Fixed Dockerfile for Apple Silicon (M4 Pro)

[vera-br]

Fixes issue #34

Changes:

• Set ARM64-specific optimisation flags
• Implemented a shallow clone of HDF5 to reduce data transfer and avoid fetch-pack disconnects during the build process

Testing:

• Successfully built and tested on Apple M4 Pro (macOS 26.1)
• All unit tests passed for ReMKiT1D v1.3.0

[Copilot]

Pull Request Overview

This PR updates the ReMKiT1D Docker container for ARM64/Apple Silicon architecture. The changes include version bump to 1.3.0, removal of Python dependencies that weren't needed, ARM64-specific compiler optimizations, improved reliability for HDF5 installation, and environment variable cleanup.

Key Changes:

• Added ARM64-specific optimization flags (-mcpu=native) to PETSc configuration
• Implemented fallback mechanism for HDF5 installation to handle git clone failures
• Removed duplicate LD_LIBRARY_PATH environment variable declarations in favor of RUN echo commands

---

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[Copilot]

These RUN echo commands only print the variable values but don't actually set them. The LD_LIBRARY_PATH environment variable is not being configured. Either remove these lines if they're debugging statements, or replace them with ENV LD_LIBRARY_PATH=/home/mpich-install/lib:/home/sundials/lib:$LD_LIBRARY_PATH to properly set the variable.

Suggested change

	RUN echo LD_LIBRARY_PATH=/home/mpich-install/lib:$LD_LIBRARY_PATH
	RUN echo LD_LIBRARY_PATH=/home/sundials/lib:$LD_LIBRARY_PATH
	ENV LD_LIBRARY_PATH=/home/mpich-install/lib:/home/sundials/lib:$LD_LIBRARY_PATH

[Copilot]

The PATH is appended with :$PATH at the end, which creates a redundant reference. This line adds /home/mpich-install/bin to PATH and then appends the entire PATH again. It should be ENV PATH=$PATH:/home/mpich-install/bin or ENV PATH=/home/mpich-install/bin:$PATH.

Suggested change

	ENV PATH=$PATH:/home/mpich-install/bin:$PATH
	ENV PATH=$PATH:/home/mpich-install/bin

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 54.20%. Comparing base (3b0aa31) to head (b9645c4).
⚠️ Report is 5 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master      #35   +/-   ##
=======================================
  Coverage   54.20%   54.20%           
=======================================
  Files         239      239           
  Lines       10124    10124           
=======================================
  Hits         5487     5487           
  Misses       4637     4637           

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[alfieadhemar]

Dockerfile succsefully compiled/verified on M2