siibra 1.0.1a0__py3-none-any.whl → 1.0.1a1__py3-none-any.whl

siibra/features/connectivity/tracing_connectivity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/dataset/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/dataset/ebrains.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/feature.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -53,7 +53,7 @@ _README_TMPL = """
 Downloaded from siibra toolsuite.
 siibra-python version: {version}
 
-All releated resources (e.g. doi, web resources) are categorized under publications.
+All related resources (e.g. doi, web resources) are categorized under publications.
 
 Name
 ----
@@ -199,9 +199,9 @@ class Feature:
     @property
     def authors(self):
         return [
-            contributer['name']
+            contributor['name']
             for ds in self.datasets
-            for contributer in ds.contributors
+            for contributor in ds.contributors
         ]
 
     @property
@@ -256,7 +256,7 @@ class Feature:
         concept: Union[structure.BrainStructure, space.Space],
     ) -> bool:
         """
-        Match the features anatomical anchor agains the given query concept.
+        Match the features anatomical anchor against the given query concept.
         Record the most recently matched concept for inspection by the caller.
         """
         # TODO: storing the last matched concept. It is not ideal, might cause problems in multithreading
@@ -509,7 +509,7 @@ class Feature:
         This will
         - call Feature.match(concept) for any registered preconfigured features
         - run any registered live queries
-        The preconfigured and live query instances are merged and returend as a list.
+        The preconfigured and live query instances are merged and returned as a list.
 
         If multiple feature types are given, recurse for each of them.
 
@@ -519,7 +519,7 @@ class Feature:
         concept: AtlasConcept
             An anatomical concept, typically a brain region or parcellation.
         feature_type: subclass of Feature, str
-            specififies the type of features ("modality")
+            specifies the type of features ("modality")
         """
         if isinstance(feature_type, list):
             # a list of feature types is given, collect match results on those
@@ -604,7 +604,7 @@ class Feature:
                 if inst.id == feature_id
             ]
             if len(candidates) == 0:
-                raise NotFoundException(f"No feature instance wth {feature_id} found.")
+                raise NotFoundException(f"No feature instance with {feature_id} found.")
             if len(candidates) == 1:
                 return candidates[0]
             else:
@@ -719,7 +719,7 @@ class Compoundable(ABC):
         """
         Compute the merge data and create a merged instance from a set of
         elements of this class. This will be used by CompoundFeature to
-        create the aggegated data and plot it. For example, to compute an
+        create the aggregated data and plot it. For example, to compute an
         average connectivity matrix from a set of subfeatures, we create a
         RegionalConnectivty feature.
         """
@@ -728,7 +728,7 @@ class Compoundable(ABC):
 
 class CompoundFeature(Feature):
     """
-    A compound aggregating mutliple features of the same type, forming its
+    A compound aggregating multiple features of the same type, forming its
     elements. The anatomical anchors and data of the features is merged.
     Features need to subclass "Compoundable" to allow aggregation
     into a compound feature.

siibra/features/image/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/image/image.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -44,7 +44,7 @@ class ImageAnchor(_anchor.AnatomicalAnchor):
         if self._location_cached is None:
             self._location_cached = self.volume.get_boundingbox(
                 clip=False
-            )  # use unclipped to preseve exisiting behaviour
+            )  # use unclipped to preserve existing behaviour
         return self._location_cached
 
     @property

siibra/features/image/sections.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/image/volume_of_interest.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/bigbrain_intensity_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/cell_density_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -60,7 +60,7 @@ class PolyLine:
         return sum(self.lengths)
 
     def sample(self, d: Union[Iterable[float], np.ndarray, float]):
-        # if d is interable, we assume a list of sample positions
+        # if d is iterable, we assume a list of sample positions
         try:
             iter(d)
         except TypeError:

siibra/features/tabular/cortical_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -37,7 +37,7 @@ class CorticalProfile(tabular.Tabular, Compoundable):
     Optionally, the depth coordinates of layer boundaries can be specified.
 
     Most attributes are modelled as properties, so dervide classes are able
-    to implement lazy loading instead of direct initialiation.
+    to implement lazy loading instead of direct initialization.
 
