lingyuzeng
c0ead42384
Implement the standard/non-standard/not-macrolactone classification layer and integrate it into analyzer, fragmenter, and CLI outputs. Port the remaining legacy package capabilities into new visualization and workflow modules, restore batch/statistics/SDF scripts on top of the flat CSV workflow, and update active docs to the new package API.
145 lines
2.7 KiB
Markdown
145 lines
2.7 KiB
Markdown
# 快速命令参考
|
||
|
||
## 📚 查看文档
|
||
|
||
```bash
|
||
# 启动文档服务器（推荐）
|
||
pixi run mkdocs serve
|
||
|
||
# 访问：http://localhost:8000
|
||
|
||
# 构建静态文档
|
||
pixi run mkdocs build
|
||
|
||
# 部署到 GitHub Pages
|
||
pixi run mkdocs gh-deploy
|
||
```
|
||
|
||
## 📦 安装项目
|
||
|
||
```bash
|
||
# 方式 1: 使用 Pixi（推荐）
|
||
pixi install
|
||
pixi shell
|
||
|
||
# 方式 2: 使用 Pip（需要先安装 RDKit）
|
||
conda install -c conda-forge rdkit
|
||
pip install -e . # 开发模式
|
||
|
||
# 方式 3: 常规安装
|
||
pip install .
|
||
```
|
||
|
||
## 🧪 测试安装
|
||
|
||
```python
|
||
from macro_lactone_toolkit import MacroLactoneAnalyzer, MacrolactoneFragmenter
|
||
from macro_lactone_toolkit.workflows import fragment_csv, results_to_dataframe
|
||
|
||
analyzer = MacroLactoneAnalyzer()
|
||
fragmenter = MacrolactoneFragmenter()
|
||
print("✓ 安装成功！")
|
||
```
|
||
|
||
## 📓 运行示例
|
||
|
||
```bash
|
||
pixi run macro-lactone-toolkit analyze --smiles 'O=C1CCCCCCCCCCCCCCO1'
|
||
python scripts/batch_process.py --input molecules.csv --output fragments.csv --errors-output errors.csv
|
||
python scripts/analyze_fragments.py --input fragments.csv --output-dir analysis
|
||
```
|
||
|
||
## 🔍 项目结构
|
||
|
||
```bash
|
||
# 查看文档文件
|
||
find docs -type f -name "*.md" | sort
|
||
|
||
# 查看源代码
|
||
ls -la src/
|
||
|
||
# 查看配置文件
|
||
cat pyproject.toml
|
||
cat mkdocs.yml
|
||
```
|
||
|
||
## 📝 文档编辑
|
||
|
||
```bash
|
||
# 编辑文档
|
||
vim docs/user-guide/fragmenter-usage.md
|
||
|
||
# 实时预览
|
||
pixi run mkdocs serve
|
||
|
||
# 构建验证
|
||
pixi run mkdocs build
|
||
```
|
||
|
||
## 🚀 发布准备
|
||
|
||
```bash
|
||
# 构建分发包
|
||
python -m build
|
||
|
||
# 检查包
|
||
twine check dist/*
|
||
|
||
# 上传到 TestPyPI（测试）
|
||
twine upload --repository testpypi dist/*
|
||
|
||
# 上传到 PyPI（正式发布）
|
||
twine upload dist/*
|
||
```
|
||
|
||
## 🛠️ 开发工具
|
||
|
||
```bash
|
||
# 格式化代码
|
||
pixi run black src/
|
||
|
||
# 检查代码质量
|
||
pixi run flake8 src/
|
||
|
||
# 运行测试
|
||
pixi run pytest
|
||
|
||
# 测试覆盖率
|
||
pixi run pytest --cov=src
|
||
```
|
||
|
||
## 📊 项目信息
|
||
|
||
```bash
|
||
# 查看 Pixi 环境
|
||
pixi list
|
||
|
||
# 查看项目信息
|
||
cat pyproject.toml | grep -A 10 '\[project\]'
|
||
|
||
# 查看版本
|
||
cat pyproject.toml | grep version
|
||
```
|
||
|
||
## 🔗 重要文件
|
||
|
||
| 文件 | 说明 |
|
||
|------|------|
|
||
| `README.md` | 项目主文档 |
|
||
| `docs/SUMMARY.md` | 当前 API 和工作流摘要 |
|
||
| `scripts/README.md` | 脚本工作流说明 |
|
||
| `src/macro_lactone_toolkit/` | 正式包实现 |
|
||
| `pyproject.toml` | Python 项目配置 |
|
||
| `mkdocs.yml` | 文档配置 |
|
||
| `pixi.toml` | Pixi 环境配置 |
|
||
|
||
## 💡 常用链接
|
||
|
||
- **本地文档**: http://localhost:8000 (运行 `pixi run mkdocs serve`)
|
||
- **GitHub**: https://github.com/yourusername/macro_split
|
||
- **PyPI**: https://pypi.org/project/macrolactone-fragmenter/
|
||
|
||
---
|
||
|
||
**需要帮助？** 查看 `docs/SUMMARY.md`、`scripts/README.md` 或运行 `pixi run mkdocs serve`
|