ion-CSP 2.1.5__tar.gz → 2.1.9__tar.gz

{ion_csp-2.1.5 → ion_csp-2.1.9}/.github/workflows/conda-env-build.yml

@@ -1,6 +1,8 @@
 name: Conda Environment Build
 
-on: [push, pull_request]
+on:
+  release:
+    types: [published]
 
 jobs:
   build-linux:

{ion_csp-2.1.5 → ion_csp-2.1.9}/CHANGELOG.md

@@ -1,177 +1,296 @@
 # Changelog
 
+## Latest Changes
+
+### 30a2f56 (2025-06-27)
+
+Optimize the file copying logic in VASP processing to ensure that copying operations are only performed when files exist
+
+### 0acedac (2025-06-27)
+
+Update the version number to 2.1.9, adjust the version detection error information in the task manager, optimize the error handling of multiple modules, optimize the EE workflow, make its operation and calling more stable, and work logic more rigorous.
+
+## V2.1.8
+
+### b534c0e (2025-06-23)
+
+Update version number to 2.1.8, optimize error handling in code, and update multiple modules to improve readability and functionality.
+
+### b68c9ac (2025-06-19)
+
+Update dependencies, improve documentation, and enhance error handling
+
+### 162ddc4 (2025-06-16)
+
+Use git hooks to automatcally update CHANGELOG.md
+
+### 80f0d24 (2025-06-16)
+
+Merge branch 'main' of https://github.com/Bagabaga007/ion_CSP
+
+### bf651e6 (2025-06-16)
+
+Update GitHub Actions workflow to trigger builds upon release, modify the steps for updating CHANGELOG to ensure proper installation of dependencies, update version number to 2.1.6, and optimize the generation format of CHANGELOG.
+
+### 5c3c950 (2025-06-16)
+
+Update update_changelog.yml
+
+### 346d034 (2025-06-16)
+
+Update update_changelog.yml
+
+### 2ea0ac4 (2025-06-16)
+
+Introduce importlib.resourses in multiple modules to improve file path management;  Fix the module import path in the task manager.
+
+## V2.1.5
+
+### 934f0fa (2025-06-16)
+
+Add dependency descriptions for the Scipy version;  Fixed missing example 2 in the examples section.
+
+### 31087de (2025-06-16)
+
+Update version to 2.1.5.
+
+### 3edd170 (2025-06-16)
+
+Added the function of automatically updating CHANGELOG; Import configuration and data files through importlib.resosourced to fix file read errors in the pypi distribution package.
+
 ## V2.1.4
+
 ### ad5c1d7 (2025-06-13)
+
 Optimize the packaging behavior when building pypi distribution packages to make them easier to use
 
 ## V2.1.3
+
 ### d503641 (2025-06-11)
+
 Updata version to 2.1.3
 
 ## V2.1.2
+
 ### 1befcf7 (2025-06-09)
+
 Implement centralized management of version numbers and automatic synchronization of multiple configuration files to ensure consistency and reliability in the construction process.
 
 ## V2.1.1
+
 ### bde5189 (2025-06-09)
+
 Refactoring the project structure, configuring packaging parameters, and modifying sub process call logic to address the issue of module path failure in PyPI distribution packages;  To modify VASP optimization steps in the workflow: 1  Rough optimization of limiting cell shape 2. Fine optimization of limiting cell shape 3. Final optimization without cell constraints
 
 ### bb0d853 (2025-05-30)
+
 Added usage and configuration examples in the project root directory. Added permission items in the CI Build workflow to enhance security. Added parameters to the example resources.yaml file to specify JOB_NAME to optimize the readability of jobs.
 
 ### 80a3e3d (2025-05-23)
+
 Add template configuration files and corresponding usage document in the config folder under the root directory
 
 ### 7f383b0 (2025-05-21)
+
 Adjust the installation method of the code, use git clone and pip install - e. commands to install the source code, and continue to optimize the use of code installed using distribution packages in the future.  Correspondingly updated the version number and the documentation content of README.md.
 
 ### 1d0d5fc (2025-05-16)
+
 Modification of conda package build yml file.
 
 ### 83f25cb (2025-05-16)
+
 Modification of conda package build yml file.
 
 ### 5540449 (2025-05-16)
+
 Remove the flake8 installation in conda package construction.
 
 ### 01af54c (2025-05-16)
+
 Update information in README.md
 
 ### cb7dcb0 (2025-05-15)
+
 Ignore the big-size dist files
 
 ### 1ff9020 (2025-05-13)
+
 Update README.md and modified the yml file for github action of conda package build
 
 ### 01f2095 (2025-05-13)
+
 Modified yml file for github actions
 
 ### 90bfd07 (2025-05-13)
+
 Modified yml file for Github actions.
 
 ### 6f29d21 (2025-05-13)
+
 After machine learning potential optimization and structure filtering, CSV files were added to summarize the sequence number, density, and energy of the filtered structures, making it easier to visualize the interface.
 