     """
 
@@ -151,7 +151,7 @@ class CorticalProfile(tabular.Tabular, Compoundable):
 
     @property
     def _layers(self):
-        """List of layers assigned to each measurments,
+        """List of layers assigned to each measurements,
         if layer boundaries are available for this features.
         """
         if self.boundaries_mapped:

siibra/features/tabular/gene_expression.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/layerwise_bigbrain_intensities.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/layerwise_cell_density.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/receptor_density_fingerprint.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,8 @@
 from .. import anchor as _anchor
 from . import tabular
 
-from ... import commons, vocabularies
+from ...commons import logger
+from ...vocabularies import RECEPTOR_SYMBOLS
 from ...retrieval import requests
 
 import pandas as pd
@@ -34,7 +35,7 @@ class ReceptorDensityFingerprint(
     DESCRIPTION = (
         "Fingerprint of densities (in fmol/mg protein) of receptors for classical neurotransmitters "
         "obtained by means of quantitative in vitro autoradiography. The fingerprint provides average "
-        "density measurments for different receptors measured in tissue samples from different subjects "
+        "density measurements for different receptors measured in tissue samples from different subjects "
         "together with the corresponding standard deviations. "
     )
 
@@ -75,9 +76,9 @@ class ReceptorDensityFingerprint(
         # Likely ill-formed tsv's
         return [
             "{} ({})".format(
-                vocabularies.RECEPTOR_SYMBOLS[t]['neurotransmitter']['label'],
-                vocabularies.RECEPTOR_SYMBOLS[t]['neurotransmitter']['name'],
-            ) if t in vocabularies.RECEPTOR_SYMBOLS else
+                RECEPTOR_SYMBOLS[t]['neurotransmitter']['label'],
+                RECEPTOR_SYMBOLS[t]['neurotransmitter']['name'],
+            ) if t in RECEPTOR_SYMBOLS else
             f"{t} (undeciphered)"
             for t in self.receptors
         ]
@@ -107,7 +108,7 @@ class ReceptorDensityFingerprint(
             std = [data[_]["density (sd)"] for _ in labels]
         except KeyError as e:
             print(str(e))
-            commons.logger.error("Could not parse fingerprint from this dictionary")
+            logger.error("Could not parse fingerprint from this dictionary")
         return {
             'unit': next(iter(units)),
             'labels': labels,
@@ -124,9 +125,11 @@ class ReceptorDensityFingerprint(
         if backend == "matplotlib":
             try:
                 import matplotlib.pyplot as plt
-            except ImportError:
-                commons.logger.error("matplotlib not available. Plotting of fingerprints disabled.")
-                return None
+            except ImportError as e:
+                logger.error(
+                    "matplotlib not available. Please install matplotlib or use or another backend such as plotly."
+                )
+                raise e
             from collections import deque
 
             # default args

siibra/features/tabular/receptor_density_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/regional_timeseries_activity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -239,7 +239,7 @@ class RegionalTimeseriesActivity(tabular.Tabular, Compoundable):
         backend="plotly", **kwargs
     ):
         """
-        Create a carpet plot ofthe timeseries data per region.
+        Create a carpet plot of the timeseries data per region.
 
         Parameters
         ----------

siibra/features/tabular/tabular.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,7 +19,7 @@ from .. import feature
 
 from .. import anchor as _anchor
 
-from ... import commons
+from ...commons import logger
 
 import pandas as pd
 from textwrap import wrap
@@ -91,9 +91,11 @@ class Tabular(feature.Feature):
         if backend == "matplotlib":
             try:
                 import matplotlib.pyplot as plt
-            except ImportError:
-                commons.logger.error("matplotlib not available. Plotting of fingerprints disabled.")
-                return None
+            except ImportError as e:
+                logger.error(
+                    "matplotlib not available. Please install matplotlib or use or another backend such as plotly."
+                )
+                raise e
             # default kwargs
             if kwargs.get("error_y") is None:
                 kwargs["yerr"] = kwargs.get("yerr", 'std' if 'std' in self.data.columns else None)

siibra/livequeries/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/livequeries/allen.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -66,7 +66,7 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
     - Each sample was subject to multiple (in fact 4) different probes.
     - The probe data structures contain the list of gene expression of a
       particular gene measured in each sample. Therefore the length of the gene
-      expression list in a probe coresponds to the number of samples taken in
+      expression list in a probe corresponds to the number of samples taken in
       the corresponding donor for the given gene.
     """
 
@@ -114,7 +114,7 @@ class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions
         Each sample is linked to a donor, brain structure, and
         ICBM coordinate.
         When querying with a brain structure, the ICBM coordinates
-        will be tested agains the region mask in ICBM space
+        will be tested against the region mask in ICBM space
         to produce a table of outputs.
         """
         LiveQuery.__init__(self, **kwargs)

siibra/livequeries/bigbrain.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,14 +12,14 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Matches BigBrain intesity profiles extracted by Wagstyl et al. to volumes."""
+"""Matches BigBrain intensity profiles extracted by Wagstyl et al. to volumes."""
 
