junifer 0.0.6.dev536__tar.gz → 0.0.7.dev18__tar.gz

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.6.dev536
+Version: 0.0.7.dev18
 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-0.0.7.dev18/docs/changes/newsfragments/333.enh

@@ -0,0 +1 @@
+Add support for Chatterjee's xi correlation in :class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/docs/whats_new.rst

@@ -10,6 +10,206 @@ What's new
 
 .. towncrier release notes start
 
+Junifer 0.0.6 (2025-03-24)
+--------------------------
+
+Bugfixes
+^^^^^^^^
+
+- Fix ``mri_binarize`` command preparation for structures with multiple indices
+  in :class:`.BrainPrint` by `Fede Raimondo`_ (:gh:`356`)
+- Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for
+  :class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_
+  (:gh:`360`)
+- Correct listing for :class:`.fMRIPrepConfoundRemover` in
+  ``junifer.pipeline.registry`` by `Synchon Mandal`_ (:gh:`369`)
+- Add ``'emomatching'`` task to :class:`.DataladAOMICPIOP2` by `Leonard Sasse`_
+  (:gh:`370`)
+- Use correct return code for ANTs commands while checking presence of external
+  commands by `Synchon Mandal`_ (:gh:`385`)
+- Use the :class:`junifer.pipeline.WorkDirManager` for temporary directories in
+  the :class:`.DataladDataGrabber` by `Fede Raimondo`_ (:gh:`386`)
+- Fix coordinates space transformation using ANTs by `Synchon Mandal`_
+  (:gh:`388`)
+- 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`_ (:gh:`398`)
+- Use correct file output suffices for AFNI-based markers by `Synchon Mandal`_
+  (:gh:`409`)
+- Fix ``t_r`` tampering by :func:`nilearn.image.clean_img` in
+  :class:`.fMRIPrepConfoundRemover` by `Fede Raimondo`_ and `Synchon Mandal`_
+  (:gh:`420`)
+- Fix coordinates fetching for Power and Dosenbach from ``junifer-data`` by
+  `Synchon Mandal`_ (:gh:`431`)
+- Remove ``Power2013`` from :class:`.CoordinatesRegistry` by `Synchon Mandal`_
+  (:gh:`436`)
+- Correct dispatch methods for ``*_data()`` functions by `Synchon Mandal`_
+  (:gh:`439`)
+
+
+API Changes
+^^^^^^^^^^^
+
+- ``get_parcellation``, ``load_parcellation``, ``list_parcellation``,
+  ``register_parcellation`` , ``get_coordinates``, ``load_coordinates``,
+  ``list_coordinates``, ``register_coordinates``, ``get_mask``, ``load_mask``,
+  ``list_mask``, ``register_mask`` have been removed in favour of
+  :func:`.get_data`, :func:`.load_data`, :func:`.list_data`,
+  :func:`.register_data` and :func:`.deregister_data` by `Synchon Mandal`_
+  (:gh:`387`)
+- :class:`.SpaceWarper`'s ``using`` now supports ``"auto"`` allowing auto tool
+  selection based on DataGrabber specification by `Synchon Mandal`_ (:gh:`390`)
+- Allow ``workdir`` to also be a mapping in YAML, with ``path`` and ``cleanup``
+  keys by `Synchon Mandal`_ (:gh:`402`)
+- Add ``source`` parameter and resurrect ``extra_input`` parameter for
+  ``compute_brain_mask`` by `Fede Raimondo`_ (:gh:`404`)
+- ``native_t1w`` parameter has been replaced with ``space`` to allow
+  :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
+  :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede
+  Raimondo`_ (:gh:`405`)
+- :meth:`.ParcellationRegistry.load` now has a new parameter ``target_space``
+  to provide parcellation in highest possible resolution if it does not match
+  the space of the parcellation by `Fede Raimondo`_ and `Synchon Mandal`_
+  (:gh:`411`)
+- Introduce new CLI parameter ``--verbose-datalad`` to control ``datalad``'s
+  logging handler by `Fede Raimondo`_ (:gh:`412`)
