junifer 0.0.8.dev295__tar.gz → 0.0.8.dev298__tar.gz

{junifer-0.0.8.dev295/junifer.egg-info → junifer-0.0.8.dev298}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev295
+Version: 0.0.8.dev298
 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>

junifer-0.0.8.dev298/docs/changes/newsfragments/523.misc

@@ -0,0 +1 @@
+Use :class:`.HDF5FeatureStorage` instead of :class:`.SQLiteFeatureStorage` in the tests and documentation, as the latter is only kept for compatibility, and fix the component registry test leaving components de-registered by `Fede Raimondo`_

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/docs/understanding/storage.rst

@@ -21,7 +21,7 @@ The :ref:`Markers <marker>` are responsible for mapping the input
 :ref:`data type <data_types>` to its output :ref:`storage type <storage_types>`
 as shown :ref:`here <extending_markers_input_output>`.
 The storage object in turn declares and provides implementation for
-specific *storage type*. For example, :class:`.SQLiteFeatureStorage` supports
+specific *storage type*. For example, :class:`.HDF5FeatureStorage` supports
 saving ``matrix``, ``vector`` and ``timeseries`` via ``store_matrix``,
 ``store_vector`` and ``store_timeseries`` methods respectively.
 
@@ -88,3 +88,10 @@ Storage Interfaces
      - ``.hdf5``
      - HDF5
      - ``matrix``, ``vector``, ``timeseries``, ``timeseries_2d``, ``scalar_table``
+
+.. note::
+
+   :class:`.HDF5FeatureStorage` is the recommended storage.
+   :class:`.SQLiteFeatureStorage` is only kept for compatibility with features
+   stored in previous versions of ``junifer`` and should not be used for new
+   analyses.

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/docs/using/running.rst

@@ -130,8 +130,8 @@ First we load the storage like so:
 
     from junifer.storage import HDF5FeatureStorage
 
-    # You need to import and use SQLiteFeatureStorage if you chose that
-    # for storage while extracting features
+    # If the features were stored with the legacy SQLiteFeatureStorage,
+    # import and use that class instead
     storage = HDF5FeatureStorage("<path/to/your/collected/file>")
 
 The best way to start analysing would be to list all the extracted features

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev295'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev295')
+__version__ = version = '0.0.8.dev298'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev298')
 
-__commit_id__ = commit_id = 'g4eb842a09'
+__commit_id__ = commit_id = 'g30ddf7410'

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/api/tests/test_functions.py

@@ -92,7 +92,7 @@ def markers() -> list[dict[str, list[str] | str]]:
 def storage() -> dict[str, str]:
     """Return a storage as a dictionary."""
     return {
-        "kind": "SQLiteFeatureStorage",
+        "kind": "HDF5FeatureStorage",
     }
 
 
@@ -158,7 +158,7 @@ def test_run_single_element(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Run operations
     with expect:
         run(
@@ -169,7 +169,7 @@ def test_run_single_element(
             elements=element,
         )
         # Check files
-        files = list(tmp_path.glob("*.sqlite"))
+        files = list(tmp_path.glob("*.hdf5"))
         assert len(files) == 1
 
 
@@ -191,7 +191,7 @@ def test_run_single_element_with_preprocessing(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     # Run operations
     run(
         workdir={"path": tmp_path, "cleanup": False},
@@ -209,7 +209,7 @@ def test_run_single_element_with_preprocessing(
         elements=["sub-01"],
     )
     # Check files
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == 1
 
 
@@ -250,7 +250,7 @@ def test_run_multi_element_multi_output(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     storage["single_output"] = False  # type: ignore
     # Run operations
     with expect:
@@ -262,7 +262,7 @@ def test_run_multi_element_multi_output(
             elements=element,
         )
         # Check files
-        files = list(tmp_path.glob("*.sqlite"))
+        files = list(tmp_path.glob("*.hdf5"))
         assert len(files) == 2
 
 
@@ -287,7 +287,7 @@ def test_run_multi_element_single_output(
 
     """
     # Set storage
-    storage["uri"] = str((tmp_path / "out.sqlite").resolve())
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
     storage["single_output"] = True  # type: ignore
     # Run operations
     run(
@@ -298,9 +298,9 @@ def test_run_multi_element_single_output(
         elements=["sub-01", "sub-03"],
     )
     # Check files
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == 1
-    assert files[0].name == "out.sqlite"
+    assert files[0].name == "out.hdf5"
 
 
 def test_run_and_collect(
@@ -324,7 +324,7 @@ def test_run_and_collect(
 
     """
     # Set storage
-    uri = tmp_path / "out.sqlite"
+    uri = tmp_path / "out.hdf5"
     storage["uri"] = str(uri.resolve())
     storage["single_output"] = False  # type: ignore
     # Run operations
@@ -343,9 +343,9 @@ def test_run_and_collect(
     )
     elements = dg.get_elements()  # type: ignore
     # This should create one file per element
-    files = list(tmp_path.glob("*.sqlite"))
+    files = list(tmp_path.glob("*.hdf5"))
     assert len(files) == len(elements)
-    # But the test.sqlite file should not exist
+    # But the test.hdf5 file should not exist
     assert not uri.exists()
     # Collect in storage
     collect(storage)
@@ -660,7 +660,7 @@ def test_reset_run(
 
