junifer 0.0.6.dev150__py3-none-any.whl → 0.0.6.dev175__py3-none-any.whl

junifer/pipeline/tests/test_pipeline_component_registry.py

@@ -0,0 +1,201 @@
+"""Provide tests for PipelineComponentRegistry."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import logging
+from abc import ABC
+from typing import Type
+
+import pytest
+
+from junifer.datagrabber.pattern import PatternDataGrabber
+from junifer.pipeline.pipeline_component_registry import (
+    PipelineComponentRegistry,
+)
+from junifer.storage import SQLiteFeatureStorage
+
+
+def test_pipeline_component_registry_singleton() -> None:
+    """Test that PipelineComponentRegistry is a singleton."""
+    registry_1 = PipelineComponentRegistry()
+    registry_2 = PipelineComponentRegistry()
+    assert id(registry_1) == id(registry_2)
+
+
+def test_pipeline_component_registry_register_invalid_step():
+    """Test invalid step name during component registration."""
+    with pytest.raises(ValueError, match="Invalid step:"):
+        PipelineComponentRegistry().register(step="foo", klass=str)
+
+
+def test_pipeline_component_registry_steps():
+    """Test steps for PipelineComponentRegistry."""
+    assert set(PipelineComponentRegistry().steps) == {
+        "datagrabber",
+        "datareader",
+        "preprocessing",
+        "marker",
+        "storage",
+    }
+
+
+def test_pipeline_component_registry_components():
+    """Test components for PipelineComponentRegistry."""
+    assert set(PipelineComponentRegistry().steps) == {
+        "datagrabber",
+        "datareader",
+        "preprocessing",
+        "marker",
+        "storage",
+    }
+
+
+@pytest.mark.parametrize(
+    "step, klass",
+    [
+        ("datagrabber", PatternDataGrabber),
+        ("storage", SQLiteFeatureStorage),
+    ],
+)
+def test_pipeline_component_registry_register(
+    caplog: pytest.LogCaptureFixture, step: str, klass: Type
+) -> None:
+    """Test register for PipelineComponentRegistry.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    step : str
+        The parametrized name of the step.
+    klass : str
+        The parametrized name of the class.
+
+    """
+    with caplog.at_level(logging.INFO):
+        # Register
+        PipelineComponentRegistry().register(step=step, klass=klass)
+        # Check logging message
+        assert "Registering" in caplog.text
+
+
+@pytest.mark.parametrize(
+    "step, klass",
+    [
+        ("datagrabber", PatternDataGrabber),
+        ("storage", SQLiteFeatureStorage),
+    ],
+)
+def test_pipeline_component_registry_deregister(
+    caplog: pytest.LogCaptureFixture, step: str, klass: Type
+) -> None:
+    """Test de-register for PipelineComponentRegistry.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    step : str
+        The parametrized name of the step.
+    klass : str
+        The parametrized name of the class.
+
+    """
+    with caplog.at_level(logging.INFO):
+        # Register
+        PipelineComponentRegistry().deregister(step=step, klass=klass)
+        # Check logging message
+        assert "De-registering" in caplog.text
+
+
+def test_pipeline_component_registry_step_components() -> None:
+    """Test step components for PipelineComponentRegistry."""
+    # Check absent name
+    assert "fizz" not in PipelineComponentRegistry().step_components(
+        step="datagrabber"
+    )
+
+    # Create new class
+    class fizz(str):
+        pass
+
+    # Register datagrabber
+    PipelineComponentRegistry().register(step="datagrabber", klass=fizz)
+    # Check registered component
+    assert "fizz" in PipelineComponentRegistry().step_components(
+        step="datagrabber"
+    )
+
+
+def test_pipeline_component_registry_get_class_invalid_name() -> None:
+    """Test get class invalid name for PipelineComponentRegistry."""
+    with pytest.raises(ValueError, match="Invalid name:"):
+        PipelineComponentRegistry().get_class(step="datagrabber", name="foo")
+
+
+def test_pipeline_component_registry_get_class():
+    """Test get class for PipelineComponentRegistry."""
+
+    # Create new class
+    class bar(str):
+        pass
+
+    # Register datagrabber
+    PipelineComponentRegistry().register(step="datagrabber", klass=bar)
+    # Get class
+    obj = PipelineComponentRegistry().get_class(step="datagrabber", name="bar")
+    assert isinstance(obj, type(bar))
+
+
+def test_pipeline_component_registry_build():
+    """Test component instance building for PipelineComponentRegistry."""
+    import numpy as np
+
+    # Define abstract base class
+    class SuperClass(ABC):
+        pass
+
+    # Define concrete class
+    class ConcreteClass(SuperClass):
+        def __init__(self, value=1):
+            self.value = value
+
+    # Register
+    PipelineComponentRegistry().register(
+        step="datagrabber", klass=ConcreteClass
+    )
+
+    # Build
+    obj = PipelineComponentRegistry().build_component_instance(
+        step="datagrabber", name="ConcreteClass", baseclass=SuperClass
+    )
+    assert isinstance(obj, ConcreteClass)
+    assert obj.value == 1
+
+    # Build
+    obj = PipelineComponentRegistry().build_component_instance(
+        step="datagrabber",
+        name="ConcreteClass",
+        baseclass=SuperClass,
+        init_params={"value": 2},
+    )
+    assert isinstance(obj, ConcreteClass)
+    assert obj.value == 2
+
+    # Check error
+    with pytest.raises(ValueError, match="Must inherit"):
+        PipelineComponentRegistry().build_component_instance(
+            step="datagrabber", name="ConcreteClass", baseclass=np.ndarray
+        )
+
+    # Check error
+    with pytest.raises(RuntimeError, match="Failed to create"):
+        PipelineComponentRegistry().build_component_instance(
+            step="datagrabber",
+            name="ConcreteClass",
+            baseclass=SuperClass,
+            init_params={"wrong": 2},
+        )

