encode-toolkit 0.3.0b8__tar.gz → 0.3.0b10__tar.gz

{encode_toolkit-0.3.0b8 → encode_toolkit-0.3.0b10}/.claude-plugin/marketplace.json

@@ -10,7 +10,7 @@
   "plugins": [
     {
       "name": "encode-toolkit",
-      "version": "0.3.0-beta.8",
+      "version": "0.3.0-beta.10",
       "source": "./plugin",
       "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases."
     }

{encode_toolkit-0.3.0b8 → encode_toolkit-0.3.0b10}/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "encode-toolkit",
   "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
-  "version": "0.3.0-beta.8",
+  "version": "0.3.0-beta.10",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"
@@ -9,7 +9,7 @@
   "homepage": "https://github.com/ammawla/encode-toolkit",
   "repository": "https://github.com/ammawla/encode-toolkit",
   "icon": "docs/icon.svg",
-  "license": "CC-BY-NC-ND-4.0",
+  "license": "CC-BY-NC-4.0",
   "keywords": [
     "genomics",
     "encode",

encode_toolkit-0.3.0b10/.cursor-plugin/marketplace.json

@@ -0,0 +1,27 @@
+{
+  "name": "ammawla",
+  "owner": {
+    "name": "Dr. Alex M. Mawla, PhD",
+    "email": "ammawla@ucdavis.edu"
+  },
+  "metadata": {
+    "description": "ENCODE Project genomics research infrastructure for Cursor",
+    "version": "0.3.0-beta.10",
+    "homepage": "https://github.com/ammawla/encode-toolkit"
+  },
+  "plugins": [
+    {
+      "name": "encode-toolkit",
+      "source": ".",
+      "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
+      "category": "science",
+      "tags": [
+        "genomics",
+        "bioinformatics",
+        "encode",
+        "epigenomics",
+        "pipelines"
+      ]
+    }
+  ]
+}

encode_toolkit-0.3.0b10/.cursor-plugin/plugin.json

@@ -0,0 +1,48 @@
+{
+  "name": "encode-toolkit",
+  "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
+  "version": "0.3.0-beta.10",
+  "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",
+  "license": "CC-BY-NC-4.0",
+  "logo": "docs/icon.svg",
+  "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"
+  ],
+  "rules": "rules",
+  "skills": "plugin/skills",
+  "commands": "commands",
+  "agents": "agents",
+  "mcpServers": {
+    "encode-toolkit": {
+      "command": "npx",
+      "args": ["-y", "encode-toolkit@latest"]
+    }
+  }
+}

