = {year}` is invalid"
         )
     if (n_rois == 268 and year == 2019) or (n_rois == 368 and year == 2015):
         raise_error(
-            f"The parameter combination `resolution = {resolution}` and "
+            f"The parameter combination `n_rois = {n_rois}` and "
             f"`year = {year}` is invalid"
         )
 
@@ -1312,11 +1312,11 @@ def merge_parcellations(
     parcellations_names: list[str],
     labels_lists: list[list[str]],
 ) -> tuple["Nifti1Image", list[str]]:
-    """Merge all parcellations from a list into one parcellation.
+    """Merge multiple parcellations.
 
     Parameters
     ----------
-    parcellations_list : list of niimg-like object
+    parcellations_list : list of Niimg-like object
         List of parcellations to merge.
     parcellations_names: list of str
         List of names for parcellations at the corresponding indices.
@@ -1326,10 +1326,10 @@ def merge_parcellations(
 
     Returns
     -------
-    parcellation : niimg-like object
+    Niimg-like object
         The parcellation that results from merging the list of input
         parcellations.
-    labels : list of str
+    list of str
         List of labels for the resultant parcellation.
 
     """

junifer/data/parcellations/tests/test_parcellations.py

@@ -13,7 +13,12 @@ import pytest
 from nilearn.image import new_img_like, resample_to_img
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
-from junifer.data import ParcellationRegistry
+from junifer.data import (
+    get_data,
+    list_data,
+    load_data,
+    register_data,
+)
 from junifer.data.parcellations import merge_parcellations
 from junifer.data.parcellations._parcellations import (
     _retrieve_aicha,
@@ -35,7 +40,8 @@ from junifer.testing.datagrabbers import (
 def test_register_built_in_check() -> None:
     """Test parcellation registration check for built-in parcellations."""
     with pytest.raises(ValueError, match=r"built-in parcellation"):
-        ParcellationRegistry().register(
+        register_data(
+            kind="parcellation",
             name="SUITxSUIT",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
@@ -46,34 +52,40 @@ def test_register_built_in_check() -> None:
 
 def test_list_incorrect() -> None:
     """Test incorrect information check for list parcellations."""
-    assert "testparc" not in ParcellationRegistry().list
+    assert "testparc" not in list_data(kind="parcellation")
 
 
 def test_register_already_registered() -> None:
     """Test parcellation registration check for already registered."""
     # Register custom parcellation
-    ParcellationRegistry().register(
+    register_data(
+        kind="parcellation",
         name="testparc",
         parcellation_path="testparc.nii.gz",
         parcels_labels=["1", "2", "3"],
         space="MNI152Lin",
     )
     assert (
-        ParcellationRegistry()
+        load_data(
-        .load("testparc", target_space="MNI152Lin", path_only=True)[2]
+            kind="parcellation",
-        .name
+            name="testparc",
+            target_space="MNI152Lin",
+            path_only=True,
+        )[2].name
         == "testparc.nii.gz"
     )
 
     # Try registering again
     with pytest.raises(ValueError, match=r"already registered."):
-        ParcellationRegistry().register(
+        register_data(
+            kind="parcellation",
             name="testparc",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
             space="MNI152Lin",
         )
-    ParcellationRegistry().register(
+    register_data(
+        kind="parcellation",
         name="testparc",
         parcellation_path="testparc2.nii.gz",
         parcels_labels=["1", "2", "3"],
@@ -82,9 +94,12 @@ def test_register_already_registered() -> None:
     )
 
     assert (
-        ParcellationRegistry()
+        load_data(
-        .load("testparc", target_space="MNI152Lin", path_only=True)[2]
+            kind="parcellation",
-        .name
+            name="testparc",
+            target_space="MNI152Lin",
+            path_only=True,
+        )[2].name
         == "testparc2.nii.gz"
     )
 
@@ -98,27 +113,44 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    schaefer, labels, schaefer_path, _ = ParcellationRegistry().load(
+    schaefer, labels, schaefer_path, _ = load_data(
-        "Schaefer100x7",
+        kind="parcellation",
-        "MNI152NLin6Asym",
+        name="Schaefer100x7",
+        target_space="MNI152NLin6Asym",
     )
     assert schaefer is not None
 
     # Test wrong number of labels
-    ParcellationRegistry().register(
+    register_data(
-        "WrongLabels", schaefer_path, labels[:10], "MNI152Lin"
+        kind="parcellation",
+        name="WrongLabels",
+        parcellation_path=schaefer_path,
+        parcels_labels=labels[:10],
+        space="MNI152Lin",
     )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 10"):
-        ParcellationRegistry().load("WrongLabels", "MNI152NLin6Asym")
+        load_data(
+            kind="parcellation",
+            name="WrongLabels",
+            target_space="MNI152NLin6Asym",
+        )
 
     # Test wrong number of labels
-    ParcellationRegistry().register(
+    register_data(
-        "WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI152Lin"
+        kind="parcellation",
+        name="WrongLabels2",
+        parcellation_path=schaefer_path,
+        parcels_labels=[*labels, "wrong"],
+        space="MNI152Lin",
     )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
-        ParcellationRegistry().load("WrongLabels2", "MNI152NLin6Asym")
+        load_data(
+            kind="parcellation",
+            name="WrongLabels2",
+            target_space="MNI152NLin6Asym",
+        )
 
     schaefer_data = schaefer.get_fdata().copy()
     schaefer_data[schaefer_data == 50] = 0
@@ -126,11 +158,19 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    ParcellationRegistry().register(
+    register_data(
-        "WrongValues", new_schaefer_path, labels[:-1], "MNI152Lin"
+        kind="parcellation",
+        name="WrongValues",
+        parcellation_path=new_schaefer_path,
+        parcels_labels=labels[:-1],
+        space="MNI152Lin",
     )
     with pytest.raises(ValueError, match=r"must have all the values in the"):
-        ParcellationRegistry().load("WrongValues", "MNI152NLin6Asym")
+        load_data(
+            kind="parcellation",
+            name="WrongValues",
+            target_space="MNI152NLin6Asym",
+        )
 
     schaefer_data = schaefer.get_fdata().copy()
     schaefer_data[schaefer_data == 50] = 200
@@ -138,11 +178,19 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    ParcellationRegistry().register(
+    register_data(
-        "WrongValues2", new_schaefer_path, labels, "MNI152Lin"
+        kind="parcellation",
+        name="WrongValues2",
+        parcellation_path=new_schaefer_path,
+        parcels_labels=labels,
+        space="MNI152Lin",
     )
     with pytest.raises(ValueError, match=r"must have all the values in the"):
-        ParcellationRegistry().load("WrongValues2", "MNI152NLin6Asym")
+        load_data(
+            kind="parcellation",
+            name="WrongValues2",
+            target_space="MNI152NLin6Asym",
+        )
 
