Convert 3 more CommunityMech writers (intelligent_snippet_fixer + enhance_strain_data + add_evidence_source)

[realmarcin]

Summary

Continues the audit-machinery rollout from #84 (initial port: 5 writers) and #85 (audit-detector blind spot fix + restore-on-failure pattern). Brings CommunityMech writer coverage from 5/16 → 8/16 gated through record_curation_event + write_validated_community.

Each converted script now:

1. Loads the community YAML via yaml.safe_load
2. Mutates the in-memory dict
3. Calls record_curation_event(doc, curator=..., action=..., changes=..., llm_assisted=...)
4. Writes via write_validated_community(doc, path) — closed-schema LinkML gate refuses any drift
5. Catches ValidationFailedError per-record so one bad doc can't kill a batch

Conversions

Script	Action label	LLM	Notes
scripts/intelligent_snippet_fixer.py	FIX_SNIPPETS_LLM	yes	Uses skip_if_recent=True so a session of auto-approved snippet fixes collapses into one curation_history entry. Pre-existing .yaml.bak_intelligent backup (from shutil.copy2 at session start) is unchanged — still the user-visible safety net.
scripts/enhance_strain_data.py	ENHANCE_STRAIN_DATA	no	Previously extract-only; added an --apply mode that writes strain_designation into matching taxonomy[*] entries via the validated writer. Default behavior preserves the historical extract-only flow (no kb/communities writes without --apply). --overwrite controls whether to replace existing curator-authored values.
scripts/add_evidence_source.py	BACKFILL_EVIDENCE_SOURCE	no	Backup-then-rename pattern from #85: original renamed to .yaml.bak_source before the validated write; on ValidationFailedError the backup is renamed back into place so the batch loop continues cleanly.

All existing CLI flags preserved (--auto, --interactive, --dry-run, --auto-approve, --only-invalid, --file, --verbose, --relaxed).

After-state audit

=== writers audit summary (16 writers) ===
  appends curation_history:   8 / 16   (was 5/16)
  has write safeguard:        11 / 16
  validates before write:     9 / 16   (was 6/16)
  wired into justfile:        1 / 16

The remaining un-converted writers (apply_strain_designations.py, apply_taxonomy_corrections.py, backfill_metals.py, clean_metals_inplace.py [in flight on a sibling PR], fix_reference_formats.py, plus a couple of src/ writers) follow the same pattern; left as future work to keep this PR focused.

Heads-up: pre-existing import errors (not changed by this PR)

scripts/add_evidence_source.py and scripts/intelligent_snippet_fixer.py import communitymech.literature_enhanced at the module top level — a module that does not exist in this repo and never has. Both scripts have always failed at the import step when invoked from CLI. This PR does not introduce or fix that; it's tracked separately. The conversion itself (imports + writer routing) is independently verifiable by ruff + ast-parse, which is what this PR verifies.

Baseline (unchanged)

check	result
uv run python scripts/validate_strict.py --quiet	0 ERROR rows / 265 files
uv run pytest tests/ -q	136 passed, 9 skipped, 7 deselected
uv run ruff check scripts/{add_evidence_source,enhance_strain_data,intelligent_snippet_fixer}.py	net -4 errors (all I001 / F401 from removing unused imports); no new findings

Test plan

• uv run python -c "import ast; ast.parse(open('scripts/<name>.py').read())" — all three parse
• uv run ruff check scripts/<name>.py — net error reduction (removed pre-existing unused imports); no new findings
• uv run python scripts/audit_writers.py — all 3 now show appends_curation_history=yes AND validates_before_write=yes
• uv run python scripts/validate_strict.py --quiet — 0 ERROR rows / 265 files
• uv run pytest tests/ — 136 passed, 9 skipped
• uv run python scripts/enhance_strain_data.py --help — new --apply / --overwrite / --kb-dir flags surface cleanly

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Continues the audit-machinery rollout from PR #84/#85 by converting three more writers (intelligent_snippet_fixer.py, enhance_strain_data.py, add_evidence_source.py) to route through record_curation_event + write_validated_community, bringing coverage from 5/16 to 8/16.

Changes:

• Convert three writers to use the curation-event + closed-schema-validated writer pattern, each with a script-specific action label
• Add --apply / --overwrite / --kb-dir flags to enhance_strain_data.py (previously extract-only); the historical default still writes nothing to kb/communities/
• Refresh reports/pipeline_writers_audit.tsv so the three converted scripts now show appends_curation_history=yes and validates_before_write=yes

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
scripts/intelligent_snippet_fixer.py	Wrap snippet-fix write in record_curation_event(skip_if_recent=True, llm_assisted=True) + write_validated_community; pre-existing .yaml.bak_intelligent backup remains the user-facing safety net
scripts/enhance_strain_data.py	Add apply_strain_data_to_community method and --apply / --overwrite / --kb-dir CLI flags; preserves curator-authored strain_designation values unless --overwrite is set
scripts/add_evidence_source.py	Summarize per-file changes in a curation event, rename original to .yaml.bak_source, write via validated writer, restore backup on ValidationFailedError
reports/pipeline_writers_audit.tsv	Update three rows to reflect new appends_curation_history / validates_before_write status

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