diff --git a/docs/changes/newsfragments/115.doc b/docs/changes/newsfragments/115.doc deleted file mode 100644 index e732e9196d..0000000000 --- a/docs/changes/newsfragments/115.doc +++ /dev/null @@ -1 +0,0 @@ -Improve sub-package level docstrings to better reflect their purposes by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/136.enh b/docs/changes/newsfragments/136.enh deleted file mode 100644 index d0a4955636..0000000000 --- a/docs/changes/newsfragments/136.enh +++ /dev/null @@ -1 +0,0 @@ -Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean aggregation function behaves exactly as :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/161.feature b/docs/changes/newsfragments/161.feature deleted file mode 100644 index 6c1e3742e5..0000000000 --- a/docs/changes/newsfragments/161.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.Smoothing` for smoothing / blurring images as a preprocessing step by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/273.feature b/docs/changes/newsfragments/273.feature deleted file mode 100644 index c876502d2c..0000000000 --- a/docs/changes/newsfragments/273.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for choosing between ``bash`` and ``zsh`` shells when queueing by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/318.misc b/docs/changes/newsfragments/318.misc deleted file mode 100644 index 57ca912e14..0000000000 --- a/docs/changes/newsfragments/318.misc +++ /dev/null @@ -1 +0,0 @@ -Improve CI to allow external tool installation to fail gracefully and update necessary dependency version and conditional checks by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/323.feature b/docs/changes/newsfragments/323.feature deleted file mode 100644 index 4da107eec5..0000000000 --- a/docs/changes/newsfragments/323.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``junifer list-elements`` to list out available elements for a DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/324.bugfix b/docs/changes/newsfragments/324.bugfix deleted file mode 100644 index ee6e3d25e6..0000000000 --- a/docs/changes/newsfragments/324.bugfix +++ /dev/null @@ -1 +0,0 @@ -Remove extra dimension from parcellations warped via ANTs to other template spaces by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/327.doc b/docs/changes/newsfragments/327.doc deleted file mode 100644 index 04a2729e86..0000000000 --- a/docs/changes/newsfragments/327.doc +++ /dev/null @@ -1 +0,0 @@ -Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/330.doc b/docs/changes/newsfragments/330.doc deleted file mode 100644 index c92c5fd4c2..0000000000 --- a/docs/changes/newsfragments/330.doc +++ /dev/null @@ -1 +0,0 @@ -Add missing DataGrabber ``types`` options in respective docstrings of :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/331.bugfix b/docs/changes/newsfragments/331.bugfix deleted file mode 100644 index 61d03f105b..0000000000 --- a/docs/changes/newsfragments/331.bugfix +++ /dev/null @@ -1 +0,0 @@ -Remove extra dimension from parcellations warped via ANTs when merging parcellations by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/332.bugfix b/docs/changes/newsfragments/332.bugfix deleted file mode 100644 index ce28dbfa90..0000000000 --- a/docs/changes/newsfragments/332.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix ``junifer reset`` to properly delete storage directory and handle ``junifer_jobs`` deletion if not empty by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/336.removal b/docs/changes/newsfragments/336.removal deleted file mode 100644 index 2ad43cabd4..0000000000 --- a/docs/changes/newsfragments/336.removal +++ /dev/null @@ -1 +0,0 @@ -Remove ``Power`` coordinates, ``fetch_icbm152_brain_gm_mask`` mask, ``BOLDWarper`` Preprocessor by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/337.misc b/docs/changes/newsfragments/337.misc deleted file mode 100644 index 9c829fc2d5..0000000000 --- a/docs/changes/newsfragments/337.misc +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/339.bugfix b/docs/changes/newsfragments/339.bugfix deleted file mode 100644 index e4e3e1c3d2..0000000000 --- a/docs/changes/newsfragments/339.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix validation failure of multiple Preprocessors with different input data types requirement by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/340.bugfix b/docs/changes/newsfragments/340.bugfix deleted file mode 100644 index 85e6f5c871..0000000000 --- a/docs/changes/newsfragments/340.bugfix +++ /dev/null @@ -1 +0,0 @@ -Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/341.enh b/docs/changes/newsfragments/341.enh deleted file mode 100644 index ce0c29356a..0000000000 --- a/docs/changes/newsfragments/341.enh +++ /dev/null @@ -1 +0,0 @@ -Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as "nested types" of the actual data type by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/342.misc b/docs/changes/newsfragments/342.misc deleted file mode 100644 index 4a479d1ac6..0000000000 --- a/docs/changes/newsfragments/342.