 
 @pytest.mark.parametrize(
@@ -195,7 +243,8 @@ def test_register(
 
     """
     # Register custom parcellation
-    ParcellationRegistry().register(
+    register_data(
+        kind="parcellation",
         name=name,
         parcellation_path=parcellation_path,
         parcels_labels=parcels_labels,
@@ -203,10 +252,13 @@ def test_register(
         overwrite=overwrite,
     )
     # List available parcellation and check registration
-    assert name in ParcellationRegistry().list
+    assert name in list_data(kind="parcellation")
     # Load registered parcellation
-    _, lbl, fname, parcellation_space = ParcellationRegistry().load(
+    _, lbl, fname, parcellation_space = load_data(
-        name=name, target_space=space, path_only=True
+        kind="parcellation",
+        name=name,
+        target_space=space,
+        path_only=True,
     )
     # Check values for registered parcellation
     assert lbl == parcels_labels
@@ -237,13 +289,17 @@ def test_list_correct(parcellation_name: str) -> None:
         The parametrized parcellation name.
 
     """
-    assert parcellation_name in ParcellationRegistry().list
+    assert parcellation_name in list_data(kind="parcellation")
 
 
 def test_load_incorrect() -> None:
     """Test loading of invalid parcellations."""
     with pytest.raises(ValueError, match=r"not found"):
-        ParcellationRegistry().load("wrongparcellation", "MNI152NLin6Asym")
+        load_data(
+            kind="parcellation",
+            name="wrongparcellation",
+            target_space="MNI152NLin6Asym",
+        )
 
 
 @pytest.mark.parametrize(
@@ -309,14 +365,15 @@ def test_schaefer(
 
     """
     parcellation_name = f"Schaefer{n_rois}x{yeo_networks}"
-    assert parcellation_name in ParcellationRegistry().list
+    assert parcellation_name in list_data(kind="parcellation")
 
     parcellation_file = (
         f"Schaefer2018_{n_rois}Parcels_{yeo_networks}Networks_order_FSLMNI152_"
         f"{int(resolution)}mm.nii.gz"
     )
     # Load parcellation
-    img, label, img_path, space = ParcellationRegistry().load(
+    img, label, img_path, space = load_data(
+        kind="parcellation",
         name=parcellation_name,
         target_space="MNI152NLin6Asym",
         resolution=resolution,
@@ -326,7 +383,8 @@ def test_schaefer(
     assert len(label) == n_rois
     assert space == "MNI152NLin6Asym"
     assert_array_equal(
-        img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
+        img.header["pixdim"][1:4],
+        3 * [resolution],  # type: ignore
     )
 
 
@@ -365,9 +423,10 @@ def test_suit(space_key: str, space: str) -> None:
         The parametrized space values.
 
     """
-    assert f"SUITx{space_key}" in ParcellationRegistry().list
+    assert f"SUITx{space_key}" in list_data(kind="parcellation")
     # Load parcellation
-    img, label, img_path, parcellation_space = ParcellationRegistry().load(
+    img, label, img_path, parcellation_space = load_data(
+        kind="parcellation",
         name=f"SUITx{space_key}",
         target_space=space,
     )
@@ -398,13 +457,14 @@ def test_tian_3T_6thgeneration(scale: int, n_label: int) -> None:
         The parametrized n_label values.
 
     """
-    parcellations = ParcellationRegistry().list
+    parcellations = list_data(kind="parcellation")
     assert "TianxS1x3TxMNI6thgeneration" in parcellations
     assert "TianxS2x3TxMNI6thgeneration" in parcellations
     assert "TianxS3x3TxMNI6thgeneration" in parcellations
     assert "TianxS4x3TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname, space = ParcellationRegistry().load(
+    img, lbl, fname, space = load_data(
+        kind="parcellation",
         name=f"TianxS{scale}x3TxMNI6thgeneration",
         target_space="MNI152NLin2009cAsym",  # force highest resolution
     )
@@ -415,7 +475,8 @@ def test_tian_3T_6thgeneration(scale: int, n_label: int) -> None:
     assert len(lbl) == n_label
     assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
     # Load parcellation
-    img, lbl, fname, space = ParcellationRegistry().load(
+    img, lbl, fname, space = load_data(
+        kind="parcellation",
         name=f"TianxS{scale}x3TxMNI6thgeneration",
         target_space="MNI152NLin6Asym",
         resolution=2,
@@ -442,13 +503,14 @@ def test_tian_3T_nonlinear2009cAsym(scale: int, n_label: int) -> None:
         The parametrized n_label values.
 
     """
-    parcellations = ParcellationRegistry().list
+    parcellations = list_data(kind="parcellation")
     assert "TianxS1x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS2x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS3x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS4x3TxMNInonlinear2009cAsym" in parcellations
     # Load parcellation
-    img, lbl, fname, space = ParcellationRegistry().load(
+    img, lbl, fname, space = load_data(
+        kind="parcellation",
         name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
         target_space="MNI152NLin6Asym",  # force highest resolution
     )
@@ -459,7 +521,8 @@ def test_tian_3T_nonlinear2009cAsym(scale: int, n_label: int) -> None:
     assert len(lbl) == n_label
     assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
     # Load parcellation
-    img, lbl, fname, space = ParcellationRegistry().load(
+    img, lbl, fname, space = load_data(
+        kind="parcellation",
         name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
         target_space="MNI152NLin2009cAsym",
         resolution=2,
@@ -486,13 +549,14 @@ def test_tian_7T_6thgeneration(scale: int, n_label: int) -> None:
         The parametrized n_label values.
 
     """
-    parcellations = ParcellationRegistry().list
+    parcellations = list_data(kind="parcellation")
     assert "TianxS1x7TxMNI6thgeneration" in parcellations
     assert "TianxS2x7TxMNI6thgeneration" in parcellations
     assert "TianxS3x7TxMNI6thgeneration" in parcellations
     assert "TianxS4x7TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname, space = ParcellationRegistry().load(
+    img, lbl, fname, space = load_data(
+        kind="parcellation",
         name=f"TianxS{scale}x7TxMNI6thgeneration",
         target_space="MNI152NLin6Asym",
     )
@@ -502,7 +566,8 @@ def test_tian_7T_6thgeneration(scale: int, n_label: int) -> None:
     assert space == "MNI152NLin6Asym"
     assert len(lbl) == n_label
     assert_array_almost_equal(
-        img.header["pixdim"][1:4], [1.6, 1.6, 1.6]  # type: ignore
+        img.header["pixdim"][1:4],
+        [1.6, 1.6, 1.6],  # type: ignore
     )
 
 
@@ -552,9 +617,10 @@ def test_aicha(version: int) -> None:
         The parametrized version values.
 
