junifer 0.0.6.dev258__tar.gz → 0.0.6.dev277__tar.gz

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev258
+Version: 0.0.6.dev277
 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.dev277/docs/changes/newsfragments/398.bugfix

@@ -0,0 +1 @@
+Fix metadata update for :class:`.MultipleDataGrabber` and adjust :meth:`.PatternDataGrabber.get_elements` to check ``list``-like data type values by `Fede Raimondo`_ and `Synchon Mandal`_

junifer-0.0.6.dev277/docs/changes/newsfragments/401.feature

@@ -0,0 +1 @@
+Introduce :class:`junifer.utils.ConfigManager` singleton class to manage global configuration by `Fede Raimondo`_

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev258'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev258')
+__version__ = version = '0.0.6.dev277'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev277')

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/api/functions.py

@@ -24,7 +24,7 @@ from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 from ..utils import logger, raise_error, yaml
 
 
-__all__ = ["run", "collect", "queue", "reset", "list_elements"]
+__all__ = ["collect", "list_elements", "queue", "reset", "run"]
 
 
 def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/cli/parser.py

@@ -15,7 +15,7 @@ import pandas as pd
 from ..utils import logger, raise_error, warn_with_log, yaml
 
 
-__all__ = ["parse_yaml", "parse_elements"]
+__all__ = ["parse_elements", "parse_yaml"]
 
 
 def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/data/masks/_masks.py

@@ -35,7 +35,7 @@ if TYPE_CHECKING:
     from nibabel.nifti1 import Nifti1Image
 
 
-__all__ = ["compute_brain_mask", "MaskRegistry"]
+__all__ = ["MaskRegistry", "compute_brain_mask"]
 
 
 # Path to the masks

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/data/template_spaces.py

@@ -16,7 +16,7 @@ from ..utils import logger, raise_error
 from .utils import closest_resolution
 
 
-__all__ = ["get_xfm", "get_template"]
+__all__ = ["get_template", "get_xfm"]
 
 
 def get_xfm(

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/multiple.py

@@ -111,8 +111,12 @@ class MultipleDataGrabber(BaseDataGrabber):
 
         # Update all the metas again
         for kind in out:
-            self.update_meta(out[kind], "datagrabber")
-            out[kind]["meta"]["datagrabber"]["datagrabbers"] = metas
+            to_update = out[kind]
+            if not isinstance(to_update, list):
+                to_update = [to_update]
+            for t_kind in to_update:
+                self.update_meta(t_kind, "datagrabber")
+                t_kind["meta"]["datagrabber"]["datagrabbers"] = metas
         return out
 
     def __enter__(self) -> "MultipleDataGrabber":

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/pattern.py

@@ -13,6 +13,7 @@ from typing import Optional, Union
 import numpy as np
 
 from ..api.decorators import register_datagrabber
+from ..typing import DataGrabberPatterns
 from ..utils import logger, raise_error
 from .base import BaseDataGrabber
 from .pattern_validation_mixin import PatternValidationMixin
@@ -171,7 +172,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
     def __init__(
         self,
         types: list[str],
-        patterns: dict[str, dict[str, str]],
+        patterns: DataGrabberPatterns,
         replacements: Union[list[str], str],
         datadir: Union[str, Path],
         confounds_format: Optional[str] = None,
@@ -478,58 +479,63 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
             t_type = self.types[t_idx]
             types_element = set()
 
