junifer 0.0.6.dev530__tar.gz → 0.0.6.dev538__tar.gz

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.6.dev530
+Version: 0.0.6.dev538
 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>
@@ -44,7 +44,7 @@ Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
-Requires-Dist: junifer_data==1.2.0
+Requires-Dist: junifer_data==1.3.0
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
 Requires-Dist: neurokit2>=0.1.7; extra == "all"
@@ -69,6 +69,7 @@ Requires-Dist: towncrier<24.7.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
 Requires-Dist: setuptools-scm>=8; extra == "docs"
+Dynamic: license-file
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/docs/extending/index.rst

@@ -30,3 +30,4 @@ DataGrabbers, Preprocessors, Markers, etc.,  following the *junifer* way.
    parcellations
    coordinates
    masks
+   plugins

junifer-0.0.6.dev538/docs/extending/plugins.rst

@@ -0,0 +1,50 @@
+.. include:: ../links.inc
+
+.. _plugins:
+
+Creating a ``junifer`` plugin
+=============================
+
+What is a plugin
+----------------
+
+Plugins are additional components that extend the functionality of ``junifer``.
+Technically, plugins can also be called as extensions, but we clearly differentiate
+them in ``junifer`` as :ref:`extensions<extending_extension>` serve a different
+purpose. ``junifer`` plugins are command line programs which can be used
+independently but also integrates with the core ``junifer`` command line interface
+(CLI) framework.
+
+When a plugin is installed, we basically inject new behaviours into the ``junifer`` CLI
+while promoting modularity and allowing for easier maintenance and updates to the core
+application. A great plugin example is `junifer-data`_ which is well-integrated
+in ``junifer`` to access assets like parcellations, coordinates and masks, but also
+remains modular enough to update its CLI without disturbing that of ``junifer``.
+
+How to make a plugin
+--------------------
+
+A key distinction between a ``junifer`` extension and a ``junifer`` plugin is that a
+plugin will have its own CLI and be a Python package in its own right, for example,
+`junifer-data`_.
+
+The following steps should lead you to make a successful plugin:
+
+#. Create CLI for your plugin. As ``junifer`` uses `click`_ for its CLI, a plugin
+   should be creating its own ``click.Group`` as shown here:
+   `<https://click.palletsprojects.com/en/stable/commands/#commands-and-groups>`_.
+
+#. Integrate the `click`_-based plugin CLI with `setuptools`_ as shown here:
+   `<https://click.palletsprojects.com/en/stable/setuptools/#setuptools-integration>`_.
+
+#. Make sure the plugin CLI independently works as intended.
+
+#. Follow the steps here:
+   `<https://setuptools.pypa.io/en/latest/userguide/entry_point.html#entry-points-for-plugins>`_
+   and make a new entry point with the *name* as the sub-command you want under ``junifer`` command
+   and the *group* as ``"junifer.ext"``. The *name* should refer to the ``click.Group`` of your
+   plugin CLI.
+
+#. After you install your plugin in the same environment as your ``junifer`` installation, you can
+   observe your plugin being added as a new sub-command under ``junifer`` and working exactly as it
+   did independently.

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/docs/links.inc

@@ -12,6 +12,7 @@
 .. _`AML`: https://www.fz-juelich.de/inm/inm-7/EN/Forschung/Applied%20Machine%20Learning/_node.html
 .. _`INM-7`: https://www.fz-juelich.de/inm/inm-7/EN/Home/home_node.html
 .. _`julearn`: https://juaml.github.io/julearn
+.. _`junifer-data`: https://github.com/juaml/junifer-data-client
 
 .. _`pandas`: https://pandas.pydata.org
 .. _`pandas.DataFrame` : https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
@@ -24,6 +25,7 @@
 .. _`nipype`: https://nipype.readthedocs.io
 .. _`datalad`: https://datalad.org
 .. _`templateflow`: https://www.templateflow.org
+.. _`click`: https://click.palletsprojects.com/en/stable/
 
 .. _`venv`: https://docs.python.org/3/tutorial/venv.html
 .. _`conda env`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
@@ -36,6 +38,7 @@
 .. _`Wikipedia`: https://wikipedia.org
 .. _`YAML`: https://yaml.org
 
