@researai/deepscientist 1.5.16 → 1.6.0

package/docs/zh/README.md

@@ -13,7 +13,7 @@ DeepScientist 灵活且易于使用，支持：
 - 本地优先、开源、一条命令安装
 - Git 驱动的 quest 仓库、Web 工作区、Studio / Canvas 与 TUI
 - 工作坊式协作：可长期自主推进，也可随时接管、协作、改代码、跑终端或记录 Notion 式笔记
-- 默认使用 Codex + `gpt-5.4`
+- 内建 `codex`、`claude`、`kimi`、`opencode` 四种 runner
 - 兼容外部 OpenAI-compatible 模型端点
 - 你可以在任何地方使用 DeepScientist：服务器（TUI）、浏览器（Web）、手机（微信或 QQ），甚至眼镜（Rokid Glasses）
 - 每个 quest 绑定一个外部 connector
@@ -77,15 +77,27 @@ DeepScientist 灵活且易于使用，支持：
 ## 如果你是第一次使用
 
 - [00 快速开始](./00_QUICK_START.md)
-  从安装、启动，到创建第一个项目，先看这一篇。
+  从安装、选择 Codex / Claude Code / Kimi Code / OpenCode runner，到启动和创建第一个项目，先看这一篇。
 - [20 工作区模式指南](./20_WORKSPACE_MODES_GUIDE.md)
   如果你最纠结的是“应该选 Copilot 还是全自动”，先看这篇。
-- [19 本地浏览器密码说明](./19_LOCAL_BROWSER_AUTH.md)
+- [31 本地浏览器密码说明](./31_LOCAL_BROWSER_AUTH.md)
   如果你想弄清楚密码弹窗是什么、密码去哪里看、怎样关闭这一层本地保护，先看这篇。
+- [32 Windows + WSL2 部署指南](./32_WINDOWS_WSL2_DEPLOYMENT_GUIDE.md)
+  如果你在 Windows 上使用 DeepScientist，并且想走推荐的 WSL2 路线，先看这篇。
 - [05 TUI 端到端指南](./05_TUI_GUIDE.md)
-  如果你主要在服务器或终端里工作，这篇会带你从 `ds --tui` 一路走到 quest、connector 和跨端协作跑通。
+  如果你主要在服务器或终端里工作，这篇会带你从 `ds --tui` 一路走到 quest、connector、跨端协作和 TUI debug 快照。
 - [15 Codex Provider 配置](./15_CODEX_PROVIDER_SETUP.md)
-  如果你准备通过 MiniMax、GLM、火山方舟、阿里百炼或其他 Codex profile 来运行 DeepScientist，先看这一篇。
+  如果你准备通过 OpenAI、Ollama、MiniMax、GLM、火山方舟、阿里百炼 Coding Plan 或其他 Codex profile 来运行 DeepScientist，先看这一篇。Gemini 只建议作为高级实验路线，通常优先走 OpenCode。
+- [24 Claude Code 配置指南](./24_CLAUDE_CODE_PROVIDER_SETUP.md)
+  如果 Claude Code 在你的机器上已经能正常工作，并且你想让 DeepScientist 直接复用它，或者你想通过 Ollama 的 Anthropic-compatible API 跑 Claude runner，先看这一篇。
+- [27 Kimi Code 配置指南](./27_KIMI_CODE_PROVIDER_SETUP.md)
+  如果官方 `kimi` CLI 在你的机器上已经能正常工作，并且你想把它作为独立 builtin runner 使用，先看这一篇。
+- [25 OpenCode 配置指南](./25_OPENCODE_PROVIDER_SETUP.md)
+  如果 OpenCode 在你的机器上已经能正常工作，并且你想让 DeepScientist 直接复用它的 provider/model 配置，尤其是接 Gemini 或 Ollama，先看这一篇。
+- [21 本地模型后端指南](./21_LOCAL_MODEL_BACKENDS_GUIDE.md)
+  如果你想通过 vLLM、Ollama、SGLang 等本地模型后端运行 DeepScientist，先看这一篇；它会帮你在 Codex、Claude Code、OpenCode 三条 runner 路线之间选路。
+- [26 引用与致谢说明](./26_CITATION_AND_ATTRIBUTION.md)
+  如果 DeepScientist 对论文或报告已经产生了实质性帮助，想看推荐引用方式、致谢模板和归因边界，就看这一篇。
 - [12 引导式工作流教程](./12_GUIDED_WORKFLOW_TOUR.md)
   按真实产品流程，逐步理解从首页到工作区应该怎么使用。
 - [02 Start Research 参考](./02_START_RESEARCH_GUIDE.md)
@@ -101,6 +113,8 @@ DeepScientist 灵活且易于使用，支持：
   当你需要配置 runner、connector、运行时默认值或主目录路径时，看这一篇。
 - [11 协议与风险说明](./11_LICENSE_AND_RISK.md)
   如果你关心开源协议、责任边界、服务器安全、结果伪造风险和 connector 泄露风险，先看这一篇。
+- [26 引用与致谢说明](./26_CITATION_AND_ATTRIBUTION.md)
+  如果你主要关心的是论文里该如何引用、如何做温和而清楚的 AI assistance 披露，优先看这篇。
 
