Skip to content

Add cell-free expression value sets for synthetic biology #70

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
cmungall merged 4 commits into from
Jun 23, 2026
Merged

Add cell-free expression value sets for synthetic biology #70

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
99797e1
Add cell-free expression value sets
claude Jun 23, 2026
00fe49f
Update CHEBI label cache for cell-free expression terms
claude Jun 23, 2026
d929b86
Anchor cell-free expression PVs to ontology terms
claude Jun 23, 2026
d9006e5
Migrate Claude Code workflows to claude-code-action@v1
claude Jun 23, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 14 additions & 31 deletions .github/workflows/claude-code-review.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

56 changes: 14 additions & 42 deletions .github/workflows/claude.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

8 changes: 8 additions & 0 deletions cache/chebi/terms.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
1 change: 1 addition & 0 deletions cache/ncit/terms.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
1 change: 1 addition & 0 deletions cache/obi/terms.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Loading
Loading