 from . import query
 
 from ..features.tabular import bigbrain_intensity_profile, layerwise_bigbrain_intensities
 from ..features import anchor as _anchor
 from ..commons import logger
-from ..locations import point, pointcloud
+from ..locations import point, pointcloud, location
 from ..core import structure
 from ..retrieval import requests, cache
 from ..retrieval.datasets import GenericDataset
@@ -123,11 +123,16 @@ class BigBrainProfileQuery(query.LiveQuery, args=[], FeatureType=bigbrain_intens
         matched = concept.intersection(mesh_vertices)  # returns a reduced PointCloud with og indices as labels
         if matched is None:
             return []
+        if isinstance(matched, point.Point):
+            matched = pointcloud.from_points([matched])
         assert isinstance(matched, pointcloud.PointCloud)
+        if isinstance(concept, location.Location):
+            mesh_as_list = mesh_vertices.as_list()
+            matched.labels = [mesh_as_list.index(v.coordinate) for v in matched]
         indices = matched.labels
         assert indices is not None
         features = []
-        for i in matched.labels:
+        for i in indices:
             anchor = _anchor.AnatomicalAnchor(
                 location=point.Point(loader._vertices[i], space='bigbrain'),
                 region=str(concept),
@@ -160,12 +165,16 @@ class LayerwiseBigBrainIntensityQuery(query.LiveQuery, args=[], FeatureType=laye
 
         loader = WagstylProfileLoader()
         mesh_vertices = pointcloud.PointCloud(loader._vertices, space='bigbrain')
-        matched = concept.intersection(mesh_vertices)  # returns a reduced PointCloud with og indices as labels
+        matched = concept.intersection(mesh_vertices)  # returns a reduced PointCloud with og indices as labels if the concept is a region
         if matched is None:
             return []
+        if isinstance(matched, point.Point):
+            matched = pointcloud.from_points([matched])
         assert isinstance(matched, pointcloud.PointCloud)
+        if isinstance(concept, location.Location):
+            mesh_as_list = mesh_vertices.as_list()
+            matched.labels = [mesh_as_list.index(v.coordinate) for v in matched]
         indices = matched.labels
-        assert indices is not None
         matched_profiles = loader._profiles[indices, :]
         boundary_depths = loader._boundary_depths[indices, :]
         # compute array of layer labels for all coefficients in profiles_left

siibra/livequeries/ebrains.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/livequeries/query.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -46,4 +46,4 @@ class LiveQuery(ABC):
 
     @abstractmethod
     def query(self, concept: AtlasConcept, **kwargs) -> List[Feature]:
-        raise NotImplementedError(f"Dervied class {self.__class__} needs to implement query()")
+        raise NotImplementedError(f"Derived class {self.__class__} needs to implement query()")

siibra/locations/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,7 +22,7 @@ from .boundingbox import BoundingBox
 
 def reassign_union(loc0: 'Location', loc1: 'Location') -> 'Location':
     """
-    Add two locations of same or diffrent type to find their union as a
+    Add two locations of same or different type to find their union as a
     Location object.
     Note
     ----

siibra/locations/boundingbox.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -148,11 +148,7 @@ class BoundingBox(location.Location):
             points_inside = [p for p in other if self.intersects(p)]
             if len(points_inside) == 0:
                 return None
-            result = pointcloud.PointCloud(
-                points_inside,
-                space=other.space,
-                sigma_mm=[p.sigma for p in points_inside]
-            )
+            result = pointcloud.from_points(points_inside)
             return result[0] if len(result) == 1 else result  # if PointCloud has single point return as a Point
 
         return other.intersection(self)
@@ -213,7 +209,7 @@ class BoundingBox(location.Location):
         X, Y, Z = np.where(mask.get_fdata() > threshold)
         h = np.ones(len(X))
 
-        # array of homogenous physical nonzero voxel coordinates
+        # array of homogeneous physical nonzero voxel coordinates
         coords = np.dot(mask.affine, np.vstack((X, Y, Z, h)))[:3, :].T
         minpoint = [min(self.minpoint[i], self.maxpoint[i]) for i in range(3)]
         maxpoint = [max(self.minpoint[i], self.maxpoint[i]) for i in range(3)]

siibra/locations/location.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/locations/point.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -108,7 +108,7 @@ class Point(location.Location):
 
