NepTrainKit 2.8.4.dev0__tar.gz → 3.0.0__tar.gz

neptrainkit-3.0.0/.gitignore

@@ -0,0 +1,34 @@
+**/__pycache__/
+/src/NepTrainKit.egg-info/
+/build
+/dist
+/docs/build
+/docs/_build
+/docs/source/locale/**/*.mo
+/docs/superpowers/
+/.tmp/docs-screenshots
+.idea/
+/src/NepTrainKit/?.py
+/src/NepTrainKit/_version.py
+/src/NepTrainKit/Log/*.log
+.pytest_cache/
+.superpowers/
+tests/_sandbox_tmp/
+tests/_localappdata/
+tests/_tmp/
+tests/_pytest_cache/
+tests/_pytest_tmp/
+tests/pytest-cache-files-*/
+/.tmp_localappdata/
+
+# Local platform builds and generated diagnostics
+**/.DS_Store
+/src/NepTrainKit/**/*.so
+/diagnostics/
+/tmp/
+
+# Outputs generated while exercising bundled test fixtures
+/tests/data/**/descriptor.pca2.json
+/tests/data/**/descriptor.pca2.npy
+/tests/data/**/nep.in
+/tests/data/nep/*.out

neptrainkit-2.8.4.dev0/.readthedocs.yml → neptrainkit-3.0.0/.readthedocs.yaml

@@ -9,18 +9,16 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "20"
-    # rust: "1.70"
-    # golang: "1.20"
 
 # Build documentation in the "docs/" directory with Sphinx
+# The parent and translation projects share this file. ``conf.py`` reads
+# READTHEDOCS_LANGUAGE so each project builds only its configured language.
 sphinx:
   configuration: docs/source/conf.py
   # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
   # builder: "dirhtml"
-  # Fail on all warnings to avoid broken references
-  # fail_on_warning: true
+  # Keep both language projects strict and fail on broken documentation.
+  fail_on_warning: true
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
@@ -32,4 +30,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-     - requirements: docs/requirements.txt
+     - requirements: docs/requirements.txt

neptrainkit-3.0.0/AGENTS.md

@@ -0,0 +1,31 @@
+# NepTrainKit Agent Notes
+
+## Project Skill
+
+This repo has a local skill at `skills/make-dataset-card-dev/SKILL.md`.
+
+Before changing Make Dataset cards, card operations, card docs, or card tests:
+
+1. Read `skills/make-dataset-card-dev/SKILL.md` from this checkout.
+2. Follow its operation/params/UI/docs/tests contract.
+3. If the global Codex skill is not installed or does not auto-trigger, say so briefly and use the repo-local `SKILL.md` as the source of truth.
+
+The skill should trigger naturally when the task is about adding, migrating, refactoring, or testing Make Dataset cards. Do not assume every developer has it installed globally; the repo-local file is the fallback.
+
+## Change Style
+
+- Keep changes surgical. Touch only files needed for the requested behavior.
+- Prefer existing helpers, card patterns, canvas backends, and result-data contracts over new abstractions.
+- Do not add optional flexibility, new dependencies, or broad refactors unless the user asks.
+- Preserve user-visible workflows unless the task explicitly changes them.
+
+## Tests
+
+- For ordinary fixes, run the smallest targeted pytest command that covers the behavior, then broaden if risk warrants it.
+- Before committing a repo change, run `git diff --check`.
+- For Make Dataset card work, also run `python skills/make-dataset-card-dev/scripts/run_card_checks.py --quick` when the script is available.
+- Keep ad hoc generated files out of Git. Use temp paths for fixtures and clean up local outputs created by tests.
+
+## Local Artifacts
+
+Treat `tmp/`, `outputs/`, `diagnostics/`, generated descriptors, copied datasets, compiled local binaries, and similar files as local artifacts unless the user explicitly asks to version them.

