Add Prymnesium parvum B12-limited SynCom

[realmarcin]

Summary

• add CommunityMech:000381 for the PMID:42549325 Prymnesium parvum CCAP 646/6 plus 15-strain bacterial SynCom
• cache PMID:42549325 full text and supplementary text, including Supplementary Table S1 strain membership
• render the legacy community page and add an append-only curation-history record
• teach scripts/cache_supplements.py to extract text from nested ZIP and XLSX supplementary files

Validation

• /Users/marcin/.pyenv/versions/3.10.12/bin/python -m pytest tests/test_cache_supplements.py
• /Users/marcin/.pyenv/versions/3.10.12/bin/python -m py_compile scripts/cache_supplements.py tests/test_cache_supplements.py
• env PYTHONPATH=src /Users/marcin/.pyenv/versions/3.10.12/bin/python scripts/validate_gtdb_coherence.py kb/communities/Prymnesium_Parvum_B12_Limited_SynCom.yaml
• env PYTHONPATH=src /Users/marcin/.pyenv/versions/3.10.12/bin/python scripts/validate_yaml_scalars.py kb/communities/Prymnesium_Parvum_B12_Limited_SynCom.yaml history/records/Prymnesium_Parvum_B12_Limited_SynCom/2026-09-15T044040Z-codex-42549325.yaml
• env PYTHONPATH=src /Users/marcin/.pyenv/versions/3.10.12/bin/python scripts/validate_cross_repo_ids.py kb/communities/Prymnesium_Parvum_B12_Limited_SynCom.yaml
• custom PMID:42549325 snippet verifier: 39 snippets checked, 0 missing
• direct OAK SQLite label check for all CHEBI, ENVO, GO, and NCBITaxon terms in the new record
• rg --hidden --no-ignore duplicate check across kb
• git diff --cached --check

Local environment notes

• scripts/validate_strict.py is blocked locally by the direct Python linkml_runtime not understanding schema bindings metadata
• validate_id_label_correspondence.py and validate_shared_taxon_ids.py are blocked/skipped locally because the direct Python lacks oaklib

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

[github-actions]

Network integrity findings

Warnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build.

Network Integrity Audit Report
================================================================================

0 error, 13 warning across 4 records with findings
Only error-severity findings fail the build.

Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'tobacco' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Fusarium oxysporum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Pinus massoniana' not found in taxonomy section (community-level scope)

Total: 3 issues (0 error, 3 warning)

Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
--------------------------------------------------------------------------------
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)
  [warning] UNKNOWN_TARGET: Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)

Total: 2 issues (0 error, 2 warning)

Space_Habitat_SevenMember_Stress_Tolerance_SynCom
--------------------------------------------------------------------------------
  [warning] DISCONNECTED: Taxon 'Acinetobacter radioresistens 50V1' has no interactions
  [warning] DISCONNECTED: Taxon 'Micrococcus luteus W4-Al-K1' has no interactions
  [warning] DISCONNECTED: Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions
  [warning] DISCONNECTED: Taxon 'Pseudomonas antarctica CMS 35T' has no interactions
  [warning] DISCONNECTED: Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions
  [warning] DISCONNECTED: Taxon 'Streptococcus halotolerans HTS9T' has no interactions

Total: 6 issues (0 error, 6 warning)

The full report is attached to the workflow run as an artifact.