+- ``target_data`` parameter of :func:`.get_template` has been replaced with
+  ``target_img`` by `Fede Raimondo`_ (:gh:`413`)
+- Add ``template_space`` parameter for ``compute_brain_mask`` and
+  ``resolution`` parameter for :func:`.get_template` by `Fede Raimondo`_
+  (:gh:`415`)
+- Add ``scrub``, ``fd_threshold`` and ``std_vars_threshold`` parameters to
+  :class:`.fMRIPrepConfoundRemover` and allow ``"scrubbing"`` key of type bool
+  for ``strategy`` by `Synchon Mandal`_ (:gh:`421`)
+
+
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+- Improve Sphinx configuration and extensions by `Synchon Mandal`_ (:gh:`358`)
+- Add documentation on analysing extracted features by `Synchon Mandal`_
+  (:gh:`359`)
+- Add documentation on how to make a ``junifer`` plugin by `Synchon Mandal`_
+  (:gh:`366`)
+
+
+Enhancements
+^^^^^^^^^^^^
+
+- Raise error when partial or complete element selectors are invalid when
+  running the pipeline by `Synchon Mandal`_ (:gh:`319`)
+- Add support for Spearman's correlation in
+  :class:`.JuniferConnectivityMeasure` by `Leonard Sasse`_ (:gh:`335`)
+- Set proper stdout encoding for :func:`.run_ext_cmd` to ease human readability
+  by `Fede Raimondo`_ (:gh:`357`)
+- Adapt usage of ``junifer-data`` client API to fetch parcellations, masks,
+  coordinates and xfms by `Synchon Mandal`_ (:gh:`363`)
+- Allow for external python files in the ``with`` section of the yaml to import
+  other files by `Fede Raimondo`_ (:gh:`367`)
+- Use ``datalad``-enabled repository for template space transform files in
+  :func:`.get_xfm` by `Synchon Mandal`_ (:gh:`368`)
+- Add a ``cleanup`` parameter to the :class:`junifer.pipeline.WorkDirManager`,
+  which allows to disable cleaning up temporary directories by `Fede Raimondo`_
+  (:gh:`389`)
+- Update ``Warp`` data type to be a list of dictionaries and adapt to allow
+  multiple transforms to be specified by `Synchon Mandal`_ (:gh:`390`)
+- Refactor the masking logic in the pipeline to account for and optimise space
+  transformations and merges by `Synchon Mandal`_ and `Fede Raimondo`_
+  (:gh:`395`)
+- Allow ``workdir`` mapping form in YAML for easy debugging of single element
+  ``run`` by disabling cleanup of :class:`junifer.pipeline.WorkDirManager` by
+  `Synchon Mandal`_ (:gh:`402`)
+- Use :func:`junifer.utils.ConfigManager` to skip time-consuming dataset ID and
+  dirty checks for :class:`.DataladDataGrabber` by `Fede Raimondo`_ (:gh:`403`)
+- Enable ``compute_brain_mask`` to use subject-specific probseg files by `Fede
+  Raimondo`_ (:gh:`404`)
+- Update :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
+  :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede
+  Raimondo`_ (:gh:`405`)
+- Update Preprocessors to sync data their paths so that the results are
+  idempotent by `Synchon Mandal`_ (:gh:`408`)
+- Ease asset storage for AFNI-based markers by `Synchon Mandal`_ (:gh:`409`)
+- Refactor the parcellation logic in the pipeline to account for and optimise
+  space transformations and merges by `Synchon Mandal`_ and `Fede Raimondo`_
+  (:gh:`411`)
+- Adapt mask warpers to use correct interpolation method based on the type of
+  data by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`416`)
+- Adapt usage of ``junifer-data`` DataLad dataset to fetch parcellations,
+  masks, coordinates and xfms by `Synchon Mandal`_ (:gh:`418`)
+- Add scrubbing support to :class:`.fMRIPrepConfoundRemover` by `Synchon
+  Mandal`_ (:gh:`421`)
+- Add commit SHA check for ``junifer_data`` to simplify data fetching by `Fede
