fix(security): complete dependency confusion fix — replace all pip install agent-os with agent-os-kernel

imran-siddique · Copilot · imran-siddique · commit 7a3fdb988346 · 2026-03-21T09:26:08.000-07:00
Replace all remaining instances of `pip install agent-os` (unregistered on PyPI) with `pip install agent-os-kernel` (the actual package) across docs, examples, TypeScript extensions, CLI source, tests, and SVG assets. Also fixes `pip install emk` references to point to `agent-os-kernel[full]` since emk is a submodule, not a standalone PyPI package. Completes the fix started in PR microsoft#325 which only covered notebooks. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
diff --git a/docs/deployment/azure-foundry-agent-service.md b/docs/deployment/azure-foundry-agent-service.md
@@ -82,7 +82,7 @@ Each middleware works independently. Use any combination based on your requireme
 pip install agent-governance-toolkit[full]
 
 # Or install individual packages
-pip install agent-os agentmesh agent-sre
+pip install agent-os-kernel agentmesh-platform agent-sre
 ```
 
 ---
diff --git a/docs/tutorials/06-execution-sandboxing.md b/docs/tutorials/06-execution-sandboxing.md
@@ -55,7 +55,7 @@ layers of defense:
 
 - Python ≥ 3.11
 - `pip install agent-runtime` (v2.0.2+)
-- For capability guards: `pip install agent-os`
+- For capability guards: `pip install agent-os-kernel`
 
 ---
 
diff --git a/packages/agent-compliance/docs/submissions/adversa-mcp-security-submission.md b/packages/agent-compliance/docs/submissions/adversa-mcp-security-submission.md
@@ -88,7 +88,7 @@ Identifies malicious schema patterns:
 
 ```bash
 # Install
-pip install agent-os
+pip install agent-os-kernel
 
 # Scan an MCP configuration file
 mcp-scan scan mcp-config.json
diff --git a/packages/agent-compliance/docs/submissions/owasp-genai-implementation-guide.md b/packages/agent-compliance/docs/submissions/owasp-genai-implementation-guide.md
@@ -11,7 +11,7 @@ The stack consists of four components:
 
 | Component | Role | Install |
 |---|---|---|
-| **Agent OS** | Governance kernel — policy, sandbox, memory, MCP security | `pip install agent-os` |
+| **Agent OS** | Governance kernel — policy, sandbox, memory, MCP security | `pip install agent-os-kernel` |
 | **AgentMesh** | Identity & trust — DIDs, SPIFFE, handshake, reputation | `pip install agentmesh` |
 | **Agent SRE** | Observability — SLOs, anomaly detection, chaos, OpenTelemetry | `pip install agent-sre` |
 | **Agent Runtime** | Runtime control — kill switch, execution rings, saga rollback | `pip install agent-runtime` |
@@ -1044,7 +1044,7 @@ This implementation guide is a community contribution to the OWASP GenAI project
 To reproduce the examples, install the stack:
 
 ```bash
-pip install agent-os agentmesh agent-sre agent-runtime
+pip install agent-os-kernel agentmesh-platform agent-sre agent-runtime
 ```
 
 All source code is available under the MIT license. PRs and issues welcome at
diff --git a/packages/agent-os/assets/demo-terminal.svg b/packages/agent-os/assets/demo-terminal.svg
@@ -43,7 +43,7 @@
   <g class="terminal" transform="translate(20, 55)">
     <!-- Line 1: pip install -->
     <g class="line1">
-      <text y="0"><tspan class="prompt">$ </tspan><tspan class="command">pip install agent-os</tspan></text>
+      <text y="0"><tspan class="prompt">$ </tspan><tspan class="command">pip install agent-os-kernel</tspan></text>
     </g>
     
     <!-- Line 2: install output -->
diff --git a/packages/agent-os/docs/index.md b/packages/agent-os/docs/index.md
@@ -59,7 +59,7 @@ Learn by doing with our Jupyter notebooks:
 
 ```bash
 # Core package
-pip install agent-os
+pip install agent-os-kernel
 
 # With all features
 pip install agent-os-kernel[full]
diff --git a/packages/agent-os/docs/troubleshooting.md b/packages/agent-os/docs/troubleshooting.md
@@ -43,7 +43,7 @@ Common issues and solutions for Agent OS.
 
 2. **Install in the correct environment:**
    ```bash
-   python -m pip install agent-os
+   python -m pip install agent-os-kernel
    ```
 
 ### Import errors with optional dependencies
diff --git a/packages/agent-os/docs/tutorials/getting-started.md b/packages/agent-os/docs/tutorials/getting-started.md
@@ -10,7 +10,7 @@
 ## Step 1: Install (30 seconds)
 
