Add tests for Rich markup escape safety in formatter

- Introduced a new test file `test_rich_escape.py` to validate the safety of Rich markup escaping in the ToolResultFormatter.
- Added tests to ensure that tool names and error messages containing brackets do not cause crashes during formatting.

.gitignore

@@ -9,6 +9,7 @@ dist/
 build/
 *.egg
 *.pytest_cache/
+.coverage
 
 # Environment
 .env

EvoScientist/EvoScientist.py

@@ -64,8 +64,6 @@ SUBAGENTS_CONFIG = Path(__file__).parent / "subagent.yaml"
 # Initialization
 # =============================================================================
 
-# Get current date
-current_date = datetime.now().strftime("%Y-%m-%d")
 
 # Generate system prompt with limits
 SYSTEM_PROMPT = get_system_prompt(
@@ -170,7 +168,7 @@ def _build_base_kwargs(base_backend, base_middleware):
     subs = load_subagents(
         SUBAGENTS_CONFIG,
         tool_registry=tool_registry,
-        prompt_refs=prompt_refs,
+        prompt_refs=_build_prompt_refs(),
     )
     _inject_subagent_middleware(subs)
     return dict(
@@ -206,7 +204,7 @@ def load_mcp_and_build_kwargs(base_backend, base_middleware):
     subs = load_subagents(
         SUBAGENTS_CONFIG,
         tool_registry=registry,
-        prompt_refs=prompt_refs,
+        prompt_refs=_build_prompt_refs(),
     )
 
     _inject_subagent_middleware(subs)
@@ -228,9 +226,13 @@ def load_mcp_and_build_kwargs(base_backend, base_middleware):
     )
 
 
-prompt_refs = {
-    "RESEARCHER_INSTRUCTIONS": RESEARCHER_INSTRUCTIONS.format(date=current_date),
-}
+def _build_prompt_refs() -> dict:
+    """Build prompt references with the current date (not frozen at import)."""
+    return {
+        "RESEARCHER_INSTRUCTIONS": RESEARCHER_INSTRUCTIONS.format(
+            date=datetime.now().strftime("%Y-%m-%d"),
+        ),
+    }
 
 base_middleware = [
     ToolErrorHandlerMiddleware(),

EvoScientist/backends.py

@@ -2,6 +2,7 @@
 
 import os
 import re
+import shlex
 import uuid
 from pathlib import Path
 
@@ -24,7 +25,6 @@ _SYSTEM_PATH_PREFIXES = (
 
 # Dangerous patterns that could escape the workspace
 BLOCKED_PATTERNS = [
-    r'\.\.',              # ../ directory traversal
     r'~/',                # home directory
     r'\bcd\s+/',          # cd to absolute path
     r'\brm\s+-rf\s+/',    # rm -rf with absolute path
@@ -42,6 +42,38 @@ BLOCKED_COMMANDS = [
 ]
 
 
+def _split_shell_commands(command: str) -> list[str]:
+    """Split a compound shell command into individual base commands.
+
+    Handles &&, ||, ;, and | operators. Returns base command names.
+    """
+    base_commands: list[str] = []
+    # Split by sequential operators first
+    for segment in re.split(r'\s*(?:&&|\|\||;)\s*', command):
+        # Then split by pipe
+        for pipe_seg in segment.split("|"):
+            pipe_seg = pipe_seg.strip()
+            if not pipe_seg:
+                continue
+            try:
+                tokens = shlex.split(pipe_seg)
+            except ValueError:
+                tokens = pipe_seg.split()
+            if tokens:
+                base_commands.append(tokens[0])
+    return base_commands
+
+
+def _has_traversal_component(command: str) -> bool:
+    """Check if command contains '..' as a path component (not substring)."""
+    from pathlib import PurePosixPath
+
+    for token in command.split():
+        if ".." in PurePosixPath(token).parts:
+            return True
+    return False
+
+
 def validate_command(command: str) -> str | None:
     """
     Validate a shell command for safety.
@@ -49,7 +81,15 @@ def validate_command(command: str) -> str | None:
     Returns:
         None if command is safe, error message string if blocked.
     """
-    # Check for directory traversal and dangerous patterns
+    # Check for '..' path traversal as a path component
+    if _has_traversal_component(command):
+        return (
+            "Command blocked: contains '..' path traversal. "
+            "All commands must operate within the workspace directory. "
+            "Use relative paths (e.g., './file.py') instead."
+        )
+
+    # Check for dangerous patterns
     for pattern in BLOCKED_PATTERNS:
         if re.search(pattern, command):
             return (
@@ -58,11 +98,11 @@ def validate_command(command: str) -> str | None:
                 f"Use relative paths (e.g., './file.py') instead."
             )
 