junifer/testing/__init__.pyi

@@ -1,4 +1,4 @@
-__all__ = ["datagrabbers", "get_testing_data"]
+__all__ = ["datagrabbers", "registry", "get_testing_data"]
 
-from . import datagrabbers
+from . import datagrabbers, registry
 from .utils import get_testing_data

junifer/testing/registry.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from ..pipeline.registry import register
+from ..pipeline import PipelineComponentRegistry
 from .datagrabbers import (
     OasisVBMTestingDataGrabber,
     PartlyCloudyTestingDataGrabber,
@@ -13,20 +13,17 @@ from .datagrabbers import (
 
 
 # Register testing DataGrabbers
-register(
+PipelineComponentRegistry().register(
     step="datagrabber",
-    name="OasisVBMTestingDataGrabber",
     klass=OasisVBMTestingDataGrabber,
 )
 
-register(
+PipelineComponentRegistry().register(
     step="datagrabber",
-    name="SPMAuditoryTestingDataGrabber",
     klass=SPMAuditoryTestingDataGrabber,
 )
 
-register(
+PipelineComponentRegistry().register(
     step="datagrabber",
-    name="PartlyCloudyTestingDataGrabber",
     klass=PartlyCloudyTestingDataGrabber,
 )

junifer/testing/tests/test_testing_registry.py

@@ -1,24 +1,16 @@
 """Provide tests for testing registry."""
 
-import importlib
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
 
-from junifer.pipeline.registry import get_step_names
+from junifer.pipeline import PipelineComponentRegistry
 
 
 def test_testing_registry() -> None:
     """Test testing registry."""
-    import junifer
-
-    importlib.reload(junifer.pipeline.registry)
-    importlib.reload(junifer)
-
-    assert "OasisVBMTestingDataGrabber" not in get_step_names("datagrabber")
-    assert "SPMAuditoryTestingDataGrabber" not in get_step_names("datagrabber")
-    assert "PartlyCloudyTestingDataGrabber" not in get_step_names(
-        "datagrabber"
-    )
-    importlib.reload(junifer.testing.registry)  # type: ignore
-
-    assert "OasisVBMTestingDataGrabber" in get_step_names("datagrabber")
-    assert "SPMAuditoryTestingDataGrabber" in get_step_names("datagrabber")
-    assert "PartlyCloudyTestingDataGrabber" in get_step_names("datagrabber")
+    assert {
+        "OasisVBMTestingDataGrabber",
+        "SPMAuditoryTestingDataGrabber",
+        "PartlyCloudyTestingDataGrabber",
+    }.issubset(set(PipelineComponentRegistry().step_components("datagrabber")))