 ### f2a8abc (2025-05-09)
+
 Modified the yml file for github actions
 
 ### b5d1bcd (2025-05-09)
+
 Merge branch 'main' of https://github.com/Bagabaga007/ion_CSP
 
 ### bfec475 (2025-05-09)
+
 Significantly optimized the program logic of the interactive entrance and fixed a large number of potential bugs. Integrate pagination display function to reduce code duplication. Add unit testing modules for this interactive entry program.
 
 ### 30c455b (2025-04-25)
+
 Create SECURITY.md
 
 ### 070c86f (2025-04-25)
+
 Add unit testing module for task_manager.
 
 ### 72ccfad (2025-04-25)
+
 Remove torchvision package dependencies to allow pip to attempt to solve the dependency conflict.
 
 ### 049d915 (2025-04-25)
+
 Fix the bug in environment.yml file
 
 ### 3866521 (2025-04-25)
+
 Adjust the depencies installation order
 
 ### ff92e05 (2025-04-25)
+
 Change some certain packages installation way to pip installation.
 
 ### 24832ea (2025-04-25)
+
 Remove invalid channel and adapt the mixed installation method.
 
 ### c2a01ee (2025-04-25)
+
 Update the corresponding information yml to resolve the conda environment configuration actions in Github
 
 ### 0675303 (2025-04-25)
+
 Add conda environment configuration
 
 ### b91ee5c (2025-04-25)
+
 Merge branch 'main' of https://github.com/Bagabaga007/ion_CSP
 
 ### 15c4628 (2025-04-25)
+
 Significantly optimized the logging system and task management of the interactive program entrance.  The specific functions implemented include: real-time process monitoring (PID tracking), automatic symbolic linking of log files, process security termination and resource cleaning, log pagination browsing (10 entries/page), module filtering (CSP/EE), and soft link parsing to display the actual path.  Greatly optimized the README.md file, providing bilingual support in both Chinese and English that is more in line with Python project specifications.
 
 ### 7b1752b (2025-04-23)
+
 Create python-package-conda.yml
 
 ### 0cf8d07 (2025-04-23)
+
 Merge branch 'main' of https://github.com/Bagabaga007/ion_CSP
 
 ### ebf54e3 (2025-04-23)
+
 Unified the interactive interface between shell and Python versions, and uploaded distribution files to Pypi
 
 ### 1cbba7e (2025-04-23)
+
 Create python-publish.yml
 
 ### 98f7382 (2025-04-22)
+
 Added Python version of interactive main function entry and corresponding app files.
 
 ### f034fbe (2025-04-21)
+
 1. Improve the dockerfile to ensure smooth operation inside the container; 2. Added a terminal interactive entrance for the program, supporting both Linux terminals and Docker environments, supporting runtime experience evaluation and ion crystal structure prediction modules, and able to capture the PID of Python programs and link logs for easy monitoring of task status and results, as well as task killing. 3. Optimize the task step logic of the EE module to avoid possible redundant Gaussian calculations, and provide batch update parameters for the config. yaml configuration file in the combined folder. 4. Generate CSV files for echo information during the structure generation stage, saving the structure generation information of each space group and the exception types when pyxtal generation fails. At the same time, based on the results of phonopy symmetry processing, remove the double atom structure generated by pyxtal and update the CSV file information.
 
 ### d079b70 (2025-04-11)
+
 After successfully completing the task using the dpdispatcher module, delete the corresponding folder for submission to save space.
 
