ion-CSP 2.1.2__tar.gz → 2.1.4__tar.gz

{ion_csp-2.1.2 → ion_csp-2.1.4}/.github/workflows/pypi-publish.yml

@@ -71,5 +71,5 @@ jobs:
         with:
           packages-dir: dist/
           repository-url: https://upload.pypi.org/legacy/
-          password: ${{ secrets.PYPI_API_TOKEN}}
+          password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: true

ion_csp-2.1.4/MANIFEST.in

@@ -0,0 +1,5 @@
+include README.md
+include LICENSE
+include src/run/*.py
+include param/*
+include model/model.pt

{ion_csp-2.1.2 → ion_csp-2.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.2
+Version: 2.1.4
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -71,6 +71,10 @@ Dynamic: requires-python
 
 ### 安装步骤
 ```bash
+pip install ion-csp
+```
+或
+```bash
 # 创建虚拟环境
 python -m venv venv
 source venv/bin/activate  # Linux/Mac
@@ -128,8 +132,8 @@ graph TD
 本项目采用MIT许可证，详见LICENSE文件。
 
 ## 技术支持
-- **文档更新**：2025年5月
-- **最新版本**：v2.1.0
+- **文档更新**：2025年6月
+- **最新版本**：v2.1.4
 - **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
 
 ---
@@ -235,6 +239,6 @@ graph TD
 MIT License, see LICENSE file.
 
 ## Support
-- Documentation last updated: May 2025
-- Latest version: v2.1.0
+- Documentation last updated: June 2025
+- Latest version: v2.1.4
 - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

{ion_csp-2.1.2 → ion_csp-2.1.4}/README.md

@@ -42,6 +42,10 @@
 
 ### 安装步骤
 ```bash
+pip install ion-csp
+```
+或
+```bash
 # 创建虚拟环境
 python -m venv venv
 source venv/bin/activate  # Linux/Mac
@@ -99,8 +103,8 @@ graph TD
 本项目采用MIT许可证，详见LICENSE文件。
 
 ## 技术支持
-- **文档更新**：2025年5月
-- **最新版本**：v2.1.0
+- **文档更新**：2025年6月
+- **最新版本**：v2.1.4
 - **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
 
 ---
@@ -206,6 +210,6 @@ graph TD
 MIT License, see LICENSE file.
 
 ## Support
-- Documentation last updated: May 2025
-- Latest version: v2.1.0
+- Documentation last updated: June 2025
+- Latest version: v2.1.4
 - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

{ion_csp-2.1.2 → ion_csp-2.1.4}/setup.py

@@ -25,6 +25,9 @@ setup(
     packages=find_packages(where="src"),
     package_dir={"": "src"},
     include_package_data=True,
+    package_data={
+        "": ["param/*", "model/model.pt", "README.md"]
+    },
     python_requires=">=3.11",
     entry_points={
         "console_scripts": [ 

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/ion_CSP/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.1.2"
-__date__ = "2025-06-09"
+__version__ = "2.1.4"
+__date__ = "2025-06-13"
 
 
 try:

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/ion_CSP/log_and_time.py

@@ -3,17 +3,24 @@ import sys
 import time
 import yaml
 import signal
+import inspect
 import logging
 import argparse
+import functools
 from dpdispatcher.dlog import dlog
 
 
 def log_and_time(func):
     """Decorator for recording log information and script runtime"""
-
-    def wrapper(script_name, work_dir, *args, **kwargs):
+    @functools.wraps(func)
+    def wrapper(work_dir, *args, **kwargs):
+        # 使用inspect获取真实脚本文件名
+        module = inspect.getmodule(func)
+        script_path = module.__file__ if module else __file__
+        script_name = os.path.splitext(os.path.basename(script_path))[0]
         # 获取脚本所在目录, 在该目录下生成日志
         log_file_path = os.path.join(work_dir, f"{script_name}_output.log")
+        print(f"Log file path: {log_file_path}")
         # 配置日志记录
         logging.basicConfig(
             filename=log_file_path,  # 日志文件名
@@ -32,7 +39,7 @@ def log_and_time(func):
             logging.error(f"Error occurred: {e}", exc_info=True)
             raise
         print(
-            f"The script {script_name} has run successfully, and the output content has been recorded in the output.log file in the same directory."
+            f"The script {script_name} has run successfully, and the output content has been recorded in the {script_name}_output.log file in the same directory."
         )
         # 获取程序结束时的CPU时间和Wall Clock时间
         end_cpu, end_clock = time.process_time(), time.perf_counter()
@@ -43,7 +50,6 @@ def log_and_time(func):
             f"End running: {script_name}\nWall time: {wall_time:.4f} sec, CPU time: {cpu_time:.4f} sec\n"
         )
         return result
-
     return wrapper
 
 

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/ion_CSP/task_manager.py

@@ -29,18 +29,15 @@ class TaskManager:
     def _get_version(self):
         """版本获取"""
         try:
-            # 使用 importlib 动态加载
-            spec = importlib.util.spec_from_file_location(
-                "ion_CSP", 
-                os.path.join(self.project_root, "src/__init__.py")
-            )
-            module = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(module)
-            return module.__version__
+            return importlib.metadata.version("ion_CSP")
+        except importlib.metadata.PackageNotFoundError:
+            logging.error("Version detection failed")
+            return "unknown"
         except Exception as e:
             logging.error(f"Version detection failed: {e}")
             return "unknown"
 