{neptrainkit-2.8.4.dev0 → neptrainkit-3.0.0}/MANIFEST.in

@@ -14,12 +14,9 @@ prune .github
 global-exclude *.log
 global-exclude *upx.exe
 global-exclude *update.exe
-global-exclude *nep_cpu*.pyd
-global-exclude *_fastxyz*.pyd
-global-exclude *nep_gpu*.pyd
-global-exclude *cuda*.dll
-global-exclude *vcomp140*.dll
-global-exclude *msvcp140*.dll
-global-exclude *libomp140.x86_64.dll
+global-exclude *.so
+global-exclude *.dylib
+global-exclude *.pyd
+global-exclude *.dll
 global-exclude src/NepTrainKit/src/**
 global-exclude src/NepTrainKit/src.qrc

neptrainkit-3.0.0/PKG-INFO

@@ -0,0 +1,150 @@
+Metadata-Version: 2.4
+Name: NepTrainKit
+Version: 3.0.0
+Summary: Visualize, diagnose, and manipulate NEP training datasets.
+Author-email: Chen Cheng bing <1747193328@qq.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/aboys-cb/NepTrainKit
+Project-URL: Documentation, https://github.com/aboys-cb/NepTrainKit
+Project-URL: Repository, https://github.com/aboys-cb/NepTrainKit
+Project-URL: Issues, https://github.com/aboys-cb/NepTrainKit/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Requires-Dist: PySide6==6.9.0
+Requires-Dist: PySide6-Fluent-Widgets>=1.7.0
+Requires-Dist: loguru>=0.7.2
+Requires-Dist: requests>=2.32.3
+Requires-Dist: packaging>=24.0
+Requires-Dist: pyqtgraph>=0.13.7
+Requires-Dist: PyOpenGL>=3.1.7
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: vispy>=0.14.3
+Requires-Dist: ase
+Requires-Dist: nep-adapters>=1.0
+Requires-Dist: scipy>=1.15.0
+Requires-Dist: SQLAlchemy>=2.0.0
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-qt>=4.2.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Requires-Dist: codecov>=2.0.0; extra == "test"
+Requires-Dist: ruff>=0.12.0; extra == "test"
+Requires-Dist: scikit-learn>=1.5.0; extra == "test"
+Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "test"
+Dynamic: license-file
+
+<div align="center">
+<a href="https://github.com/aboys-cb/NepTrainKit">
+  <img src="https://raw.githubusercontent.com/aboys-cb/NepTrainKit/master/src/NepTrainKit/src/images/logo.png" width="25%" alt="NepTrainKit logo">
+</a><br>
+<a href="https://pypi.org/project/NepTrainKit"><img src="https://img.shields.io/pypi/dm/NepTrainKit?logo=pypi&logoColor=white&color=blue&label=PyPI" alt="PyPI downloads"></a>
+<a href="https://python.org/downloads"><img src="https://img.shields.io/badge/Python-3.10--3.13-blue.svg?logo=python&logoColor=white" alt="Python version"></a>
+<a href="https://codecov.io/github/aboys-cb/NepTrainKit"><img src="https://codecov.io/github/aboys-cb/NepTrainKit/graph/badge.svg?token=HQ5FMLD91F" alt="Codecov"></a>
+<a href="https://github.com/aboys-cb/NepTrainKit/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-GPL--3.0--or--later-blue" alt="License"></a>
+<br><br>
+<strong>English</strong> | <a href="https://github.com/aboys-cb/NepTrainKit/blob/master/README.zh-CN.md">简体中文</a>
+</div>
+
+# NepTrainKit
+
+NepTrainKit is a desktop application for preparing, auditing, and visualizing training datasets for neuroevolution potentials (NEPs). It complements, rather than replaces, long-running GPUMD training or DFT calculations. Its focus is the repetitive work around those calculations: generating candidate structures, cleaning problematic samples, selecting representative configurations, and passing a well-prepared dataset back into the DFT and GPUMD workflow.
+
+## What you can do
+
+- **Make Dataset**: generate strained, perturbed, defective, surface, doped, magnetic, and solvated candidate structures with composable cards.
+- **NEP Dataset Display**: inspect structures, errors, and distributions; remove problematic samples; and export a clean subset.
+- **Representative selection**: reduce a candidate pool to a smaller, more representative set with methods such as farthest point sampling (FPS).
+- **Training-result inspection**: load NEP- and DeepMD-related outputs, locate high-error structures, and identify data gaps for the next iteration.
+- **Project tracking**: use Data Management to record models, dataset paths, and notes across multiple iterations.
