junifer 0.0.6.dev44__tar.gz → 0.0.6.dev88__tar.gz

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev44
+Version: 0.0.6.dev88
 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>
@@ -42,6 +42,7 @@ 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: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all

junifer-0.0.6.dev88/docs/changes/newsfragments/355.misc

@@ -0,0 +1 @@
+Adopt lazy-import mechanism for the package by `Synchon Mandal`_

junifer-0.0.6.dev88/docs/changes/newsfragments/367.enh

@@ -0,0 +1 @@
+Allow for external python files in the ``with`` section of the yaml to import other files by `Fede Raimondo`_

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/docs/extending/extension.rst

@@ -28,8 +28,25 @@ This is the ideal place to include ``junifer`` extensions.
 
 .. important::
 
-   Some ``junifer`` commands will not consider files imported from files included
-   in the ``with`` statement. If ``my_file.py`` imports ``my_other_file.py``,
-   some of the ``junifer`` commands will not consider ``my_other_file.py``. Either
-   place all the code in one file or add multiple files to the ``with``
-   statement.
+   Some ``junifer`` commands will not consider files imported from files
+   included in the ``with`` statement, unless this is known to junifer. If
+   ``my_file.py`` imports ``my_other_file.py``, the ``run`` command will work,
+   but ``queue`` will not create a proper job. This is because we need to 
+   let junifer know that ``my_other_file.py`` is also part of the code. To do
+   so, we need to include a special function in ``my_file.py`` which tells
+   ``junifer`` about the dependencies of the module:
+
+   .. code-block:: python
+
+      def junifer_module_deps() -> List[str]:
+        """Return the dependencies of the module.
+
+        Returns
+        -------
+        list of str
+            The list of dependencies.
+
+        """
+
+        return ["my_other_file.py"]
+

junifer-0.0.6.dev88/junifer/__init__.py

@@ -0,0 +1,10 @@
+"""Provide imports for junifer package."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/__init__.py → junifer-0.0.6.dev88/junifer/__init__.pyi

@@ -1,12 +1,22 @@
-"""Provide imports for junifer package."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "api",
+    "configs",
+    "data",
+    "datagrabber",
+    "datareader",
+    "markers",
+    "pipeline",
+    "preprocess",
+    "stats",
+    "storage",
+    "utils",
+    "external",
+    "onthefly",
+    "__version__",
+]
 
 from . import (
     api,
-    cli,
     configs,
     data,
     datagrabber,
@@ -21,21 +31,3 @@ from . import (
     onthefly,
 )
 from ._version import __version__
-
-
-__all__ = [
-    "api",
-    "cli",
-    "configs",
-    "data",
-    "datagrabber",
-    "datareader",
-    "markers",
-    "pipeline",
-    "preprocess",
-    "stats",
-    "storage",
-    "utils",
-    "external",
-    "onthefly",
-]

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev44'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev44')
+__version__ = version = '0.0.6.dev88'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev88')

junifer-0.0.6.dev88/junifer/api/__init__.py

@@ -0,0 +1,10 @@
+"""Public API components."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/api/__init__.py → junifer-0.0.6.dev88/junifer/api/__init__.pyi

@@ -1,11 +1,4 @@
-"""Public API components."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["decorators", "collect", "queue", "run", "reset", "list_elements"]
 
 from . import decorators
 from .functions import collect, list_elements, reset, run, queue
-
-
-__all__ = ["decorators", "collect", "queue", "run", "reset", "list_elements"]

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/api/functions.py

@@ -14,8 +14,7 @@ from typing import Dict, List, Optional, Tuple, Union
 from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber.base import BaseDataGrabber
 from ..markers.base import BaseMarker
-from ..markers.collection import MarkerCollection
-from ..pipeline import WorkDirManager
+from ..pipeline import MarkerCollection, WorkDirManager
 from ..pipeline.registry import build
 from ..preprocess.base import BasePreprocessor
 from ..storage.base import BaseFeatureStorage

junifer-0.0.6.dev88/junifer/api/queue_context/__init__.py

@@ -0,0 +1,9 @@
+"""Context adapters for queueing."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/api/queue_context/__init__.py → junifer-0.0.6.dev88/junifer/api/queue_context/__init__.pyi

