PyPI - junifer - Versions diffs - 0.0.4.dev829__tar.gz → 0.0.4.dev831__tar.gz - Mend

junifer 0.0.4.dev829tar.gz → 0.0.4.dev831tar.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.

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{junifer-0.0.4.dev829 → junifer-0.0.4.dev831}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev829
+Version: 0.0.4.dev831
 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-0.0.4.dev829 → junifer-0.0.4.dev831}/docs/whats_new.rst RENAMED Viewed

@@ -8,8 +8,232 @@ What's new
 .. towncrier release notes start
+Junifer 0.0.4 (2024-04-05)
+--------------------------
+Bugfixes
+^^^^^^^^
+- Make copying of assets in ``with`` block of YAML, relative to YAML and not to
+  current working directory by `Fede Raimondo`_ and `Synchon Mandal`_
+  (:gh:`224`)
+- Adapt ``junifer queue`` to properly use HTCondor >=10.4.0
+  ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`233`)
+- Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by
+  `Synchon Mandal`_ (:gh:`272`)
+- Store native warped parcellations, coordinates and masks in element-scoped
+  tempdirs for the pipeline to work by `Synchon Mandal`_ (:gh:`274`)
+- Change interpolation scheme for parcel and mask native space transformation
+  to nearest neighbour by `Synchon Mandal`_ (:gh:`276`)
+- Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for
+  coordinates transformation by `Synchon Mandal`_ (:gh:`278`)
+- Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by
+  `Synchon Mandal`_ (:gh:`280`)
+- Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect
+  for coordinates transformation to other template spaces. (:gh:`281`)
+- Propagate ReHo and fALFF maps, for aggregation to convert to other template
+  spaces when required by `Synchon Mandal`_ (:gh:`282`)
+- Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the
+  ``workdir`` parameter by `Synchon Mandal`_ (:gh:`283`)
+- Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and
+  used by markers with ``mask="inherit"`` in subject-native template space by
+  `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`284`)
+- Pass down input path if input space is "native" for ``ReHoEstimator`` and
+  ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and
+  `Synchon Mandal`_ (:gh:`286`)
+- Fix :class:`.HTCondorAdapter`'s script generation to use double quotes
+  instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_
+  (:gh:`312`)
+- Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon
+  Mandal`_ (:gh:`314`)
+- Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_
+  (:gh:`322`)
+API Changes
+^^^^^^^^^^^
+- Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_
+  (:gh:`245`)
+- Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon
+  Mandal`_ (:gh:`248`)
+- Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`,
+  :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching
+  of T1w data in subject-native space by `Synchon Mandal`_ (:gh:`252`)
+- Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and
+  ``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to
+  accept multiple preprocessors by `Synchon Mandal`_ (:gh:`263`)
+- Add ``space`` parameter to :func:`.register_coordinates`,
+  :func:`.register_parcellation` and :func:`.register_mask` and return space
+  from :func:`.load_coordinates`, :func:`.load_parcellation` and
+  :func:`.load_mask` by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
+- Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_
+  (:gh:`299`)
+- Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed
+  target data and "helper" data types as a dictionary by `Synchon Mandal`_
+  (:gh:`310`)
+- Add a positional argument ``using`` for Markers and Preprocessors having
+  implementation-based variations, in particular :class:`.ReHoParcels`,
+  :class:`.ReHoSpheres`, :class:`.ALFFParcels`, :class:`.ALFFSpheres` and
+  :class:`.BOLDWarper` by `Synchon Mandal`_ (:gh:`311`)
+- Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_
+  (:gh:`320`)
+- Change the subject and session patterns for :class:`.DataladAOMICID1000`,
+  :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and
+  :class:`.DMCC13Benchmark` so that they are consistent with their own
+  ``"participants.tsv"`` file by `Fede Raimondo`_ (:gh:`325`)
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+- Add Zenodo badge in ``README`` and improve general documentation by `Synchon
+  Mandal`_ (:gh:`247`)
+- Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix
+  listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_
+  (:gh:`251`)
+- Fixed typo in code example for adding masks from "register_custom_mask" to
+  "register_mask" by `Tobias Muganga`_ (:gh:`291`)
+- Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by
+  `Synchon Mandal`_ (:gh:`300`)
+- Improve documentation by adding information about space transformation and
+  writing custom Preprocessors by `Synchon Mandal`_ (:gh:`317`)
+Enhancements
+^^^^^^^^^^^^
+- Support element(s) to be specified via text file for ``--element`` option of
+  ``junifer run`` by `Synchon Mandal`_ (:gh:`182`)
+- Support element-scoped directory and temporary directories for
+  :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_ (:gh:`258`)
+- Improve element directory cleanup via
+  ``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon
+  Mandal`_ (:gh:`259`)
+- Improve :class:`.BasePreprocessor` for easy subclassing and adapt
+  :class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_ (:gh:`260`)
+- Add ``space`` information to existing datagrabbers, masks, parcellations and
+  coordinates by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
