encode-toolkit 0.3.0b1__tar.gz

encode_toolkit-0.3.0b1/.claude/settings.json

@@ -0,0 +1,11 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(.venv/bin/python -m pytest:*)",
+      "Bash(.venv/bin/python -c:*)",
+      "Bash(grep -c '@mcp.tool':*)",
+      "Bash(wc -l:*)",
+      "Bash(ls:*)"
+    ]
+  }
+}

encode_toolkit-0.3.0b1/.claude-plugin/plugin.json

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+{
+  "name": "encode-toolkit",
+  "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
+  "version": "0.3.0-beta.1",
+  "author": {
+    "name": "Dr. Alex M. Mawla, PhD",
+    "email": "ammawla@ucdavis.edu"
+  },
+  "homepage": "https://github.com/ammawla/encode-toolkit",
+  "repository": "https://github.com/ammawla/encode-toolkit",
+  "icon": "docs/icon.svg",
+  "license": "LicenseRef-Noncommercial",
+  "keywords": [
+    "genomics",
+    "encode",
+    "bioinformatics",
+    "epigenomics",
+    "chip-seq",
+    "atac-seq",
+    "rna-seq",
+    "wgbs",
+    "hi-c",
+    "cut-and-run",
+    "pipeline",
+    "nextflow",
+    "GTEx",
+    "ClinVar",
+    "GWAS",
+    "JASPAR",
+    "CellxGene",
+    "gnomAD",
+    "Ensembl",
+    "UCSC",
+    "provenance",
+    "biology",
+    "science"
+  ],
+  "skills": "skills/*",
+  "tools": [
+    {
+      "name": "encode_search_experiments",
+      "description": "Search ENCODE experiments with 20+ filters including assay type, organism, organ, biosample, target, and more."
+    },
+    {
+      "name": "encode_get_experiment",
+      "description": "Get full details for a specific experiment including all files, quality metrics, and audit info."
+    },
+    {
+      "name": "encode_list_files",
+      "description": "List files for a specific experiment with format/type filters."
+    },
+    {
+      "name": "encode_search_files",
+      "description": "Search files across all experiments with combined experiment + file filters."
+    },
+    {
+      "name": "encode_download_files",
+      "description": "Download specific files by accession to a local directory with MD5 verification."
+    },
+    {
+      "name": "encode_get_metadata",
+      "description": "List valid filter values for any search parameter."
+    },
+    {
+      "name": "encode_batch_download",
+      "description": "Search + download files in one step with preview mode."
+    },
+    {
+      "name": "encode_manage_credentials",
+      "description": "Store, check, or clear ENCODE credentials for restricted data access."
+    },
+    {
+      "name": "encode_get_facets",
+      "description": "Get live counts from ENCODE showing what data exists for given filters."
+    },
+    {
+      "name": "encode_get_file_info",
+      "description": "Get detailed metadata for a single file."
+    },
+    {
+      "name": "encode_track_experiment",
+      "description": "Track an experiment locally with publications, methods, and pipeline info."
+    },
+    {
+      "name": "encode_list_tracked",
+      "description": "List all tracked experiments with metadata and publication counts."
+    },
+    {
+      "name": "encode_get_citations",
+      "description": "Get publications for tracked experiments. Export as BibTeX or RIS."
+    },
+    {
+      "name": "encode_compare_experiments",
+      "description": "Analyze whether two experiments are compatible for combined analysis."
+    },
+    {
+      "name": "encode_log_derived_file",
+      "description": "Log derived files for provenance tracking back to ENCODE source data."
+    },
+    {
+      "name": "encode_get_provenance",
+      "description": "View provenance chains from derived files to source ENCODE data."
+    },
+    {
+      "name": "encode_export_data",
+      "description": "Export tracked experiments as CSV, TSV, or JSON with PMIDs for cross-referencing."
+    },
+    {
+      "name": "encode_summarize_collection",
+      "description": "Get grouped statistics of your tracked experiment collection."
+    },
+    {
+      "name": "encode_link_reference",
+      "description": "Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to experiments."
+    },
+    {
+      "name": "encode_get_references",
+      "description": "Get external references linked to experiments for cross-server workflows."
+    }
+  ]
+}