{junifer-0.0.6.dev150.dist-info → junifer-0.0.6.dev175.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev150
+Version: 0.0.6.dev175
 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-0.0.6.dev150.dist-info → junifer-0.0.6.dev175.dist-info}/RECORD

@@ -1,12 +1,12 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
-junifer/__init__.pyi,sha256=A6Janz0-4ad7zQiLsIo-jnUkpHJjzGTt_KcVsJJLSDM,454
-junifer/_version.py,sha256=2ukRDV2MPgCUZT1-vsyLzMxJAWe77kAsw8oXneXFd_c,428
+junifer/__init__.pyi,sha256=uPLuY27S7AY4kFzJX0ncCpzHnWJdztveMJpY3Di-wwQ,482
+junifer/_version.py,sha256=kxb4jDdB46TYAsROV8U-peWvw8kJsVsZHpoSPS_JLT0,428
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
 junifer/api/__init__.py,sha256=aAXW_KAEGQ8aAP5Eni2G1R4MWBF7UgjKOgM6akLuJco,252
 junifer/api/__init__.pyi,sha256=UJu55ApMFd43N0xlQyNKrYpCdzqhAxA3Jjaj0ETwCXU,169
-junifer/api/decorators.py,sha256=SkQjDYcB_cwG7AS5Q_BU1-T3b38T5RHzbW3aQHP-NzM,2723
-junifer/api/functions.py,sha256=XCw5e4FKG72NumQJyFK1R4yAdOmEOO7jTjDR0dNNi7E,13056
+junifer/api/decorators.py,sha256=nzricZsr0xawk3WDUCyKLWC6WcKN_T0SYIOkGVeoZs8,2726
+junifer/api/functions.py,sha256=Q3X5d_sB5SKcPfNLOi49GnXdln_FUqLpo1TbUK-2j1M,12792
 junifer/api/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/api/queue_context/__init__.py,sha256=glr8x4aMm4EvVrHywDIlugdNlwD1RzqV2FTDNPqYQZ4,204
 junifer/api/queue_context/__init__.pyi,sha256=LoDQFGZ9wCDmgx5a1_nhKo4zOSvqViXZ8V882DksF7U,246
@@ -39,7 +39,7 @@ junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
 junifer/api/res/fsl/img2imgcoord,sha256=Zmaw3oJYrEltcXiPyEubXry9ppAq3SND52tdDWGgeZk,49
 junifer/api/res/fsl/run_fsl_docker.sh,sha256=pq-fcNdLuvHzVIQePN4GebZGlcE2UF-xj5rBIqAMz4g,1122
 junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
-junifer/api/tests/test_functions.py,sha256=JjtdB_dFnikGdgkhtvzoJsV_jbW0X1cNRqjFk2jJmLI,17747
+junifer/api/tests/test_functions.py,sha256=1l91zo7HUAyI5Uj_Brn8P-FHCSDdBkhs3rHIs56uMbI,17805
 junifer/cli/__init__.py,sha256=DS3kZKHeVDxt6d1MLBerZ2fcAwrEBHee5JOBhOLajUI,197
 junifer/cli/__init__.pyi,sha256=PiV4znUnzSeuSSJGz-RT8N21PiMqoSMwYcypi7nt2Js,40
 junifer/cli/cli.py,sha256=LoIWiAU6e5UtcP2Hibx-PDo2QcDqEbrlvzTTSI8rPUQ,13202
@@ -119,7 +119,7 @@ junifer/datagrabber/aomic/__init__.py,sha256=ATxzXq9NBPmWowTMuL77zqrmIbbnk0Wd1iX
 junifer/datagrabber/aomic/__init__.pyi,sha256=Rp6C075fZDdKY8VIq508_g4NhVj8bWzR6zb9yln761Q,189
 junifer/datagrabber/aomic/id1000.py,sha256=wJpZiSZrsfil5w-506bOtKMWm3FllnbB8-cMvGDPiLM,7219
 junifer/datagrabber/aomic/piop1.py,sha256=AcjIueSUmhepuIfmbMEpocV7grUbJ2xKXG94O1dq2FA,9637
-junifer/datagrabber/aomic/piop2.py,sha256=cAlHfrFzFMnX2kFSaTXpRH6kgPlcpFV0R1EDi3rXqNs,9297
