MRtrix3 release 3.0.5

Fifth micro (bug fix) update following initial production release.

Please consult the main announcement and summary of changes for details.

What's Changed

• show correct version in symlinked python scripts by @jdtournier in #2548
• Revert container recipes to pull master by @jdtournier in #2544
• DICOM: Tweak terminal messages by @Lestropie in #2549
• Update Copyright notice for 2023 by @dchristiaens in #2555
• resize instead of assign of std::vector by @bjeurissen in #2568
• python library: tweak execute to work with VS Code #2472 by @Lestropie in #2566
• Fix sprintf deprecation warning on macOS by @bjeurissen in #2561
• mrview: change option name -orientationlabel to avoid conflict with -orientation by @jdtournier in #2569
• Revert "mrview: change option name -orientationlabel to avoid conflict with -orientation" by @jdtournier in #2581
• Update GitHub Actions workflow for merge queue by @jdtournier in #2588
• Add file ".git-blame-ignore-revs" by @Lestropie in #2592
• VTK surface format changes by @Lestropie in #2594
• App::get_matches(): Fix buffer overrun by @Lestropie in #2629
• Mesh::load_vtk() always open files in binary mode by @jdtournier in #2656
• mrview: fix tsf custom colour by @jdtournier in #2667
• tcksift2: Fix check for allocation of memory for weights vector by @Lestropie in #2672
• DICOM: fix multiframe encoding with explicit length sequences by @jdtournier in #2691
• Docs: Explicitly specify English language to Sphinx by @Lestropie in #2715
• ReadTheDocs: updates to fix render by @jdtournier in #2727
• add support for python importlib to locate MRtrix3 python libraries by @jdtournier in #2735
• configure: revert to -isystem rather than -idirafter by @jdtournier in #2754
• Update header copyright to 2024 by @Lestropie in #2771
• Allow filename in write_mrtrix.m to be string or char array by @lukeje in #2810
• Docs: New page on MRView "lock to image axes" by @Lestropie in #2882
• CI: Fixes for MacOSX ARM64 runner by @Lestropie in #2890
• Adapter::Reslice: Alternative resolution of complex summation by @Lestropie in #2785
• Reslice adapter: allow use with complex numbers by @jdtournier in #2768
• Add periodic checks with sanitizers by @daljit46 in #2763
• mrgrid: Fix help for -as option by @Lestropie in #2794
• run.command(): Do not hide list inputs by @Lestropie in #2803
• for_each: Add example usage demonstrating shell operator escape by @Lestropie in #2721
• mrinfo: Update author email by @Lestropie in #2698
• fod2fixel: Fix -fmls_lobe_merge_ratio by @Lestropie in #2638
• Update sanitizers workflow following testing changes by @daljit46 in #2904
• mrcalc: Support -config option by @Lestropie in #2910
• mrdegibbs: update doc to soften warning about partial Fourier by @jdtournier in #2923
• ProgressBar: Simple update method where stderr is pipe by @Lestropie in #2935
• New workflow for releases by @daljit46 in #2933
• Deprecated distutils module in Python 3.12 by @Lestropie in #2948
• Windows: Delayed writeback to host by @Lestropie in #2962
• Pipe image format: Revise error message by @Lestropie in #2600
• dwi2tensor: Preserve dw_scheme for -predicted_signal by @Lestropie in #2955
• DICOM command-line selection: abort on error reading from std::cin by @Lestropie in #2908
• population_template: Fix aggregation weights import by @Lestropie in #3001
• Python: Pylint fix consider-using-generator by @Lestropie in #3005
• Docs: Fix missing boolean types in full usage by @Lestropie in #2693
• PNG: Fix check for too few axes, memory, orientations by @Lestropie in #2713
• 5ttcheck: Fix terminal message RE: -voxels option by @Lestropie in #2411
• configure: strip FSL from PATH by @jdtournier in #2729
• Fix for mrview / singularity / NVIDIA by @celstark in #2559
• Fixes to containers FSL dependency by @Lestropie in #2929
• [ENH] Update Dockerfile by @arnaudbore in #3039
• Pylint fixes for master branch by @Lestropie in #3054
• Added info about consequences of using -white_stem in 5ttgen hsvs by @Lestropie in #3042
• dwifslpreproc: Fix for PE direction, but not readout time, in header by @Lestropie in #2722
• mrtrix3.path.wait_for(): Fix variable ghosting by @Lestropie in #2968
• voxel2mesh fixes by @Lestropie in #3049
• dwi2tensor: fix operation with -iter 1 by @Lestropie in #3056
• DICOM: add null imageIO handler to allow parsing of DICOM data even with unsupported transfer syntax by @jdtournier in #2767
• Tolerance for dw_scheme differences on header merge by @Lestropie in #3027
• DICOM: ignore image positioning tags if nested within Philips private sequence by @jdtournier in #3047
• Fix tck writer when a single streamline exceed the buffer size by @jdtournier in #3071
• DWI metadata fixes for master by @Lestropie in #3011
• fsl.check_first(): Second attempt at refinement by @Lestropie in #2609
• More robust bvecs/bvals compatibility by @Lestropie in #2602
• Fix packaging workflows on master by @daljit46 in #3086
• Final GA workflows changes for 3.0.5 by @daljit46 in #3091
• Next release 3.0.5 by @jdtournier in #3092

New Contributors

• @lukeje made their first contribution in #2810
• @celstark made their first contribution in #2559
• @arnaudbore made their first contribution in #3039

Full Changelog: 3.0.4...3.0.5