 ### 9ddb0c4 (2025-04-11)
+
 Change the version number to 2.0.0.
 
 ### c367bc3 (2025-04-09)
+
 Fully automated EE workflow
 
 ### f8e6c73 (2025-04-08)
+
 Fully automated ion CSP workflow.
 
 ### c4400f0 (2025-04-02)
+
 Delete 3_postprocessing directory
 
 ### 380eedb (2025-04-02)
+
 Delete 2_generation directory
 
 ### 05931e7 (2025-04-02)
+
 Delete 1_preparation directory
 
 ### a22b9e8 (2024-12-23)
+
 ok
 
 ### 7f6d3b1 (2024-12-23)
+
 ok
 
 ### c13cd0c (2024-12-20)
+
 ok
 
 ### 1a2b2d5 (2024-12-19)
+
 ok
 
 ### fd404eb (2024-12-19)
+
 OK
 
 ### 2d8aafd (2024-12-17)
+
 ok
 
 ### 7fbfd27 (2024-12-16)
+
 ok
 
 ### a0b84fc (2024-12-16)
+
 ok
 
 ### 9878e9d (2024-12-16)
+
 ok
 
 ### b07065c (2024-12-16)
+
 ok
 
 ### 68b6b0a (2024-12-16)
+
 ok
 
 ### f6a30b0 (2024-12-14)
+
 ok
 
 ### 0e434f6 (2024-12-14)
+
 ok
 
 ### 2bef3e2 (2024-12-12)
+
 committed
 

{ion_csp-2.1.5 → ion_csp-2.1.9}/CODE_OF_CONDUCT.md

@@ -1,12 +1,15 @@
 # Code of Conduct
 
 ## 1. Purpose
+
 We are committed to creating an open, welcoming, and inclusive community. This Code of Conduct aims to provide a safe environment for all participants, fostering positive interactions and collaboration.
 
 ## 2. Scope
+
 This Code of Conduct applies to all participants, including but not limited to: contributors, maintainers, users, and anyone involved with the project.
 
 ## 3. Expected Behavior
+
 We encourage all participants to:
 
 - **Respect Others**: Honor each person’s viewpoints, experiences, and backgrounds.
@@ -15,6 +18,7 @@ We encourage all participants to:
 - **Accept Constructive Feedback**: Be open to feedback from others and engage in discussions with an open mind.
 
 ## 4. Unacceptable Behavior
+
 The following behaviors are considered unacceptable:
 
 - **Harassment**: This includes threats, malicious attacks, sexism, racism, hate speech, etc.
@@ -22,9 +26,11 @@ The following behaviors are considered unacceptable:
 - **Disruptive Behavior**: Intentionally disrupting others' work or the community environment.
 
 ## 5. Reporting Mechanism
+
 If you witness or experience unacceptable behavior, please report it to the community maintainers promptly. We take every report seriously and will take appropriate action.
 
 ## 6. Consequences
+
 For participants who violate the Code of Conduct, we may take the following actions:
 
 - Warning
@@ -32,7 +38,9 @@ For participants who violate the Code of Conduct, we may take the following acti
 - Permanent ban from participation
 
 ## 7. Applicability
+
 This Code of Conduct applies to all activities related to the project, including online and offline interactions.
 
 ## 8. License
+
 This Code of Conduct follows the [Contributor Covenant](https://opensource.org/osd) and welcomes suggestions and improvements from anyone.

{ion_csp-2.1.5 → ion_csp-2.1.9}/LICENSE

@@ -1,4 +1,4 @@
-MIT License
+# MIT License
 
 Copyright (c) [2025] [ion_CSP]
 

{ion_csp-2.1.5 → ion_csp-2.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.5
+Version: 2.1.9
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -28,13 +28,16 @@ Dynamic: home-page
 Dynamic: license-file
 Dynamic: requires-python
 
-# Crystal Structure Design Software V2.1
+# 基于分子/离子构型的晶体结构设计软件 V2.1
 
 ## 项目概述
+
 基于分子/离子构型的晶体结构设计软件通过结合经验公式、机器学习势函数微调、第一性原理分步优化和分子/离子识别技术，实现了从分子/离子构型出发的高效晶体结构设计。该软件采用模块化设计，支持全流程自动化材料筛选，在保证预测精度的同时显著提升计算效率。
 
 ## 功能特性
+
 ### 核心功能
+
 - **双模块工作流**  
   - **EE模块**：基于经验评估的离子组合生成  
   - **CSP模块**：基于离子晶体结构预测的优化筛选  
@@ -48,13 +51,16 @@ Dynamic: requires-python
   - 软链接解析显示实际路径
 
 ### 技术特性
+
 - 跨平台支持（Linux/Docker）
 - 基于Python 3.11+的面向对象架构
 - 集成psutil进程管理
 - 结构化日志记录系统
 
 ## 安装指南
+
 ### 环境要求
+
 | 组件        | 最低版本 |
 |-------------|----------|
 | Python      | 3.11     |
@@ -71,10 +77,13 @@ Dynamic: requires-python
 | rdkit       | 2024.03.3|
 
