ducksmiles: bump to 0.5.0

[nkwork9999]

CI verified (2026-09-05)

Verified source commit: ff7c681ca14698d7ed6ec4a5d7a15fc40cefe834. Community PR head: 42d25c854f8720d561ace44082c7642e09e0c46d (tested merge commit 65f5631b4c72dbf66b1eb49c5eb62c191c1dbca3).

• Source distribution CI: success, 12 jobs passed.
• Community stable / DuckDB 1.5.5: success, 11 jobs passed.
• Community development / DuckDB 2.0-cyanoptera: success, 11 jobs passed.
• Rust PR tests: 676 passed, 1 pre-existing ignored; six Wasm-validator tests also passed.
• Actual Linux SQL test logs confirm 304 assertions in 3 cases on stable DuckDB and 3 cases passed, 0 skipped on development DuckDB. Local native execution also passed 141 statement/query checks.

Existing disabled/documentation/deployment jobs remain skipped according to the workflows; they are not counted as passed. No platform exclusions or test-disabling changes were added. These results verify builds and the executed tests, not publication or universal RDKit compatibility. Wasm checks establish side-module link integrity, not DuckDB-Wasm runtime SQL coverage.

Build and runtime compatibility fixes

• Keep DuckDB 1.5.5 and development vector APIs compatible, including nullable callbacks, mutable output access and read-only list children. Add constant/NULL, filtered-vector and multi-batch regressions.
• Mark the ten BLOB similarity callbacks and 25 dynamic-string callbacks that can throw as fallible; test expected errors, row-wise TRY recovery and connection reuse.
• Correct cross-platform Rust target selection and toolchain declarations; forward all Rust archives into the actual Wasm final link.
• Match pinned Emscripten 3.1.71 with Rust nightly-2025-02-01 and a Wasm-only std rebuild, including threaded features. Validate missing symbols and self-resolved GOT relocations against the actual binary. Wasm build contract.

Updates ducksmiles to 0.5.0 (source ref ff7c681ca14698d7ed6ec4a5d7a15fc40cefe834).

Features carried forward since 0.4.0, with SQL regression tests in the source repository:

• Bit-fingerprint similarity family over raw fingerprint BLOBs (ported from DataStructs/BitOps.cpp): dice_bit, cosine_bit, kulczynski_bit, sokal_bit, mcconnaughey_bit, asymmetric_bit, braun_blanquet_bit, russel_bit, and asymmetric tversky_bit(a, b, α, β) — joining the existing tanimoto_bit.
• mol_mr — Wildman-Crippen molar refractivity (shares the LogP atom-contribution table).
• qed — QED drug-likeness, a port of RDKit Chem.QED; reproduces the QED.py reference values closely.
• Ring-count descriptors — num_saturated_rings, num_aliphatic_rings, and the aromatic/saturated/aliphatic × heterocycle/carbocycle splits (RDKit rdMolDescriptors).

Additional changes in the current revision:

• Adds 21 structural-profile descriptors: fragment, charge and hydrogen counts; bond, ring and element statistics; heavy-atom mass and graph fractions.
• Adds a pinned RDKit 2025.09.6 suite: 4,510 distinct SMILES inputs and 94,710 scalar comparisons. Inputs include alternative spellings, isolated elements and isotopes. This is finite-corpus agreement, not universal RDKit parser/sanitizer or fingerprint compatibility.
• Fixes the reported ListVector header build failure across stable and newer DuckDB layouts.
• Adds extension.requires_toolchains: rust and correct Rust target selection for community cross-platform builds. Source CI now uses DuckDB v1.5.5 and v1.5-variegata tools.

Validation: current-ref source, community stable and community development CI all passed; exact runs, test counts and intentional skips are recorded above.

Source PR: nkwork9999/duckSMILES#14
Definitions and limits: https://github.com/nkwork9999/duckSMILES/blob/ff7c681ca14698d7ed6ec4a5d7a15fc40cefe834/PROFILE_PARITY.md

[nkwork9999]

Updated the 0.5.0 ref to the just-merged in-silico docking release (96c85cc). This version adds, on top of the existing descriptors / fingerprints / similarity / scaffold tooling:

• Drug-likeness & toxicophore filtering: admet_json, druglikeness_pass(smiles, rule) (Lipinski/Veber/Ghose/Egan/Muegge/Lead), lipinski_violations, structural_alerts_json (Brenk/PAINS catalogue).
• In-silico docking pipeline: smiles_to_pdbqt (DG + L-BFGS conformer), prepare_receptor(pdb, ph) (pH protonation + polar-H), dock(...) (flexible torsion-tree docking, Vina-style scoring + 3D affinity maps).
• Benchmark harness: roc_auc, enrichment_factor, bedroc.

Still pure Rust core (no RDKit), MIT. 546 Rust unit tests pass; full pipeline verified end-to-end against the bundled DuckDB.

[carlopi]

Closing and reopening to re-trigger CI on v1.5.4.

[sebastiaan-dev]

Hi @nkwork9999, can you take a look at the build error in the CI? It seems recurring across CI job reruns.

[nkwork9999]

Updated the source ref to nkwork9999/duckSMILES@3b5940d to address the reported build failure. The ListVector include now supports both the stable DuckDB header layout and newer layouts. The source repository CI targets DuckDB v1.5.5 with v1.5-variegata tools, and this descriptor now explicitly requests the Rust toolchain. Rust cross-target selection and formatting fixes are also included. The new community CI runs are in progress; I am checking the remaining build and SQL-test results. The 21 structural-profile descriptors have a pinned RDKit reference suite, but this update does not claim universal RDKit parser/sanitizer equivalence.

[sebastiaan-dev]

Thanks!