junifer 0.0.6.dev266__py3-none-any.whl → 0.0.6.dev277__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev266'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev266')
+__version__ = version = '0.0.6.dev277'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev277')

junifer/api/decorators.py

@@ -13,8 +13,8 @@ from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
 __all__ = [
     "register_datagrabber",
     "register_datareader",
-    "register_preprocessor",
     "register_marker",
+    "register_preprocessor",
     "register_storage",
 ]
 

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/cli/cli.py

@@ -29,19 +29,19 @@ from .utils import (
 
 
 __all__ = [
+    "afni_docker",
+    "ants_docker",
     "cli",
-    "run",
     "collect",
+    "freesurfer_docker",
+    "fsl_docker",
+    "list_elements",
     "queue",
-    "wtf",
-    "selftest",
     "reset",
-    "list_elements",
+    "run",
+    "selftest",
     "setup",
-    "afni_docker",
-    "fsl_docker",
-    "ants_docker",
-    "freesurfer_docker",
+    "wtf",
 ]
 
 

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/data/_dispatch.py

@@ -25,11 +25,11 @@ if TYPE_CHECKING:
 
 
 __all__ = [
+    "deregister_data",
     "get_data",
     "list_data",
     "load_data",
     "register_data",
-    "deregister_data",
 ]
 
 

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/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/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/storage/utils.py

@@ -15,11 +15,11 @@ from ..utils.logging import logger, raise_error
 
 
 __all__ = [
+    "element_to_prefix",
     "get_dependency_version",
+    "matrix_to_vector",
     "process_meta",
-    "element_to_prefix",
     "store_matrix_checks",
-    "matrix_to_vector",
 ]
 
 

junifer/testing/datagrabbers.py

@@ -15,8 +15,8 @@ from ..datagrabber.base import BaseDataGrabber
 
 __all__ = [
     "OasisVBMTestingDataGrabber",
-    "SPMAuditoryTestingDataGrabber",
     "PartlyCloudyTestingDataGrabber",
+    "SPMAuditoryTestingDataGrabber",
 ]
 
 

junifer/typing/__init__.pyi

@@ -9,6 +9,7 @@ __all__ = [
     "ExternalDependencies",
     "MarkerInOutMappings",
     "DataGrabberPatterns",
+    "ConfigVal",
 ]
 
 from ._typing import (
@@ -22,4 +23,5 @@ from ._typing import (
     ExternalDependencies,
     MarkerInOutMappings,
     DataGrabberPatterns,
+    ConfigVal,
 )

junifer/typing/_typing.py

@@ -19,16 +19,17 @@ if TYPE_CHECKING:
 
 
 __all__ = [
+    "ConditionalDependencies",
+    "ConfigVal",
     "DataGrabberLike",
-    "PreprocessorLike",
-    "MarkerLike",
-    "StorageLike",
-    "PipelineComponent",
+    "DataGrabberPatterns",
     "Dependencies",
-    "ConditionalDependencies",
     "ExternalDependencies",
     "MarkerInOutMappings",
-    "DataGrabberPatterns",
+    "MarkerLike",
+    "PipelineComponent",
+    "PreprocessorLike",
+    "StorageLike",
 ]
 
 
@@ -60,3 +61,4 @@ MarkerInOutMappings = MutableMapping[str, MutableMapping[str, str]]
 DataGrabberPatterns = dict[
     str, Union[dict[str, str], Sequence[dict[str, str]]]
 ]
+ConfigVal = Union[bool, int, float]

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/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/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/utils/logging.py

@@ -24,9 +24,9 @@ import datalad
 
 __all__ = [
     "WrapStdOut",
+    "configure_logging",
     "get_versions",
     "log_versions",
-    "configure_logging",
     "raise_error",
     "warn_with_log",
 ]

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/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.dev266.dist-info → junifer-0.0.6.dev277.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev266
+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.dev266.dist-info → junifer-0.0.6.dev277.dist-info}/RECORD