+- Add ``mode`` as an aggregation function option in
+  :func:`.get_aggfunc_by_name` by `Synchon Mandal`_ (:gh:`287`)
+- Adapt :class:`.BOLDWarper` to use FSL or ANTs depending on warp file
+  extension by `Synchon Mandal`_ (:gh:`293`)
+- Rewrite :func:`.compute_brain_mask` to allow variable template fetching via
+  templateflow, according to target data by `Synchon Mandal`_ (:gh:`299`)
+- Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon
+  Mandal`_ (:gh:`300`)
+- Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon
+  Mandal`_ (:gh:`302`)
+- Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_
+  (:gh:`306`)
+- Improve :class:`.PatternDataGrabber` and
+  :class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``,
+  ``format``, ``mask_item`` and other metadata description handling via YAML by
+  `Synchon Mandal`_ (:gh:`308`)
+- Improve :class:`.BasePreprocessor` by revamping
+  :meth:`.BasePreprocessor.preprocess` and ``BasePreprocessor._fit_transform``
+  to handle "helper" data types better and make the pipeline explicit where
+  data is being altered by `Synchon Mandal`_ (:gh:`310`)
+- Improve external dependency handling for :class:`.PipelineStepMixin`-derived
+  objects having implementation-based variations by `Synchon Mandal`_
+  (:gh:`311`)
+Features
+^^^^^^^^
+- Introduce complexity markers: :class:`.HurstExponent`,
+  :class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`,
+  :class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy`
+  by `Amir Omidvarnia`_ (:gh:`145`)
+- Add ``junifer reset`` to reset storage and jobs directory by `Synchon
+  Mandal`_ (:gh:`240`)
+- Add support for ``Power2013`` coordinates by `Synchon Mandal`_ (:gh:`245`)
+- Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_
+  (:gh:`249`)
+- Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_
+  (:gh:`250`)
+- Add support for subject-native space by `Synchon Mandal`_ and `Fede
+  Raimondo`_ (:gh:`252`)
+- Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage
+  working and temporary directories across pipeline by `Synchon Mandal`_
+  (:gh:`254`)
+- Introduce :func:`.get_parcellation` to fetch parcellation tailored for the
+  data by `Synchon Mandal`_ (:gh:`264`)
+- Introduce :func:`.get_coordinates` to fetch coordinates tailored for the data
+  by `Synchon Mandal`_ (:gh:`265`)
+- Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's
+  ``applywarp`` by `Synchon Mandal`_ (:gh:`266`)
+- Introduce :class:`.BOLDWarper` for warping BOLD data via FSL's ``applywarp``
+  by `Synchon Mandal`_ (:gh:`267`)
+- Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset
+  <https://openneuro.org/datasets/ds003452/versions/1.0.1>`_ by `Synchon
+  Mandal`_ (:gh:`271`)
+- Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_
+  (:gh:`275`)
+- Introduce
+  ``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper``
+  to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_ (:gh:`293`)
+- Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for
+  running external commands from FSL, ANTs and others by `Synchon Mandal`_
+  (:gh:`295`)
+- Introduce :func:`.get_xfm` to fetch transformation files for moving between
+  template spaces by `Synchon Mandal`_ (:gh:`297`)
+- Introduce :func:`.get_template` to fetch template space image tailored to a
+  target data by `Synchon Mandal`_ (:gh:`298`)
+- Add support for on-the-fly template space transformation in
+  :func:`.get_parcellation` and :func:`.get_mask` to allow parcellation and
+  mask in different template spaces to work with a ``DataGrabber``'s data in a
+  specified template space. (:gh:`299`)
+- Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``,
+  ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon
+  Mandal`_ (:gh:`301`)
+- Introduce :class:`.QueueContextAdapter` as an abstract base class for job
+  queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by
+  `Synchon Mandal`_ (:gh:`309`)
+Miscellaneous
+^^^^^^^^^^^^^
+- Update dependencies requirements by `Fede Raimondo`_ (:gh:`253`)
+- Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit``
+  config by `Synchon Mandal`_ (:gh:`261`)
+- Add support for accessing FSL via Docker wrapper along with ``flirt``,
+  ``applywarp``  and ``std2imgcoord`` commands by `Synchon Mandal`_ (:gh:`262`)
+- Improve documentation, packaging and code style by `Synchon Mandal`_
+  (:gh:`269`)
+- Add support for Python 3.12 and make Python 3.11 the base for code coverage
+  and CI checks by `Synchon Mandal`_ (:gh:`270`)
+- Add support for accessing ANTs via Docker wrapper along with
+  ``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon
+  Mandal`_ (:gh:`277`)
+- Make the external tool wrappers output to stderr instead of stdout by
+  `Synchon Mandal`_ (:gh:`279`)
+- Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by
+  `Synchon Mandal`_ (:gh:`281`)
+- Make :class:`.BOLDWarper` tool-agnostic by moving it from
+  ``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_
+  (:gh:`288`)
+- Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by
+  `Synchon Mandal`_ (:gh:`293`)
+- Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon
+  Mandal`_ (:gh:`294`)
+- Update dependency listing in ``pyproject.toml``, add
+  ``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and
+  ``FSL`` installation in CI and improve general code style by `Synchon
+  Mandal`_ (:gh:`300`)
+Deprecations and Removals
+^^^^^^^^^^^^^^^^^^^^^^^^^
+- Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon
+  Mandal`_ (:gh:`301`)
 Junifer 0.0.3 (2023-07-21)
----------------------------------
+--------------------------
 Bugfixes
 ^^^^^^^^