+  Raimondo`_ (:gh:`434`)
+
+
+Features
+^^^^^^^^
+
+- Introduce :func:`.normalize` and :func:`.reweight` functions for downstream
+  BrainPrint analysis in :mod:`.onthefly.brainprint` by `Synchon Mandal`_
+  (:gh:`354`)
+- Introduce :class:`junifer.pipeline.PipelineComponentRegistry` to centralise
+  pipeline component management by `Synchon Mandal`_ (:gh:`362`)
+- Add support for plugins by `Synchon Mandal`_ (:gh:`366`)
+- Introduce :class:`junifer.data.CoordinatesRegistry`,
+  :class:`junifer.data.ParcellationRegistry` and
+  :class:`junifer.data.MaskRegistry` to centralise data management by `Synchon
+  Mandal`_ (:gh:`387`)
+- Introduce ``junifer.typing`` sub-module to organise internal and external
+  type hints by `Synchon Mandal`_ (:gh:`392`)
+- Introduce :class:`junifer.utils.ConfigManager` singleton class to manage
+  global configuration by `Fede Raimondo`_ (:gh:`401`)
+- Introduce ``BOLD.reference`` nested type and adapt :class:`.SpaceWarper` and
+  necessary data components by `Fede Raimondo`_ (:gh:`407`)
+- Allow masks to be warped, if found, in :class:`.SpaceWarper` by `Synchon
+  Mandal`_ (:gh:`408`)
+- Add support for coloured :class:`logging.Formatter` to use with ``junifer``'s
+  :class:`logging.StreamHandler` based on environment by `Fede Raimondo`_
+  (:gh:`412`)
+- Allow storage of 2D timeseries, currently only supported by
+  HDF5FeatureStorage by `Fede Raimondo`_ (:gh:`422`)
+
+
+Miscellaneous
+^^^^^^^^^^^^^
+
+- Adopt lazy-import mechanism for the package by `Synchon Mandal`_ (:gh:`355`)
+- Refactor ``api`` sub-package and introduce new ``cli`` sub-package by
+  `Synchon Mandal`_ (:gh:`361`)
+- Add ``junifer-data`` as a dependency by `Synchon Mandal`_ (:gh:`363`)
+- Drop support for Python 3.8, add support for Python 3.13 and make Python 3.12
+  the base for code coverage by `Synchon Mandal`_ (:gh:`372`)
+- Add Dockerfile for docs CI and a corresponding action for building and
+  publishing the image by `Synchon Mandal`_ (:gh:`373`)
+- Adopt usage of custom docs CI image for building and previewing docs actions
+  by `Synchon Mandal`_ (:gh:`374`)
+- Update Dependabot GitHub Action to support groups by `Synchon Mandal`_
+  (:gh:`380`)
+- Add Dockerfile for CI and a corresponding action for building and publishing
+  the image by `Synchon Mandal`_ (:gh:`382`)
+- Adopt usage of custom CI image for testing junifer action by `Synchon
+  Mandal`_ (:gh:`383`)
+- Improve docs publishing action and add a manual trigger for it by `Synchon
+  Mandal`_ (:gh:`384`)
+- Refactor ``Singleton`` class to use a metaclass instead of a class decorator
+  by `Fede Raimondo`_ (:gh:`391`)
+- Update type hints across codebase to be Python>=3.9 compatible by `Synchon
+  Mandal`_ (:gh:`393`)
+- Update Docker image recipes and GitHub Actions workflows by `Synchon Mandal`_
+  (:gh:`396`)
+- Simplify logic for parcellation and mask space warping by `Synchon Mandal`_
+  (:gh:`414`)
+- Remove ``httpx`` as a dependency by `Synchon Mandal`_ (:gh:`418`)
+- Fix coverage in CI by `Fede Raimondo`_ (:gh:`424`)
+- Use ``junifer-data`` in CI images by `Synchon Mandal`_ (:gh:`427`)
+- Improve GitHub Actions workflows by `Synchon Mandal`_ (:gh:`428`)
+- Bump ``junifer-data`` to ``v2`` for CI workflows, remove ``Power`` and add
+  ``Seitzman2018`` to :class:`.CoordinatesRegistry` by `Synchon Mandal`_
+  (:gh:`437`)
+- Bump ``junifer-data`` to ``v2`` for Docker images by `Synchon Mandal`_
+  (:gh:`438`)
+
+
 Junifer 0.0.5 (2024-07-22)
 --------------------------
 