encode_toolkit-0.3.0b10/.github/workflows/clone-count.yml

@@ -0,0 +1,99 @@
+name: Track Clone Count
+
+on:
+  schedule:
+    - cron: "0 0 * * *"  # Daily at midnight UTC
+  workflow_dispatch:
+
+jobs:
+  clone-count:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Authenticate GitHub CLI
+        env:
+          GH_TOKEN: ${{ secrets.SECRET_TOKEN }}
+        run: echo "$GH_TOKEN" | gh auth login --with-token
+
+      - name: Fetch clone data from GitHub API
+        env:
+          GH_TOKEN: ${{ secrets.SECRET_TOKEN }}
+          GH_ACTOR: ${{ github.actor }}
+          GH_REPO: ${{ github.repository }}
+        run: |
+          curl --user "$GH_ACTOR:$GH_TOKEN" \
+            -H "Accept: application/vnd.github.v3+json" \
+            "https://api.github.com/repos/$GH_REPO/traffic/clones" \
+            > clone.json
+
+      - name: Create or retrieve gist for persistent storage
+        id: set_id
+        env:
+          GH_TOKEN: ${{ secrets.SECRET_TOKEN }}
+          GIST_ID: ${{ secrets.GIST_ID }}
+          GH_ACTOR: ${{ github.actor }}
+        run: |
+          if [ -n "$GIST_ID" ]; then
+              echo "GIST_ID found"
+              echo "GIST=$GIST_ID" >> "$GITHUB_OUTPUT"
+              curl "https://gist.githubusercontent.com/$GH_ACTOR/$GIST_ID/raw/clone.json" > clone_before.json
+              if grep -q '404: Not Found' clone_before.json; then
+                echo "GIST_ID not valid anymore. Creating another gist..."
+                gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+                echo "$gist_id" | gh secret set GIST_ID
+                echo "GIST=$gist_id" >> "$GITHUB_OUTPUT"
+                cp clone.json clone_before.json
+                git rm --ignore-unmatch CLONE.md
+              fi
+          else
+              echo "GIST_ID not found. Creating a gist..."
+              gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+              echo "$gist_id" | gh secret set GIST_ID
+              echo "GIST=$gist_id" >> "$GITHUB_OUTPUT"
+              cp clone.json clone_before.json
+          fi
+
+      - name: Accumulate clone statistics
+        run: |
+          curl https://raw.githubusercontent.com/MShawon/github-clone-count-badge/master/main.py > main.py
+          python3 main.py
+
+      - name: Update gist with accumulated data
+        env:
+          GH_TOKEN: ${{ secrets.SECRET_TOKEN }}
+          GH_ACTOR: ${{ github.actor }}
+          GH_REPO: ${{ github.repository }}
+          GIST: ${{ steps.set_id.outputs.GIST }}
+        run: |
+          content=$(sed -e 's/\\/\\\\/g' -e 's/\t/\\t/g' -e 's/"/\\"/g' -e 's/\r//g' "clone.json" | sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g')
+          echo "{\"description\": \"$GH_REPO clone statistics\", \"files\": {\"clone.json\": {\"content\": \"$content\"}}}" > post_clone.json
+          curl -s -X PATCH \
+            --user "$GH_ACTOR:$GH_TOKEN" \
+            -H "Content-Type: application/json" \
+            -d @post_clone.json "https://api.github.com/gists/$GIST" > /dev/null 2>&1
+
+          if [ ! -f CLONE.md ]; then
+            shields="https://img.shields.io/badge/dynamic/json?color=success&label=Clone&query=count&url="
+            url="https://gist.githubusercontent.com/$GH_ACTOR/$GIST/raw/clone.json"
+            repo="https://github.com/$GH_REPO"
+            {
+              echo ''
+              echo '**Badge Markdown**'
+              echo ''
+              echo '```markdown'
+              echo "[![GitHub Clones]($shields$url&logo=github)]($repo)"
+              echo '```'
+            } > CLONE.md
+
+            git add CLONE.md
+            git config --global user.name "GitHub Action"
+            git config --global user.email "action@github.com"
+            git commit -m "Create clone count badge"
+          fi
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

{encode_toolkit-0.3.0b8 → encode_toolkit-0.3.0b10}/.gitignore

@@ -41,29 +41,18 @@ node_modules/
 .claude/settings.local.json
 .claude/*.local.md
 
-# Data files (generated at runtime)
+# Runtime data
 *.db
 *.sqlite
 *.sqlite3
 credentials*
 data/
 
-# MCP Registry tokens
-.mcpregistry_*
+# OS
+.DS_Store
+Thumbs.db
 
-# Generated PDFs
+# Build artifacts
 *.pdf
-
-# PDF build artifacts
 docs/pdf-build/
-
-# Smithery
-.smithery/
-
-# npm lock (thin wrapper, no deps to lock)
 package-lock.json
-
-# OS
-.DS_Store
-Thumbs.db
-buildwithclaude/

{encode_toolkit-0.3.0b8 → encode_toolkit-0.3.0b10}/.pre-commit-config.yaml

@@ -15,9 +15,27 @@ repos:
       - id: check-json
       - id: check-added-large-files
         args: ['--maxkb=500']
+      - id: check-case-conflict
+      - id: check-merge-conflict
       - id: no-commit-to-branch
         args: ['--branch', 'main']
 
+  - repo: local
+    hooks:
+      - id: forbid-os-files
+        name: Block OS-generated files
+        entry: >-
+          bash -c 'FOUND=$(git diff --cached --name-only --diff-filter=ACR |
+          grep -E "(\.DS_Store|Thumbs\.db|desktop\.ini)$" || true);
+          if [ -n "$FOUND" ]; then
+          echo "Blocked OS-generated files from commit:";
+          echo "$FOUND";
+          echo "Run: git rm --cached <file>";
+          exit 1; fi'
+        language: system
+        always_run: true
+        pass_filenames: false
+
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.14.1
     hooks: