[ENH]: Consistency of logging

docs/changes/newsfragments/239.enh

@@ -0,0 +1 @@
+Improve logging consistency of components by `Synchon Mandal`_

junifer/api/functions.py

@@ -10,6 +10,8 @@
 import shutil
 from pathlib import Path
 
+import structlog
+
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber import BaseDataGrabber
 from ..markers import BaseMarker
@@ -27,11 +29,14 @@
     PreprocessorLike,
     StorageLike,
 )
-from ..utils import logger, raise_error, warn_with_log, yaml
+from ..utils import raise_error, warn_with_log, yaml
 
 
 __all__ = ["collect", "list_elements", "queue", "reset", "run"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="api")
+
 
 def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:
     """Get DataGrabber.

junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -9,12 +9,13 @@
 from typing import Any
 
 from ...typing import Elements
-from ...utils import logger, make_executable, raise_error, run_ext_cmd
+from ...utils import make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import (
     EnvKind,
     EnvShell,
     QueueContextAdapter,
     QueueContextEnv,
+    logger,
 )
 
 

junifer/api/queue_context/htcondor_adapter.py

@@ -10,12 +10,13 @@
 from typing import Any
 
 from ...typing import Elements
-from ...utils import logger, make_executable, raise_error, run_ext_cmd
+from ...utils import make_executable, raise_error, run_ext_cmd
 from .queue_context_adapter import (
     EnvKind,
     EnvShell,
     QueueContextAdapter,
     QueueContextEnv,
+    logger,
 )
 
 

junifer/api/queue_context/queue_context_adapter.py

@@ -19,13 +19,17 @@
 from abc import ABC, abstractmethod
 from enum import Enum
 
+import structlog
 from pydantic import BaseModel, ConfigDict
 
 from ...utils import raise_error
 
 
 __all__ = ["EnvKind", "EnvShell", "QueueContextAdapter", "QueueContextEnv"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="api")
+
 
 class EnvKind(str, Enum):
     """Accepted Python environment kind."""

junifer/cli/parser.py

@@ -10,13 +10,17 @@
 from pathlib import Path
 
 import pandas as pd
+import structlog
 
 from ..typing import Elements
-from ..utils import logger, raise_error, warn_with_log, yaml
+from ..utils import raise_error, warn_with_log, yaml
 
 
 __all__ = ["parse_elements", "parse_yaml"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="cli")
+
 
 def parse_yaml(filepath: str | Path) -> dict:  # noqa: C901
     """Parse YAML.

junifer/data/coordinates/_ants_coordinates_warper.py

@@ -9,7 +9,7 @@
 from numpy.typing import ArrayLike
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 __all__ = ["ANTsCoordinatesWarper"]
@@ -46,6 +46,9 @@ def warp(
             The transformed coordinates.
 
         """
+        # Imported here to avoid circular import
+        from ._coordinates import logger
+
         logger.debug("Using ANTs for coordinates transformation")
 
         # Create element-specific tempdir for storing post-warping assets

junifer/data/coordinates/_coordinates.py

@@ -9,10 +9,11 @@
 
 import numpy as np
 import pandas as pd
+import structlog
 from junifer_data import get
 from numpy.typing import ArrayLike
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import JUNIFER_DATA_PARAMS, get_dataset_path, get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
@@ -21,6 +22,9 @@
 
 __all__ = ["CoordinatesRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class CoordinatesRegistry(BasePipelineDataRegistry):
     """Class for coordinates data registry.

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -9,7 +9,7 @@
 from numpy.typing import ArrayLike
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 __all__ = ["FSLCoordinatesWarper"]
@@ -46,6 +46,9 @@ def warp(
             The transformed coordinates.
 