 ```bash
-pip install agent-os
+pip install agent-os-kernel
 ```
 
 ## Step 2: Create Your First Agent (2 minutes)
diff --git a/packages/agent-os/docs/tutorials/vscode-extension.md b/packages/agent-os/docs/tutorials/vscode-extension.md
@@ -509,7 +509,7 @@ jobs:
           python-version: '3.11'
       
       - name: Install AgentOS
-        run: pip install agent-os
+        run: pip install agent-os-kernel
       
       - name: Run Policy Validation
         run: agent-os validate --policy policies/ --strict
diff --git a/packages/agent-os/docs/unified-vision.md b/packages/agent-os/docs/unified-vision.md
@@ -336,7 +336,7 @@ spec:
 ### Step 1: Start with Agent OS
 
 ```bash
-pip install agent-os
+pip install agent-os-kernel
 ```
 
 ```python
diff --git a/packages/agent-os/examples/crewai-safe-mode/crewai_safe_mode.py b/packages/agent-os/examples/crewai-safe-mode/crewai_safe_mode.py
@@ -15,7 +15,7 @@
 4. Your data stays safe ✓
 
 Run:
-    pip install agent-os crewai
+    pip install agent-os-kernel crewai
     python crewai_safe_mode.py
 
 Perfect for recording a 15-second GIF showing "Access Denied"!
diff --git a/packages/agent-os/examples/crewai-safe-mode/langchain_safe_mode.py b/packages/agent-os/examples/crewai-safe-mode/langchain_safe_mode.py
@@ -15,7 +15,7 @@
 4. Your data stays safe ✓
 
 Run:
-    pip install agent-os langchain
+    pip install agent-os-kernel langchain
     python langchain_safe_mode.py
 
 For PyPI package: pip install langchain-agent-os
diff --git a/packages/agent-os/examples/hello-world/README.md b/packages/agent-os/examples/hello-world/README.md
@@ -12,7 +12,7 @@ The simplest possible Agent OS example.
 
 ```bash
 # Install
-pip install agent-os
+pip install agent-os-kernel
 
 # Run
 python agent.py
diff --git a/packages/agent-os/examples/integrations/governance_quickstart.py b/packages/agent-os/examples/integrations/governance_quickstart.py
@@ -7,7 +7,7 @@
 audit trails) to every major agent framework with a unified API.
 
 Usage:
-    pip install agent-os
+    pip install agent-os-kernel
     python governance_quickstart.py
 """
 
diff --git a/packages/agent-os/extensions/copilot/src/agentGenerator.ts b/packages/agent-os/extensions/copilot/src/agentGenerator.ts
@@ -687,7 +687,7 @@ jobs:
       
       - name: Install dependencies
         run: |
-          pip install agent-os
+          pip install agent-os-kernel
           pip install -r requirements.txt
       
       - name: Run Agent
diff --git a/packages/agent-os/extensions/copilot/src/githubIntegration.ts b/packages/agent-os/extensions/copilot/src/githubIntegration.ts
@@ -199,7 +199,7 @@ jobs:
       
       - name: Install Agent OS
         run: |
-          pip install agent-os
+          pip install agent-os-kernel
           pip install -r requirements.txt || true
       
       - name: Validate policies
@@ -270,7 +270,7 @@ jobs:
           python-version: '3.11'
       - name: Run tests
         run: |
-          pip install agent-os pytest
+          pip install agent-os-kernel pytest
           pytest tests/test_${this.toSnakeCase(spec.name)}.py -v
 
   security-scan:
@@ -279,7 +279,7 @@ jobs:
       - uses: actions/checkout@v4
       - name: Security scan
         run: |
-          pip install agent-os
+          pip install agent-os-kernel
           agentos check agents/${this.toSnakeCase(spec.name)}.py --security
 
   deploy-staging:
@@ -465,7 +465,7 @@ gh workflow run ${this.toKebabCase(spec.name)}.yml
 ### Local Development
 \`\`\`bash
 # Install dependencies
-pip install agent-os
+pip install agent-os-kernel
 
 # Run locally
 python agents/${this.toSnakeCase(spec.name)}.py
diff --git a/packages/agent-os/extensions/vscode/src/enterprise/integration/cicdIntegration.ts b/packages/agent-os/extensions/vscode/src/enterprise/integration/cicdIntegration.ts
@@ -61,7 +61,7 @@ jobs:
           python-version: '3.11'
           
       - name: Install Agent OS
-        run: pip install agent-os
+        run: pip install agent-os-kernel
         
       - name: Run Policy Validation
         run: |
@@ -89,7 +89,7 @@ agent-os-check:
   stage: security
   image: python:3.11
   before_script:
-    - pip install agent-os
+    - pip install agent-os-kernel
   script:
     - agentos check --format json --output agent-os-report.json
     - agentos check --fail-on-violation
@@ -119,7 +119,7 @@ steps:
       versionSpec: '3.11'
       
   - script: |
-      pip install agent-os
+      pip install agent-os-kernel
     displayName: 'Install Agent OS'
     
   - script: |
@@ -147,7 +147,7 @@ steps:
     stages {
         stage('Setup') {
             steps {
-                sh 'pip install agent-os'
+                sh 'pip install agent-os-kernel'
             }
         }
         
@@ -189,7 +189,7 @@ jobs:
       - checkout
       - run:
           name: Install Agent OS
-          command: pip install agent-os
+          command: pip install agent-os-kernel
       - run:
           name: Run Security Check
           command: |
diff --git a/packages/agent-os/modules/emk/README.md b/packages/agent-os/modules/emk/README.md
@@ -12,7 +12,7 @@ emk provides a simple append-only store for recording agent experiences. Episode
 ## Installation
 
