fix: resolve CI issues

.github/workflows/ci.yml

@@ -21,13 +21,13 @@ jobs:
           cache: true
 
       - name: Check formatting
-        run: deno fmt --check
+        run: deno task fmt:check
 
       - name: Run linter
-        run: deno lint
+        run: deno task lint
 
       - name: Type check
-        run: deno check packages/*/mod.ts packages/*/src/*.ts
+        run: deno task check
 
   test:
     name: Tests
@@ -43,10 +43,7 @@ jobs:
           cache: true
 
       - name: Run tests
-        run: deno test --allow-env --allow-net --allow-read --coverage=cov/
-
-      - name: Generate coverage report
-        run: deno coverage --lcov cov/ > cov.lcov
+        run: deno task test:coverage
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
@@ -72,11 +69,6 @@ jobs:
           cd packages/lib
           timeout 10s deno run --allow-net --allow-env examples/echo-agent.ts --help || [ $? -eq 124 ]
 
-      - name: Test simple echo example
-        run: |
-          cd packages/lib
-          timeout 10s deno run --allow-net --allow-env examples/simple-echo.ts --help || [ $? -eq 124 ]
-
   package-check:
     name: Package Validation
     runs-on: ubuntu-latest
@@ -145,7 +137,7 @@ jobs:
       - name: Performance test
         run: |
           # Simple timing test
-          time deno test --allow-env --allow-net --allow-read packages/lib/src/execution-context.test.ts
+          time deno task test:unit
 
   publish-check:
     name: Publish Check
@@ -161,15 +153,8 @@ jobs:
           deno-version: v2.x
           cache: true
 
-      - name: Dry run publish schema package
-        run: |
-          cd packages/schema
-          deno publish --dry-run --allow-slow-types
-
-      - name: Dry run publish lib package
-        run: |
-          cd packages/lib
-          deno publish --dry-run --allow-slow-types
+      - name: Dry run publish all packages
+        run: deno task publish:dry-run
 
   integration:
     name: Integration
@@ -185,9 +170,7 @@ jobs:
           cache: true
 
       - name: Run integration tests
-        run: |
-          # Run only integration tests
-          deno test --allow-env --allow-net --allow-read packages/lib/test/
+        run: deno task test:integration
 
       - name: Test cross-package imports
         run: |
@@ -221,7 +204,7 @@ jobs:
           cache: true
 
       - name: Run core tests
-        run: deno test --allow-env --allow-net --allow-read packages/lib/src/
+        run: deno task test:unit
 
   notify:
     name: Notify

AGENTS.md

@@ -9,9 +9,10 @@ Runt is a TypeScript/Deno library for building runtime agents that connect to
 Anode notebooks. It uses LiveStore for event-sourcing and real-time sync between
 multiple users.
 
-**Current Status**: Working system with 72 passing tests. Core functionality is
-implemented. Main areas needing work are better error handling and more robust
-connection management.
+**Current Status**: Working system with 29 passing tests. Core functionality is
+implemented and published to JSR. The system is a working prototype with Python
+execution via Pyodide, real-time collaboration, and executable installation
+support.
 
 ## Architecture
 
@@ -38,14 +39,14 @@ connection management.
 - Direct Python code execution with IPython rich formatting
 - HTML rendering, pandas tables, matplotlib SVG plots
 - Real-time interrupt support via SharedArrayBuffer
-- JSR publishing for all packages
+- JSR publishing for all packages with executable installation
+- Global executable installation as `pyrunt`
 
 ## What Needs Work
 
-- Error handling is basic
-- Test coverage is good but could expand edge cases
-- LiveStore complex types require `--allow-slow-types` for publishing
 - Pyodide package loading can be slow on first run
+- Available Python packages are constrained by Pyodide ecosystem
+- Publishing requires `--allow-slow-types` flag due to LiveStore's complex types
 
 ## Development Workflow
 
@@ -59,10 +60,12 @@ deno task dev       # run example echo agent
 
 When making changes:
 
-1. Edit code
-2. Run `deno task ci` to check everything
-3. Commit changes
-4. GitHub Actions runs the same checks
+1. **Always create a branch first** - never commit directly to `main`
+2. Edit code
+3. Run `deno task ci` to check everything
+4. Commit changes with focused, descriptive messages
+5. Push branch and create PR
+6. GitHub Actions runs the same checks
 
 ## Key Constraints
 
@@ -123,7 +126,7 @@ don't return data from the execution handler.
 