@@ -1,11 +1,5 @@
-"""Context adapters for queueing."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]
 
 from .queue_context_adapter import QueueContextAdapter
 from .htcondor_adapter import HTCondorAdapter
 from .gnu_parallel_local_adapter import GnuParallelLocalAdapter
-
-
-__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]

junifer-0.0.6.dev88/junifer/cli/__init__.py

@@ -0,0 +1,9 @@
+"""Junifer CLI components."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev88/junifer/cli/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["cli"]
+
+from .cli import cli

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/cli/cli.py

@@ -28,6 +28,23 @@ from .utils import (
 )
 
 
+__all__ = [
+    "cli",
+    "run",
+    "collect",
+    "queue",
+    "wtf",
+    "selftest",
+    "reset",
+    "list_elements",
+    "setup",
+    "afni_docker",
+    "fsl_docker",
+    "ants_docker",
+    "freesurfer_docker",
+]
+
+
 def _validate_verbose(
     ctx: click.Context, param: str, value: str
 ) -> Union[str, int]:

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/cli/parser.py

@@ -18,7 +18,7 @@ from ..utils import logger, raise_error, warn_with_log, yaml
 __all__ = ["parse_yaml", "parse_elements"]
 
 
-def parse_yaml(filepath: Union[str, Path]) -> Dict:
+def parse_yaml(filepath: Union[str, Path]) -> Dict:  # noqa: C901
     """Parse YAML.
 
     Parameters
@@ -65,14 +65,35 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                     raise_error(
                         f"File in 'with' section does not exist: {file_path}"
                     )
+                # Add the parent directory to the sys.path so that the
+                # any imports from this module work correctly
+                t_path = str(file_path.parent)
+                if t_path not in sys.path:
+                    sys.path.append(str(file_path.parent))
+
                 spec = importlib.util.spec_from_file_location(
                     t_module, file_path
                 )
                 module = importlib.util.module_from_spec(spec)  # type: ignore
                 sys.modules[t_module] = module
                 spec.loader.exec_module(module)  # type: ignore
+
                 # Add absolute path to final list
                 final_to_load.append(str(file_path.resolve()))
+
+                # Check if the module has junifer_module_deps function
+                if hasattr(module, "junifer_module_deps"):
+                    logger.debug(
+                        f"Module {t_module} has junifer_module_deps function"
+                    )
+                    # Get the dependencies
+                    deps = module.junifer_module_deps()
+                    # Add the dependencies to the final list
+                    for dep in deps:
+                        if dep not in final_to_load:
+                            final_to_load.append(
+                                str((file_path.parent / dep).resolve())
+                            )
             else:
                 logger.info(f"Importing module: {t_module}")
                 importlib.import_module(t_module)

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/cli/tests/test_cli_utils.py

@@ -47,6 +47,7 @@ def test_get_dependency_information_short() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "lazy_loader",
         "looseversion",
     ]
 
@@ -76,6 +77,7 @@ def test_get_dependency_information_long() -> None:
         "tqdm",
         "templateflow",
         "lapy",
+        "lazy_loader",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/configs/juseless/__init__.py

@@ -3,7 +3,7 @@
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-from . import datagrabbers
+import lazy_loader as lazy
 
 
-__all__ = ["datagrabbers"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev88/junifer/configs/juseless/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["datagrabbers"]
+
+from . import datagrabbers

junifer-0.0.6.dev88/junifer/configs/juseless/datagrabbers/__init__.py

@@ -0,0 +1,11 @@
+"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
+
+# 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 lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/configs/juseless/datagrabbers/__init__.py → junifer-0.0.6.dev88/junifer/configs/juseless/datagrabbers/__init__.pyi

