chore: pin latest dependency versions with uv lock

.github/workflows/ci.yml

@@ -19,19 +19,15 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.12"
-          cache: pip
+          enable-cache: true
 
       - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
-          pip install pytest pytest-asyncio pytest-cov ruff
-          pip install -e . --no-deps
+        run: uv sync --frozen --extra dev
 
       - name: Run tests
-        run: pytest -p no:cacheprovider -o addopts="" tests/ -q
+        run: uv run pytest -p no:cacheprovider -o addopts="" tests/ -q
 
   lint:
     name: Lint
@@ -42,12 +38,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.12"
+          enable-cache: true
 
-      - name: Install ruff
-        run: pip install ruff
+      - name: Install dependencies
+        run: uv sync --frozen --extra dev
 
       - name: Collect changed Python files
         env:
@@ -66,10 +62,10 @@ jobs:
 
       - name: Ruff check changed files
         run: |
-          xargs -0 -r ruff check --output-format=github \
+          xargs -0 -r uv run ruff check --output-format=github \
             < "$RUNNER_TEMP/changed-python-files"
 
       - name: Ruff format check changed files
         run: |
-          xargs -0 -r ruff format --check \
+          xargs -0 -r uv run ruff format --check \
             < "$RUNNER_TEMP/changed-python-files"

.gitignore

@@ -41,6 +41,7 @@ htmlcov/
 tests/*
 !tests/test_gitignore_filtering.py
 !tests/test_module_tree_validation.py
+!tests/test_latest_compat.py
 
 # Jupyter
 *.ipynb

.python-version

@@ -0,0 +1 @@
+3.12

DEVELOPMENT.md

@@ -38,9 +38,8 @@ codewiki/
 ├── paper/                    # Research paper source
 ├── tests/                    # Test suite
 ├── output/                   # Generated documentation output
-├── pyproject.toml           # Project metadata
-├── requirements.txt         # Python dependencies
-└── README.md                # Main documentation
+├── pyproject.toml            # Project metadata + dependencies
+└── README.md                 # Main documentation
 ```
 
 ## Development Setup
@@ -59,15 +58,15 @@ codewiki/
 git clone https://github.com/FSoft-AI4Code/CodeWiki.git
 cd CodeWiki
 
-# Create virtual environment
-python3.12 -m venv .venv
-source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+# Install uv (if not already installed)
+# curl -LsSf https://astral.sh/uv/install.sh | sh
 
-# Install in development mode
-pip install -e .
+# Create virtual environment and install dependencies (reads .python-version)
+uv sync --extra dev
+source .venv/bin/activate  # On Windows: .venv\Scripts\activate
 
-# Install development dependencies
-pip install -r requirements.txt
+# Run the test suite
+uv run pytest
 ```
 
 ## Core Components

IDE_DRIVEN_GUIDE.md

@@ -107,10 +107,10 @@ git clone https://github.com/FSoft-AI4Code/CodeWiki.git
 cd CodeWiki
 