     """
-    assert f"AICHA_v{version}" in ParcellationRegistry().list
+    assert f"AICHA_v{version}" in list_data(kind="parcellation")
     # Load parcellation
-    img, label, img_path, space = ParcellationRegistry().load(
+    img, label, img_path, space = load_data(
+        kind="parcellation",
         name=f"AICHA_v{version}",
         target_space="IXI549Space",
     )
@@ -610,9 +676,10 @@ def test_shen(
         The parametrized partial file names.
 
     """
-    assert f"Shen_{year}_{n_rois}" in ParcellationRegistry().list
+    assert f"Shen_{year}_{n_rois}" in list_data(kind="parcellation")
     # Load parcellation
-    img, label, img_path, space = ParcellationRegistry().load(
+    img, label, img_path, space = load_data(
+        kind="parcellation",
         name=f"Shen_{year}_{n_rois}",
         target_space="MNI152NLin2009cAsym",
         resolution=resolution,
@@ -622,7 +689,8 @@ def test_shen(
     assert space == "MNI152NLin2009cAsym"
     assert len(label) == n_labels
     assert_array_equal(
-        img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
+        img.header["pixdim"][1:4],
+        3 * [resolution],  # type: ignore
     )
 
 
@@ -771,7 +839,7 @@ def test_yan(
         The parametrized Kong networks values.
 
     """
-    parcellations = ParcellationRegistry().list
+    parcellations = list_data(kind="parcellation")
     if yeo_networks:
         parcellation_name = f"Yan{n_rois}xYeo{yeo_networks}"
         assert parcellation_name in parcellations
@@ -787,7 +855,8 @@ def test_yan(
             f"{int(resolution)}mm.nii.gz"
         )
     # Load parcellation
-    img, label, img_path, space = ParcellationRegistry().load(
+    img, label, img_path, space = load_data(
+        kind="parcellation",
         name=parcellation_name,
         target_space="MNI152NLin6Asym",
         resolution=resolution,
@@ -797,7 +866,8 @@ def test_yan(
     assert space == "MNI152NLin6Asym"
     assert len(label) == n_rois
     assert_array_equal(
-        img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
+        img.header["pixdim"][1:4],
+        3 * [resolution],  # type: ignore
     )
 
 
@@ -877,7 +947,7 @@ def test_brainnetome(
         The parametrized threshold values.
 
     """
-    parcellations = ParcellationRegistry().list
+    parcellations = list_data(kind="parcellation")
     parcellation_name = f"Brainnetome_thr{threshold}"
     assert parcellation_name in parcellations
 
@@ -887,7 +957,8 @@ def test_brainnetome(
 
     parcellation_file = f"BNA-maxprob-thr{threshold}-{resolution}mm.nii.gz"
     # Load parcellation
-    img, label, img_path, space = ParcellationRegistry().load(
+    img, label, img_path, space = load_data(
+        kind="parcellation",
         name=parcellation_name,
         target_space="MNI152NLin6Asym",
         resolution=resolution,
@@ -897,7 +968,8 @@ def test_brainnetome(
     assert space == "MNI152NLin6Asym"
     assert len(label) == 246
     assert_array_equal(
-        img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
+        img.header["pixdim"][1:4],
+        3 * [resolution],  # type: ignore
     )
 
 
@@ -912,11 +984,14 @@ def test_retrieve_brainnetome_incorrect_threshold() -> None:
 def test_merge_parcellations() -> None:
     """Test merging parcellations."""
     # load some parcellations for testing
-    schaefer_parcellation, schaefer_labels, _, _ = ParcellationRegistry().load(
+    schaefer_parcellation, schaefer_labels, _, _ = load_data(
-        "Schaefer100x17", target_space="MNI152NLin2009cAsym"
+        kind="parcellation",
+        name="Schaefer100x17",
+        target_space="MNI152NLin2009cAsym",
     )
-    tian_parcellation, tian_labels, _, _ = ParcellationRegistry().load(
+    tian_parcellation, tian_labels, _, _ = load_data(
-        "TianxS2x3TxMNInonlinear2009cAsym",
+        kind="parcellation",
+        name="TianxS2x3TxMNInonlinear2009cAsym",
         target_space="MNI152NLin2009cAsym",
     )
     # prepare the list of the actual parcellations
@@ -949,8 +1024,10 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
 
     """
     # Get the testing parcellation
-    parcellation, labels, _, _ = ParcellationRegistry().load(
+    parcellation, labels, _, _ = load_data(
-        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+        kind="parcellation",
+        name="Schaefer100x7",
+        target_space="MNI152NLin2009cAsym",
     )
 
     assert parcellation is not None
@@ -986,8 +1063,10 @@ def test_merge_parcellations_3D_multiple_overlapping() -> None:
     """Test merge_parcellations with multiple overlapping parcellations."""
 
     # Get the testing parcellation
-    parcellation, labels, _, _ = ParcellationRegistry().load(
+    parcellation, labels, _, _ = load_data(
-        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+        kind="parcellation",
+        name="Schaefer100x7",
+        target_space="MNI152NLin2009cAsym",
     )
 
     assert parcellation is not None
@@ -1023,8 +1102,10 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
     """Test merge_parcellations with duplicated labels."""
 