+junifer/datagrabber/aomic/piop2.py,sha256=-3M7miEtubF8Dl66OBtaPOlNiQZiVkvTOlgsEExP-ic,9298
 junifer/datagrabber/aomic/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/datagrabber/aomic/tests/test_id1000.py,sha256=AWacDroSxvRjzozFjyRlDpiJpPflYRfhDm_RANrYAKM,3283
 junifer/datagrabber/aomic/tests/test_piop1.py,sha256=J9ei2HLzdJPciysWjRo33cbZsqPF1OEDySmQWWNvYuM,4820
@@ -246,18 +246,18 @@ junifer/onthefly/_brainprint.py,sha256=-q5j5xOkuZD_f-pjWi-b8VRqM9ZXDk1TnccuQDfLw
 junifer/onthefly/read_transform.py,sha256=kZ-N_fKe9glaBTjhj_HXrdTtWXGI-fMoBpsawcOgsTw,4340
 junifer/onthefly/tests/test_read_transform.py,sha256=D2C3IpXQHdsJSF07v8rEwGntLGXjZOserlRhebJUAVM,4719
 junifer/pipeline/__init__.py,sha256=rxKQGRwc6_sts1KhVIcVVpuXeiFABf11mQQ2h5jgA3U,194
-junifer/pipeline/__init__.pyi,sha256=Er7IidlO8-sJQr2iTs8cDNCrd_sl2P4Q_bmaAJSdTcQ,338
+junifer/pipeline/__init__.pyi,sha256=hhcvNcABhtLaUQiZdTjo5sMWC3rtDkwVshL0sxD5JAE,399
 junifer/pipeline/marker_collection.py,sha256=1xcJqeOZ_IerB7PAMN1itWBv8UR6lUW9xXRoIu4qLXU,5557
+junifer/pipeline/pipeline_component_registry.py,sha256=fyGIEv30w01IhLBvKDmnxWtAi-Z9pRq-T1hpamDceyY,9481
 junifer/pipeline/pipeline_step_mixin.py,sha256=wakimkG8GC0PWkFHMHIfgzM2yak41xLrzbVRH0oe8D4,7613
 junifer/pipeline/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/pipeline/registry.py,sha256=BiUG2yKxbcqN9rrU7ATEG4U9QNFWuZnvbHgCP00h6l4,6748
 junifer/pipeline/singleton.py,sha256=c5U8Xn10MQqaXjlLzxLbw3AmSYW6aTw_iSL0rDkbuMU,1011
 junifer/pipeline/update_meta_mixin.py,sha256=A_gYCPqdPlM0Xpum9TjJowb41O7ntxQg6y4YOgYeyy4,1564
 junifer/pipeline/utils.py,sha256=CAp0P7rZST7bsJ9lSlkvZgIJebHW2cIm8VXTuu1A6tE,10291
 junifer/pipeline/workdir_manager.py,sha256=8vBKdb7FtQaGV66Ngu_ucJJPrh2xoxf_1jMeNpJKT2Y,8050
 junifer/pipeline/tests/test_marker_collection.py,sha256=edBHfmwMTXG_q0ZagApbAbkFNoegi3hVEQiNcBtZOKc,6959
+junifer/pipeline/tests/test_pipeline_component_registry.py,sha256=ww_akEhtvE1_fsWbX5Yd5w_G2Ki6w_5MInfihwwRYFk,5800
 junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=_ykZzyNzREXy-r_yv1gY_jquLZzVBl8qwYrVORCKY_k,7807
-junifer/pipeline/tests/test_registry.py,sha256=APC8PNmA3zJnMjLz90rZw_wK0hoag6St8AmQY6MUEqA,4121
 junifer/pipeline/tests/test_update_meta_mixin.py,sha256=UeWwpUi-Q5WVd36Fgfn_utXplSVXMSjLcdO2mR2xLTk,1355
 junifer/pipeline/tests/test_workdir_manager.py,sha256=E1WY4C-GDsx2c49sePqr1WR_Y3nZ1kiRn4Veu506uTs,2801
 junifer/preprocess/__init__.py,sha256=91D43p254il88g-7sSN64M7HsCvwytYoiTS_GLEr37Y,342
@@ -299,16 +299,16 @@ junifer/storage/tests/test_sqlite.py,sha256=JPfE6r34o86XkKaB6yjMVmO_2vUV40DjsaHI
 junifer/storage/tests/test_storage_base.py,sha256=YzgfspuggzXejyPIoRCPST3ZzH9Pi7dgl0IHN7kynXM,3071
