Add dairy wastewater algal-cyanobacterial panel

[realmarcin]

Summary

• add CommunityMech:000384 for the non-sterile dairy-wastewater algal/cyanobacterial cultivation panel from PMID:41561919
• capture Synechocystis sp., Desertifilum tharense, Chlorella sorokiniana, and Euglena gracilis across mono-, pairwise co-, and sequential culture treatments
• ground 50% dairy-wastewater bottle cultivation, phycosphere/free-living 16S fractionation, and PRJNA1265442 dataset metadata to OA PubMed/PMC cache snippets
• regenerate the published community page plus docs index/browser counts
• add append-only history for the new record

Validation

• PYTHONPATH=src tmp/linkml-env/bin/python scripts/validate_strict.py kb/communities/.yaml data/isolates/.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python scripts/evidence_snippet_audit.py kb/communities/Dairy_Wastewater_Algal_Cyanobacterial_Cultivation_Panel.yaml
• uvx --from linkml-term-validator linkml-term-validator validate-data kb/communities/Dairy_Wastewater_Algal_Cyanobacterial_Cultivation_Panel.yaml -s src/communitymech/schema/communitymech.yaml --labels
• uvx --from linkml-reference-validator --with "linkml>=1.9.3" linkml-reference-validator validate data kb/communities/Dairy_Wastewater_Algal_Cyanobacterial_Cultivation_Panel.yaml -s src/communitymech/schema/communitymech.yaml --config conf/reference_validator.yaml
• PYTHONPATH=src tmp/linkml-env/bin/python -m communitymech.cli audit-network --communities-dir kb/communities --check-only reported 0 errors / 13 existing warnings

Local notes

• targeted pytest had two local environment/artifact failures: uv run linkml-validate is broken in this checkout, and an ignored tmp/msystems.00113-26-s0001.pdf from earlier work trips the publication-PDF guard; direct schema validation passed for all 378 records.

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[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.