-    # Check for dangerous commands
-    for cmd in BLOCKED_COMMANDS:
-        if re.search(rf'\b{cmd}\b', command):
+    # Check for dangerous commands (pipeline-aware)
+    for base_cmd in _split_shell_commands(command):
+        if base_cmd in BLOCKED_COMMANDS:
             return (
-                f"Command blocked: '{cmd}' is not allowed in sandbox mode. "
+                f"Command blocked: '{base_cmd}' is not allowed in sandbox mode. "
                 f"Only standard development commands are permitted."
             )
 
@@ -328,7 +368,7 @@ class CustomSandboxBackend(LocalShellBackend):
 
         return super()._resolve_path(key)
 
-    def execute(self, command: str) -> ExecuteResponse:
+    def execute(self, command: str, *, timeout: int | None = None) -> ExecuteResponse:
         """
         Execute shell command in sandbox environment.
 
@@ -362,4 +402,4 @@ class CustomSandboxBackend(LocalShellBackend):
             )
 
         # Delegate to parent for subprocess execution
-        return super().execute(command)
+        return super().execute(command, timeout=timeout)

EvoScientist/cli/commands.py

@@ -10,6 +10,8 @@ from typing import Any, Optional
 import typer  # type: ignore[import-untyped]
 from rich.table import Table
 
+from rich.markup import escape
+
 from ..stream.display import console
 from ..paths import ensure_dirs, set_workspace_root
 from ._app import app, config_app, mcp_app, channel_app
@@ -213,9 +215,9 @@ def config_set(
     from ..config import set_config_value
 
     if set_config_value(key, value):
-        console.print(f"[green]Set {key}[/green]")
+        console.print(f"[green]Set {escape(key)}[/green]")
     else:
-        console.print(f"[red]Invalid key: {key}[/red]")
+        console.print(f"[red]Invalid key: {escape(key)}[/red]")
         raise typer.Exit(1)
 
 
@@ -572,7 +574,7 @@ def _configure_logging():
             if record.levelno == logging.WARNING:
                 # Use Rich console to print dim warning
                 msg = record.getMessage()
-                console.print(f"[dim yellow]\u26a0\ufe0f  Warning:[/dim yellow] [dim]{msg}[/dim]")
+                console.print(f"[dim yellow]\u26a0\ufe0f  Warning:[/dim yellow] [dim]{escape(msg)}[/dim]")
             else:
                 super().emit(record)
 

EvoScientist/cli/interactive.py

@@ -16,6 +16,7 @@ from prompt_toolkit.auto_suggest import AutoSuggestFromHistory  # type: ignore[i
 from prompt_toolkit.formatted_text import HTML  # type: ignore[import-untyped]
 from prompt_toolkit.shortcuts import CompleteStyle  # type: ignore[import-untyped]
 from prompt_toolkit.styles import Style as PtStyle  # type: ignore[import-untyped]
+from rich.markup import escape
 from rich.table import Table
 from rich.text import Text
 
@@ -236,11 +237,11 @@ def cmd_interactive(
         if len(similar) == 1:
             return similar[0]
         if len(similar) > 1:
-            console.print(f"[yellow]Ambiguous thread ID '{tid}'. Matches:[/yellow]")
+            console.print(f"[yellow]Ambiguous thread ID '{escape(tid)}'. Matches:[/yellow]")
             for s in similar:
                 console.print(f"  [cyan]{s}[/cyan]")
             return None
-        console.print(f"[red]Thread '{tid}' not found.[/red]")
+        console.print(f"[red]Thread '{escape(tid)}' not found.[/red]")
         return None
 
     async def _cmd_threads():
@@ -701,7 +702,7 @@ def cmd_interactive(
                             state["running"] = False
                             break
                         else:
-                            console.print(f"[red]Error: {e}[/red]")
+                            console.print(f"[red]Error: {escape(str(e))}[/red]")
             finally:
                 queue_task.cancel()
                 try:

EvoScientist/stream/events.py

@@ -4,6 +4,7 @@ Async generator that streams events from an agent graph,
 plus helpers for processing AI message chunks and tool results.
 """
 