     # Get the testing parcellation
-    parcellation, labels, _, _ = ParcellationRegistry().load(
+    parcellation, labels, _, _ = load_data(
-        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+        kind="parcellation",
+        name="Schaefer100x7",
+        target_space="MNI152NLin2009cAsym",
     )
 
     assert parcellation is not None
@@ -1064,15 +1145,17 @@ def test_get_single() -> None:
         bold = element_data["BOLD"]
         bold_img = bold["data"]
         # Get tailored parcellation
-        tailored_parcellation, tailored_labels = ParcellationRegistry().get(
+        tailored_parcellation, tailored_labels = get_data(
-            parcellations=["Shen_2015_268"],
+            kind="parcellation",
+            names=["Shen_2015_268"],
             target_data=bold,
         )
         # Check shape and affine with original element data
         assert tailored_parcellation.shape == bold_img.shape[:3]
         assert_array_equal(tailored_parcellation.affine, bold_img.affine)
         # Get raw parcellation
-        raw_parcellation, raw_labels, _, _ = ParcellationRegistry().load(
+        raw_parcellation, raw_labels, _, _ = load_data(
+            kind="parcellation",
             name="Shen_2015_268",
             target_space="MNI152NLin2009cAsym",
             resolution=4,
@@ -1098,8 +1181,9 @@ def test_get_multi_same_space() -> None:
         bold = element_data["BOLD"]
         bold_img = bold["data"]
         # Get tailored parcellation
-        tailored_parcellation, tailored_labels = ParcellationRegistry().get(
+        tailored_parcellation, tailored_labels = get_data(
-            parcellations=[
+            kind="parcellation",
+            names=[
                 "Shen_2015_268",
                 "TianxS1x3TxMNInonlinear2009cAsym",
             ],
@@ -1116,7 +1200,8 @@ def test_get_multi_same_space() -> None:
             "TianxS1x3TxMNInonlinear2009cAsym",
         ]
         for name in parcellations_names:
-            img, labels, _, _ = ParcellationRegistry().load(
+            img, labels, _, _ = load_data(
+                kind="parcellation",
                 name=name,
                 target_space="MNI152NLin2009cAsym",
                 resolution=4,
@@ -1152,8 +1237,9 @@ def test_get_multi_different_space() -> None:
     with OasisVBMTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         # Get tailored parcellation
-        ParcellationRegistry().get(
+        get_data(
-            parcellations=[
+            kind="parcellation",
+            names=[
                 "Schaefer100x7",
                 "TianxS1x3TxMNInonlinear2009cAsym",
             ],

junifer/data/tests/test_data_utils.py

@@ -3,7 +3,6 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-
 import numpy as np
 import pytest
 

junifer/data/utils.py

@@ -76,7 +76,7 @@ def get_native_warper(
     target_data: MutableMapping,
     other_data: MutableMapping,
     inverse: bool = False,
-) -> dict:
+) -> dict:  # pragma: no cover
     """Get correct warping specification for native space.
 
     Parameters

junifer/datagrabber/aomic/id1000.py

@@ -35,6 +35,12 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
     space : {"native", "MNI152NLin2009cAsym"}, optional
         The space to use for the data (default "MNI152NLin2009cAsym").
 
+    Raises
+    ------
+    ValueError
+        If invalid value is passed for:
+         * ``space``
+
     """
 
     def __init__(

junifer/datagrabber/aomic/piop1.py

@@ -43,7 +43,9 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
     Raises
     ------
     ValueError
-        If invalid value is passed for ``tasks``.
+        If invalid value is passed for:
+         * ``tasks``
+         * ``space``
 
     """
 
@@ -79,8 +81,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             for t in tasks:
                 if t not in all_tasks:
                     raise_error(
-                        f"{t} is not a valid task in the AOMIC PIOP1"
+                        f"{t} is not a valid task in the AOMIC PIOP1 dataset!"
-                        " dataset!"
                     )
         self.tasks = tasks
         # Descriptor for space in `anat`

junifer/datagrabber/aomic/piop2.py

@@ -43,7 +43,9 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
     Raises
     ------
     ValueError
-        If invalid value is passed for ``tasks``.
+        If invalid value is passed for:
+         * ``tasks``
+         * ``space``
 
     """
 
@@ -77,8 +79,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             for t in tasks:
                 if t not in all_tasks:
                     raise_error(
-                        f"{t} is not a valid task in the AOMIC PIOP2"
+                        f"{t} is not a valid task in the AOMIC PIOP2 dataset!"
-                        " dataset!"
                     )
         self.tasks = tasks
         # Descriptor for space in `anat`

junifer/datagrabber/pattern_datalad.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from ..api.decorators import register_datagrabber
 from ..utils import logger
 from .datalad_base import DataladDataGrabber

junifer/datagrabber/pattern_validation_mixin.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from ..typing import DataGrabberPatterns
 from ..utils import logger, raise_error, warn_with_log
 

junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -264,7 +264,7 @@ def test_DMCC13Benchmark_invalid_sessions():
     """Test DMCC13Benchmark DataGrabber invalid sessions."""
     with pytest.raises(
         ValueError,
-        match=("phonyses is not a valid session in " "the DMCC dataset"),
+        match=("phonyses is not a valid session in the DMCC dataset"),
     ):
         DMCC13Benchmark(sessions="phonyses")
 
@@ -273,9 +273,7 @@ def test_DMCC13Benchmark_invalid_tasks():
     """Test DMCC13Benchmark DataGrabber invalid tasks."""
     with pytest.raises(
         ValueError,
-        match=(
+        match=("thisisnotarealtask is not a valid task in the DMCC dataset"),
-            "thisisnotarealtask is not a valid task in " "the DMCC dataset"
-        ),
     ):
         DMCC13Benchmark(tasks="thisisnotarealtask")
 
@@ -284,9 +282,7 @@ def test_DMCC13Benchmark_phase_encodings():
     """Test DMCC13Benchmark DataGrabber invalid phase encodings."""
     with pytest.raises(
         ValueError,
-        match=(
+        match=("moonphase is not a valid phase encoding in the DMCC dataset"),
-            "moonphase is not a valid phase encoding in " "the DMCC dataset"
-        ),
     ):
         DMCC13Benchmark(phase_encodings="moonphase")
 
@@ -295,6 +291,6 @@ def test_DMCC13Benchmark_runs():
     """Test DMCC13Benchmark DataGrabber invalid runs."""
     with pytest.raises(
         ValueError,
-        match=("cerebralrun is not a valid run in " "the DMCC dataset"),
+        match=("cerebralrun is not a valid run in the DMCC dataset"),
     ):
         DMCC13Benchmark(runs="cerebralrun")

junifer/markers/base.py

@@ -229,9 +229,9 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
                     # feature data is not manipulated, only meta
                     self.update_meta(feature_data_copy, "marker")
                     # Update marker feature's metadata name
-                    feature_data_copy["meta"]["marker"][
+                    feature_data_copy["meta"]["marker"]["name"] += (
-                        "name"
+                        f"_{feature_name}"
-                    ] += f"_{feature_name}"
+                    )
 
                     if storage is not None:
                         logger.info(f"Storing in {storage}")

junifer/markers/brainprint.py

@@ -116,7 +116,7 @@ class BrainPrint(BaseMarker):
         aseg_path: Path,
         norm_path: Path,
         indices: list,
-    ) -> Path:
+    ) -> Path:  # pragma: no cover
         """Generate a surface from the aseg and label files.
 