+
+## Installation
+
+We recommend installing NepTrainKit in a dedicated Python environment. Python 3.10 through 3.13 is supported.
+
+```bash
+conda create -n nepkit python=3.10
+conda activate nepkit
+pip install NepTrainKit
+```
+
+After installation, launch the application with either command:
+
+```bash
+nepkit
+# or
+NepTrainKit
+```
+
+### NEP compute backend
+
+NepTrainKit does not compile the NEP compute backend into the application. `pip` installs the separate `nep-adapters` dependency:
+
+| Platform | Installed backend |
+| --- | --- |
+| macOS / Windows | CPU |
+| Linux x86_64 | CPU and CUDA in one wheel |
+
+The Linux CUDA path requires a compatible NVIDIA driver, but installing the wheel does not require a local CUDA toolkit or NVCC. Source builds and supported CUDA architectures are documented in the [NEPAdapters repository](https://github.com/MagTheoryLab/NEPAdapters).
+
+After launching NepTrainKit, select `Auto`, `CPU`, or `CUDA` under `Settings → NEP Backend`. `Auto` uses CUDA when the installed wheel, driver, and model support it; otherwise NepTrainKit explains why it is continuing on CPU. Explicit `CUDA` requests fail instead of silently changing backend.
+
+`Settings → NEP Settings → NEP runtime updates` can install a compatible `nep-adapters` update without replacing NepTrainKit. NepTrainKit also checks this runtime in the background whenever the app opens; no-update and network-failure cases stay silent, while an available update opens an installation prompt. Pip installations store the managed wheel under the user configuration directory; the Windows standalone build stores it under `runtime/nep-adapters/versions` beside `NepTrainKit.exe`. A wheel is activated only after SHA256 verification and a fresh-process health check, and takes effect after restart.
+
+Confirm the installed runtime with:
+
+```bash
+python -c "import nep_adapters as n; print(n.backend_status('cpu')); print(n.backend_status('cuda'))"
+```
+
+### Windows package
+
+If you prefer not to compile NepTrainKit locally, download `NepTrainKit.windows-x86_64.zip` from [GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases). This package requires 64-bit Windows on x86_64 hardware.
+
+## Documentation and support
+
+- User documentation: [neptrainkit.readthedocs.io](https://neptrainkit.readthedocs.io/en/latest/)
+- Release notes: [GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases)
+- Bug reports and feature requests: [GitHub Issues](https://github.com/aboys-cb/NepTrainKit/issues)
+- Community: [QQ group invitation](https://qm.qq.com/q/wPDQYHMhyg)
+
+If this is your first time using NepTrainKit, begin with **Quickstart** and **Cleaning candidate structures before DFT** in the user documentation. If you already know which class of configurations you need, go directly to the Make Dataset card reference.
+
+## Citation
+
+If NepTrainKit contributes to your research, please cite:
+
+```bibtex
+@article{CHEN2025109859,
+title = {NepTrain and NepTrainKit: Automated active learning and visualization toolkit for neuroevolution potentials},
+journal = {Computer Physics Communications},
+volume = {317},
+pages = {109859},
+year = {2025},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2025.109859},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465525003613},
+author = {Chengbing Chen and Yutong Li and Rui Zhao and Zhoulin Liu and Zheyong Fan and Gang Tang and Zhiyong Wang},
+}
+```
+
+## License and third-party code
+
+NepTrainKit is licensed under the GNU General Public License v3.0 or later. See [LICENSE](./LICENSE) for details.
+
+NEP computation is provided by the separate [nep-adapters](https://github.com/MagTheoryLab/NEPAdapters) dependency. NepTrainKit no longer vendors the NEP_CPU or GPUMD backend source trees.
+
+See [THIRD_PARTY_NOTICES.md](./THIRD_PARTY_NOTICES.md) for the remaining attribution in this repository. The `nep-adapters` distribution carries its own backend source notices and licenses.