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/junifer/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev536'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev536')
+__version__ = version = '0.0.7.dev18'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev18')

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,6 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import sys
+from itertools import product
 from typing import Callable, Optional
 
 import numpy as np
@@ -322,11 +324,13 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         The covariance estimator
         (default ``EmpiricalCovariance(store_precision=False)``).
     kind : {"covariance", "correlation", "spearman correlation", \
-            "partial correlation", "tangent", "precision"}, optional
+            "partial correlation", "xi correlation", "tangent", \
+            "precision"}, optional
         The matrix kind. The default value uses Pearson's correlation.
         If ``"spearman correlation"`` is used, the data will be ranked before
-        estimating the covariance. For the use of ``"tangent"`` see [1]_
-        (default "correlation").
+        estimating the covariance. For ``"xi correlation"``, the coefficient
+        is not symmetric and should be interpreted as a measure of dependence
+        [2]_ . For the use of ``"tangent"`` see [1]_ (default "correlation").
     vectorize : bool, optional
         If True, connectivity matrices are reshaped into 1D arrays and only
         their flattened lower triangular parts are returned (default False).
@@ -372,6 +376,12 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
            Springer.
            doi:10/cn2h9c.
 
+    .. [2] Chatterjee, S.
+           A new coefficient of correlation.
+           Journal of the American Statistical Association 116.536 (2021):
+           2009-2022.
+           doi:10.1080/01621459.2020.1758115.
+
     """
 
     def __init__(
@@ -420,6 +430,25 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
                 covariances_std.append(self.cov_estimator_.fit(x).covariance_)
 
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
+        elif self.kind == "xi correlation":
+            if sys.version_info < (3, 10):  # pragma: no cover
+                raise_error(
+                    klass=RuntimeError,
+                    msg=(
+                        "scipy.stats.chatterjeexi is available from "
+                        "scipy 1.15.0 and that requires Python 3.10 and above."
+                    ),
+                )
+            connectivities = []
+            for x in X:
+                n_rois = x.shape[1]
+                connectivity = np.ones((n_rois, n_rois))
+                for i, j in product(range(n_rois), range(n_rois)):
+                    if i != j:
+                        connectivity[i, j] = stats.chatterjeexi(
+                            x[:, i], x[:, j], y_continuous=True
+                        ).statistic
+                connectivities.append(connectivity)
         else:
             covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
             if self.kind in ("covariance", "tangent"):

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import copy
+import sys
 import warnings
 from math import cosh, exp, log, sinh, sqrt
 from typing import TYPE_CHECKING, Optional, Union
@@ -12,7 +13,11 @@ import numpy as np
 import pytest
 from nilearn.connectome.connectivity_matrices import sym_matrix_to_vec
 from nilearn.tests.test_signal import generate_signals
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import (
+    assert_allclose,
+    assert_array_almost_equal,
+    assert_array_equal,
+)
 from pandas import DataFrame
 from scipy import linalg
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
@@ -1088,3 +1093,42 @@ def test_connectivity_measure_standardize(
         ).fit_transform(signals)
         for m in record:
             assert match not in m.message
+
+
+@pytest.mark.skipif(
+    sys.version_info > (3, 9),
+    reason="will have correct scipy version so no error",
+)
+def test_xi_correlation_error() -> None:
+    """Check xi correlation according to paper."""
+    with pytest.raises(RuntimeError, match="scipy.stats.chatterjeexi"):
+        JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+            np.zeros((2, 2))
+        )
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 10),
+    reason=(
+        "needs scipy 1.15.0 and above which in turn requires "
+        "python 3.10 and above"
+    ),
+)
+def test_xi_correlation() -> None:
+    """Check xi correlation according to paper."""
+    rng = np.random.default_rng(25982435982346983)
+    x = rng.random(size=10)
+    y = rng.random(size=10)
+    arr = np.column_stack((x, y))
+    expected = np.array(
+        [
+            [
+                [1.0, -0.3030303],
+                [-0.18181818, 1.0],
+            ]
+        ]
+    )
+    got = JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+        [arr]
+    )
+    assert_allclose(expected, got)