+.. _`setuptools`: https://setuptools.pypa.io/en/latest/
 .. _`setuptools_scm`: https://github.com/pypa/setuptools_scm/
 
 .. _`sphinx gallery`: https://sphinx-gallery.github.io/stable/index.html

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/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.dev530 → junifer-0.0.6.dev538}/junifer/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev530'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev530')
+__version__ = version = '0.0.6.dev538'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev538')

junifer-0.0.6.dev538/junifer/cli/__init__.py

@@ -0,0 +1,24 @@
+"""Junifer CLI components."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import sys
+
+import lazy_loader as lazy
+
+
+if sys.version_info < (3, 11):  # pragma: no cover
+    from importlib_metadata import entry_points
+else:
+    from importlib.metadata import entry_points
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+
+
+# Register extensions
+from .cli import cli
+
+for ep in entry_points(group="junifer.ext"):
+    cli.add_command(ep.load(), name=ep.name)

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/junifer/cli/cli.py

@@ -111,7 +111,9 @@ def _validate_verbose(
     )
 
 
-@click.group()
+@click.group
+@click.version_option()
+@click.help_option()
 def cli() -> None:  # pragma: no cover
     """JUelich NeuroImaging FEature extractoR."""
 

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.6.dev530
+Version: 0.0.6.dev538
 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>
@@ -44,7 +44,7 @@ Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
-Requires-Dist: junifer_data==1.2.0
+Requires-Dist: junifer_data==1.3.0
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
 Requires-Dist: neurokit2>=0.1.7; extra == "all"
@@ -69,6 +69,7 @@ Requires-Dist: towncrier<24.7.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
 Requires-Dist: setuptools-scm>=8; extra == "docs"
+Dynamic: license-file
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/junifer.egg-info/SOURCES.txt

@@ -63,80 +63,6 @@ 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/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/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -145,6 +71,7 @@ docs/extending/index.rst
 docs/extending/marker.rst
 docs/extending/masks.rst
 docs/extending/parcellations.rst
+docs/extending/plugins.rst
 docs/extending/preprocessor.rst
 docs/images/junifer_logo.png
 docs/understanding/data.rst

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/junifer.egg-info/requires.txt

@@ -12,7 +12,7 @@ tqdm<4.67.0,>=4.66.1
 templateflow>=23.0.0
 lapy<2.0.0,>=1.0.0
 lazy_loader==0.4
-junifer_data==1.2.0
+junifer_data==1.3.0
 
 [:python_version < "3.9"]
 importlib_metadata

{junifer-0.0.6.dev530 → junifer-0.0.6.dev538}/pyproject.toml

@@ -52,7 +52,7 @@ dependencies = [
     "lazy_loader==0.4",
     "importlib_metadata; python_version<'3.9'",
     "looseversion==1.3.0; python_version>='3.12'",
-    "junifer_data==1.2.0",
+    "junifer_data==1.3.0",
 ]
 dynamic = ["version"]
 

junifer-0.0.6.dev530/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.dev530/docs/changes/newsfragments/335.enh

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

junifer-0.0.6.dev530/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.dev530/docs/changes/newsfragments/355.misc

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

junifer-0.0.6.dev530/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.dev530/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.dev530/docs/changes/newsfragments/358.doc

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

junifer-0.0.6.dev530/docs/changes/newsfragments/359.doc

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

junifer-0.0.6.dev530/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.dev530/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.dev530/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.dev530/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.dev530/docs/changes/newsfragments/363.misc

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

junifer-0.0.6.dev530/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.dev530/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.dev530/docs/changes/newsfragments/369.bugfix

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

junifer-0.0.6.dev530/docs/changes/newsfragments/370.bugfix

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

junifer-0.0.6.dev530/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.dev530/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.dev530/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.dev530/docs/changes/newsfragments/380.misc

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

junifer-0.0.6.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/docs/changes/newsfragments/388.bugfix

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

junifer-0.0.6.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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.dev530/docs/changes/newsfragments/396.misc

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

junifer-0.0.6.dev530/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.dev530/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.dev530/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.dev530/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.dev530/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`_