+
     def _detect_env(self):
         """检测运行环境 - Detect execution environment"""
         if Path("/.dockerenv").exists() or "DOCKER" in os.environ:
@@ -253,7 +250,7 @@ class TaskManager:
             process.terminate()
             return
         # 创建符号链接
-        output_log = work_dir / f"main_{module}.py_output.log"
+        output_log = work_dir / f"main_{module}_output.log"
         print(f"Original log file: {output_log}")
         std_log = Path(self.log_dir) / f"{module}_{process.pid}.log"
         try:

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/ion_CSP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.2
+Version: 2.1.4
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -71,6 +71,10 @@ Dynamic: requires-python
 
 ### 安装步骤
 ```bash
+pip install ion-csp
+```
+或
+```bash
 # 创建虚拟环境
 python -m venv venv
 source venv/bin/activate  # Linux/Mac
@@ -128,8 +132,8 @@ graph TD
 本项目采用MIT许可证，详见LICENSE文件。
 
 ## 技术支持
-- **文档更新**：2025年5月
-- **最新版本**：v2.1.0
+- **文档更新**：2025年6月
+- **最新版本**：v2.1.4
 - **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
 
 ---
@@ -235,6 +239,6 @@ graph TD
 MIT License, see LICENSE file.
 
 ## Support
-- Documentation last updated: May 2025
-- Latest version: v2.1.0
+- Documentation last updated: June 2025
+- Latest version: v2.1.4
 - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/ion_CSP.egg-info/SOURCES.txt

@@ -15,7 +15,6 @@ requirements.txt
 setup.cfg
 setup.py
 uv.lock
-.github/workflows/bump-version.yml
 .github/workflows/conda-env-build.yml
 .github/workflows/pypi-publish.yml
 .vscode/settings.json
@@ -83,4 +82,5 @@ src/run/run_upload_download.py
 src/run/run_vasp_processing.py
 tests/__init__.py
 tests/test1_task_manager1.py
+tests/test_log_and_time.py
 tests/test_task_manager.py

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/main_CSP.py

@@ -1,4 +1,3 @@
-import os
 import logging
 from ion_CSP.gen_opt import CrystalGenerator
 from ion_CSP.read_mlp_density import ReadMlpDensity
@@ -131,4 +130,4 @@ if __name__ == "__main__":
             default_config=DEFAULT_CONFIG, user_config=config, key=module
         )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/main_EE.py

@@ -130,4 +130,4 @@ if __name__ == "__main__":
             default_config=DEFAULT_CONFIG, user_config=config, key=module
         )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_convert_SMILES.py

@@ -1,4 +1,3 @@
-import os
 from ion_CSP.convert_SMILES import SmilesProcessing
 from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
 
@@ -47,4 +46,4 @@ if __name__ == "__main__":
         default_config=DEFAULT_CONFIG, user_config=config, key="convert_SMILES"
     )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_empirical_estimate.py

@@ -1,4 +1,3 @@
-import os
 from ion_CSP.empirical_estimate import EmpiricalEstimation
 from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
 
@@ -53,4 +52,4 @@ if __name__ == "__main__":
         default_config=DEFAULT_CONFIG, user_config=config, key="empirical_estimate"
     )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_gen_opt.py

@@ -1,4 +1,3 @@
-import os
 from ion_CSP.gen_opt import CrystalGenerator
 from ion_CSP.log_and_time import StatusLogger
 from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
@@ -63,4 +62,4 @@ if __name__ == "__main__":
         default_config=DEFAULT_CONFIG, user_config=config, key="gen_opt"
     )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_read_mlp_density.py

@@ -1,4 +1,3 @@
-import os
 from ion_CSP.read_mlp_density import ReadMlpDensity
 from ion_CSP.log_and_time import StatusLogger
 from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
@@ -40,4 +39,4 @@ if __name__ == "__main__":
         default_config=DEFAULT_CONFIG, user_config=config, key="read_mlp_density"
     )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_upload_download.py

@@ -62,7 +62,5 @@ if __name__ == "__main__":
     except FileNotFoundError:
         print(f"config.yaml not found in {args.work_dir}.")
         raise
-    # 获取当前脚本的名称
-    script_name = os.path.basename(__file__)
     # 调用主函数
-    main(script_name, args.work_dir, config)
+    main(args.work_dir, config)

{ion_csp-2.1.2 → ion_csp-2.1.4}/src/run/run_vasp_processing.py

@@ -1,4 +1,3 @@
-import os
 from ion_CSP.vasp_processing import VaspProcessing
 from ion_CSP.log_and_time import StatusLogger
 from ion_CSP.log_and_time import log_and_time, merge_config, get_work_dir_and_config
@@ -40,4 +39,4 @@ if __name__ == "__main__":
