Updated numpy

[sarthakpati]

Fixes #1033

Proposed Changes

• updated numpy version
• added support for python 3.13
• updated docker build to install git (needed for custom monai install) and use uv (for speed)

Checklist

• CONTRIBUTING guide has been followed.
• PR is based on the current GaNDLF master .
• Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
• Function/class source code documentation added/updated (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
• Code has been blacked for style consistency and linting.
• If applicable, version information has been updated in GANDLF/version.py.
• If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
• Usage documentation has been updated, if appropriate.
• Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
• If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].
• The logging library is being used and no print statements are left.

[github-actions]

MLCommons CLA bot All contributors have signed the MLCommons CLA ✍️ ✅

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.30%. Comparing base (3f9b772) to head (754c3a7).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1034   +/-   ##
=======================================
  Coverage   82.30%   82.30%           
=======================================
  Files         193      193           
  Lines       12314    12314           
=======================================
  Hits        10135    10135           
  Misses       2179     2179           

Flag	Coverage Δ
unittests	82.30% <100.00%> (ø)

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[sarthakpati]

Having space issues because MONAI is trying to install the full nvidia compute stack [ref]:

[SNIP!]
2025-08-15T19:37:51.0936021Z       Installing collected packages: nvidia-cusparselt-cu12, mpmath, wheel, typing-extensions, sympy, setuptools, packaging, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufile-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, ninja, networkx, MarkupSafe, fsspec, filelock, triton, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, jinja2, nvidia-cusolver-cu12, torch
2025-08-15T19:37:51.0939249Z       ERROR: Could not install packages due to an OSError: [Errno 28] No space left on device
[SNIP!]

Until the new version gets released, I don't think there is anything left to do.

[sarthakpati]

Current issues stem from the fact that MONAI is trying to install torch 2.8.0, but torch 2.7.1 is already installed. Unsure why this is happening.

[github-actions]

@check-spelling-bot Report

🔴 Please review

See the 📂 files view, the 📜action log, or 📝 job summary for details.

Unrecognized words (2)

dfd
pullin

These words are not needed and should be removed

ASSD bdfc deac numcodecs

To accept these unrecognized words as correct and remove the previously acknowledged and now absent words, you could run the following commands

... in a clone of the git@github.com:sarthakpati/GaNDLF.git repository
on the 1033-dep-update-numpy branch (ℹ️ how do I use this?):

curl -s -S -L 'https://raw.githubusercontent.com/check-spelling/check-spelling/main/apply.pl' |
perl - 'https://github.com/mlcommons/GaNDLF/actions/runs/17044736824/attempts/1' &&
git commit -m 'Update check-spelling metadata'

Available 📚 dictionaries could cover words not in the 📘 dictionary

Dictionary	Entries	Covers	Uniquely
cspell:java/src/java-terms.txt	920	2	2
cspell:shell/dict/shell-all-words.txt	113	1	1

Consider adding them (in .github/workflows/spellchecker.yml) in jobs:/spelling: for uses: check-spelling/check-spelling@main in its with:

      with:
        extra_dictionaries: |
          cspell:java/src/java-terms.txt
          cspell:shell/dict/shell-all-words.txt

To stop checking additional dictionaries, add (in .github/workflows/spellchecker.yml) for uses: check-spelling/check-spelling@main in its with:

check_extra_dictionaries: ""

[github-actions]

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