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for accessing FreeSurfer via Docker wrapper along with ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/343.feature b/docs/changes/newsfragments/343.feature deleted file mode 100644 index 4c13246f2e..0000000000 --- a/docs/changes/newsfragments/343.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce new storage type ``scalar_table`` and adapt :class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/344.feature b/docs/changes/newsfragments/344.feature deleted file mode 100644 index 33db2863b5..0000000000 --- a/docs/changes/newsfragments/344.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for `BrainPrint `_ marker by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/345.feature b/docs/changes/newsfragments/345.feature deleted file mode 100644 index 8973d42632..0000000000 --- a/docs/changes/newsfragments/345.feature +++ /dev/null @@ -1 +0,0 @@ -Allow Unix path expansion directives to be used in :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/346.enh b/docs/changes/newsfragments/346.enh deleted file mode 100644 index b4176a8e48..0000000000 --- a/docs/changes/newsfragments/346.enh +++ /dev/null @@ -1 +0,0 @@ -Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/346.feature b/docs/changes/newsfragments/346.feature deleted file mode 100644 index 542fb4b729..0000000000 --- a/docs/changes/newsfragments/346.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/347.misc b/docs/changes/newsfragments/347.misc deleted file mode 100644 index dcacc48413..0000000000 --- a/docs/changes/newsfragments/347.misc +++ /dev/null @@ -1 +0,0 @@ -Update core and docs dependencies by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/348.change b/docs/changes/newsfragments/348.change deleted file mode 100644 index 60b77a9e1c..0000000000 --- a/docs/changes/newsfragments/348.change +++ /dev/null @@ -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`_ diff --git a/docs/changes/newsfragments/348.enh b/docs/changes/newsfragments/348.enh deleted file mode 100644 index 592390cf94..0000000000 --- a/docs/changes/newsfragments/348.enh +++ /dev/null @@ -1 +0,0 @@ -``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`_ diff --git a/docs/changes/newsfragments/348.feature b/docs/changes/newsfragments/348.feature deleted file mode 100644 index 3705f1a86a..0000000000 --- a/docs/changes/newsfragments/348.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.JuniferConnectivityMeasure` for customising functional connectivity matrix kinds and measurements by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/349.change b/docs/changes/newsfragments/349.change deleted file mode 100644 index d121f3374b..0000000000 --- a/docs/changes/newsfragments/349.change +++ /dev/null @@ -1 +0,0 @@ -``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and fALFF by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/349.enh b/docs/changes/newsfragments/349.enh deleted file mode 100644 index 56260f91d5..0000000000 --- a/docs/changes/newsfragments/349.enh +++ /dev/null @@ -1 +0,0 @@ -Enable Markers to output multiple features by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/350.enh b/docs/changes/newsfragments/350.enh deleted file mode 100644 index 1cd260fd10..0000000000 --- a/docs/changes/newsfragments/350.enh +++ /dev/null @@ -1 +0,0 @@ -Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/351.change b/docs/changes/newsfragments/351.change deleted file mode 100644 index 1f1539bd9b..0000000000 --- a/docs/changes/newsfragments/351.change +++ /dev/null @@ -1 +0,0 @@ -Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not raise error on missing mandatory key checks for data types by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/351.enh b/docs/changes/newsfragments/351.enh deleted file mode 100644 index 462dca6708..0000000000 --- a/docs/changes/newsfragments/351.enh +++ /dev/null @@ -1 +0,0 @@ -Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in :gh:`341` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/351.feature b/docs/changes/newsfragments/351.feature deleted file mode 100644 index 939e879412..0000000000 --- a/docs/changes/newsfragments/351.feature +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/351.misc b/docs/changes/newsfragments/351.misc deleted file mode 100644 index 5e7f255a35..0000000000 --- a/docs/changes/newsfragments/351.misc +++ /dev/null @@ -1 +0,0 @@ -Integrate ``warnings`` with ``logging`` respecting filters by `Fede Raimondo`_ diff --git a/docs/whats_new.rst b/docs/whats_new.rst index 8339cdc63f..3c4350d15f 100644 --- a/docs/whats_new.rst +++ b/docs/whats_new.rst @@ -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 + `_ 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) --------------------------