junifer 0.0.5.dev110__py3-none-any.whl → 0.0.5.dev145__py3-none-any.whl

junifer/onthefly/read_transform.py

@@ -15,6 +15,9 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["read_transform"]
+
+
 def read_transform(
     storage: Type["BaseFeatureStorage"],
     transform: str,

junifer/pipeline/__init__.py

@@ -7,3 +7,11 @@ from . import registry
 from .pipeline_step_mixin import PipelineStepMixin
 from .update_meta_mixin import UpdateMetaMixin
 from .workdir_manager import WorkDirManager
+
+
+__all__ = [
+    "registry",
+    "PipelineStepMixin",
+    "UpdateMetaMixin",
+    "WorkDirManager",
+]

junifer/pipeline/pipeline_step_mixin.py

@@ -17,6 +17,9 @@ from ..utils import raise_error
 from .utils import check_ext_dependencies
 
 
+__all__ = ["PipelineStepMixin"]
+
+
 class PipelineStepMixin:
     """Mixin class for a pipeline step."""
 

junifer/pipeline/registry.py

@@ -16,6 +16,9 @@ if TYPE_CHECKING:
     from .pipeline_step_mixin import PipelineStepMixin
 
 
+__all__ = ["register", "get_step_names", "get_class", "build"]
+
+
 # Define valid steps for operation
 _VALID_STEPS: List[str] = [
     "datagrabber",

junifer/pipeline/singleton.py

@@ -6,6 +6,9 @@
 from typing import Any, Dict, Type
 
 
+__all__ = ["singleton"]
+
+
 def singleton(cls: Type) -> Type:
     """Make a class singleton.
 

junifer/pipeline/update_meta_mixin.py

@@ -7,6 +7,9 @@
 from typing import Dict
 
 
+__all__ = ["UpdateMetaMixin"]
+
+
 class UpdateMetaMixin:
     """Mixin class for updating meta."""
 

junifer/pipeline/utils.py

@@ -10,6 +10,9 @@ from typing import Any, List, Optional
 from junifer.utils.logging import raise_error, warn_with_log
 
 
+__all__ = ["check_ext_dependencies"]
+
+
 def check_ext_dependencies(
     name: str, optional: bool = False, **kwargs: Any
 ) -> bool:

junifer/pipeline/workdir_manager.py

@@ -13,6 +13,9 @@ from ..utils import logger
 from .singleton import singleton
 
 
+__all__ = ["WorkDirManager"]
+
+
 @singleton
 class WorkDirManager:
     """Class for working directory manager.

junifer/preprocess/__init__.py

@@ -9,3 +9,11 @@ from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
 from .warping import SpaceWarper
 from .smoothing import Smoothing
+
+
+__all__ = [
+    "BasePreprocessor",
+    "fMRIPrepConfoundRemover",
+    "SpaceWarper",
+    "Smoothing",
+]

junifer/preprocess/base.py

@@ -11,6 +11,9 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
 
 
+__all__ = ["BasePreprocessor"]
+
+
 class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for all preprocessors.
 
@@ -136,7 +139,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
             A single input from the Junifer Data object to preprocess.
         extra_input : dict, optional
             The other fields in the Junifer Data object. Useful for accessing
-            other data kind that needs to be used in the computation. For
+            other data type that needs to be used in the computation. For
             example, the confound removers can make use of the
             confounds if available (default None).
 

junifer/preprocess/confounds/__init__.py

@@ -5,3 +5,6 @@
 # License: AGPL
 
 from .fmriprep_confound_remover import fMRIPrepConfoundRemover
+
+
+__all__ = ["fMRIPrepConfoundRemover"]

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -27,6 +27,9 @@ from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 
 
+__all__ = ["fMRIPrepConfoundRemover"]
+
+
 FMRIPREP_BASICS = {
     "motion": [
         "trans_x",

junifer/preprocess/smoothing/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .smoothing import Smoothing
+
+
+__all__ = ["Smoothing"]

junifer/preprocess/warping/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .space_warper import SpaceWarper
+
+
+__all__ = ["SpaceWarper"]

junifer/preprocess/warping/_ants_warper.py

@@ -20,6 +20,9 @@ from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
 
 
+__all__ = ["ANTsWarper"]
+
+
 class ANTsWarper:
     """Class for space warping via ANTs antsApplyTransforms.
 

junifer/preprocess/warping/_fsl_warper.py

@@ -19,6 +19,9 @@ from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
 
 
+__all__ = ["FSLWarper"]
+
+
 class FSLWarper:
     """Class for space warping via FSL FLIRT.
 

junifer/stats.py

@@ -13,6 +13,9 @@ from scipy.stats.mstats import winsorize
 from .utils import logger, raise_error
 
