Release Bloom 8.0.0 to main

[iamh2o]

Summary

• release Bloom 8.0.0 from jem-dev to main
• pin Bloom to daylily-tapdb 9.0.10 and add defusedxml for safe spreadsheet XML parsing
• repair TapDB semantic template handling for beta actions, execution queue subjects, and Bloom prefix ownership seeding
• keep Dayhoff-facing README pin aligned to 8.0.0

Validation

• ruff check changed Python files
• ruff format --check changed Python files
• bandit -c pyproject.toml changed Python files
• uv lock --check
• python -m compileall -q bloom_lims tests container_tests
• uv build
• pytest --no-cov tests/test_config_runtime.py tests/test_route_coverage_gaps_api.py tests/test_route_coverage_gaps_gui.py tests/test_api_v1.py tests/test_gui_endpoints.py tests/test_api_atlas_bridge.py tests/test_atlas_lookup_resilience.py tests/test_queue_flow.py tests/test_run_resolver.py -> 449 passed, 35 skipped

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: e9961c942a

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Don't retire material templates after seeding

When bloom db build --overwrite reaches this cleanup, it now retires any row whose physical category differs from its semantic_category. The current template pack intentionally uses that split for active templates, e.g. config/tapdb_templates/bloom/templates.json:5911-5943 has category: "material" with semantic_category: "content"; this branch marks the just-seeded active row deleted, and the later expected-category check also deletes the old content-category variant. After an overwrite seed, lab/specimen flows that create material/... content templates will have no active template to resolve.

Useful? React with 👍 / 👎.