diff --git a/.mailmap b/.mailmap index f1a7753360..feabaee746 100644 --- a/.mailmap +++ b/.mailmap @@ -37,10 +37,13 @@ Gael Varoquaux GaelVaroquaux Gregory R. Lee Ian Nimmo-Smith Ian Nimmo-Smith Jaakko Leppäkangas jaeilepp +Jacob Roberts +Jacob Roberts Jakub Kaczmarzyk Jakub Kaczmarzyk Jasper J.F. van den Bosch Jasper Jean-Baptiste Poline jbpoline +Jérôme Dockès Jon Haitz Legarreta Jon Haitz Legarreta Gorroño Jonathan Daniel Jonathan Daniel <36337649+jond01@users.noreply.github.com> diff --git a/.zenodo.json b/.zenodo.json index 572f05d12e..a2c6ccee70 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -93,10 +93,10 @@ "orcid": "0000-0002-0807-6005" }, { - "name": "Duek, Or" + "name": "Daniel, Jonathan" }, { - "name": "Daniel, Jonathan" + "name": "Duek, Or" }, { "affiliation": "The University of Washington eScience Institute", @@ -127,6 +127,9 @@ "name": "Riddell, Cameron", "orcid": "0000-0001-8950-0375" }, + { + "name": "S\u00f3lon, Anibal" + }, { "name": "Burns, Christopher" }, @@ -140,9 +143,6 @@ "name": "Gramfort, Alexandre", "orcid": "0000-0001-9791-4404" }, - { - "name": "S\u00f3lon, Anibal" - }, { "name": "Lepp\u00e4kangas, Jaakko" }, @@ -160,6 +160,14 @@ { "name": "Subramaniam, Krish" }, + { + "affiliation": "CEA", + "name": "Papadopoulos Orfanos, Dimitri", + "orcid": "0000-0002-1242-8990" + }, + { + "name": "Van, Andrew" + }, { "affiliation": "Google", "name": "Gorgolewski, Krzysztof J.", @@ -208,6 +216,9 @@ "name": "P\u00e9rez-Garc\u00eda, Fernando", "orcid": "0000-0001-9090-3024" }, + { + "name": "Dock\u00e8s, J\u00e9r\u00f4me" + }, { "name": "Oosterhof, Nikolaas N." }, @@ -228,11 +239,6 @@ { "name": "St-Jean, Samuel" }, - { - "affiliation": "CEA", - "name": "Papadopoulos Orfanos, Dimitri", - "orcid": "0000-0002-1242-8990" - }, { "name": "Panfilov, Egor", "orcid": "0000-0002-2500-6375" @@ -253,12 +259,20 @@ { "name": "Hahn, Kevin S." }, + { + "affiliation": "Charite Universitatsmedizin Berlin, Germany", + "name": "Waller, Lea", + "orcid": "0000-0002-3239-6957" + }, { "name": "Hinds, Oliver P." }, { "name": "Fauber, Bennet" }, + { + "name": "Roberts, Jacob" + }, { "affiliation": "McGill University", "name": "Poline, Jean-Baptiste", @@ -282,6 +296,9 @@ { "name": "Moreno, Miguel Estevan" }, + { + "name": "Hrn\u010diar, Tom\u00e1\u0161" + }, { "name": "Haenel, Valentin" }, @@ -291,9 +308,6 @@ { "name": "Baratz, Zvi" }, - { - "name": "Van, Andrew" - }, { "affiliation": "Hospital for Sick Children", "name": "Darwin, Benjamin C" @@ -329,11 +343,6 @@ "affiliation": "National Technical University of Athens, Greece", "name": "Raktivan, Konstantinos" }, - { - "affiliation": "Charite Universitatsmedizin Berlin, Germany", - "name": "Waller, Lea", - "orcid": "0000-0002-3239-6957" - }, { "name": "Cal\u00e1bkov\u00e1, Mark\u00e9ta" }, @@ -354,9 +363,6 @@ { "name": "Roos, Thomas" }, - { - "name": "Hrn\u010diar, Tom\u00e1\u0161" - }, { "affiliation": "National Institute of Mental Health and Neuro-Sciences, India", "name": "Reddam, Venkateswara Reddy", diff --git a/Changelog b/Changelog index a94a806b4b..01e32bbed5 100644 --- a/Changelog +++ b/Changelog @@ -25,8 +25,90 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM). References like "pr/298" refer to github pull request numbers. +4.0.0 (To be determined) +======================== + +New feature release in the 4.0.x series. + +New features +------------ +* Add ``'mask'``, ``'compat'`` and ``'smallest'`` dtype aliases to NIfTI images + to allow for dtype specifications that can depend on the contents of the data. + ``'mask'`` is a synonym for ``uint8``. ``'compat'`` will find the nearest + Analyze-compatible (therefore widely supported) dtype that will not truncate + the data. ``'smallest'`` attempts to find the smallest integer dtype that will + contain the data. (pr/1096) (CM, reviewed by Chris Rorden and Josh Teves) +* Add ``dtype`` arguments to ``Cifti2Image`` (pr/1111) (CM) +* Allow dtypes to be passed to Analyze-like images at ``__init__()`` and + ``to_filename()`` to provide better control over output images. (pr/1082) + (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, and