 ## 如果你想通过外部协作面继续推进
 
@@ -134,22 +148,34 @@ DeepScientist 灵活且易于使用，支持：
 
 - [09 启动诊断](./09_DOCTOR.md)
   启动诊断、排查常见运行问题，先看这篇。
+- [33 Workspace Explorer Q&A](./33_WORKSPACE_EXPLORER_QA.md)
+  如果终端里能看到文件或文件夹，但 Web Explorer / Search 看不到，先看这篇确认 active worktree、`FILES` / `SCOPE`、刷新和 Git 状态边界。
 - [15 Codex Provider 配置](./15_CODEX_PROVIDER_SETUP.md)
   如果问题更像出在 Codex profile、provider endpoint、API key 或模型配置上，优先看这篇。
+- [24 Claude Code 配置指南](./24_CLAUDE_CODE_PROVIDER_SETUP.md)
+  如果问题更像出在 Claude Code 登录、配置目录、permission mode 或 Anthropic 兼容网关上，优先看这篇。
+- [27 Kimi Code 配置指南](./27_KIMI_CODE_PROVIDER_SETUP.md)
+  如果问题更像出在 Kimi Code 登录、`~/.kimi` home、agent 或 `--yolo` / thinking 配置上，优先看这篇。
+- [25 OpenCode 配置指南](./25_OPENCODE_PROVIDER_SETUP.md)
+  如果问题更像出在 OpenCode provider 登录、配置文件、模型选择、agent 或 variant 上，优先看这篇。
+- [21 本地模型后端指南](./21_LOCAL_MODEL_BACKENDS_GUIDE.md)
+  如果问题具体出在本地 OpenAI-compatible 后端以及 `/v1/responses` 支持上，优先看这篇。
 - [01 设置参考](./01_SETTINGS_REFERENCE.md)
   如果问题可能和配置、凭据或 connector 有关，再查这篇。
 
 ## 如果你在维护 DeepScientist
+- [23 BenchStore GitHub Releases 分发规范](./23_BENCHSTORE_GITHUB_RELEASES_SPEC.md)
+  如果你想把 BenchStore 的 benchmark 源码包发布到 GitHub Releases，并让用户在前端通过 Download 正常安装，先看这篇。
 
 - [90 Architecture](../en/90_ARCHITECTURE.md)
   说明系统级约束、核心契约和仓库结构。
 - [91 Development](../en/91_DEVELOPMENT.md)
-  面向维护者的开发工作流和实现说明。
+  面向维护者的开发工作流、实现说明，以及新增 MCP 工具、skills、connector 的具体清单。
 
 ## 社群交流
 
 欢迎加群讨论。
 
 <p align="center">
-  <img src="../../assets/readme/wechat.jpg" alt="DeepScientist 微信群" width="360" />
+  <img src="../../assets/readme/wechat6.jpg" alt="DeepScientist 微信群" width="360" />
 </p>

package/install.sh

@@ -112,10 +112,6 @@ else
   INSTALL_DIR="$BASE_DIR/cli"
 fi
 
-if [ "$DIR_SET" -eq 1 ] && [ "$BIN_DIR_SET" -eq 0 ] && [ -z "$ENV_BIN_DIR" ]; then
-  BIN_DIR="$BASE_DIR/bin"
-fi
-
 print_step() {
   printf '[install] %s\n' "$1"
 }
@@ -173,6 +169,22 @@ print_optional_latex_notice() {
   fi
 }
 