neptrainkit-3.0.0/README.md

@@ -0,0 +1,101 @@
+<div align="center">
+<a href="https://github.com/aboys-cb/NepTrainKit">
+  <img src="https://raw.githubusercontent.com/aboys-cb/NepTrainKit/master/src/NepTrainKit/src/images/logo.png" width="25%" alt="NepTrainKit logo">
+</a><br>
+<a href="https://pypi.org/project/NepTrainKit"><img src="https://img.shields.io/pypi/dm/NepTrainKit?logo=pypi&logoColor=white&color=blue&label=PyPI" alt="PyPI downloads"></a>
+<a href="https://python.org/downloads"><img src="https://img.shields.io/badge/Python-3.10--3.13-blue.svg?logo=python&logoColor=white" alt="Python version"></a>
+<a href="https://codecov.io/github/aboys-cb/NepTrainKit"><img src="https://codecov.io/github/aboys-cb/NepTrainKit/graph/badge.svg?token=HQ5FMLD91F" alt="Codecov"></a>
+<a href="https://github.com/aboys-cb/NepTrainKit/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-GPL--3.0--or--later-blue" alt="License"></a>
+<br><br>
+<strong>English</strong> | <a href="https://github.com/aboys-cb/NepTrainKit/blob/master/README.zh-CN.md">简体中文</a>
+</div>
+
+# NepTrainKit
+
+NepTrainKit is a desktop application for preparing, auditing, and visualizing training datasets for neuroevolution potentials (NEPs). It complements, rather than replaces, long-running GPUMD training or DFT calculations. Its focus is the repetitive work around those calculations: generating candidate structures, cleaning problematic samples, selecting representative configurations, and passing a well-prepared dataset back into the DFT and GPUMD workflow.
+
+## What you can do
+
+- **Make Dataset**: generate strained, perturbed, defective, surface, doped, magnetic, and solvated candidate structures with composable cards.
+- **NEP Dataset Display**: inspect structures, errors, and distributions; remove problematic samples; and export a clean subset.
+- **Representative selection**: reduce a candidate pool to a smaller, more representative set with methods such as farthest point sampling (FPS).
+- **Training-result inspection**: load NEP- and DeepMD-related outputs, locate high-error structures, and identify data gaps for the next iteration.
+- **Project tracking**: use Data Management to record models, dataset paths, and notes across multiple iterations.
+
+## Installation
+
+We recommend installing NepTrainKit in a dedicated Python environment. Python 3.10 through 3.13 is supported.
+
+```bash
+conda create -n nepkit python=3.10
+conda activate nepkit
+pip install NepTrainKit
+```
+
+After installation, launch the application with either command:
+
+```bash
+nepkit
+# or
+NepTrainKit
+```
+
+### NEP compute backend
+
+NepTrainKit does not compile the NEP compute backend into the application. `pip` installs the separate `nep-adapters` dependency:
+
+| Platform | Installed backend |
+| --- | --- |
+| macOS / Windows | CPU |
+| Linux x86_64 | CPU and CUDA in one wheel |
+
+The Linux CUDA path requires a compatible NVIDIA driver, but installing the wheel does not require a local CUDA toolkit or NVCC. Source builds and supported CUDA architectures are documented in the [NEPAdapters repository](https://github.com/MagTheoryLab/NEPAdapters).
+
+After launching NepTrainKit, select `Auto`, `CPU`, or `CUDA` under `Settings → NEP Backend`. `Auto` uses CUDA when the installed wheel, driver, and model support it; otherwise NepTrainKit explains why it is continuing on CPU. Explicit `CUDA` requests fail instead of silently changing backend.
+
+`Settings → NEP Settings → NEP runtime updates` can install a compatible `nep-adapters` update without replacing NepTrainKit. NepTrainKit also checks this runtime in the background whenever the app opens; no-update and network-failure cases stay silent, while an available update opens an installation prompt. Pip installations store the managed wheel under the user configuration directory; the Windows standalone build stores it under `runtime/nep-adapters/versions` beside `NepTrainKit.exe`. A wheel is activated only after SHA256 verification and a fresh-process health check, and takes effect after restart.
+
+Confirm the installed runtime with:
+
+```bash
+python -c "import nep_adapters as n; print(n.backend_status('cpu')); print(n.backend_status('cuda'))"
+```
+
+### Windows package
+
+If you prefer not to compile NepTrainKit locally, download `NepTrainKit.windows-x86_64.zip` from [GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases). This package requires 64-bit Windows on x86_64 hardware.
+
+## Documentation and support
+
+- User documentation: [neptrainkit.readthedocs.io](https://neptrainkit.readthedocs.io/en/latest/)
+- Release notes: [GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases)
+- Bug reports and feature requests: [GitHub Issues](https://github.com/aboys-cb/NepTrainKit/issues)
+- Community: [QQ group invitation](https://qm.qq.com/q/wPDQYHMhyg)
+
+If this is your first time using NepTrainKit, begin with **Quickstart** and **Cleaning candidate structures before DFT** in the user documentation. If you already know which class of configurations you need, go directly to the Make Dataset card reference.
+
+## Citation
+
+If NepTrainKit contributes to your research, please cite:
+
+```bibtex
+@article{CHEN2025109859,
+title = {NepTrain and NepTrainKit: Automated active learning and visualization toolkit for neuroevolution potentials},
+journal = {Computer Physics Communications},
+volume = {317},
+pages = {109859},
+year = {2025},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2025.109859},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465525003613},
+author = {Chengbing Chen and Yutong Li and Rui Zhao and Zhoulin Liu and Zheyong Fan and Gang Tang and Zhiyong Wang},
+}
+```
+
+## License and third-party code
+
+NepTrainKit is licensed under the GNU General Public License v3.0 or later. See [LICENSE](./LICENSE) for details.
+
+NEP computation is provided by the separate [nep-adapters](https://github.com/MagTheoryLab/NEPAdapters) dependency. NepTrainKit no longer vendors the NEP_CPU or GPUMD backend source trees.
+
+See [THIRD_PARTY_NOTICES.md](./THIRD_PARTY_NOTICES.md) for the remaining attribution in this repository. The `nep-adapters` distribution carries its own backend source notices and licenses.