 junifer/storage/tests/test_utils.py,sha256=vRGhbeOsSn2Izhjh5AaaJkp6X2EoIQVH3a-9COFVnzg,11854
 junifer/testing/__init__.py,sha256=gqfrX2c7I31VYBmH9hCUERO-61NwubT1cvy1bKM0NqU,249
-junifer/testing/__init__.pyi,sha256=16_tADqmPgoTpzYTJJr2yTf3WVrHAXcFUESRLRy0FoM,111
+junifer/testing/__init__.pyi,sha256=OFqGc5GCjoD4hPVOYNWvnvvP_RVF-oO-UQR8n9HDVtM,133
 junifer/testing/datagrabbers.py,sha256=iYS4IjYbOFQw4fH8e7HNvBOsYgVjMZNodNCLoI25oNA,6601
 junifer/testing/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/testing/registry.py,sha256=iGH3hAt36VtvnZO7UQjybHGh2FI8vo1InY3uDSct5Ps,720
+junifer/testing/registry.py,sha256=MVO-xlzSH3pAv9ySTqO1R3sNqdnfD1Qh7oA775ZxlXs,688
 junifer/testing/utils.py,sha256=TEIwdV7etWglXOFQX1O5ZR18GzfYZ0LcRqXuK-JPo8U,591
 junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv,sha256=iDY1apF5caxnyGqvBYWer5JRKQIfuOwoT-SzzsgL59s,406849
 junifer/testing/tests/test_oasisvmbtesting_datagrabber.py,sha256=BtfExi4VF-jZsi5A3hHS_EGm2O_bJoXnxWF44Z_4i24,794
 junifer/testing/tests/test_partlycloudytesting_datagrabber.py,sha256=ggU8XQQ6F0HSCh9VkbNGoaZM6CUxKXKlcuf_kGkrRF4,1297
 junifer/testing/tests/test_spmauditory_datagrabber.py,sha256=1G1emk-Ze59HiNLaYsyIz5O1YGW9darcqlzvhE-J_Mc,919
-junifer/testing/tests/test_testing_registry.py,sha256=oerticBaPRaRZm3yANzInLac0Mqph3Y0aZPQFayu7xA,827
+junifer/testing/tests/test_testing_registry.py,sha256=MK4a_q4MHieCvYhnhuPm_dH76lX0yyDOZP8tZ30aC7Y,508
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
 junifer/tests/test_stats.py,sha256=3vPMgYYpWxk8ECDFOMm3-dFBlh4XxjL83SwRBSBAHok,4155
 junifer/utils/__init__.py,sha256=I3tYaePAD_ZEU-36-TJ_OYeqW_aMmi5MZ3jmqie6RfU,260
@@ -321,10 +321,10 @@ junifer/utils/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev150.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev150.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev150.dist-info/METADATA,sha256=_jlE1Smuky__n2VceApf68x0U-cJgnAtrmtc728aXgE,8448
-junifer-0.0.6.dev150.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
-junifer-0.0.6.dev150.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev150.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev150.dist-info/RECORD,,
+junifer-0.0.6.dev175.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev175.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev175.dist-info/METADATA,sha256=CsgsHCA_JZ2DN2_3uysC3HhYOZVpzOouUOgF1l7OJxs,8448
+junifer-0.0.6.dev175.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+junifer-0.0.6.dev175.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev175.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev175.dist-info/RECORD,,