@@ -1,13 +1,13 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=fiEZu3h8Evv4yCwsFll_Ls-APBLYdJ7Qnm3jUM3IXXI,428
+junifer/_version.py,sha256=oxdSo7e4dHuWGJ6fcFCd_o22QGOenmAuWxLqOvENYXw,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/stats.py,sha256=pQCy9u4q3Wp0kMFmS0BVIfU8UCKsRqrNbyprhtlNUOg,6225
+junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
 junifer/api/__init__.py,sha256=aAXW_KAEGQ8aAP5Eni2G1R4MWBF7UgjKOgM6akLuJco,252
 junifer/api/__init__.pyi,sha256=UJu55ApMFd43N0xlQyNKrYpCdzqhAxA3Jjaj0ETwCXU,169
-junifer/api/decorators.py,sha256=kEIcJIznNG_HwrvG9i7bnM1AeZOQPbSBmgDQ3yWFmIQ,2854
-junifer/api/functions.py,sha256=GB0CODQEAx6WOEFa7g1rSbWx8_4Qw8DQRdfC4JVPkrA,12826
+junifer/api/decorators.py,sha256=xphy55NJHnMZnJ-aNA70UzHUJ3SIgh5Xc8ekcozvj3U,2854
+junifer/api/functions.py,sha256=ebKz9WVdDcVWX32p2MHiYEEN-FEcsGcRWEN6u4pFnro,12826
 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
@@ -43,8 +43,8 @@ junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvi
 junifer/api/tests/test_functions.py,sha256=aBAZ2EveiBHbAM5w6j2QxMHBze-XiVD3Td1kAE946ps,17786
 junifer/cli/__init__.py,sha256=DS3kZKHeVDxt6d1MLBerZ2fcAwrEBHee5JOBhOLajUI,197
 junifer/cli/__init__.pyi,sha256=PiV4znUnzSeuSSJGz-RT8N21PiMqoSMwYcypi7nt2Js,40
-junifer/cli/cli.py,sha256=kUAlbYIYQ5mKf_Q40Q0f73OMkkAz8B6Xy5eL6I4iY6U,13195
-junifer/cli/parser.py,sha256=3zmmdsrYzIci3TS8xGVlWeLUIgtaH2Z12OYnqG1ZKAc,8336
+junifer/cli/cli.py,sha256=kzSM-5nZWgQ4iaGbcjDkU2JgdYcUF-zsYskuq9_ewM0,13195
+junifer/cli/parser.py,sha256=Ok_ADyoDfjlAxl9NP36dtzFHp9QTL87V_cRxCa44UKs,8336
 junifer/cli/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/cli/utils.py,sha256=AbPQC0Kl-tHMNKiPxp_01gLAGD3IGoLbsq3rXyPMM-c,3116
 junifer/cli/tests/test_cli.py,sha256=AYL4my12GmFRCbI3JV7-rju32heYxAqbXNwnV8PwqVY,10982
@@ -72,10 +72,10 @@ junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=l-1y_m6NJo7JExhy
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=xJDI2QKtdjcNzpd1oVFM3guh1SFHM6jKstl7pFmzOuk,267
 junifer/data/__init__.pyi,sha256=qYszjUYcbFi_2zO23MnbA2HhTW-Ad2oh1pqPQYd6yt0,542
-junifer/data/_dispatch.py,sha256=FcEZv7ZhWD4aYWzmzd9ZyUETADUJJmqvPqZpSwRsTa4,6158
+junifer/data/_dispatch.py,sha256=O524U1R4MtbGhGJsL0HSh9EqisapBFJWK7uupXrJuMg,6158
 junifer/data/pipeline_data_registry_base.py,sha256=G8bE3WTj4D_rKC4ZKZe6E48Sd96CGea1PS3SxmTgGK4,2010
 junifer/data/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/data/template_spaces.py,sha256=Hcg4k1FL_kVhde6JJUXIQWd_fjqdtTto3nbzx8-t5Rc,6504
+junifer/data/template_spaces.py,sha256=AVNuXuCqY0w7dSrVOZURjCPFIkg0wzQsAV2ggtQFpJU,6504
 junifer/data/utils.py,sha256=5r-0QGQCNZvDM1tVcl9xyrIdgAO85mww0plpM1RUaGA,3247
 junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6RAxZdUMg,186
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
