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XpongeCPP 0.2.0

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@yuhaosimba yuhaosimba released this 29 Jul 06:00
· 18 commits to codex/xpongecpp-v1 since this release
v0.2.0
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XpongeCPP 0.2.0

Compatibility target: Xponge-origin 1.7b8.

This is a breaking feature-alignment release from XpongeCPP 0.1.6.
Supported Python versions are CPython 3.10 through 3.12.

Highlights

  • Ports the SPONGE bundle contract, native saver, legacy/bundle converters,
    restart and output handling, H5MD readers, MDAnalysis integration, and CLI
    entry points introduced through Xponge-origin 1.7b8.
  • Exposes generic RESP linear constraints, equivalence groups, constraint
    preflight, RHF/ROHF/UHF reference selection, SCF strategy controls, progress
    events, and fit metadata through the public charge API.
  • Replaces the former MCPB-specific implementation with the origin-style
    XpongeCPP.metal_assignment package. The package includes immutable
    contracts and artifacts, base and nonbonded assignment, constrained RESP,
    Hessian providers, empirical/manual/Seminario bonded fitting, hash-closed
    local parameter patches, transactional application to preassigned
    molecules, provenance, and SPONGE export mappings.
  • Aligns application semantics with Xponge-origin 1.7b8: removes the temporary
    assigned-system/apply-input materialization layer and applies
    MetalParameterPatch objects without replacing the ordinary force field.
  • Removes the XpongeCPP.MCPB API and the XpongeCPP.mcpb package. Callers
    must migrate to XpongeCPP.metal_assignment.

Verification snapshot

On Linux x86_64 with CPython 3.11:

  • bundle contract/conversion/analysis cohort: 166 passed with the discovered
    SPONGE executable;
  • after adding environment, PATH, and sibling-build discovery, the focused
    bundle converter/SPONGE zero-frame gate passed all 7 tests with the explicit
    environment override unset;
  • rebuilt RESP, bundle, and metal cohort: 238 passed, 12 optional QM/backend
    tests skipped;
  • metal-assignment origin-parity cohort: 82 passed, 23 optional
    Mokda-chemcore/backend tests skipped;
  • final combined pre-1.7b8 release/RESP/bundle/metal/numerical parity cohort:
    217 passed, 23 optional external-provider tests skipped;
  • Xponge-origin 1.7b8 patch/contract/provider/release cohort:
    85 passed, 16 optional external-provider tests skipped;
  • RESP constraints, charge models, metal RESP, base-charge, and Hessian cohort:
    99 passed, 11 optional backend tests skipped;
  • 1.7b8 local-patch constrained RESP, explicit-reference manual bonded, and
    deterministic-Hessian Seminario real-SPONGE gates pass raw-to-bundle-to-raw
    numerical comparison;
  • wheel and source distribution built successfully and passed twine check;
  • a clean wheel smoke environment imported XpongeCPP,
    XpongeCPP.io_bundle, and XpongeCPP.metal_assignment, reported version
    0.2.0, and exposed no MCPB symbol.

The repository-wide suite currently has 504 passing tests and 31 known
unrelated failures, compared with 412 passing and 32 failing in the pre-sync
baseline. The failures are tracked separately and do not occur in the bundle,
RESP, or metal-assignment parity cohorts. An actual cross-platform CI run and
a bundle-capable SPONGE runtime remain release gates rather than claims made by
this local verification snapshot. The latter has an explicit
SPONGE_BUNDLE_EXECUTABLE-controlled acceptance test and is not silently
treated as passing on legacy-only runtimes.

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