junifer/pipeline/registry.py

@@ -1,245 +0,0 @@
-"""Provide functions for registry."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import importlib
-from typing import TYPE_CHECKING, Dict, List, Optional, Union
-
-from ..utils.logging import logger, raise_error
-
-
-if TYPE_CHECKING:
-    from ..datagrabber import BaseDataGrabber
-    from ..storage import BaseFeatureStorage
-    from .pipeline_step_mixin import PipelineStepMixin
-
-
-__all__ = ["register", "get_step_names", "get_class", "build"]
-
-
-# Define valid steps for operation
-_VALID_STEPS: List[str] = [
-    "datagrabber",
-    "datareader",
-    "preprocessing",
-    "marker",
-    "storage",
-]
-
-# Step to sub-package mapping
-_STEP_TO_SUBPKG_MAPPINGS = {
-    "datagrabber": "datagrabber",
-    "datareader": "datareader",
-    "preprocessing": "preprocess",
-    "marker": "markers",
-    "storage": "storage",
-}
-
-# Define registry for valid steps
-_REGISTRY: Dict[str, Dict[str, Union[str, type]]] = {
-    "datagrabber": {
-        "HCP1200": "HCP1200",
-        "BaseDataGrabber": "BaseDataGrabber",
-        "DataladAOMICID1000": "DataladAOMICID1000",
-        "DataladAOMICPIOP1": "DataladAOMICPIOP1",
-        "DataladAOMICPIOP2": "DataladAOMICPIOP2",
-        "DataladDataGrabber": "DataladDataGrabber",
-        "DataladHCP1200": "DataladHCP1200",
-        "DMCC13Benchmark": "DMCC13Benchmark",
-        "MultipleDataGrabber": "MultipleDataGrabber",
-        "PatternDataGrabber": "PatternDataGrabber",
-        "PatternDataladDataGrabber": "PatternDataladDataGrabber",
-    },
-    "datareader": {
-        "DefaultDataReader": "DefaultDataReader",
-    },
-    "preprocessing": {
-        "BasePreprocessor": "BasePreprocessor",
-        "Smoothing": "Smoothing",
-        "SpaceWarper": "SpaceWarper",
-        "fMRIPrepConfoundRemover": "fMRIPrepConfoundRemover",
-    },
-    "marker": {
-        "ALFFParcels": "ALFFParcels",
-        "ALFFSpheres": "ALFFSpheres",
-        "BaseMarker": "BaseMarker",
-        "BrainPrint": "BrainPrint",
-        "CrossParcellationFC": "CrossParcellationFC",
-        "EdgeCentricFCParcels": "EdgeCentricFCParcels",
-        "EdgeCentricFCSpheres": "EdgeCentricFCSpheres",
-        "FunctionalConnectivityParcels": "FunctionalConnectivityParcels",
-        "FunctionalConnectivitySpheres": "FunctionalConnectivitySpheres",
-        "ParcelAggregation": "ParcelAggregation",
-        "ReHoParcels": "ReHoParcels",
-        "ReHoSpheres": "ReHoSpheres",
-        "RSSETSMarker": "RSSETSMarker",
-        "SphereAggregation": "SphereAggregation",
-        "TemporalSNRParcels": "TemporalSNRParcels",
-        "TemporalSNRSpheres": "TemporalSNRSpheres",
-    },
-    "storage": {
-        "BaseFeatureStorage": "BaseFeatureStorage",
-        "HDF5FeatureStorage": "HDF5FeatureStorage",
-        "PandasBaseFeatureStorage": "PandasBaseFeatureStorage",
-        "SQLiteFeatureStorage": "SQLiteFeatureStorage",
-    },
-}
-
-
-def register(step: str, name: str, klass: type) -> None:
-    """Register a function to be used in a pipeline step.
-
-    Parameters
-    ----------
-    step : str
-        Name of the step.
-    name : str
-        Name of the function.
-    klass : class
-        Class to be registered.
-
-    Raises
-    ------
-    ValueError
-        If the ``step`` is invalid.
-
-    """
-    # Verify step
-    if step not in _VALID_STEPS:
-        raise_error(msg=f"Invalid step: {step}", klass=ValueError)