encode_toolkit-0.3.0b1/.env.example

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+# Optional: ENCODE access credentials for restricted data
+# Get these from your ENCODE account profile at https://www.encodeproject.org/
+# These are only needed for unreleased/restricted datasets.
+# Public data (most of ENCODE) requires no authentication.
+#
+# On first use, credentials are moved to your OS keyring (macOS Keychain,
+# Linux Secret Service, Windows Credential Locker) and removed from env vars.
+ENCODE_ACCESS_KEY=
+ENCODE_SECRET_KEY=

encode_toolkit-0.3.0b1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug in ENCODE Toolkit
+title: "[Bug]: "
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting a bug! Please fill out the sections below.
+
+  - type: dropdown
+    id: component
+    attributes:
+      label: Component
+      description: Which part of ENCODE Toolkit is affected?
+      options:
+        - MCP Tools (search, download, track)
+        - Skills (analysis, pipelines, external DBs)
+        - File Downloads / MD5 verification
+        - Credential Management
+        - SQLite Tracker
+        - Installation / Setup
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: What happened?
+      description: Clear description of the bug.
+      placeholder: "When I run encode_search_experiments with..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+      description: What should have happened instead?
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Minimal steps to reproduce the issue.
+      placeholder: |
+        1. Run `encode_search_experiments(assay_title="ChIP-seq", organ="liver")`
+        2. See error...
+
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: Output of `pip show encode-toolkit | grep Version`
+      placeholder: "0.3.0b1"
+
+  - type: dropdown
+    id: python
+    attributes:
+      label: Python version
+      options:
+        - "3.13"
+        - "3.12"
+        - "3.11"
+        - "3.10"
+
+  - type: dropdown
+    id: client
+    attributes:
+      label: MCP Client
+      options:
+        - Claude Code
+        - Claude Desktop
+        - VS Code (Continue/Cline)
+        - Cursor
+        - Other

encode_toolkit-0.3.0b1/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or improvement
+title: "[Feature]: "
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for your suggestion! Help us understand what you need.
+
+  - type: dropdown
+    id: category
+    attributes:
+      label: Category
+      options:
+        - New MCP Tool
+        - New Skill
+        - New Pipeline
+        - New Database Integration
+        - Existing Tool Enhancement
+        - Existing Skill Enhancement
+        - Documentation
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem or use case
+      description: What research problem does this solve?
+      placeholder: "I'm trying to analyze ENCODE CRISPR screen data and need..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed solution
+      description: How should this work? Include example tool calls if possible.
+      placeholder: |
+        A new tool `encode_analyze_screen` that takes an experiment accession
+        and returns guide-level scores...
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: Other approaches you've thought about.

encode_toolkit-0.3.0b1/.github/PULL_REQUEST_TEMPLATE.md

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+## Summary
+
+<!-- Brief description of changes (1-3 sentences) -->
+
+## Changes
+
+<!-- Bulleted list of what was changed -->
+
+-
+
+## Type
+
+<!-- Check the relevant option -->
+
+- [ ] Bug fix
+- [ ] New feature (tool, skill, pipeline)
+- [ ] Enhancement to existing feature
+- [ ] Documentation
+- [ ] Infrastructure (CI, packaging, config)
+
+## Testing
+
+<!-- How was this tested? -->
+
+- [ ] All 506 existing tests pass (`pytest tests/ -v`)
+- [ ] New tests added for new functionality
+- [ ] Lint passes (`ruff check src/`)
+- [ ] Format passes (`ruff format --check src/`)
+- [ ] Plugin validation passes (plugin.json valid, skills load)
+
+## Checklist
+
+- [ ] CHANGELOG.md updated
+- [ ] CLAUDE.md updated (if architecture/tools changed)
+- [ ] No secrets or credentials in code
+- [ ] No breaking changes to existing tool signatures