+import asyncio
 import base64
 import mimetypes
 import os
@@ -260,15 +261,19 @@ async def stream_agent_events(
         content_blocks: list[dict[str, Any]] = []
         if message:
             content_blocks.append({"type": "text", "text": message})
+        def _read_file_b64(path: str) -> str:
+            with open(path, "rb") as fh:
+                return base64.b64encode(fh.read()).decode("ascii")
+
         file_refs: list[str] = []
         for path in media:
             ext = os.path.splitext(path)[1].lower()
-            if ext in _IMAGE_EXTS and os.path.isfile(path):
-                fsize = os.path.getsize(path)
+            is_image = ext in _IMAGE_EXTS and await asyncio.to_thread(os.path.isfile, path)
+            if is_image:
+                fsize = await asyncio.to_thread(os.path.getsize, path)
                 if fsize <= _MAX_INLINE_SIZE:
                     mime = mimetypes.guess_type(path)[0] or "image/png"
-                    with open(path, "rb") as fh:
-                        b64 = base64.b64encode(fh.read()).decode("ascii")
+                    b64 = await asyncio.to_thread(_read_file_b64, path)
                     content_blocks.append({"type": "image_url", "image_url": {
                         "url": f"data:{mime};base64,{b64}",
                     }})

EvoScientist/stream/formatter.py

@@ -9,6 +9,7 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Any, List
 
+from rich.markup import escape
 from rich.panel import Panel
 from rich.syntax import Syntax
 from rich.text import Text
@@ -123,7 +124,7 @@ class ToolResultFormatter:
         display = truncate(content, max_length)
         return [Panel(
             Text(display, style="green"),
-            title=f"{name} OK",
+            title=f"{escape(name)} OK",
             border_style="green",
         )]
 
@@ -131,7 +132,7 @@ class ToolResultFormatter:
         display = truncate(content, max_length)
         return [Panel(
             Text(display, style="red"),
-            title=f"{name} FAILED",
+            title=f"{escape(name)} FAILED",
             border_style="red",
         )]
 
@@ -155,7 +156,7 @@ class ToolResultFormatter:
         display = truncate(content, max_length)
         return [Panel(
             Markdown(display),
-            title=f"{name}",
+            title=escape(name),
             border_style="cyan dim",
         )]
 

README.md

@@ -1,14 +1,15 @@
 <!-- Add logo here -->
-<h1 align="center">
-  <img src="./assets/EvoScientist_logo.png" alt="EvoScientist Logo" height="27" style="position: relative; top: 1px;"/>
-  <strong>EvoScientist</strong>
-</h1>
-
+<div align="center">
+    <picture>
+      <source media="(prefers-color-scheme: light)" srcset=".github/images/logo-dark.svg">
+      <source media="(prefers-color-scheme: dark)" srcset=".github/images/logo-light.svg">
+      <img alt="EvoScientist Logo" src=".github/images/logo-dark.svg" width="80%">
+    </picture>
+  </a>
+</div>
 
 <div align="center">
 
-<a href="https://git.io/typing-svg"><img src="https://readme-typing-svg.demolab.com?font=Fira+Code&pause=1000&width=435&lines=Towards+Self-Evolving+AI+Scientists+for+End-to-End+Scientific+Discovery" alt="Typing SVG" /></a>
-
 [![PyPI](https://img.shields.io/badge/PyPI-EvoScientist%20v0.0.1-3da9fc?style=for-the-badge&logo=python&logoColor=3da9fc)](https://pypi.org/project/EvoScientist/)
 [![Project Page](https://img.shields.io/badge/Project-Page-ff8e3c?style=for-the-badge&logo=googlelens&logoColor=ff8e3c)]()
 [![License](https://img.shields.io/badge/License-MIT-green?style=for-the-badge)]()
@@ -16,6 +17,8 @@
 <!-- [![Gradio Demo](https://img.shields.io/badge/Gradio-Online_Demo-FFCC00?style=for-the-badge&logo=gradio&logoColor=yellow&labelColor=grey)]()
 [![Evaluation Split](https://img.shields.io/badge/HF-Test_Dataset-AECBFA?style=for-the-badge&logo=huggingface&logoColor=FFCC00&labelColor=grey)]() -->
 
