Regenerate community HTML and UMAP after recent additions#54
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Refresh docs/ to reflect recent community additions and snippet repairs: - 20 modified community pages from the snippet-repair PRs and other curation updates. - 7 new community pages from communities added since last regen (Coastal Forested Wetland, Lake Washington, MUCC Freshwater Wetland, Mushroom Spring, Prairie Pothole, Thalassiosira/Marinobacter coculture, Wetland Oxygen/Sulfate GHG microcosm). - Refreshed docs/index.html and docs/community_umap.html (252 communities embedded, 3 host-only skipped). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR regenerates the static docs/ site to reflect recent additions and snippet repairs from PRs #49–#53 and other curation. It adds 7 new community pages, updates 20 existing pages with corrected evidence snippets (verbatim substrings from cited abstracts, with some downgraded to PARTIAL or WRONG_STATEMENT), and refreshes docs/index.html (now showing 255 communities) and docs/community_umap.html.
Changes:
- Add 7 new community HTML pages (Coastal Forested Wetland, Lake Washington, MUCC, Mushroom Spring, Prairie Pothole, Thalassiosira/Marinobacter, Wetland O2/SO4 GHG).
- Update 20 community pages with repaired snippets and adjusted evidence types (SUPPORT → PARTIAL/WRONG_STATEMENT).
- Refresh
docs/index.htmlcount (248 → 255) and add new community cards.
Reviewed changes
Copilot reviewed 26 out of 27 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| docs/index.html | Updates total count to 255 and inserts cards for 7 new communities. |
| docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html | New community page. |
| docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html (via index card) | New community page reference. |
| docs/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.html (via index card) | New community page reference. |
| docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html | New community page. |
| docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html | New community page. |
| docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html | New community page. |
| docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html | New community page. |
| docs/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.html | Snippet repair (bracket stripping). |
| docs/communities/Australian_Lead_Zinc_Polymetallic.html | Snippet/evidence downgrade to PARTIAL. |
| docs/communities/BioModels_MODEL2204300001_Kefir_Community_Model.html | Snippet repair, downgrade to PARTIAL. |
| docs/communities/BioModels_MODEL2407300002_Sponge_Holobiont_Network.html | Snippet repair, downgrade to PARTIAL. |
| docs/communities/Chromium_Sulfur_Reduction_Enrichment.html | Bracket-free verbatim snippet. |
| docs/communities/Copper_Biomining_Heap_Leach.html | Snippet repair, downgrade to PARTIAL. |
| docs/communities/Dangl_SynComm_35.html | Snippet repair. |
| docs/communities/Ewaste_Bioleaching_Consortium.html | Verbatim snippet replacement. |
| docs/communities/Iberian_Pit_Lake_Stratified_Community.html | Snippet repair, downgrade to PARTIAL. |
| docs/communities/Industrial_Bioreactor_Consortium.html | Evidence downgrades (WRONG_STATEMENT, PARTIAL). |
| docs/communities/Mercury_SFA_EFPC_Sediment_Community.html | Snippet repair with .. ellipsis. |
| docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html | Snippet/evidence downgrades. |
| docs/communities/Phormidium_Alkaline_Consortium.html | Verbatim snippet repairs. |
| docs/communities/Polaromonas_Vanadium_Reduction_Community.html | Snippet/evidence downgrades to PARTIAL. |
| docs/communities/Richmond_Mine_AMD_Biofilm.html | Snippet repair, PARTIAL downgrade. |
| docs/communities/Rifle_Uranium_Reducing_Community.html | Snippet/evidence downgrades to PARTIAL. |
| docs/communities/Thermophilic_Pyrite_QS_Consortium.html | Verbatim snippet repairs. |
| docs/communities/Tinto_River_Iron_Cycling_Community.html | Snippet/evidence downgrades to PARTIAL. |
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* Regenerate community HTML and UMAP Refresh docs/ to reflect community additions and evidence updates since the last regen (PR #54). UMAP grows from 252 -> 261 embedded communities; 7 existing community pages are refreshed with the evidence additions from PRs #55, #58, #60, #61, #62, #63, #66, #67; 9 new community pages are added (2 from this session: Alaska Tundra Permafrost Iron-Redox and Saccharomyces-Acinetobacter Lignocellulose Detox; 7 from other curation work merged in between). - gen-html: 264 community pages rendered without error - gen-umap: 261 communities embedded (3 host-only skipped because none of their taxa have NCBITaxon embeddings) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #71: render evidence everywhere it lives Three template/data fixes triggered by the Copilot review on the HTML/UMAP regen: - src/communitymech/templates/community.html: - Extend the interaction-network color map and legend with PREDATION, NICHE_PARTITIONING, STRAIN_COMPETITION, and COLONIZATION_FACILITATION. Previously these enum values fell back to generic gray on the force-directed graph and were omitted from the legend, making 5+ community pages (Cellulomonas-Rhodobacter, Sphingobium-Rhodococcus, Clostridium-Carboxidivorans-Kluyveri, Rhodopseudomonas- Geobacter-Magnetite, plus any others) hard to read. - Render evidence on taxonomy entries via an "evidence-row" span. The previous template only rendered evidence inside ecological_interactions and growth_media, so evidence wired onto taxon blocks in PRs like #61 and #62 was on-disk in the YAML but invisible in the rendered HTML. - Render evidence on environmental_factors with the same expanding-row pattern. This is where PR #62 wired the Ter Horst 2021 peat-virome evidence on the SPRUCE community; it now appears in the HTML. - Add an "External Resources" section (analogous to Associated Datasets) that renders external_resources entries including their per-resource evidence. This is where PR #66 wired the Smith 2025 BioModels reproducibility paper on the Kefir BioModels community; it now appears in the HTML. - kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml: add `metals_present: [IRON]`, `metal_relevance: SIGNIFICANT`, and metal_notes describing the Fe(III) reduction / Fe(II) oxidation cycle this community is built around. The community was previously absent from the iron/metal index filter despite being entirely iron-centric. - docs/: regenerate all 264 community pages with the new template + the Alaska_Tundra metals metadata. Many pages pick up the new evidence-row block; the four pages with NICHE_PARTITIONING interactions now render those nodes with the dedicated color and include the new legend entries. Verified after regen: - SPRUCE community page now shows PMID:38515239 and PMID:34836550 (zero matches before, two each after). - Kefir BioModels community page now shows PMID:41343683 (zero matches before, two after). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Refresh `docs/` to reflect recent community additions and snippet repairs.
Test plan
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