junifer 0.0.7.dev18__py3-none-any.whl → 0.0.7.dev47__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- junifer/_version.py +2 -2
- junifer/api/decorators.py +0 -1
- junifer/api/functions.py +1 -2
- junifer/api/queue_context/gnu_parallel_local_adapter.py +4 -7
- junifer/api/queue_context/htcondor_adapter.py +6 -10
- junifer/cli/tests/test_parser.py +66 -0
- junifer/data/_dispatch.py +5 -5
- junifer/data/coordinates/_ants_coordinates_warper.py +1 -1
- junifer/data/coordinates/_coordinates.py +1 -1
- junifer/data/coordinates/_fsl_coordinates_warper.py +1 -1
- junifer/data/coordinates/tests/test_coordinates.py +38 -16
- junifer/data/masks/_ants_mask_warper.py +1 -1
- junifer/data/masks/_fsl_mask_warper.py +1 -1
- junifer/data/masks/tests/test_masks.py +66 -33
- junifer/data/parcellations/_ants_parcellation_warper.py +1 -1
- junifer/data/parcellations/_fsl_parcellation_warper.py +1 -1
- junifer/data/parcellations/_parcellations.py +7 -7
- junifer/data/parcellations/tests/test_parcellations.py +162 -76
- junifer/data/tests/test_data_utils.py +0 -1
- junifer/data/utils.py +1 -1
- junifer/datagrabber/aomic/id1000.py +6 -0
- junifer/datagrabber/aomic/piop1.py +4 -3
- junifer/datagrabber/aomic/piop2.py +4 -3
- junifer/datagrabber/pattern_datalad.py +0 -1
- junifer/datagrabber/pattern_validation_mixin.py +0 -1
- junifer/datagrabber/tests/test_dmcc13_benchmark.py +4 -8
- junifer/markers/base.py +3 -3
- junifer/markers/brainprint.py +5 -5
- junifer/markers/complexity/multiscale_entropy_auc.py +3 -3
- junifer/markers/complexity/range_entropy.py +3 -3
- junifer/markers/complexity/sample_entropy.py +3 -3
- junifer/markers/falff/falff_parcels.py +2 -6
- junifer/markers/falff/falff_spheres.py +2 -6
- junifer/markers/functional_connectivity/functional_connectivity_base.py +0 -1
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +2 -1
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +2 -1
- junifer/markers/reho/_afni_reho.py +1 -1
- junifer/markers/reho/reho_base.py +0 -1
- junifer/markers/reho/reho_parcels.py +0 -1
- junifer/markers/reho/reho_spheres.py +0 -1
- junifer/markers/temporal_snr/temporal_snr_base.py +0 -1
- junifer/markers/tests/test_markers_base.py +0 -1
- junifer/onthefly/_brainprint.py +3 -3
- junifer/onthefly/read_transform.py +1 -2
- junifer/onthefly/tests/test_read_transform.py +0 -1
- junifer/pipeline/tests/test_marker_collection.py +2 -1
- junifer/pipeline/workdir_manager.py +1 -2
- junifer/preprocess/confounds/fmriprep_confound_remover.py +1 -1
- junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +0 -1
- junifer/preprocess/smoothing/tests/test_smoothing.py +0 -1
- junifer/preprocess/warping/_ants_warper.py +2 -3
- junifer/preprocess/warping/_fsl_warper.py +1 -1
- junifer/preprocess/warping/space_warper.py +4 -2
- junifer/storage/hdf5.py +14 -2
- junifer/storage/pandas_base.py +3 -1
- junifer/storage/sqlite.py +3 -8
- junifer/storage/tests/test_hdf5.py +1 -0
- junifer/storage/tests/test_pandas_base.py +6 -3
- junifer/storage/tests/test_storage_base.py +2 -1
- junifer/utils/logging.py +38 -128
- junifer/utils/tests/test_logging.py +12 -4
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/METADATA +3 -2
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/RECORD +68 -91
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/WHEEL +1 -1
- junifer/data/coordinates/VOIs/meta/AutobiographicalMemory_VOIs.txt +0 -23
- junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt +0 -19
- junifer/data/coordinates/VOIs/meta/CogAR_VOIs.txt +0 -8
- junifer/data/coordinates/VOIs/meta/DMNBuckner_VOIs.txt +0 -6
- junifer/data/coordinates/VOIs/meta/Dosenbach2010_MNI_VOIs.txt +0 -160
- junifer/data/coordinates/VOIs/meta/Empathy_VOIs.txt +0 -22
- junifer/data/coordinates/VOIs/meta/Motor_VOIs.txt +0 -10
- junifer/data/coordinates/VOIs/meta/MultiTask_VOIs.txt +0 -9
- junifer/data/coordinates/VOIs/meta/PhysioStress_VOIs.txt +0 -18
- junifer/data/coordinates/VOIs/meta/Power2011_MNI_VOIs.txt +0 -264
- junifer/data/coordinates/VOIs/meta/Power2013_MNI_VOIs.tsv +0 -264
- junifer/data/coordinates/VOIs/meta/Rew_VOIs.txt +0 -25
- junifer/data/coordinates/VOIs/meta/Somatosensory_VOIs.txt +0 -10
- junifer/data/coordinates/VOIs/meta/ToM_VOIs.txt +0 -15
- junifer/data/coordinates/VOIs/meta/VigAtt_VOIs.txt +0 -16
- junifer/data/coordinates/VOIs/meta/WM_VOIs.txt +0 -23
- junifer/data/coordinates/VOIs/meta/eMDN_VOIs.txt +0 -17
- junifer/data/coordinates/VOIs/meta/eSAD_VOIs.txt +0 -12
- junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt +0 -16
- junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz +0 -0
- junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz +0 -0
- junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.nii.gz +0 -0
- junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz +0 -0
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/entry_points.txt +0 -0
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/licenses/AUTHORS.rst +0 -0
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/licenses/LICENSE.md +0 -0
- {junifer-0.0.7.dev18.dist-info → junifer-0.0.7.dev47.dist-info}/top_level.txt +0 -0
junifer/utils/logging.py
CHANGED
@@ -8,15 +8,14 @@ import os
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import sys
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if sys.version_info < (3, 12):
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if sys.version_info < (3, 12): # pragma: no cover