     """
     # Create storage
-    storage["uri"] = tmp_path / "test_reset_run.sqlite"  # type: ignore
+    storage["uri"] = tmp_path / "test_reset_run.hdf5"  # type: ignore
     # Run operation to generate files
     run(
         workdir=tmp_path,
@@ -711,7 +711,7 @@ def test_reset_queue(
     with monkeypatch.context() as m:
         m.chdir(tmp_path)
         # Create storage
-        storage["uri"] = "test_reset_queue.sqlite"
+        storage["uri"] = "test_reset_queue.hdf5"
         # Set job name
         if job_name is None:
             job_name = "junifer_job"

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/cli/tests/data/gmd_mean.yaml

@@ -10,5 +10,5 @@ markers:
     parcellation: TianxS2x3TxMNInonlinear2009cAsym
     method: mean
 storage:
-  kind: SQLiteFeatureStorage
-  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite
+  kind: HDF5FeatureStorage
+  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.hdf5

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/cli/tests/data/gmd_mean_htcondor.yaml

@@ -9,8 +9,8 @@ markers:
     parcellation: TianxS2x3TxMNInonlinear2009cAsym
     method: mean
 storage:
-  kind: SQLiteFeatureStorage
-  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite
+  kind: HDF5FeatureStorage
+  uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.hdf5
 queue:
   jobname: TestHTCondorQueue
   kind: HTCondor

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/cli/tests/test_cli.py

@@ -222,7 +222,7 @@ def test_queue(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
         # Working directory
         contents["workdir"] = str(tmp_path.resolve())
         # Storage
-        contents["storage"]["uri"] = str((tmp_path / "out.sqlite").resolve())
+        contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
         # Write new test config
         outfile = tmp_path / "in.yaml"
         yaml.dump(contents, stream=outfile)
@@ -274,7 +274,7 @@ def test_reset(
         # Working directory
         contents["workdir"] = str(tmp_path.resolve())
         # Storage
-        contents["storage"]["uri"] = str((tmp_path / "out.sqlite").resolve())
+        contents["storage"]["uri"] = str((tmp_path / "out.hdf5").resolve())
         # Write new test config
         outfile = tmp_path / "in.yaml"
         yaml.dump(contents, stream=outfile)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/base.py

@@ -214,7 +214,7 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
         output : dict
             The computed result as a dictionary to store.
         storage : storage-like
-            The storage class, for example, SQLiteFeatureStorage.
+            The storage class, for example, HDF5FeatureStorage.
 
         """
         s_type = self.storage_type(data_type, feature)
@@ -233,7 +233,7 @@ class BaseMarker(BaseModel, ABC, PipelineStepMixin, UpdateMetaMixin):
         input : dict
             The Junifer Data object.
         storage : storage-like, optional
-            The storage class, for example, SQLiteFeatureStorage.
+            The storage class, for example, HDF5FeatureStorage.
 
         Returns
         -------

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import HurstExponent
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = HurstExponent(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_hurst_exponent.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_hurst_exponent.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import MultiscaleEntropyAUC
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,8 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = MultiscaleEntropyAUC(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_multiscale_entropy_auc.sqlite"
+    storage = HDF5FeatureStorage(
+        uri=tmp_path / "test_multiscale_entropy_auc.hdf5"
     )
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_perm_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import PermEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = PermEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_perm_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_perm_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_range_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import RangeEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = RangeEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_range_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_range_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import RangeEntropyAUC
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = RangeEntropyAUC(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_range_entropy_auc.sqlite"
-    )
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_range_entropy_auc.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_sample_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import SampleEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,6 +83,6 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = SampleEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(uri=tmp_path / "test_sample_entropy.sqlite")
+    storage = HDF5FeatureStorage(uri=tmp_path / "test_sample_entropy.hdf5")
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -15,7 +15,7 @@ pytest.importorskip("neurokit2")
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.complexity import WeightedPermEntropy
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
 )
@@ -83,8 +83,8 @@ def test_store(element_data: dict, tmp_path: Path) -> None:
     # Initialize the marker
     marker = WeightedPermEntropy(parcellation=PARCELLATION)
     # Create storage
-    storage = SQLiteFeatureStorage(
-        uri=tmp_path / "test_weighted_perm_entropy.sqlite"
+    storage = HDF5FeatureStorage(
+        uri=tmp_path / "test_weighted_perm_entropy.hdf5"
     )
     # Compute the marker and store
     marker.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/falff/tests/test_falff_parcels.py

