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Master to dev#2893

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Lestropie merged 28 commits intodevfrom
master_to_dev
May 9, 2024
Merged

Master to dev#2893
Lestropie merged 28 commits intodevfrom
master_to_dev

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Attempting to merge the latest changes on master onto the dev branch.
Will need to cross-check the commits with the proposed changes, make sure that merge commit 3d4f392 doesn't accidentally revert anything.

For the record, I accidentally created merge commit 3d4f392 on my local dev branch, pushed it, and GitHub actually accepted it, with the following message:

remote: Bypassed rule violations for refs/heads/dev:
remote:
remote: - Changes must be made through a pull request.
remote:

I then couldn't force-push GitHub's dev back one commit because of being locked against force pushes. For now, I've gotten around this by giving myself and @jdtournier the ability to force push to dev. However GitHub should not have accepted that commit in the first place according to the branch settings.

jdtournier and others added 24 commits August 7, 2023 12:28
…cit_length_sequences

DICOM: fix multiframe encoding with explicit length sequences
Docs: Explicitly specify English language to Sphinx
This also falls back to using the (deprecated) imp module to support
Python < 3.5
add support for python importlib to locate MRtrix3 python libraries
This is to avoid failures on macos (where this test was previously being
performed) due to the python distutils package now being deprecated and
no longer available on homebrew.
configure: revert to -isystem rather than -idirafter
Update header copyright to 2024
Allow filename in write_mrtrix.m to be string or char array
Docs: New page on MRView "lock to image axes"
Multiple occurrences of "-Wunused-but-set-variable" that appeared on Mac OSX GitHub CI.
- For mrcolour, output images are clamped to [0.0,1.0] range, so use absolute tolerance rather than fractional.
- Increase tolerance on tckresample -step_size given the imprecision of the resampling operation itself.
CI: Fixes for MacOSX ARM64 runner
Conflicts:
	.github/workflows/checks.yml
	bin/dwicat
	build
	cmd/dwi2mask.cpp
	cmd/fod2fixel.cpp
	configure
	core/app.cpp
	core/file/dicom/element.cpp
	core/file/tiff.cpp
	core/file/tiff.h
	core/filter/dwi_brain_mask.h
	core/filter/fft.h
	core/fixel/types.h
	core/formats/tiff.cpp
	core/image_io/fetch_store.cpp
	core/image_io/fetch_store.h
	core/image_io/tiff.cpp
	docs/reference/commands/dwibiascorrect.rst
	docs/reference/commands/dwinormalise.rst
	package_mrtrix
	python/bin/mrtrix3.py
	run_tests
	src/dwi/directions/set.cpp
	src/gui/mrview/file_open.cpp
	src/gui/mrview/file_open.h
	src/gui/shview/file_open.h
	src/registration/transform/robust.cpp
	src/stats/permstack.cpp
	src/stats/permstack.h
	testing/cmd/testing_diff_fixel_old.cpp
	testing/cmd/testing_diff_matrix.cpp
	testing/cmd/testing_diff_mesh.cpp
	testing/cmd/testing_diff_peaks.cpp
	testing/cmd/testing_diff_tck.cpp
	testing/cmd/testing_diff_tsf.cpp
	testing/cmd/testing_unit_tests_bitset.cpp
	testing/cmd/testing_unit_tests_icls.cpp
	testing/cmd/testing_unit_tests_ordered_queue.cpp
	testing/cmd/testing_unit_tests_parse_ints.cpp
	testing/cmd/testing_unit_tests_shuffle.cpp
	testing/src/diff_images.h
	testing/src/unit_tests/tractography/roi_unit_tests.h
	testing/src/unit_tests/unit_test.h
@Lestropie Lestropie self-assigned this May 7, 2024
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As discussed in #2690

Manual cherry-pick of f21af33 due to being erroneously erased by merge commit 3d4f392.

Conflicts:
	core/file/dicom/element.cpp
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Lestropie added a commit that referenced this pull request May 7, 2024
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github-actions bot commented May 7, 2024

clang-tidy review says "All clean, LGTM! 👍"

@Lestropie Lestropie requested a review from jdtournier May 7, 2024 06:01
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github-actions bot commented May 7, 2024

clang-tidy review says "All clean, LGTM! 👍"

@Lestropie Lestropie marked this pull request as ready for review May 9, 2024 00:21
@Lestropie Lestropie enabled auto-merge May 9, 2024 00:21
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I've done a manual cross-reference of the changeset against the underlying commits, and found one small glitch from manual merge conflict resolution in python/bin/mrtrix3.py (which should disappear soon on dev anyways as part of #2741). Going to merge this to allow its merge into other PRs to unblock them, since this addresses CI failures on dev.

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github-actions bot commented May 9, 2024

clang-tidy review says "All clean, LGTM! 👍"

@Lestropie Lestropie merged commit 0d27fa4 into dev May 9, 2024
@Lestropie Lestropie deleted the master_to_dev branch May 9, 2024 00:33
@Lestropie Lestropie mentioned this pull request Jan 14, 2025
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3 participants