 # 2. Install dependencies
-pip install -e .
+uv sync --extra dev
 
 # 3. Verify
-python -c "from codewiki.mcp.server import server; print('MCP Server OK')"
+uv run python -c "from codewiki.mcp.server import server; print('MCP Server OK')"
 ```
 
 ### CodeBuddy Configuration
@@ -359,7 +359,7 @@ See the Quick Start section in [README.md](README.md) for details.
 ## FAQ
 
 **Q: MCP Server fails to start with missing dependencies?**
-A: Make sure you have run `pip install -e .` to install CodeWiki and its dependencies. The MCP Server no longer requires CLI-specific packages like `keyring` or `click`.
+A: Make sure you have run `uv sync --extra dev` to install CodeWiki and its dependencies. The MCP Server no longer requires CLI-specific packages like `keyring` or `click`.
 
 **Q: analyze_repo is slow?**
 A: Tree-sitter parsing for large repositories (>100K lines) takes some time, usually completing within 30 seconds. Use `include_patterns` / `exclude_patterns` to narrow the analysis scope. There are no component count or source code length truncation limits.

codewiki/src/be/agent_tools/str_replace_editor.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python3
 
 """Source: https://github.com/SWE-agent/SWE-agent/blob/main/tools/edit_anthropic/bin/str_replace_editor
 This tool is used to view the given source code and view/edit the documentation files in the separate docs directory.
 """
 
 import json
 import re
 import subprocess
 import sys
 from collections import defaultdict
 from pathlib import Path
 from typing import Annotated, List, Literal, Optional, Tuple
 import io
 
 import logging
@@ -19,11 +19,11 @@
 
 logger = logging.getLogger(__name__)
 
 from pydantic import BeforeValidator
 from pydantic_ai import RunContext, Tool
 
 from .deps import CodeWikiDeps
 from ..utils import validate_mermaid_diagrams
 
 
 def _coerce_json_string(value):
@@ -45,14 +45,20 @@
     return value
 
 
 ViewRange = Annotated[Optional[List[int]], BeforeValidator(_coerce_json_string)]
 InsertLine = Annotated[Optional[int], BeforeValidator(_coerce_json_string)]
 
 
 # There are some super strange "ascii can't decode x" errors,
 # that can be solved with setting the default encoding for stdout
-# (note that python3.6 doesn't have the reconfigure method)
-sys.stdout = io.TextIOWrapper(sys.stdout.buffer, encoding="utf-8")
+# (note that python3.6 doesn't have the reconfigure method).
+# Only re-wrap a real TextIOWrapper whose encoding is not already utf-8,
+# so pytest's capture object (EncodedFile) is never clobbered.
+if isinstance(sys.stdout, io.TextIOWrapper) and (
+    sys.stdout.encoding is None
+    or sys.stdout.encoding.lower() not in ("utf-8", "utf8")
+):
+    sys.stdout = io.TextIOWrapper(sys.stdout.buffer, encoding="utf-8")
 
 TRUNCATED_MESSAGE: str = "<response clipped><NOTE>To save on context only part of this file has been shown to you. You should retry this tool after you have searched inside the file with `grep -n` in order to find the line numbers of what you are looking for.</NOTE>"
 MAX_RESPONSE_LEN: int = 16000
@@ -84,7 +90,7 @@
 """
 
 
 def maybe_truncate(content: str, truncate_after: Optional[int] = MAX_RESPONSE_LEN):
     """Truncate content and append a notice if content exceeds the specified length."""
     return (
         content
@@ -127,7 +133,7 @@
 
 
 def _update_previous_errors(
     previous_errors: List[Flake8Error], replacement_window: Tuple[int, int], replacement_n_lines: int
 ) -> List[Flake8Error]:
     """Update the line numbers of the previous errors to what they would be after the edit window.
     This is a helper function for `_filter_previous_errors`.

docker/DOCKER_README.md

@@ -143,9 +143,9 @@ The Dockerfile (`docker/Dockerfile`) builds the CodeWiki image with:
 - `nodejs` and `npm` - For mermaid diagram validation
 
 ### Application Setup
-1. Copies `requirements.txt` first (for better caching)
-2. Installs Python dependencies
-3. Copies entire application code
+1. Copies `pyproject.toml`, `README.md`, and the `codewiki` package
+2. Installs the package and its dependencies via `pip install .`
+3. Copies remaining assets (`img`)
 4. Creates output directories:
    - `output/cache`
    - `output/temp`

docker/Dockerfile

@@ -12,17 +12,16 @@ RUN apt-get update && apt-get install -y \
     npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Copy requirements first for better caching
-COPY requirements.txt .
+# Copy package source and metadata, then install
+COPY pyproject.toml .
+COPY README.md .
+COPY codewiki ./codewiki
 
-# Install Python dependencies
-RUN pip install --no-cache-dir -r requirements.txt
+# Install Python dependencies and package
+RUN pip install --no-cache-dir .
 
-# Copy application code
-COPY codewiki ./codewiki
+# Copy remaining assets
 COPY img ./img
-COPY pyproject.toml .
-COPY README.md .
 
 # Create output directories
 RUN mkdir -p output/cache output/temp output/docs output/dependency_graphs

pyproject.toml

@@ -59,13 +59,7 @@ dependencies = [
     "colorama>=0.4.6",
     "logfire>=4.1.0",
     "coding-agent-wrapper>=0.1.2",
-    "mcp>=1.0.0"
-]
-
-[external]
-# Node.js is required for mermaid-py which validates mermaid diagrams in generated documentation
-build-requires = [
-    { name = "nodejs", version = ">=14.0.0" }
+    "mcp>=1.0.0,<2"
 ]
 
 [project.optional-dependencies]

skills/codewiki-wiki-generator/SKILL.md

@@ -30,7 +30,7 @@ If tools are unavailable, prompt the user to install and configure CodeWiki:
 
 ```bash
 git clone https://github.com/FSoft-AI4Code/CodeWiki.git
-cd CodeWiki && pip install -e .
+cd CodeWiki && uv sync --extra dev
 ```
 
 Then add to MCP configuration: