Release Junifer 0.0.2 #217
44 changed files with 132 additions and 43 deletions
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Organize functional connectivity markers in ``junifer.markers.functional_connectivity`` by `Synchon Mandal`_
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Fix a bug in which relative storage URIs will be computed relative to the CWD and not to the location of the YAML file by `Fede Raimondo`_.
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Expose a :func:`.merge_parcellations` function to merge a list of parcellations by `Leonard Sasse`_
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Add support for HDF5 feature storage via :class:`.HDF5FeatureStorage` by `Synchon Mandal`_
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Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_
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@ -1 +0,0 @@
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Add ``confounds_format`` parameter to :class:`.PatternDataGrabber` constructor for improved handling of confounds specified via ``BOLD_confounds`` data type by `Synchon Mandal`_
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Fix ``junifer run`` to respect preprocess step specified in the pipeline by `Synchon Mandal`_
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@ -1 +0,0 @@
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Allow :class:`.PartlyCloudyTestingDataGrabber` to be accessible via ``import junifer.testing.registry`` by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add :class:`.TemporalSNRParcels` and :class:`.TemporalSNRSpheres` by `Leonard Sasse`_
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@ -1 +0,0 @@
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Update docstrings and fix typo in log message by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add more documentation on registering parcellations, coordinates, and masks by `Leonard Sasse`_
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@ -1 +0,0 @@
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Add support for ``Power`` coordinates by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``, ``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_
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@ -1 +0,0 @@
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Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in the aomic sub-package by `Leonard Sasse`_
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Rename ``store_table()`` to ``store_vector()`` for storage-like objects and adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for storage. Also, improve the logic of storing vectors by `Synchon Mandal`_
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Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede Raimondo`_
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Add ``ica_fix`` parameter to :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers to allow for selecting data processed with ICA+FIX. Default value is ``False`` which changes behaviour since 0.0.1 release. By `Fede Raimondo`_
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Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a specific type (e.g.: ``BOLD``) will fail if another non-supported type (e.g.: ``BOLD_confounds``) is present in the data object by `Fede Raimondo`_
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Improved logging output for preprocessing, collecting and pipeline building from YAML by `Fede Raimondo`_
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Fix :class:`.ALFFParcels`, :class:`.ALFFSpheres`, :class:`.ReHoSpheres` and :class:`.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
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@ -1 +0,0 @@
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Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_
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@ -1 +0,0 @@
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Fix several markers that did not properly handle the ``extra_input`` parameter by `Fede Raimondo`_
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Expose ``allow_overlap`` parameter in :class:`.SphereAggregation` and related markers by `Fede Raimondo`_
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Allow for empty spheres in :class:`.JuniferNiftiSpheresMasker`, that will result in NaNs. Also, modify the behaviour of the ``collect`` parameter in HTCondor ``queue`` function to run a collect job even if some of the previous jobs fail. This is useful to collect the results of a pipeline even if some of the jobs fail by `Fede Raimondo`_
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Add aggregation function :func:`.count` that returns the number of elements in a given axis. This allows to count the number of voxels per sphere/parcel when used as ``method`` in markers by `Fede Raimondo`_
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Fix a bug in which relative paths in the YAML ``with`` directive would be computed relative to the current working directory of the process instead of the location of the YAML file by `Fede Raimondo`_.