+print_runner_notice() {
+  printf '\n'
+  printf 'Runner selection:\n'
+  printf '  - You do not need to choose every runner during installation.\n'
+  printf '  - Start with the default Codex lane first: %s\n' "$BIN_DIR/ds"
+  printf '  - After the Web workspace opens, you can configure or switch runners from Settings.\n'
+  printf '  - One-off launch examples when the CLI already works in your shell:\n'
+  printf '      %s --runner claude\n' "$BIN_DIR/ds"
+  printf '      %s --runner kimi\n' "$BIN_DIR/ds"
+  printf '      %s --runner opencode\n' "$BIN_DIR/ds"
+  printf '  - Diagnostics examples:\n'
+  printf '      %s doctor --runner claude\n' "$BIN_DIR/ds"
+  printf '      %s doctor --runner kimi\n' "$BIN_DIR/ds"
+  printf '      %s doctor --runner opencode\n' "$BIN_DIR/ds"
+}
+
 resolve_path() {
   if command -v python3 >/dev/null 2>&1; then
     python3 - "$1" <<'PY'
@@ -213,6 +225,80 @@ safe_remove_dir() {
   rm -rf "$target"
 }
 
+invalidate_runtime_python_env() {
+  local runtime_dir="$BASE_DIR/runtime/python-env"
+  if [ ! -d "$runtime_dir/lib" ]; then
+    return
+  fi
+  local removed=0
+  while IFS= read -r -d '' target; do
+    rm -rf "$target"
+    removed=1
+  done < <(find "$runtime_dir/lib" -maxdepth 3 -type d \
+    \( -name 'deepscientist' -o -name 'deepscientist-*.dist-info' \) \
+    -print0 2>/dev/null)
+  if [ "$removed" -eq 1 ]; then
+    print_step "Invalidated runtime Python env; next 'ds' start will reinstall deepscientist"
+  fi
+}
+
+source_copy_excludes() {
+  cat <<'EOF'
+./.git
+./.claude
+./.pytest_cache
+./.mypy_cache
+./.ruff_cache
+./.venv
+./build
+./node_modules
+./ui
+./test-results
+./runtime
+./src/ui/node_modules
+./src/ui/lib/node_modules
+./src/ui/test-results
+./src/ui/vendor/novel-headless/node_modules
+./src/ui/vendor/novel-headless/.turbo
+./src/tui/node_modules
+./src/deepscientist.egg-info
+./Codex
+./*.tgz
+./*.log
+./*.pid
+./*.rootbak
+./*.rootbak/
+./dist.bak.*
+EOF
+}
+
+tar_exclude_args() {
+  while IFS= read -r pattern; do
+    [ -n "$pattern" ] || continue
+    printf '%s\0' "--exclude=$pattern"
+  done < <(source_copy_excludes)
+}
+
+rsync_exclude_args() {
+  while IFS= read -r pattern; do
+    [ -n "$pattern" ] || continue
+    pattern="${pattern#./}"
+    case "$pattern" in
+      */*|\**)
+        ;;
+      *)
+        pattern="/$pattern"
+        ;;
+    esac
+    case "$pattern" in
+      \**)
+        pattern="/$pattern"
+        ;;
+    esac
+    printf '%s\0' "--exclude=$pattern"
+  done < <(source_copy_excludes)
+}
+
 stop_existing_install() {
   if [ -x "$INSTALL_DIR/bin/ds" ]; then
     "$INSTALL_DIR/bin/ds" --stop >/dev/null 2>&1 || true
@@ -226,20 +312,21 @@ stop_existing_install() {
 copy_source_tree() {
   local target="$1"
   mkdir -p "$target"
-  if command -v tar >/dev/null 2>&1; then
-    tar -C "$SOURCE_ROOT" -cf - \
-      --exclude='./.git' \
-      --exclude='./.pytest_cache' \
-      --exclude='./build' \
-      --exclude='./node_modules' \
-      --exclude='./ui' \
-      --exclude='./src/ui/node_modules' \
-      --exclude='./src/ui/lib/node_modules' \
-      --exclude='./src/tui/node_modules' \
-      --exclude='./src/deepscientist.egg-info' \
-      . | tar -C "$target" -xf -
+  if command -v rsync >/dev/null 2>&1; then
+    local -a excludes=()
+    while IFS= read -r -d '' item; do
+      excludes+=("$item")
+    done < <(rsync_exclude_args)
+    rsync -a --delete "${excludes[@]}" "$SOURCE_ROOT"/ "$target"/
+  elif command -v tar >/dev/null 2>&1; then
+    local -a excludes=()
+    while IFS= read -r -d '' item; do
+      excludes+=("$item")
+    done < <(tar_exclude_args)
+    tar -C "$SOURCE_ROOT" -cf - "${excludes[@]}" . | tar -C "$target" -xf -
   else
     cp -R "$SOURCE_ROOT"/. "$target"/
+    prune_tree "$target"
   fi
 }
 
