PyPI - junifer - Versions diffs - 0.0.5.dev240__tar.gz → 0.0.6.dev3__tar.gz - Mend

junifer 0.0.5.dev240tar.gz → 0.0.6.dev3tar.gz

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.

Files changed (412) hide show

{junifer-0.0.5.dev240 → junifer-0.0.6.dev3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev240
+Version: 0.0.6.dev3
 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.dev3/docs/changes/newsfragments/356.bugfix ADDED Viewed

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

{junifer-0.0.5.dev240 → junifer-0.0.6.dev3}/docs/whats_new.rst RENAMED Viewed

@@ -8,6 +8,127 @@ What's new
 .. towncrier release notes start
+Junifer 0.0.5 (2024-07-22)
+--------------------------
+Bugfixes
+^^^^^^^^
+- Remove extra dimension from parcellations warped via ANTs to other template
+  spaces by `Synchon Mandal`_ (:gh:`324`)
+- Remove extra dimension from parcellations warped via ANTs when merging
+  parcellations by `Synchon Mandal`_ (:gh:`331`)
+- Fix ``junifer reset`` to properly delete storage directory and handle
+  ``junifer_jobs`` deletion if not empty by `Synchon Mandal`_ (:gh:`332`)
+- Fix validation failure of multiple Preprocessors with different input data
+  types requirement by `Synchon Mandal`_ (:gh:`339`)
+- Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_
+  (:gh:`340`)
+API Changes
+^^^^^^^^^^^
+- For :class:`.CrossParcellationFC`, ``aggregation_method`` and
+  ``correlation_method`` have been renamed to ``agg_method`` and
+  ``corr_method`` respectively and ``agg_method_params`` has been added; for
+  ``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`,
+  :class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and
+  :class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have
+  been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon
+  Mandal`_ (:gh:`348`)
+- ``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and
+  :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and
+  fALFF by `Synchon Mandal`_ (:gh:`349`)
+- Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not
+  raise error on missing mandatory key checks for data types by `Synchon
+  Mandal`_ (:gh:`351`)
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+- Improve sub-package level docstrings to better reflect their purposes by
+  `Synchon Mandal`_ (:gh:`115`)
+- Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_ (:gh:`327`)
+- Add missing DataGrabber ``types`` options in respective docstrings of
+  :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`,
+  :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon
+  Mandal`_ (:gh:`330`)
+Enhancements
+^^^^^^^^^^^^
+- Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean
+  aggregation function behaves exactly as
+  :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_ (:gh:`136`)
+- Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as
+  "nested types" of the actual data type by `Synchon Mandal`_ (:gh:`341`)
+- Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
+  :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon
+  Mandal`_ (:gh:`346`)
+- ``FunctionalConnectivity``-family Markers now use
+  :class:`sklearn.covariance.EmpiricalCovariance` as the default covariance
+  estimator and ``correlation`` as the default connecivity matrix kind by
+  `Synchon Mandal`_ (:gh:`348`)
+- Enable Markers to output multiple features by `Synchon Mandal`_ (:gh:`349`)
+- Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_ (:gh:`350`)
+- Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in
+  :gh:`341` by `Synchon Mandal`_ (:gh:`351`)
+Features
+^^^^^^^^
+- Introduce :class:`.Smoothing` for smoothing / blurring images as a
+  preprocessing step by `Synchon Mandal`_ (:gh:`161`)
+- Add support for choosing between ``bash`` and ``zsh`` shells when queueing by
+  `Synchon Mandal`_ (:gh:`273`)
+- Add ``junifer list-elements`` to list out available elements for a
+  DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_
+  (:gh:`323`)
+- Introduce new storage type ``scalar_table`` and adapt
+  :class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_ (:gh:`343`)
+- Add support for `BrainPrint
+  <https://github.com/Deep-MI/BrainPrint?tab=readme-ov-file>`_ marker by
+  `Synchon Mandal`_ (:gh:`344`)
+- Allow Unix path expansion directives to be used in
+  :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_ (:gh:`345`)
+- Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by
+  `Synchon Mandal`_ (:gh:`346`)
+- Introduce :class:`.JuniferConnectivityMeasure` for customising functional
+  connectivity matrix kinds and measurements by `Synchon Mandal`_ (:gh:`348`)
+- Introduce :class:`.PatternValidationMixin` to simplify validation for
+  pattern-based DataGrabbers and :func:`.deep_update` for updating dictionary
+  with varying width and depth by `Synchon Mandal`_ (:gh:`351`)
+Miscellaneous
+^^^^^^^^^^^^^
+- Improve CI to allow external tool installation to fail gracefully and update
+  necessary dependency version and conditional checks by `Synchon Mandal`_
+  (:gh:`318`)
+- Update ``pre-commit`` dependency versions, add ``blacken-docs`` to
+  ``pre-commit``, add ``__all__`` for modules, sub-packages and package, update
+  ``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_
+  (:gh:`337`)
+- Add support for accessing FreeSurfer via Docker wrapper along with
+  ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by
+  `Synchon Mandal`_ (:gh:`342`)
+- Update core and docs dependencies by `Synchon Mandal`_ (:gh:`347`)
+- Integrate ``warnings`` with ``logging`` respecting filters by `Fede
+  Raimondo`_ (:gh:`351`)
+Deprecations and Removals
+^^^^^^^^^^^^^^^^^^^^^^^^^
+- Remove ``Power`` coordinates, ``fetch_icbm152_brain_gm_mask`` mask,
+  ``BOLDWarper`` Preprocessor by `Synchon Mandal`_ (:gh:`336`)
 Junifer 0.0.4 (2024-04-05)
 --------------------------

{junifer-0.0.5.dev240 → junifer-0.0.6.dev3}/junifer/_version.py RENAMED Viewed

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
-__version__ = version = '0.0.5.dev240'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev240')
+__version__ = version = '0.0.6.dev3'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev3')

{junifer-0.0.5.dev240 → junifer-0.0.6.dev3}/junifer/markers/brainprint.py RENAMED Viewed

@@ -143,7 +143,7 @@ class BrainPrint(BaseMarker):
         mri_binarize_cmd = [
             "mri_binarize",
             f"--i {aseg_path.resolve()}",
-            f"--match {''.join(indices)}",
+            f"--match {' '.join(indices)}",
             f"--o {mri_binarize_output_path.resolve()}",
         ]
         # Call mri_binarize command

{junifer-0.0.5.dev240 → junifer-0.0.6.dev3}/junifer.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev240
+Version: 0.0.6.dev3
 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-0.0.5.dev240 → junifer-0.0.6.dev3}/junifer.egg-info/SOURCES.txt RENAMED Viewed

@@ -57,39 +57,7 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
-docs/changes/newsfragments/115.doc
-docs/changes/newsfragments/136.enh
-docs/changes/newsfragments/161.feature
-docs/changes/newsfragments/273.feature
-docs/changes/newsfragments/318.misc
-docs/changes/newsfragments/323.feature
-docs/changes/newsfragments/324.bugfix
-docs/changes/newsfragments/327.doc
-docs/changes/newsfragments/330.doc
-docs/changes/newsfragments/331.bugfix
-docs/changes/newsfragments/332.bugfix
-docs/changes/newsfragments/336.removal
-docs/changes/newsfragments/337.misc
-docs/changes/newsfragments/339.bugfix
-docs/changes/newsfragments/340.bugfix
-docs/changes/newsfragments/341.enh
-docs/changes/newsfragments/342.misc
-docs/changes/newsfragments/343.feature
-docs/changes/newsfragments/344.feature
-docs/changes/newsfragments/345.feature
-docs/changes/newsfragments/346.enh
-docs/changes/newsfragments/346.feature
-docs/changes/newsfragments/347.misc
-docs/changes/newsfragments/348.change
-docs/changes/newsfragments/348.enh
-docs/changes/newsfragments/348.feature
-docs/changes/newsfragments/349.change
-docs/changes/newsfragments/349.enh
-docs/changes/newsfragments/350.enh
-docs/changes/newsfragments/351.change
-docs/changes/newsfragments/351.enh
-docs/changes/newsfragments/351.feature
-docs/changes/newsfragments/351.misc
+docs/changes/newsfragments/356.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

junifer-0.0.5.dev240/docs/changes/newsfragments/115.doc DELETED Viewed

	@@ -1 +0,0 @@
1	- Improve sub-package level docstrings to better reflect their purposes by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/136.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean aggregation function behaves exactly as :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/161.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Introduce :class:`.Smoothing` for smoothing / blurring images as a preprocessing step by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/273.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Add support for choosing between ``bash`` and ``zsh`` shells when queueing by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/318.misc DELETED Viewed

