diff --git a/docs/changes/newsfragments/132.change b/docs/changes/newsfragments/132.change deleted file mode 100644 index 812977e21..000000000 --- a/docs/changes/newsfragments/132.change +++ /dev/null @@ -1 +0,0 @@ -Expose ``types`` parameter for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.JuselessUCLA` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/132.enh b/docs/changes/newsfragments/132.enh deleted file mode 100644 index 1a389c9ca..000000000 --- a/docs/changes/newsfragments/132.enh +++ /dev/null @@ -1 +0,0 @@ -Change validation of ``types`` against ``patterns`` to allow a subset of ``patterns``'s types to be used for ``DataGrabber`` data fetch by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/173.feature b/docs/changes/newsfragments/173.feature deleted file mode 100644 index 5f28763c8..000000000 --- a/docs/changes/newsfragments/173.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``AICHA v1`` and ``AICHA v2`` parcellations to ``junifer.data`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/184.feature b/docs/changes/newsfragments/184.feature deleted file mode 100644 index 5747528d3..000000000 --- a/docs/changes/newsfragments/184.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``Shen 2013``, ``Shen 2015`` and ``Shen 2019`` parcellations to ``junifer.data`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/220.doc b/docs/changes/newsfragments/220.doc deleted file mode 100644 index 10d77bb23..000000000 --- a/docs/changes/newsfragments/220.doc +++ /dev/null @@ -1 +0,0 @@ -Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/222.change b/docs/changes/newsfragments/222.change deleted file mode 100644 index 7771cf404..000000000 --- a/docs/changes/newsfragments/222.change +++ /dev/null @@ -1 +0,0 @@ -Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/222.enh b/docs/changes/newsfragments/222.enh deleted file mode 100644 index 7ba6a197e..000000000 --- a/docs/changes/newsfragments/222.enh +++ /dev/null @@ -1 +0,0 @@ -Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/223.bugfix b/docs/changes/newsfragments/223.bugfix deleted file mode 100644 index 8fa64e86e..000000000 --- a/docs/changes/newsfragments/223.bugfix +++ /dev/null @@ -1 +0,0 @@ -Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/223.enh b/docs/changes/newsfragments/223.enh deleted file mode 100644 index 0014eed50..000000000 --- a/docs/changes/newsfragments/223.enh +++ /dev/null @@ -1 +0,0 @@ -Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/225.feature b/docs/changes/newsfragments/225.feature deleted file mode 100644 index 8ca78d515..000000000 --- a/docs/changes/newsfragments/225.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``Yan 2023`` parcellation to ``junifer.data`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/226.enh b/docs/changes/newsfragments/226.enh deleted file mode 100644 index a97ed7436..000000000 --- a/docs/changes/newsfragments/226.enh +++ /dev/null @@ -1 +0,0 @@ -Adopt ``DataGrabber`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_ \ No newline at end of file diff --git a/docs/changes/newsfragments/227.enh b/docs/changes/newsfragments/227.enh deleted file mode 100644 index 51e1b7bc1..000000000 --- a/docs/changes/newsfragments/227.enh +++ /dev/null @@ -1 +0,0 @@ -Adopt ``DataReader`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_ \ No newline at end of file diff --git a/docs/changes/newsfragments/228.misc b/docs/changes/newsfragments/228.misc deleted file mode 100644 index c8e1a1cfd..000000000 --- a/docs/changes/newsfragments/228.misc +++ /dev/null @@ -1 +0,0 @@ -Consistent docstrings for pytest fixtures used in the test suite by `Synchon Mandal`_ \ No newline at end of file diff --git a/docs/changes/newsfragments/229.misc b/docs/changes/newsfragments/229.misc deleted file mode 100644 index ac42da01f..000000000 --- a/docs/changes/newsfragments/229.misc +++ /dev/null @@ -1 +0,0 @@ -Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/230.misc b/docs/changes/newsfragments/230.misc deleted file mode 100644 index d29c02341..000000000 --- a/docs/changes/newsfragments/230.misc +++ /dev/null @@ -1 +0,0 @@ -Improve ``codespell`` support by fixing typos in documentation by `Synchon Mandal`_ \ No newline at end of file diff --git a/docs/changes/newsfragments/232.misc b/docs/changes/newsfragments/232.misc deleted file mode 100644 index 55628be7a..000000000 --- a/docs/changes/newsfragments/232.misc +++ /dev/null @@ -1 +0,0 @@ -Adopt ``pre-commmit`` for adding and managing git pre-commit hooks by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/234.enh b/docs/changes/newsfragments/234.enh deleted file mode 100644 index 60eddbb85..000000000 --- a/docs/changes/newsfragments/234.enh +++ /dev/null @@ -1 +0,0 @@ -Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/235.bugfix b/docs/changes/newsfragments/235.bugfix deleted file mode 100644 index 297845f83..000000000 --- a/docs/changes/newsfragments/235.bugfix +++ /dev/null @@ -1 +0,0 @@ -Handle ``datalad.IncompleteResultsError`` exception for partial clone in :class:`.DataladDataGrabber` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/236.change b/docs/changes/newsfragments/236.change deleted file mode 100644 index 83d746f0f..000000000 --- a/docs/changes/newsfragments/236.change +++ /dev/null @@ -1 +0,0 @@ -Add :meth:`.BaseFeatureStorage.read` method for storage-like objects by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/236.enh b/docs/changes/newsfragments/236.enh deleted file mode 100644 index 86734a2eb..000000000 --- a/docs/changes/newsfragments/236.enh +++ /dev/null @@ -1 +0,0 @@ -Adapt :meth:`.HDF5FeatureStorage.read_df` due to addition of :meth:`.HDF5FeatureStorage.read` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/237.feature b/docs/changes/newsfragments/237.feature deleted file mode 100644 index 1a7dbd91d..000000000 --- a/docs/changes/newsfragments/237.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :mod:`.onthefly` sub-module and :func:`.read_transform` for quick transform operations on stored data by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/238.misc b/docs/changes/newsfragments/238.misc deleted file mode 100644 index 7e598e512..000000000 --- a/docs/changes/newsfragments/238.misc +++ /dev/null @@ -1 +0,0 @@ -Improve docstrings and code style and parametrize remaining tests for ``junifer.data.parcellations`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/241.misc b/docs/changes/newsfragments/241.misc deleted file mode 100644 index 52a028811..000000000 --- a/docs/changes/newsfragments/241.misc +++ /dev/null @@ -1 +0,0 @@ -Bump ``numpy`` version constraint to ``>=1.24,<1.26`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/242.doc b/docs/changes/newsfragments/242.doc deleted file mode 100644 index 0fab06f7a..000000000 --- a/docs/changes/newsfragments/242.doc +++ /dev/null @@ -1 +0,0 @@ -Update ``julearn`` example under ``examples`` by `Synchon Mandal`_ diff --git a/docs/whats_new.rst b/docs/whats_new.rst index 7caa0e4a0..9f06dbe2d 100644 --- a/docs/whats_new.rst +++ b/docs/whats_new.rst @@ -8,6 +8,91 @@ What's new .. towncrier release notes start +Junifer 0.0.3 (2023-07-21) +--------------------------------- + +Bugfixes +^^^^^^^^ + +- Enable YAML 1.2 support and allow multiline strings in YAML which would not + work earlier by `Synchon Mandal`_ (:gh:`223`) +- Handle ``datalad.IncompleteResultsError`` exception for partial clone in + :class:`.DataladDataGrabber` by `Synchon Mandal`_ (:gh:`235`) + + +API Changes +^^^^^^^^^^^ + +- Expose ``types`` parameter for :class:`.DataladAOMICID1000`, + :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and + :class:`.JuselessUCLA` by `Synchon Mandal`_ (:gh:`132`) +- Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to + :class:`.SPMAuditoryTestingDataGrabber` and + ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to + :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ (:gh:`222`) +- Add :meth:`.BaseFeatureStorage.read` method for storage-like objects by + `Synchon Mandal`_ (:gh:`236`) + + +Improved Documentation +^^^^^^^^^^^^^^^^^^^^^^ + +- Improve general prose, formatting and code blocks in docs and set line length + for ``.rst`` files to 80 by `Synchon Mandal`_ (:gh:`220`) +- Update ``julearn`` example under ``examples`` by `Synchon Mandal`_ + (:gh:`242`) + + +Enhancements +^^^^^^^^^^^^ + +- Change validation of ``types`` against ``patterns`` to allow a subset of + ``patterns``'s types to be used for ``DataGrabber`` data fetch by `Synchon + Mandal`_ (:gh:`132`) +- Rename instances of "Datagrabber" to "DataGrabber" especially in + ``junifer.testing`` to be consistent by `Synchon Mandal`_ (:gh:`222`) +- Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon + Mandal`_ (:gh:`223`) +- Adopt ``DataGrabber`` consistently throughout codebase to match with the + documentation by `Synchon Mandal`_ (:gh:`226`) +- Adopt ``DataReader`` consistently throughout codebase to match with the + documentation by `Synchon Mandal`_ (:gh:`227`) +- Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon + Mandal`_ (:gh:`234`) +- Adapt :meth:`.HDF5FeatureStorage.read_df` due to addition of + :meth:`.HDF5FeatureStorage.read` by `Synchon Mandal`_ (:gh:`236`) + + +Features +^^^^^^^^ + +- Add ``AICHA v1`` and ``AICHA v2`` parcellations to ``junifer.data`` by + `Synchon Mandal`_ (:gh:`173`) +- Add ``Shen 2013``, ``Shen 2015`` and ``Shen 2019`` parcellations to + ``junifer.data`` by `Synchon Mandal`_ (:gh:`184`) +- Add ``Yan 2023`` parcellation to ``junifer.data`` by `Synchon Mandal`_ + (:gh:`225`) +- Introduce :mod:`.onthefly` sub-module and :func:`.read_transform` for quick + transform operations on stored data by `Synchon Mandal`_ (:gh:`237`) + + +Misc +^^^^ + +- Consistent docstrings for pytest fixtures used in the test suite by `Synchon + Mandal`_ (:gh:`228`) +- Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_ + (:gh:`229`) +- Improve ``codespell`` support by fixing typos in documentation by `Synchon + Mandal`_ (:gh:`230`) +- Adopt ``pre-commit`` for adding and managing git pre-commit hooks by + `Synchon Mandal`_ (:gh:`232`) +- Improve docstrings and code style and parametrize remaining tests for + ``junifer.data.parcellations`` by `Synchon Mandal`_ (:gh:`238`) +- Bump ``numpy`` version constraint to ``>=1.24,<1.26`` by `Synchon Mandal`_ + (:gh:`241`) + + Junifer 0.0.2 (2023-03-31) -------------------------- @@ -140,15 +225,9 @@ Features when used as ``method`` in markers by `Fede Raimondo`_ (:gh:`190`) -junifer 0.0.1 (2022-12-20) +Junifer 0.0.1 (2022-12-20) -------------------------- -API Changes -^^^^^^^^^^^ - -- Change the ``single_output`` default parameter in storage classes from - ``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`) - Bugfixes ^^^^^^^^ @@ -168,6 +247,14 @@ Bugfixes - Fix a bug in which the generated DAG for HTCondor will not work by `Fede Raimondo`_ (:gh:`143`) + +API Changes +^^^^^^^^^^^ + +- Change the ``single_output`` default parameter in storage classes from + ``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`) + + Improved Documentation ^^^^^^^^^^^^^^^^^^^^^^ @@ -181,6 +268,7 @@ Improved Documentation - Change documentation template to furo. Fix references and standardize documentation by `Fede Raimondo`_ (:gh:`114`) + Enhancements ^^^^^^^^^^^^ @@ -217,6 +305,7 @@ Enhancements - Refactor :class:`.PipelineStepMixin` to improve its implementation and validation for pipeline steps by `Synchon Mandal`_ (:gh:`152`) + Features ^^^^^^^^ @@ -283,6 +372,7 @@ Features - Implement :class:`.ALFFParcels` and :class:`.ALFFSpheres` markers by `Fede Raimondo`_ (:gh:`35`) + Misc ^^^^