@@ -1,17 +1,3 @@
-"""Custom DataGrabbers for FZJ INM-7's beloved juseless."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM
-from .camcan_vbm import JuselessDataladCamCANVBM
-from .ixi_vbm import JuselessDataladIXIVBM
-from .ucla import JuselessUCLA
-from .ukb_vbm import JuselessDataladUKBVBM
-
-
 __all__ = [
     "JuselessDataladAOMICID1000VBM",
     "JuselessDataladCamCANVBM",
@@ -19,3 +5,9 @@ __all__ = [
     "JuselessUCLA",
     "JuselessDataladUKBVBM",
 ]
+
+from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM
+from .camcan_vbm import JuselessDataladCamCANVBM
+from .ixi_vbm import JuselessDataladIXIVBM
+from .ucla import JuselessUCLA
+from .ukb_vbm import JuselessDataladUKBVBM

junifer-0.0.6.dev88/junifer/data/__init__.py

@@ -0,0 +1,10 @@
+"""Parcellations, coordinates and masks."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/data/__init__.py → junifer-0.0.6.dev88/junifer/data/__init__.pyi

@@ -1,8 +1,21 @@
-"""Parcellations, coordinates and masks."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "list_coordinates",
+    "load_coordinates",
+    "register_coordinates",
+    "get_coordinates",
+    "list_parcellations",
+    "load_parcellation",
+    "register_parcellation",
+    "merge_parcellations",
+    "get_parcellation",
+    "list_masks",
+    "load_mask",
+    "register_mask",
+    "get_mask",
+    "get_template",
+    "get_xfm",
+    "utils",
+]
 
 from .coordinates import (
     list_coordinates,
@@ -28,23 +41,3 @@ from .masks import (
 from .template_spaces import get_template, get_xfm
 
 from . import utils
-
-
-__all__ = [
-    "list_coordinates",
-    "load_coordinates",
-    "register_coordinates",
-    "get_coordinates",
-    "list_parcellations",
-    "load_parcellation",
-    "register_parcellation",
-    "merge_parcellations",
-    "get_parcellation",
-    "list_masks",
-    "load_mask",
-    "register_mask",
-    "get_mask",
-    "get_template",
-    "get_xfm",
-    "utils",
-]

junifer-0.0.6.dev88/junifer/datagrabber/__init__.py

@@ -0,0 +1,11 @@
+"""DataGrabbers for datasets' data description."""
+
+# 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 lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/datagrabber/__init__.py → junifer-0.0.6.dev88/junifer/datagrabber/__init__.pyi

@@ -1,24 +1,3 @@
-"""DataGrabbers for datasets' data description."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-
-# These 4 need to be in this order, otherwise it is a circular import
-from .base import BaseDataGrabber
-from .datalad_base import DataladDataGrabber
-from .pattern import PatternDataGrabber
-from .pattern_datalad import PatternDataladDataGrabber
-
-from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
-from .hcp1200 import HCP1200, DataladHCP1200
-from .multiple import MultipleDataGrabber
-from .dmcc13_benchmark import DMCC13Benchmark
-
-from .pattern_validation_mixin import PatternValidationMixin
-
 __all__ = [
     "BaseDataGrabber",
     "DataladDataGrabber",
@@ -33,3 +12,16 @@ __all__ = [
     "DMCC13Benchmark",
     "PatternValidationMixin",
 ]
+
+# These 4 need to be in this order, otherwise it is a circular import
+from .base import BaseDataGrabber
+from .datalad_base import DataladDataGrabber
+from .pattern import PatternDataGrabber
+from .pattern_datalad import PatternDataladDataGrabber
+
+from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
+from .hcp1200 import HCP1200, DataladHCP1200
+from .multiple import MultipleDataGrabber
+from .dmcc13_benchmark import DMCC13Benchmark
+
+from .pattern_validation_mixin import PatternValidationMixin

junifer-0.0.6.dev88/junifer/datagrabber/aomic/__init__.py

@@ -0,0 +1,10 @@
+"""Provide imports for aomic sub-package."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/datagrabber/aomic/__init__.py → junifer-0.0.6.dev88/junifer/datagrabber/aomic/__init__.pyi

