Update dependencies

[naegelejd]

• Bump Python from 3.9 -> 3.13
• Bump ISMRMRD to 1.15.0
• Bump HDF5 to 1.14
• Bump Yardl to 0.6.6
• Compile MRD C++ with C++20
• Remove mentions of mamba (libmamba-solver is built into Conda now)
• Bump xtensor to 0.27.1
• Remove xtensor-fftw because it is not being maintained (replaced with FFTW3)

[Copilot]

Pull request overview

This PR updates major dependencies across the MRD project, including Python 3.9 → 3.13, ISMRMRD 1.14.2 → 1.15.0, HDF5 1.10 → 1.14, xtensor 0.25.0 → 0.27.1, and Yardl 0.6.4 → 0.6.6. It also migrates C++ compilation to C++20, removes xtensor-fftw in favor of direct FFTW3 usage, replaces the fmt library with std::format, and updates deprecated Python datetime APIs.

Changes:

• Bump Python from 3.9 to 3.13 and update deprecated datetime APIs
• Update C++ dependencies (ISMRMRD, HDF5, xtensor) and implement custom FFTW wrappers replacing xtensor-fftw
• Migrate to C++20 and replace fmt library with std::format
• Update build configurations to remove mamba references (now built into conda)

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
environment.yml	Update conda dependencies including Python, ISMRMRD, HDF5, xtensor, and remove xtensor-fftw
cpp/CMakeLists.txt	Update default C++ standard to C++20
cpp/mrd/CMakeLists.txt	Add C++17 requirement for generated code
cpp/conda/meta.yaml	Update C++ package dependencies
cpp/conda/build.sh	Set C++ standard to 20 for conda builds
cpp/mrd-tools/fftw_wrappers.h	New file implementing FFTW wrapper functions to replace xtensor-fftw
cpp/mrd-tools/CMakeLists.txt	Remove fmt dependency, add warning suppression for GCC 15+
cpp/mrd-tools/*.cc	Update includes for xtensor 0.27.1 and replace xtensor-fftw with custom wrappers
cpp/mrd/yardl/detail/ndarray/impl.h	Add version-conditional includes for xtensor compatibility
python/mrd/yardl_types.py	Replace deprecated utcfromtimestamp with fromtimestamp(tz=UTC)
python/mrd/_binary.py	Replace deprecated datetime API and use complex instead of ComplexFloat
python/mrd/tools/phantom.py	Refactor acquisition creation to use factory function
python/mrd/types.py	Update type annotations for Python 3.13 compatibility
python/mrd/_dtypes.py	Add Annotated type support
.github/workflows/mrd_build.yml	Update Yardl version to 0.6.6
.github/actions/configure-mrd-build-environment/action.yml	Remove use-mamba flag
docker/Dockerfile	Update base image to Ubuntu 24.04, update Miniforge, replace mamba with conda
.devcontainer/Dockerfile	Update Miniforge and Yardl versions, replace mamba with conda
docs/*/quickstart.md	Update installation instructions to use conda instead of mamba
VERSION	Bump version from 2.1.2-preview to 2.2.0

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[johnstairs]

Should we also increase the required Python version as well in pyproject.toml?

[naegelejd]

I don't think so actually. The MRD Python library is still compatible with Python 3.9, so it advertises that it requires any Python >= 3.9.

The changes here enable us to use Python 3.13 in the devcontainer and CI pipeline (which, for example, uncovered a bug in phantom.py).

What do you think?

[johnstairs]

Yeah, that's fine. At some point, we can bump it to take advantage of newer features, but it doesn't have to be now. Should we have testing that verifies that it works with older versions?

[naegelejd]

OK, yes, backward compatibility with Python should be tested.

Instead, I'll do what you first suggested. MRD will require Python >= 3.13. I think this is appropriate.