 ### 安装步骤
+
 ```bash
 pip install ion-csp
 ```
+
 或
+
 ```bash
 # 创建虚拟环境
 python -m venv venv
@@ -87,29 +96,39 @@ pip install -e .
 ```
 
 ## 快速入门
+
 ### 交互模式
+
 ```bash
 ion-csp
 ```
+
 启动交互式命令行界面，支持以下操作：
+
 - 模块选择
 - 日志查看
 - 进程管理
 
 ### 脚本调用
+
 #### EE模块示例
+
 ```bash
 ./scripts/main_EE.sh examples/example_1
 ```
+
 从SMILES表格生成离子组合
 
 #### CSP模块示例
+
 ```bash
 ./scripts/main_CSP.sh examples/example_2
 ```
+
 从离子组合生成并优化晶体结构
 
 ## 技术架构
+
 ```mermaid
 graph TD
     A[用户界面] --> B[任务管理器]
@@ -118,34 +137,32 @@ graph TD
     B --> E[日志系统]
     B --> F[任务调度]
     C --> G[经验评估引擎]
-    D --> H[晶体预测引擎]
+    D --> H[离子晶体结构预测引擎]
     E --> I[结构化日志]
     F --> J[进程终止]
 ```
 
 ## 贡献指南
+
 1. Fork仓库并创建特性分支
 2. 编写单元测试覆盖新功能
 3. 提交Pull Request时注明关联Issue
 4. 遵循PEP8代码规范
 
 ## 许可证
-本项目采用MIT许可证，详见LICENSE文件。
 
-## 技术支持
-- **文档更新**：2025年6月
-- **最新版本**：v2.1.5
-- **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
+本项目采用MIT许可证，详见LICENSE文件。
 
 ---
 
-# Crystal Structure Design Software V2.1
-
 ## Project Overview
+
 This software enables efficient crystal structure design from molecular/ion configurations by integrating empirical formulas, tuned machine learning potentials, stepwise first-principles optimization, and molecular/ion recognition techniques. The modular architecture ensures extensibility and maintainability while maintaining prediction accuracy.
 
 ## Key Features
+
 ### Core Functionalities
+
 - **Dual-Module Workflow**
   - **EE Module**: Empirical evaluation-based ion combination generation
   - **CSP Module**: Ion crystal structure prediction and optimization
@@ -159,13 +176,16 @@ This software enables efficient crystal structure design from molecular/ion conf
   - Symlink resolution for actual log paths
 
 ### Technical Specifications
+
 - Cross-platform support (Linux/Docker)
 - Object-oriented architecture with Python 3.11+
 - Integrated process management via psutil
 - Structured logging system
 
 ## Installation
+
 ### Prerequisites
+
 | Component   | Min Version |
 |-------------|-------------|
 | Python      | 3.11     |
@@ -182,6 +202,7 @@ This software enables efficient crystal structure design from molecular/ion conf
 | rdkit       | 2024.03.3|
 
 ### Installation Steps
+
 ```bash
 # Create virtual environment
 python -m venv venv
@@ -194,29 +215,39 @@ pip install -e .
 ```
 
 ## Quick Start
+
 ### Interactive Mode
+
 ```bash
 ion-csp
 ```
+
 Launches CLI interface with:
+
 - Module selection
 - Log management
 - Process control
 
 ### Script Execution
+
 #### EE Module Example
+
 ```bash
 ./scripts/main_EE.sh examples/example_1
 ```
+
 Generates ion combinations from SMILES tables
 
 #### CSP Module Example
+
 ```bash
 ./scripts/main_CSP.sh examples/example_2
 ```
+
 Optimizes crystal structures from ion combinations
 
 ## Technical Architecture
+
 ```mermaid
 graph TD
     A[User Interface] --> B[Task Manager]
@@ -225,21 +256,18 @@ graph TD
     B --> E[Log System]
     B --> F[Task Scheduler]
     C --> G[Empirical Evaluation Engine]
-    D --> H[Crystal Prediction Engine]
+    D --> H[Ionic Crystal Structure Prediction Engine]
     E --> I[Structured Logs]
     F --> J[Process Termination]
 ```
 
 ## Contribution Guide
+
 1. Fork repository and create feature branch
 2. Write unit tests for new features
 3. Submit PR with issue reference
 4. Follow PEP8 coding standards
 
 ## License
-MIT License, see LICENSE file.
 
-## Support
-- Documentation last updated: June 2025
-- Latest version: v2.1.5
-- Issue tracker: https://github.com/bagabaga007/ion_CSP/issues
+MIT License, see LICENSE file.