neptrainkit-3.0.0/README.zh-CN.md

@@ -0,0 +1,101 @@
+<div align="center">
+<a href="https://github.com/aboys-cb/NepTrainKit">
+  <img src="https://raw.githubusercontent.com/aboys-cb/NepTrainKit/master/src/NepTrainKit/src/images/logo.png" width="25%" alt="NepTrainKit 标志">
+</a><br>
+<a href="https://pypi.org/project/NepTrainKit"><img src="https://img.shields.io/pypi/dm/NepTrainKit?logo=pypi&logoColor=white&color=blue&label=PyPI" alt="PyPI 下载量"></a>
+<a href="https://python.org/downloads"><img src="https://img.shields.io/badge/Python-3.10--3.13-blue.svg?logo=python&logoColor=white" alt="Python 版本"></a>
+<a href="https://codecov.io/github/aboys-cb/NepTrainKit"><img src="https://codecov.io/github/aboys-cb/NepTrainKit/graph/badge.svg?token=HQ5FMLD91F" alt="Codecov"></a>
+<a href="https://github.com/aboys-cb/NepTrainKit/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-GPL--3.0--or--later-blue" alt="许可证"></a>
+<br><br>
+<a href="https://github.com/aboys-cb/NepTrainKit/blob/master/README.md">English</a> | <strong>简体中文</strong>
+</div>
+
+# NepTrainKit
+
+NepTrainKit 是面向神经演化势（NEP）训练集准备、评估和可视化的桌面工具。它不替代 GPUMD 的长时间训练，也不替代 DFT 计算；它负责训练前后最容易反复手工处理的部分：生成候选结构、清理异常样本、筛选代表结构，并把准备好的数据接回 DFT 和 GPUMD 工作流。
+
+## 主要功能
+
+- **Make Dataset**：通过可组合的卡片生成应变、扰动、缺陷、表面、掺杂、磁性和溶剂化候选结构。
+- **NEP Dataset Display**：查看结构、误差和分布，删除异常样本，并导出干净的数据子集。
+- **代表性筛选**：使用最远点采样（FPS）等方法，从候选池中选出更少、更有代表性的结构。
+- **训练结果回看**：加载 NEP 和 DeepMD 相关输出，定位高误差结构，识别下一轮需要补充的数据。
+- **项目记录**：使用 Data Management 记录多轮迭代中的模型、数据路径和备注。
+
+## 安装
+
+建议在独立的 Python 环境中安装 NepTrainKit。当前版本支持 Python 3.10 到 3.13。
+
+```bash
+conda create -n nepkit python=3.10
+conda activate nepkit
+pip install NepTrainKit
+```
+
+安装完成后，可以使用任一命令启动：
+
+```bash
+nepkit
+# 或
+NepTrainKit
+```
+
+### NEP 计算后端
+
+NepTrainKit 不再把 NEP 计算后端编译进应用程序。执行 `pip install NepTrainKit` 时，会安装独立的 `nep-adapters` 依赖：
+
+| 平台 | 安装的后端 |
+| --- | --- |
+| macOS / Windows | CPU |
+| Linux x86_64 | 同一个 wheel 包含 CPU 和 CUDA |
+
+Linux CUDA 路径需要兼容的 NVIDIA 驱动，但安装 wheel 不要求本机安装 CUDA Toolkit 或 NVCC。源码构建和受支持的 CUDA 架构见 [NEPAdapters 仓库](https://github.com/MagTheoryLab/NEPAdapters)。