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Fix an issue with datalad cache and locks in which the user-specific configuration might create a conflict in high throughput systems by `Fede Raimondo`_
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Fix a bug in which :class:`.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique by `Fede Raimondo`_
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Allow for empty parcels in :class:`.ParcelAggregation`, that will result in NaNs by `Fede Raimondo`_
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Fix a bug in which :func:`.count` will not be correctly applied across an axis by `Fede Raimondo`_
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Improve metadata and data I/O for :class:`.HDF5FeatureStorage` by `Synchon Mandal`_
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Fix an issue with datalad cache and locks in which the overriden settings in Junifer were not propagated to subprocesses, resulting in using the default settings by `Fede Raimondo`_
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Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase class, because of missing extra_input parameter by `Leonard Sasse`_
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Force datalad to be non-interactive on *queued* jobs by `Fede Raimondo`_
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Migrate and document changelog creation and maintenance via ``towncrier`` by `Synchon Mandal`_
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Add copy button to documentation code blocks by `Synchon Mandal`_
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Add sections *starting* and *help* in the documentation by `Fede Raimondo`_
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Add missing ``abstractmethod`` decorators for ``get_valid_inputs`` methods of :class:`.BaseMarker` and :class:`.BasePreprocessor` by `Synchon Mandal`_
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Fix the output of :class:`.RSSETSMarker` to be 2D by `Synchon Mandal`_
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Rename ``AmplitudeLowFrequencyFluctuationParcels`` and ``AmplitudeLowFrequencyFluctuationSpheres`` to :class:`.ALFFParcels` and :class:`.ALFFSpheres` by `Synchon Mandal`_
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Shorten Sphinx references across code and docs, and add ``black`` shield in README by `Synchon Mandal`_
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Add :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres` by `Leonard Sasse`_
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@ -8,6 +8,138 @@ What's new
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.. towncrier release notes start
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Junifer 0.0.2 (2023-03-31)
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--------------------------
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Bugfixes
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^^^^^^^^
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- Fix a bug in which relative storage URIs will be computed relative to the CWD
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and not to the location of the YAML file by `Fede Raimondo`_. (:gh:`127`)
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- Fix ``junifer run`` to respect preprocess step specified in the pipeline by
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`Synchon Mandal`_ (:gh:`159`)
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- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in
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:class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede
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Raimondo`_ (:gh:`183`)
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- Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a
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specific type (e.g.: ``BOLD``) will fail if another non-supported type (e.g.:
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``BOLD_confounds``) is present in the data object by `Fede Raimondo`_
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(:gh:`185`)
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- Fix :class:`.ALFFParcels`, :class:`.ALFFSpheres`, :class:`.ReHoSpheres` and
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:class:`.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
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(:gh:`187`)
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- Fix several markers that did not properly handle the ``extra_input``
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parameter by `Fede Raimondo`_ (:gh:`189`)
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- Fix a bug in which relative paths in the YAML ``with`` directive would be
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computed relative to the current working directory of the process instead of
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the location of the YAML file by `Fede Raimondo`_. (:gh:`191`)
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- Fix an issue with datalad cache and locks in which the user-specific
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configuration might create a conflict in high throughput systems by `Fede
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Raimondo`_ (:gh:`192`)
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- Fix a bug in which :class:`.ParcelAggregation` could yield duplicated column
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names if two or more parcels were used and label names were not unique by
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`Fede Raimondo`_ (:gh:`194`)
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- Fix a bug in which :func:`.count` will not be correctly applied across an
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axis by `Fede Raimondo`_ (:gh:`195`)
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- Fix an issue with datalad cache and locks in which the overriden settings in
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Junifer were not propagated to subprocesses, resulting in using the default
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settings by `Fede Raimondo`_ (:gh:`199`)
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- Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase
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class, because of missing extra_input parameter by `Leonard Sasse`_
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(:gh:`200`)
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- Fix the output of :class:`.RSSETSMarker` to be 2D by `Synchon Mandal`_
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(:gh:`215`)
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API Changes
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^^^^^^^^^^^
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- Add ``confounds_format`` parameter to :class:`.PatternDataGrabber`
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constructor for improved handling of confounds specified via
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``BOLD_confounds`` data type by `Synchon Mandal`_ (:gh:`158`)
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- Rename ``store_table()`` to ``store_vector()`` for storage-like objects and
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adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for
