linkml-reference-validator 0.1.0__tar.gz

linkml_reference_validator-0.1.0/.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: 34d23a0
+_src_path: monarch-project-copier
+copyright_year: '2025'
+email: cjmungall@lbl.gov
+full_name: Chris Mungall
+gh_action_docs_preview: false
+github_handle: cmungall
+github_org: linkml
+license: Apache-2.0
+project_description: Validation of supporting text from references and publications
+project_name: linkml-reference-validator
+project_slug: linkml_reference_validator
+

linkml_reference_validator-0.1.0/.editorconfig

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+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false

linkml_reference_validator-0.1.0/.github/actions/claude-code-action/action.yml

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+name: "Claude Code Action"
+description: "Run Claude Code in GitHub Actions workflows"
+
+inputs:
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: true
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  prompt:
+    description: "The prompt to send to Claude Code"
+    required: false
+    default: ""
+  prompt_file:
+    description: "Path to a file containing the prompt to send to Claude Code"
+    required: false
+    default: ""
+  allowed_tools:
+    description: "Comma-separated list of allowed tools for Claude Code to use"
+    required: false
+    default: ""
+  output_file:
+    description: "File to save Claude Code output to (optional)"
+    required: false
+    default: ""
+  timeout_minutes:
+    description: "Timeout in minutes for Claude Code execution"
+    required: false
+    default: "10"
+  install_github_mcp:
+    description: "Whether to install the GitHub MCP server"
+    required: false
+    default: "false"
+  install_artl_mcp:
+    description: "Whether to install the ARTL MCP server"
+    required: false
+    default: "false"
+
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install uvx
+      shell: bash
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        source $HOME/.cargo/env
+        which uvx || echo "uvx not found in PATH, installing via pip"
+        pip install uv || true
+
+    - name: Install Claude Code
+      shell: bash
+      run: npm install -g @anthropic-ai/claude-code
+
+    - name: Install GitHub MCP Server
+      if: inputs.install_github_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json github '{
+          "command": "docker",
+          "args": [
+            "run",
+            "-i",
+            "--rm",
+            "-e",
+            "GITHUB_PERSONAL_ACCESS_TOKEN",
+            "ghcr.io/github/github-mcp-server:sha-ff3036d"
+          ],
+          "env": {
+            "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ inputs.GITHUB_TOKEN }}"
+          }
+        }'
+
+    - name: Install ARTL MCP Server
+      if: inputs.install_artl_mcp == 'true'
+      shell: bash
+      run: |
+        claude mcp add-json artl '{
+          "command": "uvx",
+          "args": [
+            "artl-mcp"
+          ]
+        }'
+
+    - name: Prepare Prompt File
+      shell: bash
+      id: prepare_prompt
+      run: |
+        # Check if either prompt or prompt_file is provided
+        if [ -z "${{ inputs.prompt }}" ] && [ -z "${{ inputs.prompt_file }}" ]; then
+          echo "::error::Neither 'prompt' nor 'prompt_file' was provided. At least one is required."
+          exit 1
+        fi
+
+        # Determine which prompt source to use
+        if [ ! -z "${{ inputs.prompt_file }}" ]; then
+          # Check if the prompt file exists
+          if [ ! -f "${{ inputs.prompt_file }}" ]; then
+            echo "::error::Prompt file '${{ inputs.prompt_file }}' does not exist."
+            exit 1
+          fi
+
+          # Use the provided prompt file
+          PROMPT_PATH="${{ inputs.prompt_file }}"
+        else
+          mkdir -p /tmp/claude-action
+          PROMPT_PATH="/tmp/claude-action/prompt.txt"
+          echo "${{ inputs.prompt }}" > "$PROMPT_PATH"
+        fi
+
+        # Verify the prompt file is not empty
+        if [ ! -s "$PROMPT_PATH" ]; then
+          echo "::error::Prompt is empty. Please provide a non-empty prompt."
+          exit 1
+        fi
+
+        # Save the prompt path for the next step
+        echo "PROMPT_PATH=$PROMPT_PATH" >> $GITHUB_ENV
+
+    - name: Run Claude Code
+      shell: bash
+      id: run_claude
+      run: |
+        ALLOWED_TOOLS_ARG=""
+        if [ ! -z "${{ inputs.allowed_tools }}" ]; then
+          ALLOWED_TOOLS_ARG="--allowedTools ${{ inputs.allowed_tools }}"
+        fi
+
+        # Set a timeout to ensure the command doesn't run indefinitely
+        timeout_seconds=$((${{ inputs.timeout_minutes }} * 60))
+
+        if [ -z "${{ inputs.output_file }}" ]; then
+          # Run Claude Code and output to console
+          timeout $timeout_seconds claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }}
+        else
+          # Run Claude Code and tee output to console and file
+          timeout $timeout_seconds claude \
+            -p \
+            --verbose \
+            --output-format stream-json \
+            "$(cat ${{ env.PROMPT_PATH }})" \
+            ${{ inputs.allowed_tools != '' && format('--allowedTools "{0}"', inputs.allowed_tools) || '' }} | tee output.txt
+
+          # Process output.txt into JSON in a separate step
+          jq -s '.' output.txt > output.json
+
+          # Extract the result from the last item in the array (system message)
+          jq -r '.[-1].result' output.json > "${{ inputs.output_file }}"
+
+          echo "Complete output saved to output.json, final response saved to ${{ inputs.output_file }}"
+        fi
+      
+      env:
+        ANTHROPIC_API_KEY: "."
+        ANTHROPIC_AUTH_TOKEN: ${{ inputs.cborg_api_key }}
+        GITHUB_TOKEN: ${{ inputs.github_token }}
+        ANTHROPIC_BASE_URL: "https://api.cborg.lbl.gov"
+        DISABLE_NON_ESSENTIAL_MODEL_CALLS: "1"