+
+启动后，可以在 `Settings → NEP Backend` 中选择 `Auto`、`CPU` 或 `CUDA`。`Auto` 会在 wheel、驱动和模型都支持时使用 CUDA；否则 NepTrainKit 会说明原因并继续使用 CPU。明确选择 `CUDA` 时如果不可用会直接报错，不会静默切换后端。
+
+`设置 → NEP 设置 → NEP 运行时更新` 可以单独检查并安装兼容的 `nep-adapters` 更新，无需更新 NepTrainKit。每次打开软件后还会在后台检查运行时：没有更新或网络检查失败时保持静默，发现新版本时弹出安装提示。pip 安装版把更新后的 wheel 解压到用户配置目录；Windows 独立版放在 `NepTrainKit.exe` 旁的 `runtime/nep-adapters/versions`。新版本通过 SHA256 和独立进程健康检查后才会激活，并在重启程序后生效。
+
+可以用下面的命令确认当前运行时：
+
+```bash
+python -c "import nep_adapters as n; print(n.backend_status('cpu')); print(n.backend_status('cuda'))"
+```
+
+### Windows 可执行包
+
+如果不想在本地编译，可以从 [GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases) 下载 `NepTrainKit.windows-x86_64.zip`。该包要求 x86_64 架构的 64 位 Windows。
+
+## 文档与支持
+
+- 用户文档：[neptrainkit.readthedocs.io](https://neptrainkit.readthedocs.io/zh-cn/latest/)
+- 更新说明：[GitHub Releases](https://github.com/aboys-cb/NepTrainKit/releases)
+- 问题反馈与功能建议：[GitHub Issues](https://github.com/aboys-cb/NepTrainKit/issues)
+- 社区交流：[QQ 群链接](https://qm.qq.com/q/wPDQYHMhyg)
+
+第一次使用时，建议先阅读用户文档中的“快速开始”和“候选结构清洗后再进入 DFT”。如果已经知道需要补充哪类结构，可以直接查阅 Make Dataset 卡片手册。
+
+## 引用
+
+如果 NepTrainKit 对你的研究有所帮助，请引用：
+
+```bibtex
+@article{CHEN2025109859,
+title = {NepTrain and NepTrainKit: Automated active learning and visualization toolkit for neuroevolution potentials},
+journal = {Computer Physics Communications},
+volume = {317},
+pages = {109859},
+year = {2025},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2025.109859},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465525003613},
+author = {Chengbing Chen and Yutong Li and Rui Zhao and Zhoulin Liu and Zheyong Fan and Gang Tang and Zhiyong Wang},
+}
+```
+
+## 许可证和第三方代码
+
+本仓库使用 GNU General Public License v3.0 or later，详见 [LICENSE](./LICENSE)。
+
+NEP 计算由独立依赖 [nep-adapters](https://github.com/MagTheoryLab/NEPAdapters) 提供。NepTrainKit 已不再内置 NEP_CPU 或 GPUMD 后端源码。
+
+本仓库仍需保留的来源说明见 [THIRD_PARTY_NOTICES.md](./THIRD_PARTY_NOTICES.md)。`nep-adapters` 发行包会携带其后端源码对应的许可证和来源说明。