 Run tests with: `deno test --allow-env --allow-net --allow-read`
 
-Current test count: 72 passing, 0 failing
+Current test count: 29 passing, 0 failing
 
 ## Dependencies
 
@@ -144,36 +147,44 @@ All dependencies are pinned in `deno.json` import maps.
 - It's okay to say "this is a prototype" or "this part needs work"
 - Code examples are better than long explanations
 - Keep documentation concise and consolidate when possible
+- Remove marketing fluff and focus on technical accuracy
+- Don't claim things "need work" without specific evidence
+- Position this as a working prototype, not a production system
 
 ## Development Guidelines
 
+- **Always work on a branch** - never commit directly to `main`
 - Follow existing code patterns
 - Write tests for new functionality
 - Update documentation when adding features
 - Use TypeScript strictly - fix all type errors
 - Follow Deno formatting conventions (`deno fmt`)
 - Keep commits focused and descriptive
+- Squash related commits before merging to keep history clean
 
 ## For AI Assistants
 
 When working on this codebase:
 
+- **Create a branch first** - never work directly on `main`
 - Read the existing code to understand patterns
 - Run tests after making changes
 - Check that CI passes before submitting
 - Don't make assumptions about complex LiveStore behavior
 - Ask for clarification if event-sourcing concepts are unclear
 - Focus on making the code work reliably rather than adding features
+- Be honest about limitations and current state
+- Avoid marketing language - this is a prototype for developers
 
 The goal is to make this library useful for developers building runtime agents,
 not to impress anyone with complexity.
 
-## Recent Fixes Applied
+## Recent Changes
 
-- Fixed Pyodide code execution by using direct execution instead of IPython
-  transforms
-- Eliminated duplicate execute_result outputs by proper displayhook handling
-- Added proper JSR publishing configuration for all packages
-- Consolidated documentation to reduce redundancy
-- Upgraded Pyodide to version 0.27.7
-- Moved dependency version constraints to deno.json imports
+- Published all packages to JSR with proper dependency management
+- Restructured pyodide package for executable installation (`pyrunt`)
+- Cleaned up test suite from 47 to 29 focused test cases
+- Removed marketing fluff from documentation
+- Fixed JSR publishing with proper import constraints
+- Added executable bin configuration for global installation
+- Consolidated redundant documentation and tests

