Updated opm

[grenkoca]

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 ✍️ ✅

[grenkoca]

@sarthakpati @benmalef

This pull request updates the backend of OPM to streamline the patch extraction, add a grid mining function, and enable loading patches in memory. It also (hopefully) resolves merge conflicts between the updated_OPM branch and add_dsa_annotations_merged branch, consolidating improvements to the patch mining system with DSA annotation support.

Let's see how this goes...

[sarthakpati]

Thanks, @grenkoca. Marking this PR as draft until we figure out the CI stuff.

[github-actions]

@check-spelling-bot Report

🔴 Please review

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

Unrecognized words (4)

downsampled
maxx
maxy
svs

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 [email protected]:grenkoca/GaNDLF.git repository
on the updated_OPM 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/17108155948/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: ""

[codecov]

Codecov Report

❌ Patch coverage is 10.24259% with 333 lines in your changes missing coverage. Please review.
✅ Project coverage is 69.53%. Comparing base (3f9b772) to head (6ec1771).

Files with missing lines	Patch %	Lines
GANDLF/data/patch_miner/opm/patch_manager.py	2.61%	149 Missing ⚠️
GANDLF/data/patch_miner/opm/dsa_annotations.py	18.36%	120 Missing ⚠️
GANDLF/data/patch_miner/opm/patch.py	8.51%	43 Missing ⚠️
GANDLF/cli/patch_extraction.py	12.50%	21 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #1019       +/-   ##
===========================================
- Coverage   82.30%   69.53%   -12.77%     
===========================================
  Files         193      194        +1     
  Lines       12314    12621      +307     
===========================================
- Hits        10135     8776     -1359     
- Misses       2179     3845     +1666     

Flag	Coverage Δ
unittests	69.53% <10.24%> (-12.77%)	⬇️

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[github-actions]

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