-            # Get the pattern dict
-            t_pattern = self.patterns[t_type]
-            # Conditional fetch of base pattern for getting elements
-            pattern = None
-            # Try for data type pattern
-            pattern = t_pattern.get("pattern")
-            # Try for nested data type pattern
-            if pattern is None and self.partial_pattern_ok:
-                for v in t_pattern.values():
-                    if isinstance(v, dict) and "pattern" in v:
-                        pattern = v["pattern"]
-                        break
-
-            # Replace the pattern
-            (
-                re_pattern,
-                glob_pattern,
-                t_replacements,
-            ) = self._replace_patterns_regex(pattern)
-            for fname in self.datadir.glob(glob_pattern):
-                suffix = fname.relative_to(self.datadir).as_posix()
-                m = re.match(re_pattern, suffix)
-                if m is not None:
-                    # Find the groups of replacements present in the pattern
-                    # If one replacement is not present, set it to None.
-                    # We will take care of this in the intersection
-                    t_element = tuple([m.group(k) for k in t_replacements])
-                    if len(self.replacements) == 1:
-                        t_element = t_element[0]
-                    types_element.add(t_element)
-            # TODO: does this make sense as elements is always None
-            if elements is None:
-                elements = types_element
-            else:
-                # Do the intersection by filtering out elements in which
-                # the replacements are not None
-                if t_replacements == self.replacements:
-                    elements.intersection(types_element)
+            # Data type dictionary
+            patterns = self.patterns[t_type]
+            # Conditional for list dtype vals like Warp
+            if not isinstance(patterns, list):
+                patterns = [patterns]
+            for t_pattern in patterns:
+                # Conditional fetch of base pattern for getting elements
+                pattern = None
+                # Try for data type pattern
+                pattern = t_pattern.get("pattern")
+                # Try for nested data type pattern
+                if pattern is None and self.partial_pattern_ok:
+                    for v in t_pattern.values():
+                        if isinstance(v, dict) and "pattern" in v:
+                            pattern = v["pattern"]
+                            break
+
+                # Replace the pattern
+                (
+                    re_pattern,
+                    glob_pattern,
+                    t_replacements,
+                ) = self._replace_patterns_regex(pattern)
+                for fname in self.datadir.glob(glob_pattern):
+                    suffix = fname.relative_to(self.datadir).as_posix()
+                    m = re.match(re_pattern, suffix)
+                    if m is not None:
+                        # Find the groups of replacements present in the
+                        # pattern. If one replacement is not present, set it
+                        # to None. We will take care of this in the
+                        # intersection.
+                        t_element = tuple([m.group(k) for k in t_replacements])
+                        if len(self.replacements) == 1:
+                            t_element = t_element[0]
+                        types_element.add(t_element)
+                # TODO: does this make sense as elements is always None
+                if elements is None:
+                    elements = types_element
                 else:
-                    t_repl_idx = [
-                        i
-                        for i, v in enumerate(self.replacements)
-                        if v in t_replacements
-                    ]
-                    new_elements = set()
-                    for t_element in elements:
-                        if (
-                            tuple(np.array(t_element)[t_repl_idx])
-                            in types_element
-                        ):
-                            new_elements.add(t_element)
-                    elements = new_elements
+                    # Do the intersection by filtering out elements in which
+                    # the replacements are not None
+                    if t_replacements == self.replacements:
+                        elements.intersection(types_element)
+                    else:
+                        t_repl_idx = [
+                            i
+                            for i, v in enumerate(self.replacements)
+                            if v in t_replacements
+                        ]
+                        new_elements = set()
+                        for t_element in elements:
+                            if (
+                                tuple(np.array(t_element)[t_repl_idx])
+                                in types_element
+                            ):
+                                new_elements.add(t_element)
+                        elements = new_elements
         if elements is None:
             elements = set()
         return list(elements)

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/pattern_validation_mixin.py

@@ -3,8 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union
 
+from ..typing import DataGrabberPatterns
 from ..utils import logger, raise_error, warn_with_log
 
 
@@ -96,7 +96,7 @@ class PatternValidationMixin:
     def _validate_replacements(
         self,
         replacements: list[str],
-        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
+        patterns: DataGrabberPatterns,
         partial_pattern_ok: bool,
     ) -> None:
         """Validate the replacements.
@@ -263,7 +263,7 @@ class PatternValidationMixin:
         self,
         types: list[str],
         replacements: list[str],
-        patterns: dict[str, Union[dict[str, str], list[dict[str, str]]]],
+        patterns: DataGrabberPatterns,
         partial_pattern_ok: bool = False,
     ) -> None:
         """Validate the patterns.