@@ -1,12 +1,5 @@
-"""Provide imports for aomic sub-package."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-# License: AGPL
+__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]
 
 from .id1000 import DataladAOMICID1000
 from .piop1 import DataladAOMICPIOP1
 from .piop2 import DataladAOMICPIOP2
-
-
-__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/datagrabber/hcp1200/__init__.py

@@ -3,8 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .hcp1200 import HCP1200
-from .datalad_hcp1200 import DataladHCP1200
+import lazy_loader as lazy
 
 
-__all__ = ["HCP1200", "DataladHCP1200"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev88/junifer/datagrabber/hcp1200/__init__.pyi

@@ -0,0 +1,4 @@
+__all__ = ["HCP1200", "DataladHCP1200"]
+
+from .hcp1200 import HCP1200
+from .datalad_hcp1200 import DataladHCP1200

{junifer-0.0.6.dev44 → junifer-0.0.6.dev88}/junifer/datareader/__init__.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from .default import DefaultDataReader
+import lazy_loader as lazy
 
 
-__all__ = ["DefaultDataReader"]
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev88/junifer/datareader/__init__.pyi

@@ -0,0 +1,3 @@
+__all__ = ["DefaultDataReader"]
+
+from .default import DefaultDataReader

junifer-0.0.6.dev88/junifer/external/nilearn/__init__.py

@@ -0,0 +1,9 @@
+"""Custom objects adapted from nilearn."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/external/nilearn/__init__.py → junifer-0.0.6.dev88/junifer/external/nilearn/__init__.pyi

@@ -1,10 +1,4 @@
-"""Custom objects adapted from nilearn."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = ["JuniferNiftiSpheresMasker", "JuniferConnectivityMeasure"]
 
 from .junifer_nifti_spheres_masker import JuniferNiftiSpheresMasker
 from .junifer_connectivity_measure import JuniferConnectivityMeasure
-
-
-__all__ = ["JuniferNiftiSpheresMasker", "JuniferConnectivityMeasure"]

junifer-0.0.6.dev88/junifer/markers/__init__.py

@@ -0,0 +1,11 @@
+"""Markers for feature extraction."""
+
+# 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 lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.6.dev44/junifer/markers/__init__.py → junifer-0.0.6.dev88/junifer/markers/__init__.pyi

@@ -1,12 +1,23 @@
-"""Markers for feature extraction."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
+__all__ = [
+    "BaseMarker",
+    "RSSETSMarker",
+    "ParcelAggregation",
+    "SphereAggregation",
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+    "ReHoParcels",
+    "ReHoSpheres",
+    "ALFFParcels",
+    "ALFFSpheres",
+    "TemporalSNRParcels",
+    "TemporalSNRSpheres",
+    "BrainPrint",
+]
 
 from .base import BaseMarker
-from .collection import MarkerCollection
 from .ets_rss import RSSETSMarker
 from .parcel_aggregation import ParcelAggregation
 from .sphere_aggregation import SphereAggregation
@@ -24,24 +35,3 @@ from .temporal_snr import (
     TemporalSNRSpheres,
 )
 from .brainprint import BrainPrint
-
-
-__all__ = [
-    "BaseMarker",
-    "MarkerCollection",
-    "RSSETSMarker",
-    "ParcelAggregation",
-    "SphereAggregation",
-    "FunctionalConnectivityParcels",
-    "FunctionalConnectivitySpheres",
-    "CrossParcellationFC",
-    "EdgeCentricFCParcels",
-    "EdgeCentricFCSpheres",
-    "ReHoParcels",
-    "ReHoSpheres",
-    "ALFFParcels",
-    "ALFFSpheres",
-    "TemporalSNRParcels",
-    "TemporalSNRSpheres",
-    "BrainPrint",
-]