docs/changes/newsfragments/401.feature

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

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__ = [
-    "cli",
-    "run",
-    "collect",
-    "queue",
-    "wtf",
-    "selftest",
-    "reset",
-    "list_elements",
-    "setup",
     "afni_docker",
-    "fsl_docker",
     "ants_docker",
+    "cli",
+    "collect",
     "freesurfer_docker",
+    "fsl_docker",
+    "list_elements",
+    "queue",
+    "reset",
+    "run",
+    "selftest",
+    "setup",
+    "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__ = [
-    "get_dependency_version",
-    "process_meta",
     "element_to_prefix",
-    "store_matrix_checks",
+    "get_dependency_version",
     "matrix_to_vector",
+    "process_meta",
+    "store_matrix_checks",
 ]
 
 

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__ = [
-    "DataGrabberLike",
-    "PreprocessorLike",
-    "MarkerLike",
-    "StorageLike",
-    "PipelineComponent",
-    "Dependencies",
     "ConditionalDependencies",
+    "ConfigVal",
+    "DataGrabberLike",
+    "DataGrabberPatterns",
+    "Dependencies",
     "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")