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/tests/test_datalad_base.py

@@ -14,8 +14,8 @@ from junifer.datagrabber import DataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
-        "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
+        "commit": "3f288c8725207ae0c9b3616e093e78cda192b570",
+        "id": "582b9696-f13f-42e4-9587-b4e62aa2a8e7",
     },
     "example_bids_ses": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids-ses",

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/tests/test_multiple.py

@@ -29,7 +29,7 @@ def test_MultipleDataGrabber() -> None:
     dg1 = PatternDataladDataGrabber(
         rootdir=rootdir,
         uri=repo_uri,
-        types=["T1w"],
+        types=["T1w", "Warp"],
         patterns={
             "T1w": {
                 "pattern": (
@@ -44,6 +44,28 @@ def test_MultipleDataGrabber() -> None:
                     "space": "native",
                 },
             },
+            "Warp": [
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-MNI152NLin2009cAsym_to-T1w_"
+                        "xfm.h5"
+                    ),
+                    "src": "MNI152NLin2009cAsym",
+                    "dst": "native",
+                    "warper": "ants",
+                },
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-T1w_to-MNI152NLin2009cAsym_"
+                        "xfm.h5"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin2009cAsym",
+                    "warper": "ants",
+                },
+            ],
         },
         replacements=replacements,
     )
@@ -75,6 +97,7 @@ def test_MultipleDataGrabber() -> None:
 
     types = dg.get_types()
     assert "T1w" in types
+    assert "Warp" in types
     assert "BOLD" in types
 
     expected_subs = [
@@ -90,6 +113,7 @@ def test_MultipleDataGrabber() -> None:
         elem = dg[("sub-01", "ses-01")]
         # Check data types
         assert "T1w" in elem
+        assert "Warp" in elem
         assert "BOLD" in elem
         # Check meta
         assert "meta" in elem["BOLD"]
@@ -111,7 +135,7 @@ def test_MultipleDataGrabber_no_intersection() -> None:
     dg1 = PatternDataladDataGrabber(
         rootdir=rootdir,
         uri=_testing_dataset["example_bids"]["uri"],
-        types=["T1w"],
+        types=["T1w", "Warp"],
         patterns={
             "T1w": {
                 "pattern": (
@@ -119,6 +143,28 @@ def test_MultipleDataGrabber_no_intersection() -> None:
                 ),
                 "space": "native",
             },
+            "Warp": [
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-MNI152NLin2009cAsym_to-T1w_"
+                        "xfm.h5"
+                    ),
+                    "src": "MNI152NLin2009cAsym",
+                    "dst": "native",
+                    "warper": "ants",
+                },
+                {
+                    "pattern": (
+                        "{subject}/{session}/anat/"
+                        "{subject}_{session}_from-T1w_to-MNI152NLin2009cAsym_"
+                        "xfm.h5"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin2009cAsym",
+                    "warper": "ants",
+                },
+            ],
         },
         replacements=replacements,
     )

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/datagrabber/tests/test_pattern_datalad.py

@@ -15,7 +15,7 @@ from junifer.datagrabber import PatternDataladDataGrabber
 _testing_dataset = {
     "example_bids": {
         "uri": "https://gin.g-node.org/juaml/datalad-example-bids",
-        "commit": "b87897cbe51bf0ee5514becaa5c7dd76491db5ad",
+        "commit": "3f288c8725207ae0c9b3616e093e78cda192b570",
         "id": "8fddff30-6993-420a-9d1e-b5b028c59468",
     },
     "example_bids_ses": {

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/stats.py

@@ -13,7 +13,7 @@ from scipy.stats.mstats import winsorize
 from .utils import logger, raise_error
 
 
-__all__ = ["get_aggfunc_by_name", "count", "winsorized_mean", "select"]
+__all__ = ["count", "get_aggfunc_by_name", "select", "winsorized_mean"]
 
 
 def get_aggfunc_by_name(

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/typing/__init__.pyi

@@ -8,6 +8,8 @@ __all__ = [
     "ConditionalDependencies",
     "ExternalDependencies",
     "MarkerInOutMappings",
+    "DataGrabberPatterns",
+    "ConfigVal",
 ]
 
 from ._typing import (
@@ -20,4 +22,6 @@ from ._typing import (
     ConditionalDependencies,
     ExternalDependencies,
     MarkerInOutMappings,
+    DataGrabberPatterns,
+    ConfigVal,
 )