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storage. Also, improve the logic of storing vectors by `Synchon Mandal`_
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(:gh:`181`)
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- Add ``ica_fix`` parameter to :class:`.DataladHCP1200` and :class:`.HCP1200`
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datagrabbers to allow for selecting data processed with ICA+FIX. Default
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value is ``False`` which changes behaviour since 0.0.1 release. By `Fede
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Raimondo`_ (:gh:`183`)
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- Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_
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(:gh:`188`)
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- Expose ``allow_overlap`` parameter in :class:`.SphereAggregation` and
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related markers by `Fede Raimondo`_ (:gh:`190`)
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- Rename ``AmplitudeLowFrequencyFluctuationParcels`` and
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``AmplitudeLowFrequencyFluctuationSpheres`` to :class:`.ALFFParcels` and
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:class:`.ALFFSpheres` by `Synchon Mandal`_ (:gh:`216`)
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Improved Documentation
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^^^^^^^^^^^^^^^^^^^^^^
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- Add more documentation on registering parcellations, coordinates, and masks
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by `Leonard Sasse`_ (:gh:`166`)
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- Migrate and document changelog creation and maintenance via ``towncrier`` by
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`Synchon Mandal`_ (:gh:`203`)
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- Add copy button to documentation code blocks by `Synchon Mandal`_ (:gh:`205`)
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- Add sections *starting* and *help* in the documentation by `Fede Raimondo`_
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(:gh:`210`)
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- Shorten Sphinx references across code and docs, and add ``black`` shield in
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README by `Synchon Mandal`_ (:gh:`218`)
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Enhancements
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^^^^^^^^^^^^
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- Organize functional connectivity markers in
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``junifer.markers.functional_connectivity`` by `Synchon Mandal`_ (:gh:`107`)
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- Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_
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(:gh:`155`)
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- Allow :class:`.PartlyCloudyTestingDataGrabber` to be accessible via ``import
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junifer.testing.registry`` by `Synchon Mandal`_ (:gh:`160`)
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- Update docstrings and fix typo in log message by `Synchon Mandal`_
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(:gh:`165`)
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- Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in
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the aomic sub-package by `Leonard Sasse`_ (:gh:`177`)
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- Improved logging output for preprocessing, collecting and pipeline building
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from YAML by `Fede Raimondo`_ (:gh:`185`)
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- Allow for empty spheres in :class:`.JuniferNiftiSpheresMasker`, that will
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result in NaNs. Also, modify the behaviour of the ``collect`` parameter in
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HTCondor ``queue`` function to run a collect job even if some of the previous
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jobs fail. This is useful to collect the results of a pipeline even if some
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of the jobs fail by `Fede Raimondo`_ (:gh:`190`)
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- Allow for empty parcels in :class:`.ParcelAggregation`, that will result in
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NaNs by `Fede Raimondo`_ (:gh:`194`)
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- Improve metadata and data I/O for :class:`.HDF5FeatureStorage` by `Synchon
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Mandal`_ (:gh:`196`)
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- Force datalad to be non-interactive on *queued* jobs by `Fede Raimondo`_
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(:gh:`201`)
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- Add missing ``abstractmethod`` decorators for ``get_valid_inputs`` methods of
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:class:`.BaseMarker` and :class:`.BasePreprocessor` by `Synchon Mandal`_
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(:gh:`214`)
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Features
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^^^^^^^^
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- Add :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres` by
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`Leonard Sasse`_ (:gh:`64`)
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- Expose a :func:`.merge_parcellations` function to merge a list of
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parcellations by `Leonard Sasse`_ (:gh:`146`)
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- Add support for HDF5 feature storage via :class:`.HDF5FeatureStorage` by
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`Synchon Mandal`_ (:gh:`147`)
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- Add :class:`.TemporalSNRParcels` and :class:`.TemporalSNRSpheres` by `Leonard
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Sasse`_ (:gh:`163`)
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- Add support for ``Power`` coordinates by `Synchon Mandal`_ (:gh:`167`)
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- Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_ (:gh:`168`)
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- Add support for nilearn computed masks (``compute_epi_mask``,
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``compute_brain_mask``, ``compute_background_mask``,
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``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_ (:gh:`175`)
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- Add aggregation function :func:`.count` that returns the number of elements
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in a given axis. This allows to count the number of voxels per sphere/parcel
|
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when used as ``method`` in markers by `Fede Raimondo`_ (:gh:`190`)
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junifer 0.0.1 (2022-12-20)
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--------------------------
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