Merge pull request #70 from linkml/claude/cool-gates-ow9b2g

Add cell-free expression value sets for synthetic biology

Author: cmungall

.github/workflows/claude-code-review.yml

@@ -27,52 +27,35 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
 
       - name: Run Claude Code Review
         id: claude-review
-        uses: anthropics/claude-code-action@beta
+        uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
 
-          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1)
-          # model: "claude-opus-4-1-20250805"
+          # In v1, providing a `prompt` runs in automation mode, which does NOT
+          # post a comment by default. track_progress restores the v0.x
+          # "post the review as a PR comment" behavior and auto-injects PR context.
+          track_progress: true
 
-          # Direct prompt for automated review (no @claude mention needed)
-          direct_prompt: |
+          # Prompt for the automated review (no @claude mention needed).
+          prompt: |
             Please review this pull request and provide feedback on:
             - Code quality and best practices
             - Potential bugs or issues
             - Performance considerations
             - Security concerns
             - Test coverage
-            
+
             Be constructive and helpful in your feedback.
 
-          # Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR
-          # use_sticky_comment: true
-          
-          # Optional: Customize review based on file types
-          # direct_prompt: |
-          #   Review this PR focusing on:
-          #   - For TypeScript files: Type safety and proper interface usage
-          #   - For API endpoints: Security, input validation, and error handling
-          #   - For React components: Performance, accessibility, and best practices
-          #   - For tests: Coverage, edge cases, and test quality
-          
-          # Optional: Different prompts for different authors
-          # direct_prompt: |
-          #   ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' && 
-          #   'Welcome! Please review this PR from a first-time contributor. Be encouraging and provide detailed explanations for any suggestions.' ||
-          #   'Please provide a thorough code review focusing on our coding standards and best practices.' }}
-          
-          # Optional: Add specific tools for running tests or linting
-          # allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)"
-          
-          # Optional: Skip review for certain conditions
-          # if: |
-          #   !contains(github.event.pull_request.title, '[skip-review]') &&
-          #   !contains(github.event.pull_request.title, '[WIP]')
+          # Args passed through to the Claude CLI. Use the `opus` alias rather
+          # than a dated model id so the workflow tracks the current Opus and
+          # won't 404 when a specific version is retired.
+          claude_args: |
+            --model opus
 

.github/workflows/claude.yml

@@ -31,65 +31,37 @@ jobs:
       actions: read # Required for Claude to read CI results on PRs
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
-            
+
       - name: Install python tools
         run: |
           uv sync
 
       - name: Run Claude Code
         id: claude
-        uses: anthropics/claude-code-action@beta
-        
+        uses: anthropics/claude-code-action@v1
+
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
-          mcp_config: |
-            {
-              "mcpServers": {
-                "ols": {
-                  "command": "uvx",
-                  "args": [
-                    "ols-mcp"
-                  ]
-                },
-                "sequential-thinking": {
-                  "command": "npx",
-                  "args": [
-                    "-y",
-                    "@modelcontextprotocol/server-sequential-thinking"
-                  ]
-                }
-              }
-            }
 
           # This is an optional setting that allows Claude to read CI results on PRs
           additional_permissions: |
             actions: read
-          
-          # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1)
-          # model: "claude-opus-4-1-20250805"
-          
+
+          # In v1 the model, MCP servers, and allowed tools are passed through to
+          # the Claude CLI via claude_args (the v0.x model / mcp_config /
+          # allowed_tools inputs were removed). The `opus` alias tracks the
+          # current Opus so this won't 404 when a dated model id is retired.
+          claude_args: |
+            --model opus
+            --mcp-config '{"mcpServers":{"ols":{"command":"uvx","args":["ols-mcp"]},"sequential-thinking":{"command":"npx","args":["-y","@modelcontextprotocol/server-sequential-thinking"]}}}'
+            --allowedTools "Bash(*),FileEdit,Edit,MultiEdit,WebSearch,WebFetch,mcp__ols_mcp__search_all_ontologies,mcp__ols_mcp__get_terms_from_ontology"
+
           # Optional: Customize the trigger phrase (default: @claude)
           # trigger_phrase: "/claude"
-          
-          # Optional: Trigger when specific user is assigned to an issue
-          # assignee_trigger: "claude-bot"
-          
-          # Optional: Allow Claude to run specific commands
-          allowed_tools: "Bash(*),FileEdit,Edit,MultiEdit,WebSearch,WebFetch,mcp__ols_mcp__search_all_ontologies,mcp__ols_mcp__get_terms_from_ontology"
-          
-          # Optional: Add custom instructions for Claude to customize its behavior for your project
-          # custom_instructions: |
-          #   Follow our coding standards
-          #   Ensure all new code has tests
-          #   Use TypeScript for new files
-          
-          # Optional: Custom environment variables for Claude
-          # claude_env: |
-          #   NODE_ENV: test
 

cache/chebi/terms.csv

@@ -253,3 +253,11 @@ CHEBI:33371,technetium-99,2026-02-14T13:12:45.429091
 CHEBI:33388,plutonium atom,2026-02-14T13:12:45.429768
 CHEBI:33389,americium atom,2026-02-14T13:12:45.430292
 CHEBI:52636,iodine-129 atom,2026-02-14T13:12:45.431463
+CHEBI:17287,N-phosphocreatine,2026-06-23T05:39:54.423305
+CHEBI:18021,phosphoenolpyruvate,2026-06-23T05:39:54.424513
+CHEBI:15350,acetyl dihydrogen phosphate,2026-06-23T05:39:54.425221
+CHEBI:17794,3-phospho-D-glyceric acid,2026-06-23T05:39:54.425989
+CHEBI:17634,D-glucose,2026-06-23T05:39:54.426683
+CHEBI:14314,D-glucose 6-phosphate,2026-06-23T05:39:54.427283
+CHEBI:17306,maltose,2026-06-23T05:39:54.427948
+CHEBI:15361,pyruvate,2026-06-23T05:39:54.428673

cache/ncit/terms.csv

@@ -428,3 +428,4 @@ NCIT:C68769,Decontamination,2026-02-15T15:46:36.956886
 NCIT:C28239,Cobalt Co-60,2026-02-15T15:46:57.873654
 NCIT:C120576,Improvised Nuclear Device,2026-02-15T15:47:04.484150
 NCIT:C120580,Radiological Dispersal Device,2026-02-15T15:47:13.265115
+NCIT:C16350,Biosensors,2026-06-23T05:48:32.996687

cache/obi/terms.csv

@@ -81,3 +81,4 @@ OBI:0302736,comet assay,2026-02-22T14:59:17.858350
 OBI:0302886,centrifugation,2026-06-11T16:05:52.111915
 OBI:0000626,DNA sequencing assay,2026-06-11T16:09:55.501188
 OBI:0002107,bio-layer interferometry assay,2026-06-11T16:12:09.434877
+OBI:0000719,vaccine production,2026-06-23T05:48:33.992380