@@ -106,7 +106,7 @@ junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQ
 junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
 junifer/data/masks/_ants_mask_warper.py,sha256=yGjC-b6Ui-MpPG3FpRnI8pEAxjMUfSSuUGVIeazjN7I,5078
 junifer/data/masks/_fsl_mask_warper.py,sha256=_7UkX3-wFXQs4KwxopO-QjMyB6aeq1GAkiGSGpG-OzM,2412
-junifer/data/masks/_masks.py,sha256=VsWY4GOrTOV6XsX-Usl8H_6s8AT6LLveBvLBUr6woFE,20729
+junifer/data/masks/_masks.py,sha256=96NKsSSosD6r03Jb2N1xQoyOc2Vl5miokcQdSeuM6SY,20729
 junifer/data/masks/tests/test_masks.py,sha256=1Zm09ZSdUlR278DTCZeVuxuQntryefsnYYPP02MttVE,16120
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
@@ -306,7 +306,7 @@ junifer/storage/hdf5.py,sha256=1nK4su0S1ND-cMMP0jhf66yf0I0JwHp1gicDjZhXw9s,38001
 junifer/storage/pandas_base.py,sha256=v3iRuoXJzBChZYkjR4OHJp99NM0BPTpYkw1TAX52Nto,7529
 junifer/storage/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/storage/sqlite.py,sha256=QzkKB1pD4qNjrMe0bB7ATHnPgNjteTrP3ULCE_XuwD0,21269
-junifer/storage/utils.py,sha256=bUtf13ADjlNOq0alYKXMWYPQaOSeSJ5R7tBmFZc6Cgo,7390
+junifer/storage/utils.py,sha256=3wpiHeyGJ74neICgKmSrlpSZcyl5Hm1y3_49-Sj9tWg,7390
 junifer/storage/tests/test_hdf5.py,sha256=vHMludIWJJ-4_i1kMYqLfdCrHJkYe7Dd9ZXLTjt-MOQ,31481
 junifer/storage/tests/test_pandas_base.py,sha256=y_TfUGpuXkj_39yVon3rMDxMeBrZXs58ZW6OSty5LNw,4058
 junifer/storage/tests/test_sqlite.py,sha256=0TQIcqHPgk67ALsR-98CA73ulDPsR2t9wGXYaem983w,28312
@@ -314,7 +314,7 @@ junifer/storage/tests/test_storage_base.py,sha256=YzgfspuggzXejyPIoRCPST3ZzH9Pi7
 junifer/storage/tests/test_utils.py,sha256=k2HxD9cC-NczasEWjPZUiIy6mpbelR8KIUXWtkp_uws,11862
 junifer/testing/__init__.py,sha256=gqfrX2c7I31VYBmH9hCUERO-61NwubT1cvy1bKM0NqU,249
 junifer/testing/__init__.pyi,sha256=OFqGc5GCjoD4hPVOYNWvnvvP_RVF-oO-UQR8n9HDVtM,133
-junifer/testing/datagrabbers.py,sha256=I5fwaKS3JtFLP1Xyt3Hs6PTVFVTQViYTiTQWL8U3MP8,6571
+junifer/testing/datagrabbers.py,sha256=ui2VwArMjx4KUD2Cf8PRJOExvDHfPntuuuhEEwWwTZ4,6571
 junifer/testing/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/testing/registry.py,sha256=MVO-xlzSH3pAv9ySTqO1R3sNqdnfD1Qh7oA775ZxlXs,688
 junifer/testing/utils.py,sha256=TEIwdV7etWglXOFQX1O5ZR18GzfYZ0LcRqXuK-JPo8U,591
@@ -326,23 +326,25 @@ junifer/testing/tests/test_testing_registry.py,sha256=MK4a_q4MHieCvYhnhuPm_dH76l
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
 junifer/tests/test_stats.py,sha256=NljoGFu2JOPADbi9W0WeUHwpf8nZSdOkcCgCv-Z1fY4,4149
 junifer/typing/__init__.py,sha256=e0UbuxozXUIxz8h8pLokMOxZV629Q1lnA7vvgm95WF0,215
-junifer/typing/__init__.pyi,sha256=WbwaRGYrmDCnHtHDvxDshnEu_jh1fUjAd5VMOnpa1u4,504
-junifer/typing/_typing.py,sha256=cgQQq7CAFPeZTxko-22mWF2cp_S82JVNLTwMg0vsMAw,1507
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