Parallel memory hardening#8

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reece-maticebio:parallel-memory-hardening

Commits on May 11, 2026

setup as installalable package. added tests. refactored modules into python modules for python scripting
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more explicit documentation of python modules for running hierachical hotnet
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Commits on May 15, 2026

Add per-score golden snapshot test as refactor safety net

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Add Store + Codec protocols and MemoryStore (W1.3)

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Auto-discover Python sources in meson.build via tools/list_sources.py

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Add config dataclasses (W1.4)

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Fix raise Warning bugs and switch pipeline to logging (W1.7+W1.8)

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Rename hhio -> file_io with backward-compat shim (W1.6)

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Move legacy clustering test script out of src/ (W1.2)

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Extract CLI from compute modules into hierarchical_hotnet.cli (Wave 2)

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Add DiskStore + ScoreMap/Hierarchy codecs (W3.1)

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Thread Store through permute_scores_many and construct_hierarchies (W3.2+W3.3)

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Wire workdir + reuse into run_pipeline; lazy hierarchy iteration (W3.4+W3.5)

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Reshape module layout: core/ and parallel/ subpackages (Wave 4)

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Centralize Fortran/Python backend dispatch into backends/ (Phase 6)

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Unify CLI into a single hhnet entry with subcommands (W2.9)

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README: document workdir/reuse, HHNET_BACKEND, and network-permutation scope

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Commits on May 18, 2026

Commits on May 19, 2026

Ignore input edge weights by default (use_edge_weights=False)

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Commits on May 20, 2026

Drop isolated nodes from pipeline input with a warning

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Commits on May 21, 2026