         Parameters
@@ -191,7 +191,7 @@ class BrainPrint(BaseMarker):
         self,
         aseg_path: Path,
         norm_path: Path,
-    ) -> dict[str, Path]:
+    ) -> dict[str, Path]:  # pragma: no cover
         """Create surfaces from FreeSurfer aseg labels.
 
         Parameters
@@ -266,7 +266,7 @@ class BrainPrint(BaseMarker):
         rh_white_path: Path,
         lh_pial_path: Path,
         rh_pial_path: Path,
-    ) -> dict[str, Path]:
+    ) -> dict[str, Path]:  # pragma: no cover
         """Create cortical surfaces from FreeSurfer labels.
 
         Parameters
@@ -308,7 +308,7 @@ class BrainPrint(BaseMarker):
     def _fix_nan(
         self,
         input_data: list[Union[float, str, npt.ArrayLike]],
-    ) -> np.ndarray:
+    ) -> np.ndarray:  # pragma: no cover
         """Convert BrainPrint output with string NaN to ``numpy.nan``.
 
         Parameters
@@ -330,7 +330,7 @@ class BrainPrint(BaseMarker):
         self,
         input: dict[str, Any],
         extra_input: Optional[dict] = None,
-    ) -> dict:
+    ) -> dict:  # pragma: no cover
         """Compute.
 
         Parameters

junifer/markers/complexity/multiscale_entropy_auc.py

@@ -114,9 +114,9 @@ class MultiscaleEntropyAUC(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(scale, int), "Scale must be integer."
-        assert isinstance(
+        assert isinstance(tol, float), (
-            tol, float
+            "Tolerance must be a positive float number."
-        ), "Tolerance must be a positive float number."
+        )
 
         _, n_roi = extracted_bold_values.shape
         MSEn_auc_roi = np.zeros((n_roi, 1))

junifer/markers/complexity/range_entropy.py

@@ -114,9 +114,9 @@ class RangeEntropy(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(delay, int), "Delay must be integer."
-        assert isinstance(
+        assert isinstance(tolerance, float), (
-            tolerance, float
+            "Tolerance must be a float number between 0 and 1."
-        ), "Tolerance must be a float number between 0 and 1."
+        )
 
         _, n_roi = extracted_bold_values.shape
         range_en_roi = np.zeros((n_roi, 1))

junifer/markers/complexity/sample_entropy.py

@@ -115,9 +115,9 @@ class SampleEntropy(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(delay, int), "Delay must be integer."
-        assert isinstance(
+        assert isinstance(tol, float), (
-            tol, float
+            "Tolerance must be a positive float number."
-        ), "Tolerance must be a positive float number."
+        )
 
         _, n_roi = extracted_bold_values.shape
         samp_en_roi = np.zeros((n_roi, 1))

junifer/markers/falff/falff_parcels.py

@@ -151,9 +151,7 @@ class ALFFParcels(ALFFBase):
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
-                )[
+                )["aggregation"],
-                    "aggregation"
-                ],
             },
             "falff": {
                 **ParcelAggregation(
@@ -165,8 +163,6 @@ class ALFFParcels(ALFFBase):
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,
-                )[
+                )["aggregation"],
-                    "aggregation"
-                ],
             },
         }

junifer/markers/falff/falff_spheres.py

@@ -164,9 +164,7 @@ class ALFFSpheres(ALFFBase):
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
-                )[
+                )["aggregation"],
-                    "aggregation"
-                ],
             },
             "falff": {
                 **SphereAggregation(
@@ -180,8 +178,6 @@ class ALFFSpheres(ALFFBase):
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,
-                )[
+                )["aggregation"],
-                    "aggregation"
-                ],
             },
         }

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from abc import abstractmethod
 from typing import Any, ClassVar, Optional, Union
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -91,7 +91,8 @@ def test_FunctionalConnectivityParcels(
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
+            cov_estimator=cov_estimator,
+            kind="correlation",  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -92,7 +92,8 @@ def test_FunctionalConnectivitySpheres(
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
+            cov_estimator=cov_estimator,
+            kind="correlation",  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal

junifer/markers/reho/_afni_reho.py

@@ -41,7 +41,7 @@ class AFNIReHo(metaclass=Singleton):
         },
     ]
 
-    def __del__(self) -> None:
+    def __del__(self) -> None:  # pragma: no cover
         """Terminate the class."""
         # Clear the computation cache
         logger.debug("Clearing cache for ReHo computation via AFNI")

junifer/markers/reho/reho_base.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,

junifer/markers/reho/reho_parcels.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Any, Optional, Union
 
 import numpy as np

junifer/markers/reho/reho_spheres.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Any, Optional, Union
 
 import numpy as np

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -3,7 +3,6 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-
 from abc import abstractmethod
 from typing import Any, ClassVar, Optional, Union
 

junifer/markers/tests/test_markers_base.py

@@ -20,7 +20,6 @@ def test_base_marker_subclassing() -> None:
 
     # Create concrete class
     class MyBaseMarker(BaseMarker):
-
         _MARKER_INOUT_MAPPINGS = {  # noqa: RUF012
             "BOLD": {
                 "feat_1": "timeseries",

junifer/onthefly/_brainprint.py

@@ -19,7 +19,7 @@ def normalize(
     storage: StorageLike,
     features: dict[str, dict[str, Optional[str]]],
     kind: str,
-) -> pd.DataFrame:
+) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and normalize either surfaces or volumes.
 
     Parameters
@@ -79,7 +79,7 @@ def normalize(
         )
     else:
         raise_error(
-            "Invalid value for `kind`, should be one of: " f"{valid_kind}"
+            f"Invalid value for `kind`, should be one of: {valid_kind}"
         )
 
     return normalized_df
@@ -89,7 +89,7 @@ def reweight(
     storage: StorageLike,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
-) -> pd.DataFrame:
+) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and reweight eigenvalues.
 