@@ -15,7 +15,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ALFFImpl, ALFFParcels
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -90,9 +90,7 @@ def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "falff_parcels.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_parcels.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/falff/tests/test_falff_spheres.py

@@ -15,7 +15,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ALFFImpl, ALFFSpheres
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -93,9 +93,7 @@ def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "falff_spheres.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "falff_spheres.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -13,7 +13,7 @@ from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import CrossParcellationFC
 from junifer.pipeline import WorkDirManager
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -85,9 +85,8 @@ def test_store(tmp_path: Path) -> None:
             parcellation_two=parcellation_two,
             corr_method="spearman",
         )
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_crossparcellation.sqlite",
-            upsert=Upsert.Ignore,
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_crossparcellation.hdf5",
         )
         # Fit transform marker on data with storage
         crossparcellation.fit_transform(input=element_data, storage=storage)

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -11,7 +11,7 @@ import pytest
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCParcels
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -67,8 +67,8 @@ def test_EdgeCentricFCParcels(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_parcels.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -11,7 +11,7 @@ import pytest
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCSpheres
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -69,8 +69,8 @@ def test_EdgeCentricFCSpheres(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_spheres.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -20,7 +20,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import (
     FunctionalConnectivityParcels,
 )
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -105,8 +105,8 @@ def test_FunctionalConnectivityParcels(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_parcels.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -21,7 +21,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivitySpheres,
 )
-from junifer.storage import SQLiteFeatureStorage, Upsert
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -106,8 +106,8 @@ def test_FunctionalConnectivitySpheres(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_spheres.sqlite", upsert=Upsert.Ignore
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/reho/tests/test_reho_parcels.py

@@ -14,7 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ReHoImpl, ReHoParcels
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import (
     ADHDTestingDataGrabber,
     PartlyCloudyTestingDataGrabber,
@@ -74,9 +74,7 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "reho_parcels.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "reho_parcels.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/reho/tests/test_reho_spheres.py

@@ -14,7 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.markers import ReHoImpl, ReHoSpheres
 from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
@@ -72,9 +72,7 @@ def test_ReHoSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
             # Reset log capture
             caplog.clear()
             # Initialize storage
-            storage = SQLiteFeatureStorage(
-                uri=tmp_path / "reho_spheres.sqlite"
-            )
+            storage = HDF5FeatureStorage(uri=tmp_path / "reho_spheres.hdf5")
             # Fit transform marker on data with storage
             marker.fit_transform(
                 input=element_data,

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/tests/test_ets_rss.py

@@ -14,7 +14,7 @@ from nilearn.maskers import NiftiLabelsMasker
 from junifer.data import ParcellationRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.ets_rss import RSSETSMarker
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
@@ -69,7 +69,7 @@ def test_store(tmp_path: Path) -> None:
         # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         # Create storage
-        storage = SQLiteFeatureStorage(uri=tmp_path / "test_rss_ets.sqlite")
+        storage = HDF5FeatureStorage(uri=tmp_path / "test_rss_ets.hdf5")
         # Compute the RSSETSMarker and store
         _ = RSSETSMarker(parcellation=PARCELLATION).fit_transform(
             input=element_data, storage=storage

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/tests/test_maps_aggregation.py

@@ -183,7 +183,7 @@ def test_MapsAggregation_storage(tmp_path: Path) -> None:
         element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
         storage = HDF5FeatureStorage(
-            uri=tmp_path / "test_maps_storage_4D.sqlite"
+            uri=tmp_path / "test_maps_storage_4D.hdf5"
         )
         marker = MapsAggregation(
             maps="Smith_rsn_10",

{junifer-0.0.8.dev295 → junifer-0.0.8.dev298}/junifer/markers/tests/test_parcel_aggregation.py

@@ -20,7 +20,7 @@ from junifer.data import MaskRegistry, ParcellationRegistry
 from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.parcel_aggregation import ParcelAggregation
-from junifer.storage import SQLiteFeatureStorage, StorageType, Upsert
+from junifer.storage import HDF5FeatureStorage, StorageType
 from junifer.testing.datagrabbers import (
     PartlyCloudyTestingDataGrabber,
     UCLACNPVBMTestingDataGrabber,
@@ -275,9 +275,8 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
     # Store 3D
     with PartlyCloudyTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_parcel_storage_3D.sqlite",
-            upsert=Upsert.Ignore,
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_parcel_storage_3D.hdf5",
         )
         marker = ParcelAggregation(
             parcellation="TianxS1x3TxMNInonlinear2009cAsym",
@@ -297,9 +296,8 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
     # Store 4D
     with PartlyCloudyTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_parcel_storage_4D.sqlite",
-            upsert=Upsert.Ignore,
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_parcel_storage_4D.hdf5",
         )
         marker = ParcelAggregation(
             parcellation="TianxS1x3TxMNInonlinear2009cAsym",