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/typing/_typing.py

@@ -19,15 +19,17 @@ if TYPE_CHECKING:
 
 
 __all__ = [
+    "ConditionalDependencies",
+    "ConfigVal",
     "DataGrabberLike",
-    "PreprocessorLike",
-    "MarkerLike",
-    "StorageLike",
-    "PipelineComponent",
+    "DataGrabberPatterns",
     "Dependencies",
-    "ConditionalDependencies",
     "ExternalDependencies",
     "MarkerInOutMappings",
+    "MarkerLike",
+    "PipelineComponent",
+    "PreprocessorLike",
+    "StorageLike",
 ]
 
 
@@ -56,3 +58,7 @@ ConditionalDependencies = Sequence[
 ]
 ExternalDependencies = Sequence[MutableMapping[str, Union[str, Sequence[str]]]]
 MarkerInOutMappings = MutableMapping[str, MutableMapping[str, str]]
+DataGrabberPatterns = dict[
+    str, Union[dict[str, str], Sequence[dict[str, str]]]
+]
+ConfigVal = Union[bool, int, float]

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/utils/__init__.pyi

@@ -1,15 +1,18 @@
 __all__ = [
     "make_executable",
     "configure_logging",
+    "config",
     "logger",
     "raise_error",
     "warn_with_log",
     "run_ext_cmd",
     "deep_update",
     "yaml",
+    "ConfigManager",
 ]
 
 from .fs import make_executable
 from .logging import configure_logging, logger, raise_error, warn_with_log
+from ._config import config, ConfigManager
 from .helpers import run_ext_cmd, deep_update
 from ._yaml import yaml

junifer-0.0.6.dev277/junifer/utils/_config.py

@@ -0,0 +1,110 @@
+"""Provide junifer global configuration."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import os
+from typing import Optional
+
+from ..typing import ConfigVal
+from .logging import logger
+from .singleton import Singleton
+
+
+__all__ = ["ConfigManager", "config"]
+
+
+class ConfigManager(metaclass=Singleton):
+    """Manage configuration parameters.
+
+    Attributes
+    ----------
+    _config : dict
+        Configuration parameters.
+
+    """
+
+    def __init__(self) -> None:
+        """Initialize the class."""
+        self._config = {}
+        # Initial setup from process env
+        self._reload()
+
+    def _reload(self) -> None:
+        """Reload env vars."""
+        for t_var in os.environ:
+            if t_var.startswith("JUNIFER_"):
+                # Set correct type
+                var_value = os.environ[t_var]
+                # bool
+                if var_value.lower() == "true":
+                    var_value = True
+                elif var_value.lower() == "false":
+                    var_value = False
+                # numeric
+                else:
+                    try:
+                        var_value = int(var_value)
+                    except ValueError:
+                        try:
+                            var_value = float(var_value)
+                        except ValueError:
+                            pass
+                # Set value
+                var_name = (
+                    t_var.replace("JUNIFER_", "").lower().replace("_", ".")
+                )
+                logger.debug(
+                    f"Setting `{var_name}` from environment to "
+                    f"`{var_value}` (type: {type(var_value)})"
+                )
+                self._config[var_name] = var_value
+
+    def get(self, key: str, default: Optional[ConfigVal] = None) -> ConfigVal:
+        """Get configuration parameter.
+
+        Parameters
+        ----------
+        key : str
+            The configuration key to get.
+        default : bool or int or float or None, optional
+            The default value to return if the key is not found (default None).
+
+        Returns
+        -------
+        bool or int or float
+            The configuration value.
+
+        """
+        return self._config.get(key, default)
+
+    def set(self, key: str, val: ConfigVal) -> None:
+        """Set configuration parameter.
+
+        Parameters
+        ----------
+        key : str
+            The configuration key to set.
+        val : bool or int or float
+            The value to set ``key`` to.
+
+        """
+        logger.debug(f"Setting `{key}` to `{val}` (type: {type(val)})")
+        self._config[key] = val
+
+    def delete(self, key: str) -> None:
+        """Delete configuration parameter.
+
+        Parameters
+        ----------
+        key : str
+            The configuration key to delete.
+
+        """
+        logger.debug(f"Deleting `{key}` from config")
+        _ = self._config.pop(key)
+
+
+# Initialize here to access from anywhere
+config = ConfigManager()