{junifer-0.0.4.dev829 → junifer-0.0.4.dev831}/junifer/_version.py RENAMED Viewed

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
-__version__ = version = '0.0.4.dev829'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev829')
+__version__ = version = '0.0.4.dev831'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev831')

{junifer-0.0.4.dev829 → junifer-0.0.4.dev831}/junifer.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev829
+Version: 0.0.4.dev831
 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-0.0.4.dev829 → junifer-0.0.4.dev831}/junifer.egg-info/SOURCES.txt RENAMED Viewed

@@ -57,85 +57,8 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
-docs/changes/newsfragments/145.feature
-docs/changes/newsfragments/182.enh
-docs/changes/newsfragments/224.bugfix
-docs/changes/newsfragments/233.bugfix
-docs/changes/newsfragments/240.feature
-docs/changes/newsfragments/245.change
-docs/changes/newsfragments/245.feature
-docs/changes/newsfragments/247.doc
-docs/changes/newsfragments/248.change
-docs/changes/newsfragments/249.feature
-docs/changes/newsfragments/250.feature
-docs/changes/newsfragments/251.doc
-docs/changes/newsfragments/252.change
-docs/changes/newsfragments/252.feature
-docs/changes/newsfragments/253.misc
-docs/changes/newsfragments/254.feature
-docs/changes/newsfragments/258.enh
-docs/changes/newsfragments/259.enh
-docs/changes/newsfragments/260.enh
-docs/changes/newsfragments/261.misc
-docs/changes/newsfragments/262.misc
-docs/changes/newsfragments/263.change
-docs/changes/newsfragments/264.feature
-docs/changes/newsfragments/265.feature
-docs/changes/newsfragments/266.feature
-docs/changes/newsfragments/267.feature
-docs/changes/newsfragments/268.change
-docs/changes/newsfragments/268.enh
-docs/changes/newsfragments/269.misc
-docs/changes/newsfragments/270.misc
-docs/changes/newsfragments/271.feature
-docs/changes/newsfragments/272.bugfix
-docs/changes/newsfragments/274.bugfix
-docs/changes/newsfragments/275.feature
-docs/changes/newsfragments/276.bugfix
-docs/changes/newsfragments/277.misc
-docs/changes/newsfragments/278.bugfix
-docs/changes/newsfragments/279.misc
-docs/changes/newsfragments/280.bugfix
-docs/changes/newsfragments/281.bugfix
-docs/changes/newsfragments/281.misc
-docs/changes/newsfragments/282.bugfix
-docs/changes/newsfragments/283.bugfix
-docs/changes/newsfragments/284.bugfix
-docs/changes/newsfragments/286.bugfix
-docs/changes/newsfragments/287.enh
-docs/changes/newsfragments/288.misc
-docs/changes/newsfragments/291.doc
-docs/changes/newsfragments/293.enh
-docs/changes/newsfragments/293.feature
-docs/changes/newsfragments/293.misc
-docs/changes/newsfragments/294.misc
-docs/changes/newsfragments/295.feature
-docs/changes/newsfragments/297.feature
-docs/changes/newsfragments/298.feature
-docs/changes/newsfragments/299.change
-docs/changes/newsfragments/299.enh
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-docs/changes/newsfragments/300.doc
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-docs/changes/newsfragments/300.misc
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-docs/changes/newsfragments/301.removal
-docs/changes/newsfragments/302.enh
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-docs/changes/newsfragments/308.enh
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-docs/changes/newsfragments/310.change
-docs/changes/newsfragments/310.enh
-docs/changes/newsfragments/311.change
-docs/changes/newsfragments/311.enh
-docs/changes/newsfragments/312.bugfix
-docs/changes/newsfragments/314.bugfix
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 docs/changes/newsfragments/320.fix
 docs/changes/newsfragments/321.fix
-docs/changes/newsfragments/322.bugfix
-docs/changes/newsfragments/325.change
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