encode_toolkit-0.3.0b1/.github/dependabot.yml

@@ -0,0 +1,25 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"
+    open-pull-requests-limit: 5
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "ci"
+    open-pull-requests-limit: 3
+
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    labels:
+      - "dependencies"
+    open-pull-requests-limit: 2

encode_toolkit-0.3.0b1/.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install ruff
+        run: pip install ruff
+
+      - name: Check formatting
+        run: ruff format --check src/ tests/
+
+      - name: Check linting
+        run: ruff check src/ tests/

encode_toolkit-0.3.0b1/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install build tools
+        run: pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Verify package
+        run: twine check dist/*
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install and test
+        run: |
+          pip install -e ".[dev]"
+          pytest tests/ -v --tb=short
+
+  github-release:
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Determine if prerelease
+        id: check
+        run: |
+          TAG_NAME="${GITHUB_REF#refs/tags/}"
+          if echo "$TAG_NAME" | grep -qE 'beta|rc|alpha'; then
+            echo "prerelease=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "prerelease=false" >> "$GITHUB_OUTPUT"
+          fi
+        env:
+          GITHUB_REF: ${{ github.ref }}
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: dist/*
+          prerelease: ${{ steps.check.outputs.prerelease == 'true' }}
+
+  pypi-publish:
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  npm-publish:
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    environment: release
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          registry-url: "https://registry.npmjs.org"
+
+      - name: Publish to npm
+        run: npm publish --access public
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}

encode_toolkit-0.3.0b1/.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests with coverage
+        run: pytest tests/ -v --tb=short --cov=encode_connector --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage
+        if: matrix.python-version == '3.13'
+        uses: codecov/codecov-action@v4
+        with:
+          file: coverage.xml
+          fail_ci_if_error: false

encode_toolkit-0.3.0b1/.github/workflows/validate.yml

@@ -0,0 +1,55 @@
+name: Plugin Validation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Verify server imports
+        run: python -c "from encode_connector.server.main import mcp; print('Server module imports OK')"
+
+      - name: Validate plugin.json
+        run: |
+          python -c "
+          import json
+          d = json.load(open('.claude-plugin/plugin.json'))
+          assert 'name' in d
+          assert 'version' in d
+          print(f'plugin.json valid: {d[\"name\"]} v{d[\"version\"]}')
+          "
+
+      - name: Validate skill structure
+        run: |
+          python -c "
+          import os
+          skills_dir = 'skills'
+          count = 0
+          for skill in sorted(os.listdir(skills_dir)):
+              skill_path = os.path.join(skills_dir, skill, 'SKILL.md')
+              if os.path.isfile(skill_path):
+                  count += 1
+                  print(f'  OK: {skill}')
+              else:
+                  print(f'  MISSING SKILL.md: {skill}')
+          print(f'Total skills validated: {count}')
+          "
+
+      - name: Run tests
+        run: pytest tests/ -v --tb=short

encode_toolkit-0.3.0b1/.gitignore

@@ -0,0 +1,53 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+*.egg
+*.so
+dist/
+build/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+
+# Environment variables
+.env
+.env.*
+!.env.example
+
+# Encrypted credential files
+*.enc
+
+# Testing & linting
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# Node
+node_modules/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Claude Code local files
+.claude/settings.local.json
+.claude/*.local.md
+
+# Data files (generated at runtime)
+*.db
+*.sqlite
+*.sqlite3
+credentials*
+data/
+
+# OS
+.DS_Store
+Thumbs.db

encode_toolkit-0.3.0b1/.mcp.json

@@ -0,0 +1,8 @@
+{
+  "mcpServers": {
+    "encode": {
+      "command": "encode-toolkit",
+      "args": []
+    }
+  }
+}

encode_toolkit-0.3.0b1/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.6
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-added-large-files
+        args: ['--maxkb=500']
+      - id: no-commit-to-branch
+        args: ['--branch', 'main']
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        additional_dependencies: [pydantic, httpx]
+        args: [--ignore-missing-imports]
+        files: ^src/