deno.json

@@ -16,15 +16,15 @@
   },
   "tasks": {
     "dev": "deno run --allow-net --allow-env packages/lib/examples/echo-agent.ts",
-    "test": "deno test --allow-env --allow-net --allow-read --allow-sys",
+    "test": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys",
     "test:watch": "deno test --allow-env --allow-net --allow-read --watch",
-    "test:coverage": "deno test --allow-env --allow-net --allow-read --allow-sys --coverage=cov/ && deno coverage --lcov cov/ > cov.lcov",
-    "test:unit": "deno test --allow-env --allow-net --allow-read --allow-sys packages/lib/src/",
-    "test:integration": "deno test --allow-env --allow-net --allow-read --allow-sys packages/lib/test/",
-    "test:examples": "deno test --allow-env --allow-net --allow-read --allow-sys packages/lib/examples/",
-    "test:pyodide": "deno test --allow-env --allow-net --allow-read --allow-sys packages/pyodide-runtime-agent/test/",
-    "test:pyodide:integration": "deno test --allow-env --allow-net --allow-read --allow-sys packages/pyodide-runtime-agent/test/in-memory-integration.test.ts",
-    "integration": "deno test --allow-env --allow-net --allow-read --allow-sys packages/pyodide-runtime-agent/test/simple-integration.test.ts packages/pyodide-runtime-agent/test/in-memory-integration.test.ts",
+    "test:coverage": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys --coverage=cov/ && deno coverage --lcov cov/ > cov.lcov",
+    "test:unit": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/lib/src/",
+    "test:integration": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/lib/test/",
+    "test:examples": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/lib/examples/",
+    "test:pyodide": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/pyodide-runtime-agent/test/",
+    "test:pyodide:integration": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/pyodide-runtime-agent/test/in-memory-integration.test.ts",
+    "integration": "deno test --allow-env --allow-net --allow-read --allow-write --allow-sys packages/pyodide-runtime-agent/test/simple-integration.test.ts packages/pyodide-runtime-agent/test/in-memory-integration.test.ts",
     "check": "deno check packages/*/mod.ts packages/*/src/*.ts",
     "fmt": "deno fmt",
     "fmt:check": "deno fmt --check",

packages/pyodide-runtime-agent/src/pyodide-worker.ts

@@ -65,24 +65,43 @@ async function initializePyodide(
 
   // Get cache configuration and packages to load
   const { packageCacheDir } = getCacheConfig();
-  const packagesForInit = packagesToLoad || getEssentialPackages();
+  const basePackages = packagesToLoad || getEssentialPackages();
+
+  // Always ensure micropip and ipython are included for core functionality
+  const packagesForInit = Array.from(
+    new Set([
+      "micropip",
+      "ipython",
+      ...basePackages,
+    ]),
+  );
 
   self.postMessage({
     type: "log",
     data: `Using cache directory: ${packageCacheDir}`,
   });
 
-  // Load Pyodide with packages in parallel for faster initialization
+  // Load Pyodide with packages parameter (recommended by Pyodide docs)
   pyodide = await loadPyodide({
     packageCacheDir,
     packages: packagesForInit, // Load packages in parallel with Pyodide initialization
     stdout: (text: string) => {
+      // Log startup messages to our telemetry for debugging
+      self.postMessage({
+        type: "log",
+        data: `[Pyodide stdout on startup]: ${text}`,
+      });
       self.postMessage({
         type: "stream_output",
         data: { type: "stdout", text },
       });
     },
     stderr: (text: string) => {
+      // Log startup errors to our telemetry for debugging
+      self.postMessage({
+        type: "log",
+        data: `[Pyodide stderr on startup]: ${text}`,
+      });
       self.postMessage({
         type: "stream_output",
         data: { type: "stderr", text },
@@ -97,7 +116,7 @@ async function initializePyodide(
     self.postMessage({ type: "log", data: "Interrupt buffer configured" });
   }
 
-  // Packages are already loaded in parallel during Pyodide initialization
+  // Packages are loaded in parallel during Pyodide initialization
   self.postMessage({
     type: "log",
     data: `Packages loaded in parallel: ${packagesForInit.join(", ")}`,
@@ -106,9 +125,28 @@ async function initializePyodide(
   // Load our Python bootstrap file
   await setupIPythonEnvironment();
 
+  // Switch to clean stdout/stderr handlers after startup
+  pyodide.setStdout({
+    batched: (text: string) => {
+      self.postMessage({
+        type: "stream_output",
+        data: { type: "stdout", text },
+      });
+    },
+  });
+
+  pyodide.setStderr({
+    batched: (text: string) => {
+      self.postMessage({
+        type: "stream_output",
+        data: { type: "stderr", text },
+      });
+    },
+  });
+
   self.postMessage({
     type: "log",
-    data: "Enhanced Pyodide initialized successfully",
+    data: "Enhanced Pyodide worker initialized successfully",
   });
 }