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -143,14 +143,17 @@ class FunctionalConnectivityBase(BaseMarker):
             },
         )
         # Create dictionary for output
+        labels = aggregation["aggregation"]["col_names"]
         return {
             "functional_connectivity": {
                 "data": connectivity.fit_transform(
                     [aggregation["aggregation"]["data"]]
                 )[0],
-                # Create column names
-                "row_names": aggregation["aggregation"]["col_names"],
-                "col_names": aggregation["aggregation"]["col_names"],
-                "matrix_kind": "tril",
+                "row_names": labels,
+                "col_names": labels,
+                # xi correlation coefficient is not symmetric
+                "matrix_kind": (
+                    "full" if self.conn_method == "xi correlation" else "tril"
+                ),
             },
         }

{junifer-0.0.6.dev536 → junifer-0.0.7.dev18}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.6.dev536
+Version: 0.0.7.dev18
 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.dev536 → junifer-0.0.7.dev18}/junifer.egg-info/SOURCES.txt

@@ -63,82 +63,7 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
-docs/changes/newsfragments/319.enh
-docs/changes/newsfragments/335.enh
-docs/changes/newsfragments/354.feature
-docs/changes/newsfragments/355.misc
-docs/changes/newsfragments/356.bugfix
-docs/changes/newsfragments/357.enh
-docs/changes/newsfragments/358.doc
-docs/changes/newsfragments/359.doc
-docs/changes/newsfragments/360.bugfix
-docs/changes/newsfragments/361.misc
-docs/changes/newsfragments/362.feature
-docs/changes/newsfragments/363.enh
-docs/changes/newsfragments/363.misc
-docs/changes/newsfragments/366.doc
-docs/changes/newsfragments/366.feature
-docs/changes/newsfragments/367.enh
-docs/changes/newsfragments/368.enh
-docs/changes/newsfragments/369.bugfix
-docs/changes/newsfragments/370.bugfix
-docs/changes/newsfragments/372.misc
-docs/changes/newsfragments/373.misc
-docs/changes/newsfragments/374.misc
-docs/changes/newsfragments/380.misc
-docs/changes/newsfragments/382.misc
-docs/changes/newsfragments/383.misc
-docs/changes/newsfragments/384.misc
-docs/changes/newsfragments/385.bugfix
-docs/changes/newsfragments/386.bugfix
-docs/changes/newsfragments/387.change
-docs/changes/newsfragments/387.feature
-docs/changes/newsfragments/388.bugfix
-docs/changes/newsfragments/389.enh
-docs/changes/newsfragments/390.change
-docs/changes/newsfragments/390.enh
-docs/changes/newsfragments/391.misc
-docs/changes/newsfragments/392.feature
-docs/changes/newsfragments/393.misc
-docs/changes/newsfragments/395.enh
-docs/changes/newsfragments/396.misc
-docs/changes/newsfragments/398.bugfix
-docs/changes/newsfragments/401.feature
-docs/changes/newsfragments/402.change
-docs/changes/newsfragments/402.enh
-docs/changes/newsfragments/403.enh
-docs/changes/newsfragments/404.change
-docs/changes/newsfragments/404.enh
-docs/changes/newsfragments/405.change
-docs/changes/newsfragments/405.enh
-docs/changes/newsfragments/407.feature
-docs/changes/newsfragments/408.enh
-docs/changes/newsfragments/408.feature
-docs/changes/newsfragments/409.bugfix
-docs/changes/newsfragments/409.enh
-docs/changes/newsfragments/411.change
-docs/changes/newsfragments/411.enh
-docs/changes/newsfragments/412.change
-docs/changes/newsfragments/412.feature
-docs/changes/newsfragments/413.change
-docs/changes/newsfragments/414.misc
-docs/changes/newsfragments/415.change
-docs/changes/newsfragments/416.enh
-docs/changes/newsfragments/418.enh
-docs/changes/newsfragments/418.misc
-docs/changes/newsfragments/420.bugfix
-docs/changes/newsfragments/421.change
-docs/changes/newsfragments/421.enh
-docs/changes/newsfragments/422.feature
-docs/changes/newsfragments/424.misc
-docs/changes/newsfragments/427.misc
-docs/changes/newsfragments/428.misc
-docs/changes/newsfragments/431.bugfix
-docs/changes/newsfragments/434.enh
-docs/changes/newsfragments/436.bugfix
-docs/changes/newsfragments/437.misc
-docs/changes/newsfragments/438.misc
-docs/changes/newsfragments/439.bugfix
+docs/changes/newsfragments/333.enh
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