 ```bash
-pip install emk
+pip install agent-os-kernel[full]  # emk is included as a submodule
 ```
 
 ## Quick Start
diff --git a/packages/agent-os/modules/emk/emk/hf_utils.py b/packages/agent-os/modules/emk/emk/hf_utils.py
@@ -7,7 +7,7 @@
 results to/from the Hugging Face Hub for sharing and reproducibility.
 
 Requirements:
-    pip install emk[huggingface]
+    pip install agent-os-kernel[full]  # includes emk with huggingface support
 
 Example:
     >>> from emk.hf_utils import upload_episodes_to_hub
@@ -52,7 +52,7 @@ def _check_hf_hub() -> None:
     if not _HF_HUB_AVAILABLE:
         raise ImportError(
             "huggingface_hub is required for this functionality. "
-            "Install it with: pip install emk[huggingface]"
+            "Install it with: pip install agent-os-kernel[full]"
         )
 
 
diff --git a/packages/agent-os/src/agent_os/cli/__init__.py b/packages/agent-os/src/agent_os/cli/__init__.py
@@ -202,7 +202,7 @@ def handle_invalid_policy(name: str) -> str:
 
 def handle_missing_dependency(package: str, extra: str = "") -> str:
     """Error message when an optional dependency is missing."""
-    install_cmd = f"pip install agent-os[{extra}]" if extra else f"pip install {package}"
+    install_cmd = f"pip install agent-os-kernel[{extra}]" if extra else f"pip install {package}"
     return format_error(
         f"Required package not installed: {package}",
         suggestion=f"Install with: {install_cmd}",
diff --git a/packages/agent-os/tests/test_cli.py b/packages/agent-os/tests/test_cli.py
@@ -524,7 +524,7 @@ def test_handle_missing_dependency(self):
         from agent_os.cli import handle_missing_dependency
 
         msg = handle_missing_dependency("redis", extra="redis")
-        assert "pip install agent-os[redis]" in msg
+        assert "pip install agent-os-kernel[redis]" in msg
 
     def test_handle_connection_error(self):
         """Test connection-error helper includes host:port."""
diff --git a/packages/agentmesh-integrations/copilot-governance/README.md b/packages/agentmesh-integrations/copilot-governance/README.md
@@ -197,7 +197,7 @@ npm install @agentmesh/mastra
 
 **Python agents:**
 ```bash
-pip install agent-os
+pip install agent-os-kernel
 ```
 
 See the [Agent Governance Toolkit](https://github.com/microsoft/agent-governance-toolkit) for the full documentation.
diff --git a/packages/agentmesh-integrations/copilot-governance/src/reviewer.ts b/packages/agentmesh-integrations/copilot-governance/src/reviewer.ts
@@ -563,7 +563,7 @@ export function formatReviewResult(result: ReviewResult): string {
   lines.push(
     "> 📦 Add governance to your agent in minutes: " +
       "`npm install @agentmesh/mastra` (TypeScript) or " +
-      "`pip install agent-os` (Python)."
+      "`pip install agent-os-kernel` (Python)."
   );
 
   return lines.join("\n");