     Parameters

junifer/onthefly/read_transform.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Optional
 
 import pandas as pd
@@ -85,7 +84,7 @@ def read_transform(
         # Check bctpy import
         try:
             import bct
-        except ImportError as err:
+        except ImportError as err:  # pragma: no cover
             raise_error(msg=str(err), klass=ImportError)
 
         # Warning about function usage

junifer/onthefly/tests/test_read_transform.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import logging
 from pathlib import Path
 

junifer/pipeline/tests/test_marker_collection.py

@@ -186,7 +186,8 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
         assert out is None
 
     mc2 = MarkerCollection(
-        markers=markers, datareader=DefaultDataReader()  # type: ignore
+        markers=markers,
+        datareader=DefaultDataReader(),  # type: ignore
     )
     mc2.validate(dg)
     assert mc2._storage is None

junifer/pipeline/workdir_manager.py

@@ -197,8 +197,7 @@ class WorkDirManager(metaclass=Singleton):
             return
         if self._elementdir is not None:
             logger.debug(
-                "Deleting element directory at "
+                f"Deleting element directory at {self._elementdir.resolve()!s}"
-                f"{self._elementdir.resolve()!s}"
             )
             shutil.rmtree(self._elementdir, ignore_errors=True)
             self._elementdir = None

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -572,7 +572,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         if bold_img.get_fdata().shape[3] != len(confound_df):
             raise_error(
                 "Image time series and confounds have different length!\n"
-                f"\tImage time series: { bold_img.get_fdata().shape[3]}\n"
+                f"\tImage time series: {bold_img.get_fdata().shape[3]}\n"
                 f"\tConfounds: {len(confound_df)}"
             )
 

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import numpy as np
 import pandas as pd
 import pytest

junifer/preprocess/smoothing/tests/test_smoothing.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import pytest
 
 from junifer.datareader import DefaultDataReader

junifer/preprocess/warping/_ants_warper.py

@@ -72,7 +72,7 @@ class ANTsWarper:
         )
 
         # Native space warping
-        if reference == "T1w":
+        if reference == "T1w":  # pragma: no cover
             logger.debug("Using ANTs for space warping")
 
             # Get the min of the voxel sizes from input and use it as the
@@ -237,8 +237,7 @@ class ANTsWarper:
             if input.get("mask") is not None:
                 # Create a tempfile for warped mask output
                 apply_transforms_mask_out_path = element_tempdir / (
-                    f"warped_mask_from_{input['space']}_to_"
+                    f"warped_mask_from_{input['space']}_to_{reference}.nii.gz"
-                    f"{reference}.nii.gz"
                 )
                 # Set antsApplyTransforms command
                 apply_transforms_mask_cmd = [

junifer/preprocess/warping/_fsl_warper.py

@@ -40,7 +40,7 @@ class FSLWarper:
         self,
         input: dict[str, Any],
         extra_input: dict[str, Any],
-    ) -> dict[str, Any]:
+    ) -> dict[str, Any]:  # pragma: no cover
         """Preprocess using FSL.
 
         Parameters

junifer/preprocess/warping/space_warper.py

@@ -77,7 +77,7 @@ class SpaceWarper(BasePreprocessor):
         self.reference = reference
         # Set required data types based on reference and
         # initialize superclass
-        if self.reference == "T1w":
+        if self.reference == "T1w":  # pragma: no cover
             required_data_types = [self.reference, "Warp"]
             # Listify on
             if not isinstance(on, list):
@@ -170,7 +170,9 @@ class SpaceWarper(BasePreprocessor):
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
+        if (
+            self.using in ["fsl", "ants", "auto"] and self.reference == "T1w"
+        ):  # pragma: no cover
             # Check for extra inputs
             if extra_input is None:
                 raise_error(

junifer/storage/pandas_base.py

@@ -187,7 +187,9 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         )
         # Prepare new dataframe
         df = pd.DataFrame(
-            data=data, columns=col_names, index=idx  # type: ignore
+            data=data,
+            columns=col_names,
+            index=idx,  # type: ignore
         )
         # Store dataframe
         self.store_df(meta_md5=meta_md5, element=element, df=df)

junifer/storage/sqlite.py

@@ -229,9 +229,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         # Format index names for retrieved data
         meta_df.index = meta_df.index.str.replace(r"meta_", "")
         # Convert dataframe to dictionary
-        out: dict[str, dict[str, str]] = meta_df.to_dict(
+        out: dict[str, dict[str, str]] = meta_df.to_dict(orient="index")  # type: ignore
-            orient="index"
-        )  # type: ignore
         # Format output
         for md5, t_meta in out.items():
             for k, v in t_meta.items():
@@ -536,8 +534,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
                 klass=IOError,
             )
         logger.info(
-            "Collecting data from "
+            f"Collecting data from {self.uri.parent}/*{self.uri.name}"  # type: ignore
-            f"{self.uri.parent}/*{self.uri.name}"  # type: ignore
         )
         # Create new instance
         out_storage = SQLiteFeatureStorage(uri=self.uri, upsert="ignore")
@@ -596,9 +593,7 @@ def _generate_update_statements(table, index_col, rows_to_update):
     for i, (_, keys) in enumerate(pk_indb.iterrows()):
         stmt = (
             table.update()
-            .where(
+            .where(and_(col == keys[j] for j, col in enumerate(pk_cols)))  # type: ignore
-                and_(col == keys[j] for j, col in enumerate(pk_cols))
-            )  # type: ignore
             .values(new_records[i])
         )
         stmts.append(stmt)

junifer/storage/tests/test_pandas_base.py

@@ -37,7 +37,8 @@ def test_element_to_index() -> None:
     assert index.levels[1].name == "idx"  # type: ignore
     # Check second index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[1].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[1].values)  # type: ignore
     )
     # Check second index level values shape
     assert index.levels[1].values.shape == (10,)  # type: ignore
@@ -69,7 +70,8 @@ def test_element_to_index() -> None:
     assert index.levels[1].name == "scan"  # type: ignore
     # Check second index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[1].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[1].values)  # type: ignore
     )
     # Check second index level values shape
     assert index.levels[1].values.shape == (7,)  # type: ignore
@@ -97,7 +99,8 @@ def test_element_to_index() -> None:
     assert index.levels[2].name == "idx"  # type: ignore
     # Check third index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[2].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[2].values)  # type: ignore
     )
     # Check third index level values shape
     assert index.levels[2].values.shape == (10,)  # type: ignore

junifer/storage/tests/test_storage_base.py

@@ -13,7 +13,8 @@ def test_BaseFeatureStorage_abstractness() -> None:
     """Test BaseFeatureStorage is abstract base class."""
     with pytest.raises(TypeError, match=r"abstract"):
         BaseFeatureStorage(
-            uri="/tmp", storage_types=["matrix"]  # type: ignore
+            uri="/tmp",
+            storage_types=["matrix"],  # type: ignore
         )
 
 

junifer/utils/logging.py

@@ -8,15 +8,14 @@ import os
 import sys
 
 
-if sys.version_info < (3, 12):
+if sys.version_info < (3, 12):  # pragma: no cover
     from distutils.version import LooseVersion
-else:  # pragma: no cover
+else:
     from looseversion import LooseVersion
 
 import logging
 import warnings
 from pathlib import Path
-from subprocess import PIPE, Popen, TimeoutExpired
 from typing import ClassVar, NoReturn, Optional, Union
 from warnings import warn
 
@@ -77,7 +76,7 @@ class WrapStdOut(logging.StreamHandler):
         # just stdout) in order for this to work (tested on OSX and Linux)
         if hasattr(sys.stdout, name):
             return getattr(sys.stdout, name)
-        else:
+        else:  # pragma: no cover
             raise AttributeError(f"'file' object has not attribute '{name}'")
 
 
@@ -107,11 +106,13 @@ class ColorFormatter(logging.Formatter):
     COLOR_SEQ: str = "\033[1;%dm"
     BOLD_SEQ: str = "\033[1m"
 
-    def __init__(self, fmt: str, datefmt: Optional[str] = None) -> None:
+    def __init__(
+        self, fmt: str, datefmt: Optional[str] = None
+    ) -> None:  # pragma: no cover
         """Initialize the ColorFormatter."""
         logging.Formatter.__init__(self, fmt, datefmt)
 
-    def format(self, record: logging.LogRecord) -> str:
+    def format(self, record: logging.LogRecord) -> str:  # pragma: no cover
         """Format the log record.
 
         Parameters
@@ -134,45 +135,6 @@ class ColorFormatter(logging.Formatter):
         return logging.Formatter.format(self, record)
 
 
-def _get_git_head(path: Path) -> str:
-    """Aux function to read HEAD from git.
-
-    Parameters
-    ----------
-    path : pathlib.Path
-        The path to read git HEAD from.
-
-    Returns
-    -------
-    str
-        Empty string if timeout expired for subprocess command execution else
-        git HEAD information.
-
-    Raises
-    ------
-    FileNotFoundError
-        If ``path`` is invalid.
-
-    """
-    if not path.exists():
-        raise_error(
-            msg=f"This path does not exist: {path}", klass=FileNotFoundError
-        )
-    command = f"cd {path}; git rev-parse --verify HEAD"
-    process = Popen(
-        args=command,
-        stdout=PIPE,
-        shell=True,
-    )
-    try:
-        stdout, _ = process.communicate(timeout=10)
-        proc_stdout = stdout.strip().decode()
-    except TimeoutExpired:
-        process.kill()
-        proc_stdout = ""
-    return proc_stdout
-
-
 def get_versions() -> dict:
     """Import stuff and get versions if module.
 
@@ -182,52 +144,22 @@ def get_versions() -> dict:
         The module names and corresponding versions.
 
     """
+    # Setup dictionary to track versions of modules
     module_versions = {}
     for name, module in sys.modules.copy().items():
         # Bypassing sub-modules of packages and
         # allowing ruamel.yaml
         if "." in name and name != "ruamel.yaml":
             continue
-        if name in ["_curses"]:
+        # Get version or None as string
-            continue
         vstring = str(getattr(module, "__version__", None))
-        module_version = LooseVersion(vstring)
+        # Get module version
-        module_version = getattr(module_version, "vstring", None)
+        module_version = getattr(LooseVersion(vstring), "vstring", None)
-        if module_version is None:
-            module_version = None
-        elif "git" in module_version:
-            git_path = Path(module.__file__).resolve().parent  # type: ignore
-            head = _get_git_head(git_path)
-            module_version += f"-HEAD:{head}"
-
         module_versions[name] = module_version
     return module_versions
 
 
-# def get_ext_versions(tbox_path: Path) -> Dict:
+def _close_handlers(logger: logging.Logger) -> None:  # pragma: no cover
-#     """Get versions of external tools used by junifer.
-
-#     Parameters
-#     ----------
-#     tbox_path : pathlib.Path
-#         The path to external toolboxes.
-
-#     Returns
-#     -------
-#     dict
-#         The dependency information.
-
-#     """
-#     versions = {}
-#     # spm_path = tbox_path / 'spm12'
-#     # if spm_path.exists():
-#     #     head = _get_git_head(spm_path)
-#     #     module_version = 'SPM12-HEAD:{}'.format(head)
-#     #     versions['spm'] = module_version
-#     return versions
-
-
-def _close_handlers(logger: logging.Logger) -> None:
     """Safely close relevant handlers for logger.
 
     Parameters
@@ -243,55 +175,37 @@ def _close_handlers(logger: logging.Logger) -> None:
             logger.removeHandler(handler)
 
 
-def _safe_log(versions: dict, name: str) -> None:
+def log_versions() -> None:
-    """Log with safety.
+    """Log versions of dependencies and junifer."""
-
-    Parameters
-    ----------
-    versions : dict
-        The dictionary with keys as dependency names and values as the
-        versions.
-    name : str
-        The dependency to look up in `versions`.
-
-    """
-    if name in versions:
-        logger.info(f"{name}: {versions[name]}")
-
-
-def log_versions(tbox_path: Optional[Path] = None) -> None:
-    """Log versions of dependencies and junifer.
-
-    If `tbox_path` is specified, can also log versions of external toolboxes.
-
-    Parameters
-    ----------
-    tbox_path : pathlib.Path, optional
-        The path to external toolboxes (default None).
-
-    """
     # Get versions of all found packages
     versions = get_versions()
-
+    # Set packages to log
+    pkgs_to_log = [
+        "click",
+        "numpy",
+        "scipy",
+        "datalad",
+        "pandas",
+        "nibabel",
+        "nilearn",
+        "sqlalchemy",
+        "ruamel.yaml",
+        "h5py",
+        "tqdm",
+        "templateflow",
+        "lapy",
+        "junifer_data",
+        "junifer",
+    ]
+    # Log
     logger.info("===== Lib Versions =====")
-    _safe_log(versions, "numpy")
+    for pkg in pkgs_to_log:
-    _safe_log(versions, "scipy")
+        if pkg in versions:
-    _safe_log(versions, "pandas")
+            logger.info(f"{pkg}: {versions[pkg]}")
-    _safe_log(versions, "nipype")
-    _safe_log(versions, "nitime")
-    _safe_log(versions, "nilearn")
-    _safe_log(versions, "nibabel")
-    _safe_log(versions, "junifer")
     logger.info("========================")
 
-    if tbox_path is not None:
-        # ext_versions = get_ext_versions(tbox_path)
-        # logger.info('spm: {}'.format(ext_versions['spm']))
-        # logger.info('========================')
-        pass
 
-
+def _can_use_color(handler: logging.Handler) -> bool:  # pragma: no cover
-def _can_use_color(handler: logging.Handler) -> bool:
     """Check if color can be used in the logging output.
 
     Parameters
@@ -391,11 +305,7 @@ def configure_logging(
     # Set logging format
     if output_format is None:
         output_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-        # (
+    if _can_use_color(lh):  # pragma: no cover
-        #     "%(asctime)s [%(levelname)s] %(message)s "
-        #     "(%(filename)s:%(lineno)s)"
-        # )
-    if _can_use_color(lh):
         formatter = ColorFormatter(fmt=output_format)
     else:
         formatter = logging.Formatter(fmt=output_format)

junifer/utils/tests/test_logging.py

@@ -68,7 +68,9 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Warn message" in line for line in lines)
         assert any("Error message" in line for line in lines)
 
-    configure_logging(fname=tmp_path / "test2.log", level="INFO")
+    configure_logging(
+        fname=str((tmp_path / "test2.log").resolve()), level="INFO"
+    )
     logger.debug("Debug message")
     logger.info("Info message")
     logger.warning("Warn message")
@@ -81,7 +83,9 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Warn message" in line for line in lines)
         assert any("Error message" in line for line in lines)
 
-    configure_logging(fname=tmp_path / "test3.log", level="WARNING")
+    configure_logging(
+        fname=tmp_path / "test3.log", level="WARNING", level_datalad="WARNING"
+    )
     logger.debug("Debug message")
     logger.info("Info message")
     logger.warning("Warn message")
@@ -94,7 +98,7 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Warn message" in line for line in lines)
         assert any("Error message" in line for line in lines)
 
-    configure_logging(fname=tmp_path / "test4.log", level="ERROR")
+    configure_logging(fname=tmp_path / "test4.log", level=logging.ERROR)
     logger.debug("Debug message")
     logger.info("Info message")
     logger.warning("Warn message")
@@ -107,7 +111,11 @@ def test_log_file(tmp_path: Path) -> None:
         assert any("Error message" in line for line in lines)
 
     with pytest.warns(UserWarning, match="to avoid this message"):
-        configure_logging(fname=tmp_path / "test4.log", level="WARNING")
+        configure_logging(
+            fname=tmp_path / "test4.log",
+            level="WARNING",
+            level_datalad=logging.WARNING,
+        )
         logger.debug("Debug2 message")
         logger.info("Info2 message")
         logger.warning("Warn2 message")

pyproject.toml

@@ -75,7 +75,12 @@ onthefly = [
     "bctpy==0.6.0"
 ]
 neurokit2 = ["neurokit2>=0.1.7"]
-dev = ["tox", "pre-commit"]
+dev = [
+    "tox",
+    "pre-commit",
+    "ruff",
+    "towncrier",
+]
 docs = [
     "seaborn>=0.13.0,<0.14.0",
     "sphinx>=7.3.0,<8.1.0",
@@ -107,16 +112,6 @@ version_scheme = "guess-next-dev"
 local_scheme = "no-local-version"
 write_to = "junifer/_version.py"
 
-[tool.black]
-line-length = 79
-target-version = ["py39", "py310", "py311", "py312", "py313"]
-extend-exclude = """
-(
-  junifer/external/h5io
-  | junifer/external/BrainPrint
-)
-"""
-
 [tool.codespell]
 skip = "*/auto_examples/*,*.html,.git/,*.pyc,*/_build/*,*/h5io/*,*/BrainPrint/*"
 count = ""
@@ -136,6 +131,7 @@ extend-exclude = [
     "examples",
     "tools",
 ]
+target-version = "py39"
 
 [tool.ruff.lint]
 select = [
@@ -275,3 +271,31 @@ showcontent = true
 [tool.towncrier.fragment.change]
 name = "API Changes"
 showcontent = true
+
+[tool.coverage.paths]
+source = [
+    "junifer",
+    "*/site-packages/junifer",
+]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/setup.py",
+    "*/_version.py",
+    "*/tests/*",
+    "*/junifer/configs/*",
+    "*/junifer/external/h5io/*",
+    "*/junifer/external/BrainPrint/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+    # Type checking if statements should not be considered
+    "if TYPE_CHECKING:",
+    # Don't complain if non-runnable code isn't run:
+    "if __name__ == .__main__.:",
+]
+precision = 2

tox.ini

@@ -1,5 +1,13 @@
 [tox]
-envlist = ruff, black, test, coverage, codespell, py3{9,10,11,12,13}
+requires =
+    tox>=4
+env_list =
+    ruff,
+    changelog,
+    test,
+    coverage,
+    codespell,
+    py3{9,10,11,12,13}
 isolated_build = true
 
 [gh-actions]
@@ -22,20 +30,27 @@ commands =
     pytest
 
 [testenv:ruff]
+description = run ruff
 skip_install = true
 deps =
     ruff>=0.1.0
 commands =
+    ruff format {toxinidir}
     ruff check {toxinidir}
 
-[testenv:black]
+[testenv:changelog]
+description = show changelog
 skip_install = true
+# See https://github.com/sphinx-contrib/sphinxcontrib-towncrier/issues/92
+# Pin also present in pyproject.toml
 deps =
-    black
+    towncrier<24.7
+    lazy_loader==0.4
 commands =
-    black --check --diff {toxinidir}/junifer {toxinidir}/setup.py
+    towncrier build --draft
 
 [testenv:test]
+description = run tests
 skip_install = false
 passenv =
     HOME
@@ -45,6 +60,7 @@ commands =
     pytest
 
 [testenv:coverage]
+description = run tests with coverage
 skip_install = false
 deps =
     bctpy==0.6.0
@@ -52,42 +68,13 @@ deps =
     pytest
     pytest-cov
 commands =
-    pytest --cov={envsitepackagesdir}/junifer --cov-report=xml --cov-report=term {envsitepackagesdir}/junifer
+    pytest --cov={envsitepackagesdir}/junifer --cov-report=xml --cov-report=term --cov-config=pyproject.toml {envsitepackagesdir}/junifer
 
 [testenv:codespell]
+description = run codespell
 skip_install = true
 deps =
     codespell
     tomli
 commands =
     codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ {toxinidir}/README.md
-
-################
-# Tool configs #
-################
-
-[coverage:paths]
-source =
-    junifer
-    */site-packages/junifer
-
-[coverage:run]
-branch = true
-omit =
-    */setup.py
-    */_version.py
-    */tests/*
-    */junifer/configs/*
-    */junifer/external/h5io/*
-    */junifer/external/BrainPrint/*
-parallel = false
-
-[coverage:report]
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-    # Type checking if statements should not be considered
-    if TYPE_CHECKING:
-    # Don't complain if non-runnable code isn't run:
-    if __name__ == .__main__.:
-precision = 2