linkml_reference_validator-0.1.0/.github/actions/claude-issue-summarize-action/action.yml

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+name: "Claude Issue summarize Action"
+description: "Automatically Summarize GitHub issues using Claude Code"
+
+inputs:
+  timeout_minutes:
+    description: "Timeout in minutes for execution"
+    required: false
+    default: "5"
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: true
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Checkout repository code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Create prompt file
+      shell: bash
+      run: |
+        mkdir -p /tmp/claude-prompts
+        cat > /tmp/claude-prompts/claude-issue-summarize-prompt.txt << 'EOF'
+        You're an Summarization assistant for GitHub issues. Your task is to analyze the issue, look up related issues, and summarize the issue.
+
+        Remember that this repo is primarily a note-taking and memory device for Chris Mungall, so anything you can do to enhance and enrich that would be helpful.
+
+        IMPORTANT: Don't make any PRs. You should ONLY post a response, IN THE SAME ISSUE.
+
+        Issue Information:
+        - REPO: ${{ github.repository }}
+        - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+        TASK OVERVIEW:
+
+        1. First, use your judgement to determine the course of action.
+            - If the issue is an epic or has links to other issues, read those issues, and summarize them. Summarize their status etc. Given an overall summary.
+            - If the issue is an idea or a vague high level description, run with the idea, do deep research, give heloful suggestions with links to relevant papers etc.
+            - If there are links in the issue to websites, database entities, etc, then look these up.
+            - If there are links or references to papers, then looks these up and summarize (don't guess content - if you can't access the paper, then say "I can't access the paper")
+            - Try using artl-mcp to get paper fulltext.
+            - If you want a more powerful AI agent to take on this one and make a PR, use this magic phrase: `@dragon-ai-agent please <INSTRUCTIONS>`
+
+        2. Next, use the GitHub tools to get context about the issue:
+           - You have access to these github tools:
+             - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+             - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+             - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+             - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+             - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+           - You can also use web searching and fetching.
+
+        - It's okay to not add any information if the issue is not clear.
+        EOF
+
+    - name: Run Claude Code
+      uses: ./.github/actions/claude-code-action
+      with:
+        prompt_file: /tmp/claude-prompts/claude-issue-summarize-prompt.txt
+        allowed_tools: "Bash(gh label list),WebFetch,Fetch,LS,mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__add_issue_comment,mcp__github__search_issues,mcp__github__list_issues"
+        install_github_mcp: "true"
+        install_artl_mcp: "true"
+        timeout_minutes: ${{ inputs.timeout_minutes }}
+        anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        cborg_api_key: ${{ inputs.cborg_api_key }}
+        github_token: ${{ inputs.github_token }}

linkml_reference_validator-0.1.0/.github/actions/claude-issue-triage-action/action.yml