junifer-0.0.6.dev536/docs/changes/newsfragments/319.enh

@@ -1 +0,0 @@
-Raise error when partial or complete element selectors are invalid when running the pipeline by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/335.enh

@@ -1 +0,0 @@
-Add support for Spearman's correlation in :class:`.JuniferConnectivityMeasure` by `Leonard Sasse`_

junifer-0.0.6.dev536/docs/changes/newsfragments/354.feature

@@ -1 +0,0 @@
-Introduce :func:`.normalize` and :func:`.reweight` functions for downstream BrainPrint analysis in :mod:`.onthefly.brainprint` by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/355.misc

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

junifer-0.0.6.dev536/docs/changes/newsfragments/356.bugfix

@@ -1 +0,0 @@
-Fix ``mri_binarize`` command preparation for structures with multiple indices in :class:`.BrainPrint` by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/357.enh

@@ -1 +0,0 @@
-Set proper stdout encoding for :func:`.run_ext_cmd` to ease human readability by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/358.doc

@@ -1 +0,0 @@
-Improve Sphinx configuration and extensions by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/359.doc

@@ -1 +0,0 @@
-Add documentation on analysing extracted features by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/360.bugfix

@@ -1 +0,0 @@
-Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for :class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/361.misc

@@ -1 +0,0 @@
-Refactor ``api`` sub-package and introduce new ``cli`` sub-package by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/362.feature

@@ -1 +0,0 @@
-Introduce :class:`junifer.pipeline.PipelineComponentRegistry` to centralise pipeline component management by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/363.enh

@@ -1 +0,0 @@
-Adapt usage of ``junifer-data`` client API to fetch parcellations, masks, coordinates and xfms by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/363.misc

@@ -1 +0,0 @@
-Add ``junifer-data`` as a dependency by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/366.doc

@@ -1 +0,0 @@
-Add documentation on how to make a ``junifer`` plugin by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/366.feature

@@ -1 +0,0 @@
-Add support for plugins by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/367.enh

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

junifer-0.0.6.dev536/docs/changes/newsfragments/368.enh

@@ -1 +0,0 @@
-Use ``datalad``-enabled repository for template space transform files in :func:`.get_xfm` by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/369.bugfix

@@ -1 +0,0 @@
-Correct listing for :class:`.fMRIPrepConfoundRemover` in ``junifer.pipeline.registry`` by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/370.bugfix

@@ -1 +0,0 @@
-Add ``'emomatching'`` task to :class:`.DataladAOMICPIOP2` by `Leonard Sasse`_

junifer-0.0.6.dev536/docs/changes/newsfragments/372.misc

@@ -1 +0,0 @@
-Drop support for Python 3.8, add support for Python 3.13 and make Python 3.12 the base for code coverage by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/373.misc

@@ -1 +0,0 @@
-Add Dockerfile for docs CI and a corresponding action for building and publishing the image by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/374.misc

@@ -1 +0,0 @@
-Adopt usage of custom docs CI image for building and previewing docs actions by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/380.misc

