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.. -*- mode: rst -*-
.. vim:ft=rst
.. _changelog:
NIPY Changelog
--------------
NIPY is not only a module for neuroimaing analysis but an umbrella for
other Python neuroimaging-related projects -- see
https://github.com/nipy and http://www.nipy.org for more information
about their releases.
'Close gh-' statements refer to GitHub issues that are available at::
http://github.com/nipy/nipy/issues
The full VCS changelog is available here:
http://github.com/nipy/nipy/commits/main
Releases
~~~~~~~~
Abbreviated authors are:
* MB - Matthew Brett
* BT - Bertrand Thirion
* AR - Alexis Roche
* GV - Gaël Varoquaux
* YH - Yarik Halchenko
* JBP - Jean-Baptiste Poline
* JT - Jonathan Taylor
* BB - Ben Beasley
* CM - Chris Markiewicz
* JM - Jarrod Millman
* SvdW - Stéfan van der Walt
* 0.6.1 (Saturday 5 October 2024)
Compatibility release for Numpy 2.0
* Port code for Numpy 2.0 compatibility (MB)
* Update for test precision on Sympy 1.13 (MB)
* Clean up consts and casts in C code (BB)
* Refactoring to functools.cached_property, style and CI updates (CM)
* CI and automated style check updates (Dimitri Papadopoulos Orfanos)
* Fix for Viz example (Nicholas Tolley)
* Add spin tooling for working with repository checkout (SvdW)
* Fix shebangs for some development scripts (Étienne Mollier)
* 0.6.0 (Thursday 21 December 2023)
Bugfix, refactoring and compatibility release.
Much thankless maintenance duty particularly by CM. Oh wait - not thankless
- thank you!
* Huge cleanup of old dependencies for installation and build (BB).
* Allow for Nibabel deprecations and removals, particularly ``get_data``
(BB).
* Build refactor to ``pyproject.toml`` (CM)
* Various cleanups in spelling and script mechanics (Dimitri Papadopoulos).
* Move to pytest / pytest-doctestplus for testing (JM, MB).
* Various improvements to development process and CI (JM, MB, SvdW).
* Port build process from Numpy distutils to Meson (SvdW).
* Drop Python 2 support.
* Various bugfixes for modern Numpy (BB, MB).
* Drop Cython C files and depend on Cython for build (MB).
* Fixes to temporary files in Mayavi calls (fazledyn-or, CM).
* 0.5.0 (Saturday 27 March 2021)
Bugfix, refactoring and compatibility release.
* Heroic work to update Nipy for recent versions of Numpy, Sympy, Nose,
Scipy, and numpydoc - many thanks to Matteo Visconti di Oleggio Castello.
* Some fixes to harmonize interpolation with recent changes / fixes in
interpolation in Scipy (MB).
* Move script installation logic to use setuptools (MB).
* Some more updates for modern Numpy (MB).
* Fixes for changes in Sympy, by updating some formulae to use Piecewise
(YH).
* 0.4.2 (Saturday 17 February 2018)
Bugfix, refactoring and compatibility release.
* Fixes for compatibility with released versions of Sympy and Numpy,
including some incorrect results from the Euler calculations;
* Fixes for deprecated escape sequences in docstrings (thanks to Klaus
Sembritzki);
* Fixes for compatibility with Windows in various configurations, now
tested with Appveyor builds;
* Various continuous integration and doc build fixes;
* The advent of Windows wheels on release - most credit to the Scipy folks
for building Scipy on Windows.
* 0.4.1 (Friday 10 February 2017)
Bugfix, refactoring and compatibility release.
* New discrete cosine transform functions for building basis sets;
* Fixes for compatibility with Python 3.6;
* Fixes for compatibility with Numpy 1.12 (1.12 no longer allows floating
point values for indexing and other places where an integer value is
required);
* Fixes for compatibility with Sympy 1.0;
* Drop compatibility with Python 2.6, 3.2, 3.3;
* Add ability to pass plotting arguments to ``plot_anat`` function (Matteo
Visconti dOC);
* Some helpers for working with OpenFMRI datasets;
* Signal upcoming change in return shape from ``make_recarray`` when passing
in an array for values. Allow user to select upcoming behavior with
keyword argument;
* Bug fix for axis selection when using record arrays in numpies <= 1.7.1;
* Add flag to allow SpaceTimeRealign to read TR from image headers;
* 0.4.0 (Saturday 18 October 2015)
Bugfix, refactoring and compatibility release.
* Full port to Python 3 using single code-base;
* Various fixes for modern numpy, scipy, sympy, nibabel compatibility;
* Refactor space-time realignment (AR);
* Change in interface for slice-timing options in space-time realign
(AR+MB);
* New ``nipy_4d_realign`` script to run space-time realign (Ariel Rokem);
* Drop requirement for BLAS / LAPACK external library at build-time (AR);
* Move much code out of nipy.labs into main tree (AR, BT);
* Deprecate remaining code in nipy.labs (AR, BT);
* Updates to landmark learning code including API (BT);
* Various fixes to design matrix machinery (BT, Michael Waskom);
* Fix to two-sample permutation test suggested by github user jwirsich (BF);
* Refactoring and fixes to design matrix drift calculations (JBP);
* Extending API of resampling code to allow more ndimage kwargs (JBP);
* Start of new example on OpenFMRI ds105 dataset (JT);
* New ``block_design`` function for designs with specified onsets (JT);
* New ``show_contrast`` function for reviewing contrasts (JT);
* Fix for bug in ``nipy_diagnose`` script / ``screens`` module giving
incorrect PCA output;
* Added SPM HRF to other HRF options;
* Redesign concept of an image "space" with new image space modules,
functions, classes;
* Various fixes for correct installation provided or suggested by YH;
* Some visualization changes by Elvis Dohmatob;
* 0.3.0 (Saturday 2 February 2013)
Bugfix, refactoring and compatibility release.
* Addition of EM algorithm for mixed effects analysis (BT)
* New high-level GLM class interface (BT)
* nipy diagnostic scripts save PCA and tsdifana vectors to npz file
* Python 3 compatibility through 3.3 (MB)
* Fixes for compatibility with upcoming Numpy 1.7
* Fixes to background and axis specification in visualization tools (GV, BT)
* Fixes and tests for installed nipy scripts (MB)
* Fix to optimization parameters for Realign4D - thanks to `bpinsard`
* Fix 0 in affine diagonal for TR=0 in affines by default (MB)
* Allow saving of nipy images loaded from nifti files that lack explicit
affine (MB)
* Allow `slice_order=None` to `FmriRealign4D` when not doing time
interpolation (AR); check for valid slice order specification (YH)
* Refactoring of quantile routine to move code out of C library (AR)
* Fix bug in resampling of unsigned int images (AR)
* Custom doctest machinery to work round differences of dtype repr on
different platforms, and to skip doctests with optional dependencies (MB)
* Script to run examples for testing (MB)
* Fix for accidental integer division of frametimes in design matrix
generation (Fabian Pedregosa)
* Various other fixes and refactorings with thanks from (AR, BT, MB, YH,
Yannick Schwartz, Virgile Fritsch)
* 0.2.0 (Sunday 22 July 2012)
The first ever official release.
- > 30 contributors
- > 6 years in development
- 192 issues closed on github
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