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+name: "Claude Issue Triage Action"
+description: "Automatically triage GitHub issues using Claude Code"
+
+inputs:
+  timeout_minutes:
+    description: "Timeout in minutes for execution"
+    required: false
+    default: "5"
+  anthropic_api_key:
+    description: "Anthropic API key"
+    required: true
+  cborg_api_key:
+    description: "CBORG API key"
+    required: true
+  github_token:
+    description: "GitHub token with repo and issues permissions"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Checkout repository code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Create prompt file
+      shell: bash
+      run: |
+        mkdir -p /tmp/claude-prompts
+        cat > /tmp/claude-prompts/claude-issue-triage-prompt.txt << 'EOF'
+        You're an issue triage assistant for GitHub issues. Your task is to analyze the issue and select appropriate labels from the provided list.
+
+        IMPORTANT: Don't post any comments or messages to the issue. Your only action should be to apply labels.
+
+        Issue Information:
+        - REPO: ${{ github.repository }}
+        - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+        TASK OVERVIEW:
+
+        1. First, fetch the list of labels available in this repository by running: `gh label list`. Run exactly this command with nothing else.
+
+        2. Next, use the GitHub tools to get context about the issue:
+           - You have access to these tools:
+             - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+             - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+             - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+             - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+             - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+           - Start by using mcp__github__get_issue to get the issue details
+
+        3. Analyze the issue content, considering:
+           - The issue title and description
+           - The type of issue (bug report, feature request, question, etc.)
+           - Technical areas mentioned
+           - Severity or priority indicators
+           - User impact
+           - Components affected
+
+        4. Select appropriate labels from the available labels list provided above:
+           - Choose labels that accurately reflect the issue's nature
+           - Be specific but comprehensive
+           - Select priority labels if you can determine urgency (high-priority, med-priority, or low-priority)
+           - Consider platform labels (android, ios) if applicable
+           - If you find similar issues using mcp__github__search_issues, consider using a "duplicate" label if appropriate. Only do so if the issue is a duplicate of another OPEN issue.
+
+        5. Apply the selected labels:
+           - Use mcp__github__update_issue to apply your selected labels
+           - DO NOT post any comments explaining your decision
+           - DO NOT communicate directly with users
+           - If no labels are clearly applicable, do not apply any labels
+
+        IMPORTANT GUIDELINES:
+        - Be thorough in your analysis
+        - Only select labels from the provided list above
+        - DO NOT post any comments to the issue
+        - Your ONLY action should be to apply labels using mcp__github__update_issue
+        - It's okay to not add any labels if none are clearly applicable
+        EOF
+
+    - name: Run Claude Code
+      uses: ./.github/actions/claude-code-action
+      with:
+        prompt_file: /tmp/claude-prompts/claude-issue-triage-prompt.txt
+        allowed_tools: "Bash(gh label list),mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__search_issues,mcp__github__list_issues"
+        install_github_mcp: "true"
+        timeout_minutes: ${{ inputs.timeout_minutes }}
+        anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        cborg_api_key: ${{ inputs.cborg_api_key }}
+        github_token: ${{ inputs.github_token }}

linkml_reference_validator-0.1.0/.github/ai-controllers.json

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+["cmungall"]

linkml_reference_validator-0.1.0/.github/copilot-setup-steps.yml

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+name: "Copilot Setup Steps"
+
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Install Python tools
+      run: |
+        uv sync
+        source .venv/bin/activate
+      shell: bash
+      

linkml_reference_validator-0.1.0/.github/dependabot.yml

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+# Please see the documentation for all configuration options:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly

linkml_reference_validator-0.1.0/.github/workflows/deploy-docs.yaml

@@ -0,0 +1,57 @@
+---
+name: Deploy docs
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions: {}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # allow to generate an OpenID Connect (OIDC) token
+
+    steps:
+      # https://github.com/actions/checkout
+      - name: Checkout
+        uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
+
+      - name: Configure git for the bot
+        # Gives the bot that commits to gh-pages a name & email address
+        # so that the commits have an author in the commit log.
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email github-actions[bot]@users.noreply.github.com
+
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.4.3
+        with:
+          python-version: 3.13
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python
+        uses: actions/setup-python@v5.6.0
+        with:
+          python-version: 3.13
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install dependencies
+        run: uv sync --dev --no-progress
+
+      - name: Generate schema documentation
+        run: |
+          uv run mkdocs gh-deploy

linkml_reference_validator-0.1.0/.github/workflows/main.yaml

@@ -0,0 +1,55 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+---
+name: Build and test
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches: [main]
+  pull_request:
+
+env:
+  FORCE_COLOR: "1" # Make tools pretty.
+
+#permissions: {}
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
+
+    steps:
+
+      # https://github.com/actions/checkout
+      - name: Check out repository
+        uses: actions/checkout@v4.2.2
+        with:
+          persist-credentials: false
+
+      # https://github.com/astral-sh/setup-uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.4.3
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      # https://github.com/actions/setup-python
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5.6.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install just
+        run: |
+          uv tool install rust-just
+
+      - name: Install project
+        run: uv sync --dev
+
+      - name: Run test suite
+        run: just test

linkml_reference_validator-0.1.0/.github/workflows/pypi-publish.yaml

@@ -0,0 +1,35 @@
+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Build source and wheel archives
+        run: uv build
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true