         """
+        # Imported here to avoid circular import
+        from ._coordinates import logger
+
         logger.debug("Using FSL for coordinates transformation")
 
         # Create element-specific tempdir for storing post-warping assets

junifer/data/maps/_ants_maps_warper.py

@@ -9,7 +9,7 @@
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -71,6 +71,9 @@ def warp(
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         # Create element-scoped tempdir so that warped maps is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/maps/_fsl_maps_warper.py

@@ -9,7 +9,7 @@
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -53,6 +53,9 @@ def warp(
             The transformed maps image.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         logger.debug("Using FSL for maps transformation")
 
         # Create element-scoped tempdir so that warped maps is

junifer/data/maps/_maps.py

@@ -9,9 +9,10 @@
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import (
     JUNIFER_DATA_PARAMS,
@@ -29,6 +30,9 @@
 
 __all__ = ["MapsRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class MapsRegistry(BasePipelineDataRegistry):
     """Class for maps data registry.

junifer/data/masks/_ants_mask_warper.py

@@ -10,7 +10,7 @@
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -92,6 +92,9 @@ def warp(
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/masks/_fsl_mask_warper.py

@@ -10,7 +10,7 @@
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -74,6 +74,9 @@ def warp(
             The transformed mask image.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         logger.debug("Using FSL for mask transformation")
 
         # Create element-scoped tempdir so that warped mask is

junifer/data/masks/_masks.py

@@ -15,14 +15,15 @@
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 from nilearn.masking import (
     compute_background_mask,
     compute_epi_mask,
     intersect_masks,
 )
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
 from ..utils import (
@@ -41,6 +42,9 @@
 
 __all__ = ["MaskRegistry", "compute_brain_mask"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 def compute_brain_mask(
     target_data: dict[str, Any],

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -9,7 +9,7 @@
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -71,6 +71,9 @@ def warp(
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._parcellations import logger
+
         # Create element-scoped tempdir so that warped parcellation is
         # available later as nibabel stores file path reference for
         # loading on computation

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -9,7 +9,7 @@
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -53,6 +53,9 @@ def warp(
             The transformed parcellation image.
 
         """
+        # Imported here to avoid circular import
+        from ._parcellations import logger
+
         logger.debug("Using FSL for parcellation transformation")
 
         # Create element-scoped tempdir so that warped parcellation is

junifer/data/parcellations/_parcellations.py

@@ -13,9 +13,10 @@
 import nilearn.image as nimg
 import numpy as np
 import pandas as pd
+import structlog
 from junifer_data import get
 
-from ...utils import logger, raise_error, warn_with_log
+from ...utils import raise_error, warn_with_log
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import (
     JUNIFER_DATA_PARAMS,
@@ -36,6 +37,9 @@
     "merge_parcellations",
 ]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class ParcellationRegistry(BasePipelineDataRegistry):
     """Class for parcellation data registry.
@@ -58,8 +62,12 @@ def __init__(self) -> None:
         # The built-in parcellations are files that are shipped with the
         # junifer-data dataset.
         # Make built-in and external dictionaries for validation later
-        self._builtin = {}
-        self._external = {}
+        self._builtin: dict[
+            str, dict[str, str | int | Path | list[str] | list[int]]
+        ] = {}
+        self._external: dict[
+            str, dict[str, str | int | Path | list[str] | list[int]]
+        ] = {}
 
         # Add SUIT
         self._builtin.update(

junifer/data/template_spaces.py

@@ -8,15 +8,19 @@
 
 import nibabel as nib
 import numpy as np
+import structlog
 from junifer_data import get
 from templateflow import api as tflow
 
-from ..utils import logger, raise_error
+from ..utils import raise_error
 from .utils import JUNIFER_DATA_PARAMS, closest_resolution, get_dataset_path
 
 
 __all__ = ["get_template", "get_xfm"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
     """Fetch warp files to convert from ``src`` to ``dst``.

junifer/data/utils.py

@@ -8,8 +8,9 @@
 from pathlib import Path
 
 import numpy as np
+import structlog
 
-from ..utils import config, logger, raise_error
+from ..utils import config, raise_error
 
 
 __all__ = [
@@ -21,6 +22,8 @@
     "get_native_warper",
 ]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
 
 # junifer-data version constant
 JUNIFER_DATA_VERSION = "7"