Document the retired chemistry provider

[dhsohn]

Motivation

Commit 932c0607e16e9192f69625bc430a3a628a3961af removed SMILES insertion, Molecule Info, the 3D preview, XYZ export, reaction mapping, the rdkit extra, and machine.json output. The user guides, packaging notes, and the observation-provider claim still described those features.

Changes

• Current guides and packaging instructions no longer tell people to install a chemistry extra or to run the removed handoff commands. MOL export is documented as refusing abbreviation expansion. Legacy calculation plans stay readable, and save still refuses when a plan would be dropped.
• ADR 0035 records that retirement. Chemvas does not write machine.json and does not record a replacement provider, a core version, or an execution approval for any other project.
• __version__ stays 0.25.0.dev0. Release preparation is described separately from tagging and publishing. The Windows bundle spec still requires a numeric major.minor.patch before a bundle or tag.
• tests/test_docs_sync.py rejects the removed install strings and commands in the current guides.
• Follow-up commit dff496f (review fixes for two documentation defects):
  • FIRST_SCHEME / README: the chain-to-new-C-to-terminal step now states two bonds explicitly, and only the second product bond is a double bond. tests/test_first_scheme_guide.py replays the guide's tool order and checks 8 atoms and 8 bonds.
  • CONTRIBUTING / AGENTS: aligned with the real Linux test job, coverage, and run_test_files.sh. The docs check fails if a deleted check path reappears.

Verification

Identity before the edit: task bc-72e73971-e173-51a5-8db2-557df848b1b8, origin github.com/dhsohn/Chemvas, checkout 932c0607e16e9192f69625bc430a3a628a3961af, parent 04ed9e26fbb848268026cc1ea21987032d8616ef.

Current head: dff496f32a026e137aa79351cb1f94684d37919a (previous commit b24717f43212023ae55494f9bc67f44e71d6ce38; its 20-test run is superseded and is not evidence for this head).

bash scripts/check.sh tests/test_first_scheme_guide.py tests/test_docs_sync.py

Linux, Qt offscreen, RDKit not installed. Selected files only, not a full-suite baseline.

• Ruff, Ruff format, mypy: passed
• tests/test_first_scheme_guide.py + tests/test_docs_sync.py: 22 passed

CI on dff496f (Actions run 37322231134): completed, conclusion success (2026-10-05 14:20 UTC).

• secret-scan: success
• Wheel smoke test: success
• Windows native packaging tests: success
• test (3.12): success, completed 14:20:32 UTC
• test (3.13): success, completed 14:19:35 UTC

The macOS full-suite and Cocoa results recorded on 932c0607 belong to that commit. They are not evidence for this documentation change. The rewritten quickstart was not recorded on a live canvas.

Review scope

The two documentation defects were reviewed as resolved on dff496f and approved for that scope only. This is not native QA of the full tutorial and not release completion.

Related issue

None.

Checklist

• make check passes — the whole local gate: lint, formatting, mypy, and the file-isolated test suite
• Added/updated tests for the change
• Did not cross an architecture boundary (tests/test_architecture_boundaries.py still passes)
• Updated CHANGELOG.md (under Unreleased) if user-visible
• Updated docs/README if behavior or usage changed

Notes for reviewers

Remaining conditions:

• Full make check has not been run on this commit.
• No merge to main, no tag, no PyPI publish, and no Windows installer build. 0.25.0.dev0 cannot build the Windows bundle until the version is a numeric triple.
• Downstream provider adoption is outside this repository.
• walkthrough-chemistry.gif is labeled historical and is not current UI evidence.

Slack Thread