@@ -247,14 +334,26 @@ prune_tree() {
   local target="$1"
   rm -rf \
     "$target/.git" \
+    "$target/.claude" \
     "$target/.pytest_cache" \
+    "$target/.mypy_cache" \
+    "$target/.ruff_cache" \
+    "$target/.venv" \
     "$target/build" \
     "$target/node_modules" \
     "$target/ui" \
+    "$target/test-results" \
+    "$target/runtime" \
     "$target/src/ui/node_modules" \
     "$target/src/ui/lib/node_modules" \
+    "$target/src/ui/test-results" \
+    "$target/src/ui/vendor/novel-headless/node_modules" \
+    "$target/src/ui/vendor/novel-headless/.turbo" \
     "$target/src/tui/node_modules" \
-    "$target/src/deepscientist.egg-info"
+    "$target/src/deepscientist.egg-info" \
+    "$target/Codex"
+  find "$target" -maxdepth 1 -type f \( -name '*.tgz' -o -name '*.log' -o -name '*.pid' -o -name '*.rootbak' \) -delete
+  find "$target" -maxdepth 1 -type d \( -name '*.rootbak' -o -name 'dist.bak.*' \) -prune -exec rm -rf {} +
   find "$target" -type d -name '__pycache__' -prune -exec rm -rf {} +
   find "$target" -type f \( -name '*.pyc' -o -name '*.pyo' \) -delete
 }
@@ -265,14 +364,14 @@ build_ui() {
     return
   fi
   print_step "Building web UI in install tree"
-  npm --prefix "$1/src/ui" install --include=dev --no-audit --no-fund
+  npm --prefix "$1/src/ui" ci --include=dev --no-audit --no-fund
   npm --prefix "$1/src/ui" run build
   rm -rf "$1/src/ui/node_modules" "$1/src/ui/lib/node_modules"
 }
 
 install_root_runtime() {
   print_step "Installing root runtime dependencies in install tree"
-  npm --prefix "$1" install --omit=dev --no-audit --no-fund
+  npm --prefix "$1" ci --omit=dev --no-audit --no-fund
 }
 
 build_tui() {
@@ -289,7 +388,7 @@ build_tui() {
     return
   fi
   print_step "Building TUI in install tree"
-  npm --prefix "$1/src/tui" install --include=dev --no-audit --no-fund
+  npm --prefix "$1/src/tui" ci --include=dev --no-audit --no-fund
   npm --prefix "$1/src/tui" run build
   npm --prefix "$1/src/tui" prune --omit=dev --no-audit --no-fund
 }
@@ -431,6 +530,47 @@ EOF
   chmod +x "$target_path"
 }
 
+record_install_index() {
+  node - "$BASE_DIR" "$INSTALL_DIR" "$BIN_DIR" <<'NODE'
+const fs = require('node:fs');
+const os = require('node:os');
+const path = require('node:path');
+
+const home = path.resolve(process.argv[2] || '');
+const installDir = path.resolve(process.argv[3] || '');
+const binDir = path.resolve(process.argv[4] || '');
+const indexPath = path.join(os.homedir(), '.deepscientist', 'install-index.json');
+const wrapperPaths = ['ds', 'ds-cli', 'research', 'resear'].map((name) => path.join(binDir, name));
+const entry = {
+  home,
+  install_mode: 'install-local',
+  install_dir: installDir,
+  package_root: installDir,
+  launcher_path: path.join(installDir, 'bin', 'ds.js'),
+  wrapper_paths: wrapperPaths,
+  updated_at: new Date().toISOString(),
+  created_at: new Date().toISOString(),
+};
+let installs = [];
+try {
+  const payload = JSON.parse(fs.readFileSync(indexPath, 'utf8'));
+  installs = Array.isArray(payload?.installs) ? payload.installs : [];
+} catch {}
+const sameEntry = (item) =>
+  String(item?.home || '') === home
+  && String(item?.install_dir || '') === installDir
+  && String(item?.install_mode || '') === 'install-local';
+const existing = installs.find((item) => sameEntry(item));
+if (existing && existing.created_at) {
+  entry.created_at = existing.created_at;
+}
+installs = installs.filter((item) => !sameEntry(item));
+installs.push(entry);
+fs.mkdirSync(path.dirname(indexPath), { recursive: true });
+fs.writeFileSync(indexPath, `${JSON.stringify({ installs }, null, 2)}\n`, 'utf8');
+NODE
+}
+
 require_command node
 require_command npm
 
@@ -460,12 +600,15 @@ safe_remove_dir "$INSTALL_DIR"
 mv "$STAGING_DIR" "$INSTALL_DIR"
 trap - EXIT
 