MB) +* Allow compressed GIFTI images (MB, reviewed by CM) +* Add zstd compression support (pr/1005) (Andrew Van, reviewed by CM) +* Support ``ExternalFileBinary`` GIFTI data arrays (PM, reviewed by CM) + +Enhancements +------------ +* Document ``InTemporaryDirectory`` as non-thread-safe (pr/1103) (Jacob Roberts, + reviewed by MB) +* Unify Caret-XML-style metadata structure (GiftiMetaData, Cifti2MetaData) + as dict-like (pr/1091) (CM, reviewed by Josh Teves and Hao-Ting Wang) +* Add ``__repr__`` methods to GIFTI objects (pr/1092) (CM, + reviewed by Josh Teves and Hao-Ting Wang) +* Create gzip header deterministically by default (pr/1024) (CM, reviewed by YOH) +* Provide clear error message when files with zip extensions don't match + file contents (pr/1013) (Jérôme Dockès, reviewed by CM) + +Bug fixes +--------- +* Re-import externals/netcdf.py from scipy to resolve numpy API change (pr/1110) + (CM) +* Resize ArraySequence.data without helper function to avoid reference increment + (pr/1093) (MC, reviewed by CM) + +Maintenance +----------- +* Update submodule URLs to use https over git protocol (pr/1097) (CM) +* Published BIAP 9: CoordinateImage API (pr/1084) (CM) +* Drop uses of deprecated ``distutils`` (pr/1073) (CM, reviewed by MB) +* Suppress LGTM false alarm "Clear-text logging of sensitive information" + (pr/1052) (Dimitri Papadopoulos, reviewed by CM) +* Test on Python 3.10 (pr/1047) (CM) +* Fix typos found by codespell (pr/1040, pr/1044) + (Dimitri Papadopoulos, reviewed by CM) +* Run stable tests weekly, pre-release tests nightly (pr/1025) (CM) +* Documentation updates to establish/clarify governance and decision + making (pr/1019, pr/1020, pr/1022, pr/1018, pr/1017, pr/1016) (MB and CM) + +API changes and deprecations +---------------------------- +* Writing NIfTIs with 64-bit integer dtypes is getting harder. + Passing ``(u)int64`` arrays to ``Nifti1Image`` and subclasses will warn unless + a ``header`` or ``dtype`` option is passed; in the future this will become an + error. + Additionally, passing ``int`` or ``'int'`` to ``set_data_dtype()`` now raises + an error, requiring an explicit numpy dtype to make 64-bit integer images. + (pr/1082) (CM, following discussions with Chris Rorden, Josh Teves, Jerome Dockes, + and MB) +* Drop support for Python 3.6, Numpy < 1.17 (pr/1079) (CM) +* Fully removed the following APIs, which have raised errors on use + since 3.0 (pr/980) (CM, reviewed by Jonathan Daniel) + * ``nibabel.trackvis`` + * ``nibabel.volumeutils.calculate_scale`` + * ``nibabel.volumeutils.can_cast`` + * ``nibabel.volumeutils.scale_min_max`` + * ``nibabel.dataobj_images.DataobjImage.get_shape`` + * ``nibabel.minc1.MincImage`` (use ``Minc1Image``) + * ``nibabel.minc1.MincFile`` (use ``Minc1File``) + * ``nibabel.filebasedimages.FileBasedImage.from_files`` + * ``nibabel.filebasedimages.FileBasedImage.filespec_to_files`` + * ``nibabel.filebasedimages.FileBasedImage.to_filespec`` + * ``nibabel.filebasedimages.FileBasedImage.to_files`` + * ``nibabel.arrayproxy.ArrayProxy.header`` + * ``keep_file_open=="auto"`` parameter to load method (now must be boolean) + + 3.2.2 (Monday 7 February 2022) -================================= +============================== Bug fix release in the 3.2.x series. @@ -557,7 +639,7 @@ Maintenance * Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB) * Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM) * Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM) -* Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by +* Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by Yaroslav Halchenko, MB) * Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615) (Chris Cheng, reviewed by MB, Yaroslav Halchenko) diff --git a/doc/source/index.rst b/doc/source/index.rst index 4e1821cae8..8eb8a9c7d5 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -117,6 +117,8 @@ contributed code and discussion (in rough order of appearance): * Lea Waller * Tomáš Hrnčiar * Andrew Van +* Jérôme Dockès +* Jacob Roberts License reprise ===============