	@@ -1 +0,0 @@
1	- Improve CI to allow external tool installation to fail gracefully and update necessary dependency version and conditional checks by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/323.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Add ``junifer list-elements`` to list out available elements for a DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/324.bugfix DELETED Viewed

	@@ -1 +0,0 @@
1	- Remove extra dimension from parcellations warped via ANTs to other template spaces by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/327.doc DELETED Viewed

	@@ -1 +0,0 @@
1	- Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/330.doc DELETED Viewed

	@@ -1 +0,0 @@
1	- Add missing DataGrabber ``types`` options in respective docstrings of :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/331.bugfix DELETED Viewed

	@@ -1 +0,0 @@
1	- Remove extra dimension from parcellations warped via ANTs when merging parcellations by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/332.bugfix DELETED Viewed

	@@ -1 +0,0 @@
1	- Fix ``junifer reset`` to properly delete storage directory and handle ``junifer_jobs`` deletion if not empty by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/336.removal DELETED Viewed

	@@ -1 +0,0 @@
1	- Remove ``Power`` coordinates, ``fetch_icbm152_brain_gm_mask`` mask, ``BOLDWarper`` Preprocessor by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/337.misc DELETED Viewed

	@@ -1 +0,0 @@
1	- Update ``pre-commit`` dependency versions, add ``blacken-docs`` to ``pre-commit``, add ``__all__`` for modules, sub-packages and package, update ``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/339.bugfix DELETED Viewed

	@@ -1 +0,0 @@
1	- Fix validation failure of multiple Preprocessors with different input data types requirement by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/340.bugfix DELETED Viewed

	@@ -1 +0,0 @@
1	- Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/341.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as "nested types" of the actual data type by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/342.misc DELETED Viewed

	@@ -1 +0,0 @@
1	- Add support for accessing FreeSurfer via Docker wrapper along with ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/343.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Introduce new storage type ``scalar_table`` and adapt :class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/344.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Add support for `BrainPrint <https://github.com/Deep-MI/BrainPrint?tab=readme-ov-file>`_ marker by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/345.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Allow Unix path expansion directives to be used in :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/346.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/346.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/347.misc DELETED Viewed

	@@ -1 +0,0 @@
1	- Update core and docs dependencies by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/348.change DELETED Viewed

@@ -1 +0,0 @@

- For :class:`.CrossParcellationFC`, ``aggregation_method`` and ``correlation_method`` have been renamed to ``agg_method`` and ``corr_method`` respectively and ``agg_method_params`` has been added; for ``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`, :class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/348.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- ``FunctionalConnectivity``-family Markers now use :class:`sklearn.covariance.EmpiricalCovariance` as the default covariance estimator and ``correlation`` as the default connecivity matrix kind by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/348.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Introduce :class:`.JuniferConnectivityMeasure` for customising functional connectivity matrix kinds and measurements by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/349.change DELETED Viewed

	@@ -1 +0,0 @@
1	- ``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and fALFF by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/349.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Enable Markers to output multiple features by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/350.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/351.change DELETED Viewed

	@@ -1 +0,0 @@
1	- Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not raise error on missing mandatory key checks for data types by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/351.enh DELETED Viewed

	@@ -1 +0,0 @@
1	- Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in :gh:`341` by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/351.feature DELETED Viewed

	@@ -1 +0,0 @@
1	- Introduce :class:`.PatternValidationMixin` to simplify validation for pattern-based DataGrabbers and :func:`.deep_update` for updating dictionary with varying width and depth by `Synchon Mandal`_

junifer-0.0.5.dev240/docs/changes/newsfragments/351.misc DELETED Viewed

	@@ -1 +0,0 @@
1	- Integrate ``warnings`` with ``logging`` respecting filters by `Fede Raimondo`_

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