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	@@ -1 +0,0 @@
1	- Introduce complexity markers: :class:`.HurstExponent`, :class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`, :class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy` by `Amir Omidvarnia`_

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	@@ -1 +0,0 @@
1	- Support element(s) to be specified via text file for ``--element`` option of ``junifer run`` by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Make copying of assets in ``with`` block of YAML, relative to YAML and not to current working directory by `Fede Raimondo`_ and `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Adapt ``junifer queue`` to properly use HTCondor >=10.4.0 ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_

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1	- Add ``junifer reset`` to reset storage and jobs directory by `Synchon Mandal`_

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1	- Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Add support for ``Power2013`` coordinates by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Add Zenodo badge in ``README`` and improve general documentation by `Synchon Mandal`_

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1	- Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon Mandal`_

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1	- Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_

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1	- Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching of T1w data in subject-native space by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Add support for subject-native space by `Synchon Mandal`_ and `Fede Raimondo`_

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1	- Update dependencies requirements by `Fede Raimondo`_

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1	- Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage working and temporary directories across pipeline by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Support element-scoped directory and temporary directories for :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Improve element directory cleanup via ``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Improve :class:`.BasePreprocessor` for easy subclassing and adapt :class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit`` config by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Add support for accessing FSL via Docker wrapper along with ``flirt``, ``applywarp`` and ``std2imgcoord`` commands by `Synchon Mandal`_

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	@@ -1 +0,0 @@
1	- Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and ``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to accept multiple preprocessors by `Synchon Mandal`_

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1	- Introduce :func:`.get_parcellation` to fetch parcellation tailored for the data by `Synchon Mandal`_

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1	- Introduce :func:`.get_coordinates` to fetch coordinates tailored for the data by `Synchon Mandal`_

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1	- Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's ``applywarp`` by `Synchon Mandal`_

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1	- Introduce :class:`.BOLDWarper` for warping BOLD data via FSL's ``applywarp`` by `Synchon Mandal`_

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1	- Add ``space`` parameter to :func:`.register_coordinates`, :func:`.register_parcellation` and :func:`.register_mask` and return space from :func:`.load_coordinates`, :func:`.load_parcellation` and :func:`.load_mask` by `Synchon Mandal`_ and `Fede Raimondo`_

junifer-0.0.4.dev829/docs/changes/newsfragments/268.enh DELETED Viewed

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1	- Add ``space`` information to existing datagrabbers, masks, parcellations and coordinates by `Synchon Mandal`_ and `Fede Raimondo`_

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1	- Improve documentation, packaging and code style by `Synchon Mandal`_

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1	- Add support for Python 3.12 and make Python 3.11 the base for code coverage and CI checks by `Synchon Mandal`_