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/utils/helpers.py

@@ -10,7 +10,7 @@ import sys
 from .logging import logger, raise_error
 
 
-__all__ = ["run_ext_cmd", "deep_update"]
+__all__ = ["deep_update", "run_ext_cmd"]
 
 
 def run_ext_cmd(name: str, cmd: list[str]) -> None:

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer/utils/singleton.py

@@ -8,7 +8,7 @@ from abc import ABCMeta
 from typing import Any, ClassVar
 
 
-__all__ = ["Singleton", "ABCSingleton"]
+__all__ = ["ABCSingleton", "Singleton"]
 
 
 class Singleton(type):

junifer-0.0.6.dev277/junifer/utils/tests/test_config.py

@@ -0,0 +1,59 @@
+"""Provide tests for ConfigManager."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import os
+
+import pytest
+
+from junifer.typing import ConfigVal
+from junifer.utils import config
+from junifer.utils._config import ConfigManager
+
+
+def test_config_manager_singleton() -> None:
+    """Test that ConfigManager is a singleton."""
+    config_mgr_1 = ConfigManager()
+    config_mgr_2 = ConfigManager()
+    assert id(config_mgr_1) == id(config_mgr_2)
+
+
+def test_config_manager() -> None:
+    """Test config operations for ConfigManager."""
+    # Get non-existing with default
+    assert config.get(key="scooby") is None
+    # Set
+    config.set(key="scooby", val=True)
+    # Get existing
+    assert config.get("scooby")
+    # Delete
+    config.delete("scooby")
+    # Get non-existing with default
+    assert config.get(key="scooby") is None
+
+
+@pytest.mark.parametrize(
+    "val, expected_val",
+    [("TRUE", True), ("FALSE", False), ("1", 1), ("0.0", 0.0)],
+)
+def test_config_manager_env_reload(val: str, expected_val: ConfigVal) -> None:
+    """Test config parsing from env reload.
+
+    Parameters
+    ----------
+    val : str
+        The parametrized values.
+    expected_val : bool or int or float
+        The parametrized expected value.
+
+    """
+    # Set env var
+    os.environ["JUNIFER_TESTME"] = val
+    # Check
+    config._reload()
+    assert config.get("testme") == expected_val
+    # Cleanup
+    del os.environ["JUNIFER_TESTME"]
+    config.delete("testme")

{junifer-0.0.6.dev258 → junifer-0.0.6.dev277}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev258
+Version: 0.0.6.dev277
 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.dev258 → junifer-0.0.6.dev277}/junifer.egg-info/SOURCES.txt

@@ -94,6 +94,8 @@ docs/changes/newsfragments/390.enh
 docs/changes/newsfragments/391.misc
 docs/changes/newsfragments/392.feature
 docs/changes/newsfragments/393.misc
+docs/changes/newsfragments/398.bugfix
+docs/changes/newsfragments/401.feature
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -467,12 +469,14 @@ junifer/typing/__init__.pyi
 junifer/typing/_typing.py
 junifer/utils/__init__.py
 junifer/utils/__init__.pyi
+junifer/utils/_config.py
 junifer/utils/_yaml.py
 junifer/utils/fs.py
 junifer/utils/helpers.py
 junifer/utils/logging.py
 junifer/utils/py.typed
 junifer/utils/singleton.py
+junifer/utils/tests/test_config.py
 junifer/utils/tests/test_fs.py
 junifer/utils/tests/test_helpers.py
 junifer/utils/tests/test_logging.py