+<a href="https://git.io/typing-svg"><img src="https://readme-typing-svg.demolab.com?font=Fira+Code&pause=1000&width=435&lines=Towards+Self-Evolving+AI+Scientists+for+End-to-End+Scientific+Discovery" alt="Typing SVG" /></a>
+
 </div>
 
 ## 🔥 News

pyproject.toml

@@ -16,9 +16,9 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dependencies = [
-    "deepagents>=0.4.1",
-    "langchain>=1.2.7",
-    "langchain-anthropic>=1.3.1",
+    "deepagents>=0.4.3",
+    "langchain>=1.2.10",
+    "langchain-anthropic>=1.3.3",
     "langchain-openai>=0.3",
     "langchain-nvidia-ai-endpoints>=0.3",
     "langchain-google-genai>=4.2",

tests/test_backends.py

@@ -297,3 +297,73 @@ class TestExecuteStderr:
         resp = backend.execute("echo ok")
         assert resp.exit_code == 0
         assert "Exit code:" not in resp.output
+
+
+# === execute() timeout kwarg ===
+
+class TestExecuteTimeout:
+    def test_execute_accepts_timeout_kwarg(self, tmp_workspace):
+        backend = CustomSandboxBackend(root_dir=tmp_workspace, virtual_mode=True)
+        resp = backend.execute("echo hello", timeout=60)
+        assert resp.exit_code == 0
+        assert "hello" in resp.output
+
+    def test_execute_timeout_none_uses_default(self, tmp_workspace):
+        backend = CustomSandboxBackend(root_dir=tmp_workspace, virtual_mode=True)
+        resp = backend.execute("echo ok", timeout=None)
+        assert resp.exit_code == 0
+
+    def test_execute_accepts_timeout_introspection(self):
+        from deepagents.backends.protocol import execute_accepts_timeout
+        execute_accepts_timeout.cache_clear()
+        assert execute_accepts_timeout(CustomSandboxBackend) is True
+
+
+# === '..' traversal false-positive fix ===
+
+class TestTraversalFalsePositiveFix:
+    def test_dotdot_in_filename_allowed(self):
+        assert validate_command("echo foo..bar.txt") is None
+
+    def test_dotdot_path_component_still_blocked(self):
+        result = validate_command("cat ../secret")
+        assert result is not None
+        assert "blocked" in result.lower()
+
+    def test_dotdot_nested_still_blocked(self):
+        result = validate_command("cat foo/../../etc/passwd")
+        assert result is not None
+
+
+# === Pipeline command validation ===
+
+class TestPipelineCommandValidation:
+    def test_pipe_blocked_command(self):
+        """sudo after pipe should be caught."""
+        result = validate_command("echo hi | sudo tee /etc/passwd")
+        assert result is not None
+        assert "sudo" in result
+
+    def test_chained_blocked_command(self):
+        """chmod after && should be caught."""
+        result = validate_command("echo ok && chmod 777 file")
+        assert result is not None
+        assert "chmod" in result
+
+    def test_semicolon_blocked_command(self):
+        """dd after ; should be caught."""
+        result = validate_command("echo start ; dd if=/dev/zero of=disk")
+        assert result is not None
+        assert "dd" in result
+
+    def test_safe_pipe_allowed(self):
+        """Normal pipes should be fine."""
+        assert validate_command("cat file.txt | grep pattern") is None
+
+    def test_safe_chain_allowed(self):
+        """Normal && chains should be fine."""
+        assert validate_command("mkdir build && cd build") is None
+
+    def test_quoted_pipe_not_split(self):
+        """Pipe inside quotes is not a shell operator."""
+        assert validate_command("echo 'hello | world'") is None

tests/test_rich_escape.py

@@ -0,0 +1,18 @@
+"""Tests for Rich markup escape safety in formatter."""
+
+from EvoScientist.stream.formatter import ToolResultFormatter
+
+
+class TestRichMarkupEscape:
+    def test_panel_title_with_brackets(self):
+        """Tool name with brackets shouldn't crash formatter."""
+        formatter = ToolResultFormatter()
+        result = formatter.format("arr[0]", "[OK]\nDone", max_length=800)
+        # Should not raise — content is safely rendered
+        assert result.elements
+
+    def test_error_format_with_brackets(self):
+        """Error content with markup-like text shouldn't crash."""
+        formatter = ToolResultFormatter()
+        result = formatter.format("test", "Error: expected [int] got [str]", max_length=800)
+        assert result.elements