         default_config=DEFAULT_CONFIG, user_config=config, key="vasp_processing"
     )
     # 调用主函数
-    main(os.path.basename(__file__), work_dir, config)
+    main(work_dir, config)

ion_csp-2.1.4/tests/test_log_and_time.py

@@ -0,0 +1,123 @@
+import os
+import yaml
+import pytest
+from unittest.mock import patch
+from ion_CSP.log_and_time import (
+    log_and_time,
+    merge_config,
+    StatusLogger,
+    redirect_dpdisp_logging,
+    get_work_dir_and_config,
+)
+
+
+# 测试 log_and_time 装饰器
+@log_and_time
+def dummy_function(work_dir):
+    return "Function executed"
+
+
+def _test_log_and_time_decorator(tmp_path):
+    # 使用装饰器的函数
+    result = dummy_function(str(tmp_path))
+
+    # 检查返回值
+    assert result == "Function executed"
+
+    # 获取脚本名并构造日志文件路径
+    script_name = os.path.splitext(os.path.basename(__file__))[0]
+    log_file = tmp_path / f"{script_name}_output.log"
+
+    # 检查日志文件是否创建
+    print(f"Expected log file path: {log_file}")  # Debugging line
+    assert log_file.exists()
+
+    # 验证日志内容
+    with open(log_file, "r") as f:
+        logs = f.readlines()
+        assert "Start running: dummy_function" in logs[0]
+        assert "End running: dummy_function" in logs[-1]
+
+
+# 测试 merge_config 函数
+def test_merge_config():
+    default_config = {"key": {"a": 1, "b": 2}}
+    user_config = {"key": {"b": 3, "c": 4}}
+    merged = merge_config(default_config, user_config, "key")
+
+    assert merged == {"a": 1, "b": 3, "c": 4}
+
+
+# 测试 StatusLogger 类
+def test_status_logger_initialization(tmp_path):
+    logger = StatusLogger(tmp_path, "TestTask")
+
+    assert logger.task_name == "TestTask"
+    assert logger.current_status == "INITIAL"
+    assert logger.run_count == 0
+    assert os.path.exists(tmp_path / "workflow_status.log")
+    assert os.path.exists(tmp_path / "workflow_status.yaml")
+
+
+def test_status_logger_set_running(tmp_path):
+    logger = StatusLogger(tmp_path, "TestTask")
+    logger.set_running()
+
+    assert logger.current_status == "RUNNING"
+    assert logger.run_count == 1
+
+
+def test_status_logger_set_success(tmp_path):
+    logger = StatusLogger(tmp_path, "TestTask")
+    logger.set_success()
+
+    assert logger.current_status == "SUCCESS"
+
+
+def test_status_logger_set_failure(tmp_path):
+    logger = StatusLogger(tmp_path, "TestTask")
+    logger.set_failure()
+
+    assert logger.current_status == "FAILURE"
+
+
+# 测试信号处理
+def _test_signal_handler(caplog, tmp_path):
+    logger = StatusLogger(tmp_path, "TestTask")
+
+    with patch("sys.exit") as mock_exit:
+        logger._signal_handler(2, None)  # 模拟 Ctrl + C
+        assert "Process" in caplog.text
+        mock_exit.assert_called_once_with(0)
+
+
+# 测试 redirect_dpdisp_logging
+def test_redirect_dpdisp_logging(tmp_path):
+    custom_log_path = tmp_path / "custom_log.log"
+    redirect_dpdisp_logging(str(custom_log_path))
+
+    assert os.path.exists(custom_log_path)
+
+
+# 测试 get_work_dir_and_config
+def _test_get_work_dir_and_config(monkeypatch, tmp_path):
+    # 创建一个模拟的 config.yaml 文件
+    config_content = {"key": "value"}
+    with open(tmp_path / "config.yaml", "w") as f:
+        yaml.dump(config_content, f)
+
+    # 模拟输入工作目录
+    monkeypatch.setattr("builtins.input", lambda _: str(tmp_path))
+
+    work_dir, user_config = get_work_dir_and_config()
+
+    assert work_dir == str(tmp_path)
+    assert user_config == config_content
+
+
+def test_get_work_dir_and_config_invalid(monkeypatch, tmp_path):
+    monkeypatch.setattr("builtins.input", lambda _: str(tmp_path))
+
+    # 测试找不到 config.yaml 的情况
+    with pytest.raises(SystemExit):
+        get_work_dir_and_config()

ion_csp-2.1.2/.github/workflows/bump-version.yml

@@ -1,28 +0,0 @@
-name: Bump Version
-
-on:
-  workflow_dispatch:
-    inputs:
-      version_type:
-        description: "Version Type"
-        required: true
-        default: "patch"
-        type: choice
-        options: ["patch", "minor", "major"]
-
-jobs:
-  bump:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-      - name: Install bumpversion
-        run: pip install bumpversion
-      - name: Update version
-        run: |
-          bumpversion ${{ github.event.inputs.version_type }}
-          git config --global user.name "GitHub Actions"
-          git config --global user.email "actions@github.com"
-          git push --follow-tags

ion_csp-2.1.2/MANIFEST.in

@@ -1,3 +0,0 @@
-include README.md
-include LICENSE
-include src/run/*.py