Latest Results
feat: add transition evidence to HDF5 timelines (#2499)
## Summary
- extend the opt-in HDF5 timeline introduced in #2498 to schema 1.1 with
one evidence row per inferred connected reaction instance
- link each aggregate reaction count to its reactant and product
molecule IDs, require those instances at frames `t` and `t + 1`, and
store the exact canonical bond-order differences between their molecule
graphs
- add frozen public reader records, schema-aware validation, semantic
manifests, a machine-readable descriptor, documentation, and corruption
tests while retaining schema 1.0 read and validation support
- keep CSV-only reaction-event output unchanged; instance IDs are
requested from workers only when the HDF5 timeline is enabled
## Semantics and limits
Transition evidence records ReacNetGenerator's inferred
connected-component assignment and the corresponding stored molecule
graphs. It provides audit provenance for aggregate counts; it is not
transition-state evidence, a barrier or kinetics estimate, or
independent chemical ground truth. The timeline remains opt-in and does
not store coordinates. One connected instance can exceed the configured
numeric scan block size, and schema 1.1 files grow with the number of
inferred instances.
## Validation
- `python -m pytest tests/test_timedoutput.py
tests/test_timedoutput_validation.py -q` (`74 passed`)
- affected reaction/indexed/pipeline regression set (`48 passed`)
- GitHub Actions checks for tox, type checking, CodeQL, documentation,
source distribution, and Linux, macOS, and Windows wheel builds
- `ty==0.0.15` and Ruff 0.16.4 checks
- relevant pre-commit hooks for all changed files, including mdformat,
Velin, JSON checks, Ruff, and Ruff format
- Sphinx HTML build in the tox docs environment
- wheel build, clean Python 3.13 installation, and installed schema
descriptor smoke check (`1.1`)
Coding agent: Codex
Codex version: codex-cli 0.145.0
Model: gpt-6-astra
Reasoning effort: medium
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Timed-output timelines now support schema 1.1 with auditable,
instance-level reaction evidence.
- Evidence includes participating molecules and inferred formed, broken,
or order-changed bonds.
- Transition evidence can be read incrementally.
- Existing schema 1.0 aggregate-only timelines remain supported.
- **Validation**
- Added checks for participant integrity, atom conservation, bond
changes, and reaction-count consistency.
- **Documentation**
- Updated command-line help and API documentation for schema 1.1 and
transition evidence.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
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