@@ -1 +0,0 @@
-Update Dependabot GitHub Action to support groups by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/382.misc

@@ -1 +0,0 @@
-Add Dockerfile for CI and a corresponding action for building and publishing the image by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/383.misc

@@ -1 +0,0 @@
-Adopt usage of custom CI image for testing junifer action by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/384.misc

@@ -1 +0,0 @@
-Improve docs publishing action and add a manual trigger for it by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/385.bugfix

@@ -1 +0,0 @@
-Use correct return code for ANTs commands while checking presence of external commands by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/386.bugfix

@@ -1 +0,0 @@
-Use the :class:`junifer.pipeline.WorkDirManager` for temporary directories in the :class:`.DataladDataGrabber` by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/387.change

@@ -1 +0,0 @@
-``get_parcellation``, ``load_parcellation``, ``list_parcellation``, ``register_parcellation`` , ``get_coordinates``, ``load_coordinates``, ``list_coordinates``, ``register_coordinates``, ``get_mask``, ``load_mask``, ``list_mask``, ``register_mask`` have been removed in favour of :func:`.get_data`, :func:`.load_data`, :func:`.list_data`, :func:`.register_data` and :func:`.deregister_data` by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/387.feature

@@ -1 +0,0 @@
-Introduce :class:`junifer.data.CoordinatesRegistry`, :class:`junifer.data.ParcellationRegistry` and :class:`junifer.data.MaskRegistry` to centralise data management by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/388.bugfix

@@ -1 +0,0 @@
-Fix coordinates space transformation using ANTs by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/389.enh

@@ -1 +0,0 @@
-Add a ``cleanup`` parameter to the :class:`junifer.pipeline.WorkDirManager`, which allows to disable cleaning up temporary directories by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/390.change

@@ -1 +0,0 @@
-:class:`.SpaceWarper`'s ``using`` now supports ``"auto"`` allowing auto tool selection based on DataGrabber specification by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/390.enh

@@ -1 +0,0 @@
-Update ``Warp`` data type to be a list of dictionaries and adapt to allow multiple transforms to be specified by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/391.misc

@@ -1 +0,0 @@
-Refactor ``Singleton`` class to use a metaclass instead of a class decorator by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/392.feature

@@ -1 +0,0 @@
-Introduce ``junifer.typing`` sub-module to organise internal and external type hints by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/393.misc

@@ -1 +0,0 @@
-Update type hints across codebase to be Python>=3.9 compatible by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/395.enh

@@ -1 +0,0 @@
-Refactor the masking logic in the pipeline to account for and optimise space transformations and merges by `Synchon Mandal`_ and `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/396.misc

@@ -1 +0,0 @@
-Update Docker image recipes and GitHub Actions workflows by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/398.bugfix

@@ -1 +0,0 @@
-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.dev536/docs/changes/newsfragments/401.feature

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

junifer-0.0.6.dev536/docs/changes/newsfragments/402.change

@@ -1 +0,0 @@
-Allow ``workdir`` to also be a mapping in YAML, with ``path`` and ``cleanup`` keys by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/402.enh

@@ -1 +0,0 @@
-Allow ``workdir`` mapping form in YAML for easy debugging of single element ``run`` by disabling cleanup of :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_

junifer-0.0.6.dev536/docs/changes/newsfragments/403.enh

@@ -1 +0,0 @@
-Use :func:`junifer.utils.ConfigManager` to skip time-consuming dataset ID and dirty checks for :class:`.DataladDataGrabber` by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/404.change

@@ -1 +0,0 @@
-Add ``source`` parameter and resurrect ``extra_input`` parameter for ``compute_brain_mask`` by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/404.enh

@@ -1 +0,0 @@
-Enable ``compute_brain_mask`` to use subject-specific probseg files by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/405.change

@@ -1 +0,0 @@
-``native_t1w`` parameter has been replaced with ``space`` to allow :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede Raimondo`_

junifer-0.0.6.dev536/docs/changes/newsfragments/405.enh

@@ -1 +0,0 @@
-Update :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede Raimondo`_