encode-toolkit 0.3.0b2__tar.gz → 0.3.0b3__tar.gz

{encode_toolkit-0.3.0b2 → encode_toolkit-0.3.0b3}/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "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.2",
+  "version": "0.3.0-beta.3",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"

{encode_toolkit-0.3.0b2 → encode_toolkit-0.3.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: encode-toolkit
-Version: 0.3.0b2
+Version: 0.3.0b3
 Summary: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
 Project-URL: Homepage, https://github.com/ammawla/encode-toolkit
 Project-URL: Repository, https://github.com/ammawla/encode-toolkit
@@ -46,9 +46,14 @@ Description-Content-Type: text/markdown
 [![Security](https://img.shields.io/badge/security-no_telemetry-blue)]()
 [![Claude Code](https://img.shields.io/badge/Claude_Code-plugin-blueviolet)](https://claude.com/claude-code)
 [![Provenance](https://img.shields.io/badge/provenance-full_audit_trail-green)]()
-[![PyPI version](https://img.shields.io/pypi/v/encode-toolkit.svg)](https://pypi.org/project/encode-toolkit/)
+[![PyPI version](https://img.shields.io/pypi/v/encode-toolkit.svg?include_prereleases)](https://pypi.org/project/encode-toolkit/)
+[![npm version](https://img.shields.io/npm/v/encode-toolkit.svg)](https://www.npmjs.com/package/encode-toolkit)
 [![smithery badge](https://smithery.ai/badge/encode-toolkit)](https://smithery.ai/server/encode-toolkit)
 
+<a href="https://glama.ai/mcp/servers/ammawla/encode-toolkit">
+  <img width="380" height="200" src="https://glama.ai/mcp/servers/ammawla/encode-toolkit/badge" />
+</a>
+
 Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
 
 > Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.

{encode_toolkit-0.3.0b2 → encode_toolkit-0.3.0b3}/README.md

@@ -13,9 +13,14 @@
 [![Security](https://img.shields.io/badge/security-no_telemetry-blue)]()
 [![Claude Code](https://img.shields.io/badge/Claude_Code-plugin-blueviolet)](https://claude.com/claude-code)
 [![Provenance](https://img.shields.io/badge/provenance-full_audit_trail-green)]()
-[![PyPI version](https://img.shields.io/pypi/v/encode-toolkit.svg)](https://pypi.org/project/encode-toolkit/)
+[![PyPI version](https://img.shields.io/pypi/v/encode-toolkit.svg?include_prereleases)](https://pypi.org/project/encode-toolkit/)
+[![npm version](https://img.shields.io/npm/v/encode-toolkit.svg)](https://www.npmjs.com/package/encode-toolkit)
 [![smithery badge](https://smithery.ai/badge/encode-toolkit)](https://smithery.ai/server/encode-toolkit)
 
+<a href="https://glama.ai/mcp/servers/ammawla/encode-toolkit">
+  <img width="380" height="200" src="https://glama.ai/mcp/servers/ammawla/encode-toolkit/badge" />
+</a>
+
 Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
 
 > Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.

encode_toolkit-0.3.0b3/glama.json

@@ -0,0 +1,6 @@
+{
+  "$schema": "https://glama.ai/mcp/schemas/server.json",
+  "maintainers": [
+    "ammawla"
+  ]
+}

{encode_toolkit-0.3.0b2 → encode_toolkit-0.3.0b3}/package.json

@@ -1,6 +1,6 @@
 {
   "name": "encode-toolkit",
-  "version": "0.3.0-beta.2",
+  "version": "0.3.0-beta.3",
   "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
   "main": "index.js",
   "bin": {

{encode_toolkit-0.3.0b2 → encode_toolkit-0.3.0b3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "encode-toolkit"
-version = "0.3.0b2"
+version = "0.3.0b3"
 description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
 readme = "README.md"
 license = "LicenseRef-Noncommercial"

encode_toolkit-0.3.0b3/smithery.yaml

@@ -0,0 +1,10 @@
+# Smithery configuration file: https://smithery.ai/docs/config#smitheryyaml
+
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction:
+    |-
+    config => ({ command: 'uvx', args: ['encode-toolkit'] })

encode_toolkit-0.3.0b2/smithery.yaml

@@ -1,24 +0,0 @@
-# Smithery configuration for encode-toolkit
-# https://smithery.ai/docs/config
-
-startCommand:
-  type: stdio
-  configSchema:
-    type: object
-    properties:
-      ENCODE_ACCESS_KEY:
-        type: string
-        description: "Optional ENCODE API access key for restricted data"
-      ENCODE_SECRET_KEY:
-        type: string
-        description: "Optional ENCODE API secret key for restricted data"
-    required: []
-  commandFunction: |-
-    (config) => ({
-      command: "uvx",
-      args: ["encode-toolkit"],
-      env: {
-        ...(config.ENCODE_ACCESS_KEY ? { ENCODE_ACCESS_KEY: config.ENCODE_ACCESS_KEY } : {}),
-        ...(config.ENCODE_SECRET_KEY ? { ENCODE_SECRET_KEY: config.ENCODE_SECRET_KEY } : {})
-      }
-    })