-
-    logger.info(f"Registering {name} in {step}")
-    _REGISTRY[step][name] = klass
-
-
-def get_step_names(step: str) -> List[str]:
-    """Get the names of the registered functions for a given step.
-
-    Parameters
-    ----------
-    step : str
-        Name of the step.
-
-    Returns
-    -------
-    list
-        List of registered function names.
-
-    Raises
-    ------
-    ValueError
-        If the ``step`` is invalid.
-
-    """
-    # Verify step
-    if step not in _VALID_STEPS:
-        raise_error(msg=f"Invalid step: {step}", klass=ValueError)
-
-    return list(_REGISTRY[step].keys())
-
-
-def get_class(step: str, name: str) -> type:
-    """Get the class of the registered function for a given step.
-
-    Parameters
-    ----------
-    step : str
-        Name of the step.
-    name : str
-        Name of the function.
-
-    Returns
-    -------
-    class
-        Registered function class.
-
-    Raises
-    ------
-    ValueError
-        If the ``step`` or ``name`` is invalid.
-
-    """
-    # Verify step
-    if step not in _VALID_STEPS:
-        raise_error(msg=f"Invalid step: {step}", klass=ValueError)
-    # Verify step name
-    if name not in _REGISTRY[step]:
-        raise_error(msg=f"Invalid name: {name}", klass=ValueError)
-
-    # Check if first-time import, then import it
-    if isinstance(_REGISTRY[step][name], str):
-        klass = getattr(
-            importlib.import_module(
-                f"junifer.{_STEP_TO_SUBPKG_MAPPINGS[step]}"
-            ),
-            name,
-        )
-    else:
-        klass = _REGISTRY[step][name]
-
-    return klass
-
-
-def build(
-    step: str,
-    name: str,
-    baseclass: type,
-    init_params: Optional[Dict] = None,
-) -> Union["BaseDataGrabber", "PipelineStepMixin", "BaseFeatureStorage"]:
-    """Ensure that the given object is an instance of the given class.
-
-    Parameters
-    ----------
-    step : str
-        Name of the step.
-    name : str
-        Name of the function.
-    baseclass : class
-        Class to be checked against.
-    init_params : dict or None, optional
-        Parameters to pass to the base class constructor (default None).
-
-    Returns
-    -------
-    object
-        An instance of the given base class.
-
-    Raises
-    ------
-    RuntimeError
-        If there is a problem creating the instance.
-    ValueError
-        If the created object with the given name is not an instance of the
-        base class.
-
-    """
-    # Set default init parameters
-    if init_params is None:
-        init_params = {}
-    # Get class of the registered function
-    logger.debug(f"Building {step}/{name}")
-    klass = get_class(step=step, name=name)
-    logger.debug(f"\tClass: {klass.__name__}")
-    logger.debug(f"\tInit params: {init_params}")
-    try:
-        # Create instance of the class
-        object_ = klass(**init_params)
-    except (ValueError, TypeError) as e:
-        raise_error(
-            msg=f"Failed to create {step} ({name}). Error: {e}",
-            klass=RuntimeError,
-            exception=e,
-        )
-    # Verify created instance belongs to the base class
-    if not isinstance(object_, baseclass):
-        raise_error(
-            msg=(
-                f"Invalid {step} ({object_.__class__.__name__}). "
-                f"Must inherit from {baseclass.__name__}"
-            ),
-            klass=ValueError,
-        )
-    return object_