 
+__all__ = ["get_aggfunc_by_name", "count", "winsorized_mean", "select"]
+
+
 def get_aggfunc_by_name(
     name: str, func_params: Optional[Dict[str, Any]] = None
 ) -> Callable:

junifer/storage/__init__.py

@@ -8,3 +8,11 @@ from .base import BaseFeatureStorage
 from .pandas_base import PandasBaseFeatureStorage
 from .sqlite import SQLiteFeatureStorage
 from .hdf5 import HDF5FeatureStorage
+
+
+__all__ = [
+    "BaseFeatureStorage",
+    "PandasBaseFeatureStorage",
+    "SQLiteFeatureStorage",
+    "HDF5FeatureStorage",
+]

junifer/storage/base.py

@@ -15,6 +15,9 @@ from ..utils import raise_error
 from .utils import process_meta
 
 
+__all__ = ["BaseFeatureStorage"]
+
+
 class BaseFeatureStorage(ABC):
     """Abstract base class for feature storage.
 

junifer/storage/hdf5.py

@@ -26,6 +26,9 @@ from .base import BaseFeatureStorage
 from .utils import element_to_prefix, matrix_to_vector, store_matrix_checks
 
 
+__all__ = ["HDF5FeatureStorage"]
+
+
 def _create_chunk(
     chunk_data: List[np.ndarray],
     kind: str,

junifer/storage/pandas_base.py

@@ -15,6 +15,9 @@ from ..utils import raise_error
 from .base import BaseFeatureStorage
 
 
+__all__ = ["PandasBaseFeatureStorage"]
+
+
 class PandasBaseFeatureStorage(BaseFeatureStorage):
     """Abstract base class for feature storage via pandas.
 

junifer/storage/sqlite.py

@@ -25,6 +25,9 @@ if TYPE_CHECKING:
     from sqlalchemy.engine import Engine
 
 
+__all__ = ["SQLiteFeatureStorage"]
+
+
 @register_storage
 class SQLiteFeatureStorage(PandasBaseFeatureStorage):
     """Concrete implementation for feature storage via SQLite.

junifer/storage/utils.py

@@ -14,6 +14,15 @@ import numpy as np
 from ..utils.logging import logger, raise_error
 
 
+__all__ = [
+    "get_dependency_version",
+    "process_meta",
+    "element_to_prefix",
+    "store_matrix_checks",
+    "matrix_to_vector",
+]
+
+
 def get_dependency_version(dependency: str) -> str:
     """Get dependency version.
 

junifer/testing/__init__.py

@@ -6,3 +6,6 @@
 
 from . import datagrabbers
 from .utils import get_testing_data
+
+
+__all__ = ["datagrabbers", "get_testing_data"]

junifer/testing/datagrabbers.py

@@ -14,6 +14,13 @@ from nilearn import datasets, image
 from ..datagrabber.base import BaseDataGrabber
 
 
+__all__ = [
+    "OasisVBMTestingDataGrabber",
+    "SPMAuditoryTestingDataGrabber",
+    "PartlyCloudyTestingDataGrabber",
+]
+
+
 class OasisVBMTestingDataGrabber(BaseDataGrabber):
     """DataGrabber for Oasis VBM testing data.
 

junifer/testing/utils.py

@@ -6,6 +6,9 @@
 from pathlib import Path
 
 
+__all__ = ["get_testing_data"]
+
+
 def get_testing_data(fname: str) -> Path:
     """Get the path to a testing data file.
 

junifer/utils/__init__.py

@@ -7,3 +7,13 @@
 from .fs import make_executable
 from .logging import configure_logging, logger, raise_error, warn_with_log
 from .helpers import run_ext_cmd
+
+
+__all__ = [
+    "make_executable",
+    "configure_logging",
+    "logger",
+    "raise_error",
+    "warn_with_log",
+    "run_ext_cmd",
+]

junifer/utils/fs.py

@@ -8,6 +8,9 @@ import stat
 from pathlib import Path
 
 
+__all__ = ["make_executable"]
+
+
 def make_executable(path: Path) -> None:
     """Make ``path`` executable.
 

junifer/utils/helpers.py

@@ -9,6 +9,9 @@ from typing import List
 from .logging import logger, raise_error
 
 
+__all__ = ["run_ext_cmd"]
+
+
 def run_ext_cmd(name: str, cmd: List[str]) -> None:
     """Run external command via subprocess.
 

junifer/utils/logging.py

@@ -19,6 +19,16 @@ from warnings import warn
 import datalad
 
 
+__all__ = [
+    "WrapStdOut",
+    "get_versions",
+    "log_versions",
+    "configure_logging",
+    "raise_error",
+    "warn_with_log",
+]
+
+
 logger = logging.getLogger("JUNIFER")
 
 # Set up datalad logger level to warning by default

{junifer-0.0.5.dev110.dist-info → junifer-0.0.5.dev145.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev110
+Version: 0.0.5.dev145
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -41,6 +41,7 @@ Requires-Dist: h5py >=3.10
 Requires-Dist: httpx[http2] ==0.26.0
 Requires-Dist: tqdm ==4.66.1
 Requires-Dist: templateflow >=23.0.0
+Requires-Dist: lapy <2.0.0,>=1.0.0
 Requires-Dist: importlib-metadata ; python_version < "3.10"
 Requires-Dist: looseversion ==1.3.0 ; python_version >= "3.12"
 Provides-Extra: all