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from distutils.version import LooseVersion
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else:
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else:
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from looseversion import LooseVersion
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import logging
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import warnings
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from pathlib import Path
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from subprocess import PIPE, Popen, TimeoutExpired
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from typing import ClassVar, NoReturn, Optional, Union
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from warnings import warn
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@@ -77,7 +76,7 @@ class WrapStdOut(logging.StreamHandler):
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# just stdout) in order for this to work (tested on OSX and Linux)
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if hasattr(sys.stdout, name):
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return getattr(sys.stdout, name)
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else:
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else: # pragma: no cover
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raise AttributeError(f"'file' object has not attribute '{name}'")
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COLOR_SEQ: str = "\033[1;%dm"
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BOLD_SEQ: str = "\033[1m"
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def __init__(
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def __init__(
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self, fmt: str, datefmt: Optional[str] = None
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) -> None: # pragma: no cover
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"""Initialize the ColorFormatter."""
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logging.Formatter.__init__(self, fmt, datefmt)
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def format(self, record: logging.LogRecord) -> str:
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def format(self, record: logging.LogRecord) -> str: # pragma: no cover
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"""Format the log record.
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Parameters
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return logging.Formatter.format(self, record)
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def _get_git_head(path: Path) -> str:
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"""Aux function to read HEAD from git.
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Parameters
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----------
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path : pathlib.Path
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The path to read git HEAD from.
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Returns
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-------
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str
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Empty string if timeout expired for subprocess command execution else
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git HEAD information.
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Raises
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------
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FileNotFoundError
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If ``path`` is invalid.
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"""
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if not path.exists():
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raise_error(
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msg=f"This path does not exist: {path}", klass=FileNotFoundError
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)
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command = f"cd {path}; git rev-parse --verify HEAD"
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process = Popen(
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args=command,
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stdout=PIPE,
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shell=True,
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)
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try:
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stdout, _ = process.communicate(timeout=10)
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proc_stdout = stdout.strip().decode()
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except TimeoutExpired:
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process.kill()
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proc_stdout = ""
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return proc_stdout
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def get_versions() -> dict:
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"""Import stuff and get versions if module.
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The module names and corresponding versions.
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"""
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# Setup dictionary to track versions of modules
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module_versions = {}
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for name, module in sys.modules.copy().items():
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# Bypassing sub-modules of packages and
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# allowing ruamel.yaml
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if "." in name and name != "ruamel.yaml":
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continue
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continue
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# Get version or None as string
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vstring = str(getattr(module, "__version__", None))
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module_version = getattr(
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if module_version is None:
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module_version = None
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elif "git" in module_version:
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git_path = Path(module.__file__).resolve().parent # type: ignore
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head = _get_git_head(git_path)
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module_version += f"-HEAD:{head}"
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# Get module version
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module_version = getattr(LooseVersion(vstring), "vstring", None)
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module_versions[name] = module_version
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return module_versions
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# """Get versions of external tools used by junifer.
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# Parameters
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# ----------
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# tbox_path : pathlib.Path
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# The path to external toolboxes.
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# Returns
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# -------
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# dict
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# The dependency information.
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# """
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# versions = {}
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# # spm_path = tbox_path / 'spm12'
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# # if spm_path.exists():
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# # head = _get_git_head(spm_path)
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# # module_version = 'SPM12-HEAD:{}'.format(head)
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# # versions['spm'] = module_version
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# return versions
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def _close_handlers(logger: logging.Logger) -> None:
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def _close_handlers(logger: logging.Logger) -> None: # pragma: no cover
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"""Safely close relevant handlers for logger.
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logger.removeHandler(handler)
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def
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"""Log
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versions : dict
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The dictionary with keys as dependency names and values as the
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versions.
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name : str
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The dependency to look up in `versions`.
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"""
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if name in versions:
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logger.info(f"{name}: {versions[name]}")
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def log_versions(tbox_path: Optional[Path] = None) -> None:
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"""Log versions of dependencies and junifer.
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If `tbox_path` is specified, can also log versions of external toolboxes.
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----------
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tbox_path : pathlib.Path, optional
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The path to external toolboxes (default None).
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"""
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def log_versions() -> None:
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"""Log versions of dependencies and junifer."""
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# Get versions of all found packages
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versions = get_versions()
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# Set packages to log
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pkgs_to_log = [
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"click",
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"numpy",
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"scipy",
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"datalad",
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"pandas",
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"nibabel",
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"nilearn",
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"sqlalchemy",
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"ruamel.yaml",
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"h5py",
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"tqdm",
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"templateflow",
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"lapy",
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"junifer_data",
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"junifer",
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]
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# Log
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logger.info("===== Lib Versions =====")
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_safe_log(versions, "nipype")
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_safe_log(versions, "nitime")
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_safe_log(versions, "nilearn")
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_safe_log(versions, "nibabel")
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_safe_log(versions, "junifer")
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for pkg in pkgs_to_log:
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if pkg in versions:
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logger.info(f"{pkg}: {versions[pkg]}")
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logger.info("========================")
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if tbox_path is not None:
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# ext_versions = get_ext_versions(tbox_path)
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# logger.info('spm: {}'.format(ext_versions['spm']))
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# logger.info('========================')
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pass
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def _can_use_color(handler: logging.Handler) -> bool:
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def _can_use_color(handler: logging.Handler) -> bool: # pragma: no cover
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"""Check if color can be used in the logging output.
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Parameters
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# Set logging format
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output_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
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# "%(asctime)s [%(levelname)s] %(message)s "
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# "(%(filename)s:%(lineno)s)"
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# )
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if _can_use_color(lh):
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if _can_use_color(lh): # pragma: no cover
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formatter = ColorFormatter(fmt=output_format)
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formatter = logging.Formatter(fmt=output_format)
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assert any("Warn message" in line for line in lines)
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assert any("Error message" in line for line in lines)
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configure_logging(
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configure_logging(
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fname=str((tmp_path / "test2.log").resolve()), level="INFO"
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)
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logger.debug("Debug message")
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logger.info("Info message")
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logger.warning("Warn message")
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assert any("Warn message" in line for line in lines)
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configure_logging(
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configure_logging(
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fname=tmp_path / "test3.log", level="WARNING", level_datalad="WARNING"
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)
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logger.debug("Debug message")
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logger.info("Info message")
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logger.warning("Warn message")
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configure_logging(fname=tmp_path / "test4.log", level=
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configure_logging(fname=tmp_path / "test4.log", level=logging.ERROR)
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logger.debug("Debug message")
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logger.info("Info message")
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with pytest.warns(UserWarning, match="to avoid this message"):
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configure_logging(
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configure_logging(
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