     @property
     def homogeneous(self):
-        """The homogenous coordinate of this point as a 4-tuple,
+        """The homogeneous coordinate of this point as a 4-tuple,
         obtained by appending '1' to the original 3-tuple."""
         return np.atleast_2d(self.coordinate + (1,))
 
@@ -157,7 +157,7 @@ class Point(location.Location):
         return self.sigma**3 * np.pi * 4. / 3.
 
     def __sub__(self, other):
-        """Substract the coordinates of two points to get
+        """Subtract the coordinates of two points to get
         a new point representing the offset vector. Alternatively,
         subtract an integer from the all coordinates of this point
         to create a new one.

siibra/locations/pointcloud.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -32,7 +32,7 @@ except ImportError:
     _HAS_HDBSCAN = False
     logger.warning(
         f"HDBSCAN is not available with your version {sklearn.__version__} of sckit-learn."
-        "`PointCloud.find_clusters()` will not be avaiable."
+        "`PointCloud.find_clusters()` will not be available."
     )
 
 
@@ -120,18 +120,13 @@ class PointCloud(location.Location):
         if not isinstance(other, (point.Point, PointCloud, _boundingbox.BoundingBox)):
             return other.intersection(self)
 
-        intersections = [(i, p) for i, p in enumerate(self) if p.intersects(other)]
-        if len(intersections) == 0:
+        if isinstance(other, PointCloud):
+            intersecting_points = [p for p in self if p.coordinate in other.coordinates]
+        else:
+            intersecting_points = [p for p in self if p.intersects(other)]
+        if len(intersecting_points) == 0:
             return None
-        ids, points = zip(*intersections)
-        labels = None if self.labels is None else [self.labels[i] for i in ids]
-        sigma = [p.sigma for p in points]
-        intersection = PointCloud(
-            points,
-            space=self.space,
-            sigma_mm=sigma,
-            labels=labels
-        )
+        intersection = from_points(intersecting_points)
         return intersection[0] if len(intersection) == 1 else intersection
 
     @property
@@ -320,7 +315,7 @@ class PointCloud(location.Location):
         if not _HAS_HDBSCAN:
             raise RuntimeError(
                 f"HDBSCAN is not available with your version {sklearn.__version__} "
-                "of sckit-learn. `PointCloud.find_clusters()` will not be avaiable."
+                "of sckit-learn. `PointCloud.find_clusters()` will not be available."
             )
         points = np.array(self.as_list())
         N = points.shape[0]

siibra/retrieval/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/retrieval/cache.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/retrieval/datasets.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -319,12 +319,12 @@ class EbrainsV3Dataset(EbrainsBaseDataset):
     @property
     def contributors(self):
         if self._contributers is None:
-            contributers = {}
+            contributors = {}
             for version_id in self.version_ids:
-                contributers.update(
+                contributors.update(
                     {c['@id']: c for c in EbrainsV3DatasetVersion(version_id).contributors}
                 )
-            self._contributers = list(contributers.values())
+            self._contributers = list(contributors.values())
         return self._contributers
 
     @property

siibra/retrieval/exceptions/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/retrieval/repositories.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -196,7 +196,7 @@ class GithubConnector(RepositoryConnector):
                 if len(matched_reftags) == 1:
                     self._want_commit_cached = matched_reftags[0]["commit"]
                 else:
-                    raise RuntimeError(f"Found {len(matched_reftags)} mathces to {reftag}")
+                    raise RuntimeError(f"Found {len(matched_reftags)} matches to {reftag}")
                 self._tag_checked = True
             except Exception:
                 logger.warning("Could not connect to GitHub repository.", exc_info=1)
@@ -258,7 +258,7 @@ class GitlabConnector(RepositoryConnector):
             n.b. only archive_mode should only be set for trusted domains. Extraction of archive can result in files created outside the path
             see https://docs.python.org/3/library/tarfile.html#tarfile.TarFile.extractall
         """
-        # TODO: the query builder needs to check wether the reftag is a branch, and then not cache.
+        # TODO: the query builder needs to check whether the reftag is a branch, and then not cache.
         assert server.startswith("http")
         RepositoryConnector.__init__(
             self, base_url=f"{server}/api/v4/projects/{project}/repository"
@@ -584,7 +584,7 @@ class EbrainsPublicDatasetConnector(RepositoryConnector):
             Part of dataset title as an alternative dataset specification (will ignore dataset_id then)
         in_progress: bool (default:False)
             If true, will request datasets that are still under curation.
-            Will only work when autenticated with an appropriately privileged
+            Will only work when authenticated with an appropriately privileged
             user account.
         """
         self.dataset_id = dataset_id