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1	- Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset <https://openneuro.org/datasets/ds003452/versions/1.0.1>`_ by `Synchon Mandal`_

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1	- Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by `Synchon Mandal`_

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1	- Store native warped parcellations, coordinates and masks in element-scoped tempdirs for the pipeline to work by `Synchon Mandal`_

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1	- Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_

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1	- Change interpolation scheme for parcel and mask native space transformation to nearest neighbour by `Synchon Mandal`_

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1	- Add support for accessing ANTs via Docker wrapper along with ``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon Mandal`_

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1	- Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_

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1	- Make the external tool wrappers output to stderr instead of stdout by `Synchon Mandal`_

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1	- Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by `Synchon Mandal`_

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1	- Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect for coordinates transformation to other template spaces.

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1	- Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by `Synchon Mandal`_

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1	- Propagate ReHo and fALFF maps, for aggregation to convert to other template spaces when required by `Synchon Mandal`_

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1	- Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the ``workdir`` parameter by `Synchon Mandal`_

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1	- Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and used by markers with ``mask="inherit"`` in subject-native template space by `Fede Raimondo`_ and `Synchon Mandal`_

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1	- Pass down input path if input space is "native" for ``ReHoEstimator`` and ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and `Synchon Mandal`_

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1	- Add ``mode`` as an aggregation function option in :func:`.get_aggfunc_by_name` by `Synchon Mandal`_

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1	- Make :class:`.BOLDWarper` tool-agnostic by moving it from ``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_

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1	- Fixed typo in code example for adding masks from "register_custom_mask" to "register_mask" by `Tobias Muganga`_

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1	- Adapt :class:`.BOLDWarper` to use FSL or ANTs depending on warp file extension by `Synchon Mandal`_

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1	- Introduce ``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper`` to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_

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1	- Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by `Synchon Mandal`_

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1	- Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon Mandal`_

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1	- Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for running external commands from FSL, ANTs and others by `Synchon Mandal`_

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1	- Introduce :func:`.get_xfm` to fetch transformation files for moving between template spaces by `Synchon Mandal`_

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1	- Introduce :func:`.get_template` to fetch template space image tailored to a target data by `Synchon Mandal`_

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1	- Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_

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1	- Rewrite :func:`.compute_brain_mask` to allow variable template fetching via templateflow, according to target data by `Synchon Mandal`_

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1	- Add support for on-the-fly template space transformation in :func:`.get_parcellation` and :func:`.get_mask` to allow parcellation and mask in different template spaces to work with a ``DataGrabber``'s data in a specified template space.

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1	- Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by `Synchon Mandal`_

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1	- Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon Mandal`_

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1	- Update dependency listing in ``pyproject.toml``, add ``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and ``FSL`` installation in CI and improve general code style by `Synchon Mandal`_

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1	- Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_

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1	- Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_

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1	- Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon Mandal`_

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1	- Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_

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1	- Improve :class:`.PatternDataGrabber` and :class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``, ``format``, ``mask_item`` and other metadata description handling via YAML by `Synchon Mandal`_

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1	- Introduce :class:`.QueueContextAdapter` as an abstract base class for job queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by `Synchon Mandal`_

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1	- Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed target data and "helper" data types as a dictionary by `Synchon Mandal`_

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1	- Improve :class:`.BasePreprocessor` by revamping :meth:`.BasePreprocessor.preprocess` and ``BasePreprocessor._fit_transform`` to handle "helper" data types better and make the pipeline explicit where data is being altered by `Synchon Mandal`_

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1	- Add a positional argument ``using`` for Markers and Preprocessors having implementation-based variations, in particular :class:`.ReHoParcels`, :class:`.ReHoSpheres`, :class:`.ALFFParcels`, :class:`.ALFFSpheres` and :class:`.BOLDWarper` by `Synchon Mandal`_

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1	- Improve external dependency handling for :class:`.PipelineStepMixin`-derived objects having implementation-based variations by `Synchon Mandal`_

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1	- Fix :class:`.HTCondorAdapter`'s script generation to use double quotes instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_

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1	- Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon Mandal`_

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1	- Improve documentation by adding information about space transformation and writing custom Preprocessors by `Synchon Mandal`_

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1	- Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_

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1	- Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_

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1	- Change the subject and session patterns for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` so that they are consistent with their own ``"participants.tsv"`` file by `Fede Raimondo`_

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