+invalidate_runtime_python_env
+
 print_step "Writing launcher wrappers"
 mkdir -p "$BIN_DIR"
 write_global_wrapper "$BIN_DIR/ds" "ds"
 write_global_wrapper "$BIN_DIR/ds-cli" "ds-cli"
 write_global_wrapper "$BIN_DIR/research" "research"
 write_global_wrapper "$BIN_DIR/resear" "resear"
+record_install_index
 
 print_step "Install complete"
 printf 'Install dir: %s\n' "$INSTALL_DIR"
@@ -475,6 +618,11 @@ printf 'Start web workspace: %s\n' "$BIN_DIR/ds --web"
 printf 'Default start: %s\n' "$BIN_DIR/ds"
 printf 'When `ds` starts, it prints the local Web URL and opens it automatically when supported.\n'
 printf 'If `uv` is missing, the first `ds` start will bootstrap a local copy automatically under the DeepScientist home.\n'
+print_runner_notice
+if [ "$DIR_SET" -eq 1 ] && [ "$BIN_DIR_SET" -eq 0 ] && [ -z "$ENV_BIN_DIR" ]; then
+  printf 'Custom install dir detected; launcher wrappers were still refreshed in the default global bin dir: %s\n' "$BIN_DIR"
+  printf 'If you prefer install-local wrappers instead, rerun with: --bin-dir %s/bin\n' "$BASE_DIR"
+fi
 if [ "$WITH_TINYTEX" -eq 1 ]; then
   print_step "Installing TinyTeX pdflatex runtime"
   "$INSTALL_DIR/bin/ds" latex install-runtime

package/package.json

@@ -1,10 +1,11 @@
 {
   "name": "@researai/deepscientist",
-  "version": "1.5.16",
+  "version": "1.6.0",
   "description": "DeepScientist is not just a fully open-source autonomous scientific discovery system. It is also a research map that keeps growing from every round.",
   "license": "Apache-2.0",
   "files": [
     "AGENTS.md",
+    "AISB/",
     "README.md",
     "docs/",
     "install.sh",
@@ -35,9 +36,11 @@
     "research": "bin/ds.js"
   },
   "dependencies": {
+    "@anthropic-ai/claude-code": "^2.1.109",
     "@openai/codex": "^0.114.0",
     "ink": "npm:@jrichman/ink@6.4.6",
     "ink-gradient": "^3.0.0",
+    "opencode-ai": "^1.14.28",
     "qrcode": "^1.5.4",
     "react": "^19.2.0",
     "react-dom": "^19.2.0",
@@ -47,6 +50,7 @@
     "ds": "node ./bin/ds.js",
     "start": "node ./bin/ds.js daemon",
     "install:local": "bash ./install.sh",
+    "preuninstall": "node ./bin/ds.js uninstall --yes --origin npm",
     "ui:install": "npm --prefix src/ui install",
     "ui:dev": "npm --prefix src/ui run dev",
     "ui:build": "npm --prefix src/ui run build",

package/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deepscientist"
-version = "1.5.16"
+version = "1.6.0"
 description = "DeepScientist Core skeleton"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -14,6 +14,7 @@ authors = [
 ]
 dependencies = [
   "cryptography>=42,<46",
+  "httpx>=0.27,<1",
   "lark-oapi>=1.5,<2",
   "mcp>=1.19,<2",
   "Pillow>=10,<12",

package/src/deepscientist/__init__.py

@@ -5,4 +5,4 @@ __all__ = ["__version__"]
 try:
     __version__ = _package_version("deepscientist")
 except PackageNotFoundError:  # pragma: no cover - source checkout fallback
-    __version__ = "1.5.16"
+    __version__ = "1.6.0"

package/src/deepscientist/acp/envelope.py

@@ -142,6 +142,19 @@ def build_session_update(
             "reply_to_interaction_id": event.get("reply_to_interaction_id"),
             "client_message_id": event.get("client_message_id"),
             "delivery_state": event.get("delivery_state"),
+            "message_id": event.get("message_id"),
+            "read_state": event.get("read_state"),
+            "read_reason": event.get("read_reason"),
+            "read_at": event.get("read_at"),
+        }
+    elif event_type == "conversation.message_state":
+        update_kind = "message_state"
+        update_payload["message_state"] = {
+            "message_id": event.get("message_id"),
+            "client_message_id": event.get("client_message_id"),
+            "read_state": event.get("read_state"),
+            "read_reason": event.get("read_reason"),
+            "read_at": event.get("read_at"),
         }
     elif event_type == "artifact.recorded":
         update_kind = "artifact"

package/src/deepscientist/admin/__init__.py

@@ -0,0 +1,3 @@
+from .tasks import AdminTaskService
+
+__all__ = ["AdminTaskService"]