neptrainkit-3.0.0/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,34 @@
+Third‑Party Notices
+
+This document lists third-party code or designs retained directly in the
+NepTrainKit repository. NEP compute backends are distributed separately by
+`nep-adapters` and are not vendored here.
+
+nep-adapters
+
+- Repository: https://github.com/MagTheoryLab/NEPAdapters
+- Role: Runtime dependency supplying CPU and CUDA NEP compute backends.
+- Packaging: The dependency carries the applicable NEP_CPU and GPUMD source
+  notices and licenses. Those backend source trees are not part of the
+  NepTrainKit distribution.
+
+GPUMD Energy Reference Aligner
+
+- Repository: https://github.com/brucefan1983/GPUMD
+- License: GNU General Public License v3.0 or later (GPL‑3.0‑or‑later)
+- The energy reference alignment workflow in
+  `src/NepTrainKit/core/energy_shift.py` is conceptually adapted from GPUMD's
+  `tools/Analysis_and_Processing/energy-reference-aligner`.
+
+License Summary
+
+- The root of this repository includes `LICENSE` (GPL‑3.0). Consistent with the
+  upstream projects, this project is distributed under GPL‑3.0‑or‑later terms.
+- Per the GPL, all redistributions and modifications must remain under the GPL and
+  must retain copyright and license notices.
+
+Disclaimer
+
+- The above summaries are provided for convenience and do not replace the full
+  text of the licenses. See `LICENSE` and the upstream repositories for the
+  complete license terms.

{neptrainkit-2.8.4.dev0 → neptrainkit-3.0.0}/pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
 "wheel",
 "numpy",
-"setuptools>=68.0.0",
+"setuptools>=77.0.0",
 "pybind11>=2.12.0",
 "setuptools-scm>=8.2.0"
 ]
@@ -14,12 +14,11 @@ name = "NepTrainKit"
 authors = [{ name = "Chen Cheng bing", email = "1747193328@qq.com" }]
 dynamic = ["version"]
 
-description = """
-NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.
-"""
+description = "Visualize, diagnose, and manipulate NEP training datasets."
 readme = "README.md"
-requires-python = ">=3.10"
-license = { "text"="GPL-3.0" }
+requires-python = ">=3.10,<3.14"
+license = "GPL-3.0-or-later"
+license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
@@ -28,7 +27,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Topic :: Scientific/Engineering :: Physics",
@@ -39,13 +38,14 @@ dependencies = [
 "PySide6-Fluent-Widgets>=1.7.0",
 "loguru>=0.7.2",
 "requests>=2.32.3",
+"packaging>=24.0",
 "pyqtgraph>=0.13.7",
 "PyOpenGL>=3.1.7",
 "numpy>=1.26.0",
 "vispy>=0.14.3",
 "ase",
+"nep-adapters>=1.0",
 "scipy>=1.15.0",
-"pybind11",
 "SQLAlchemy>=2.0.0"
 ]
 [project.optional-dependencies]
@@ -53,7 +53,10 @@ test = [
     "pytest>=7.0",
     "pytest-qt>=4.2.0",
     "pytest-cov>=4.0.0",
-    "codecov>=2.0.0"
+    "codecov>=2.0.0",
+    "ruff>=0.12.0",
+    "scikit-learn>=1.5.0",
+    "tomli>=2.0; python_version < '3.11'"
 ]
 
 [project.urls]
@@ -76,7 +79,9 @@ where = ["src"]
 include = ["NepTrainKit", "NepTrainKit.*" ]
 
 [tool.setuptools.package-data]
+"NepTrainKit" = ["translations/*.qm", "translations/*.ts"]
 "NepTrainKit.Config" = ["config.sqlite","ptable.json","nep.json","nep89.txt" ]
+"NepTrainKit.core.dataset" = ["catalogs/*.json"]
 
 [tool.setuptools_scm]
 

{neptrainkit-2.8.4.dev0 → neptrainkit-3.0.0}/requirements.txt

@@ -3,9 +3,11 @@ numpy==1.26.0
 PySide6-Fluent-Widgets==1.8.7
 loguru==0.7.2
 requests==2.32.3
+packaging>=24.0
 pyqtgraph==0.13.7
 PyOpenGL==3.1.7
 vispy==0.15.2
 ase
+nep-adapters>=1.0
 scipy==1.15.0
 SQLAlchemy==2.0.43

neptrainkit-3.0.0/setup.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+"""Build NepTrainKit's application-native helpers.
+
+NEP compute backends are supplied exclusively by the ``nep-adapters``
+dependency and are intentionally not built in this package.
+"""
+
+from __future__ import annotations
+
+import os
+import sys
+
+import pybind11
+from setuptools import Extension, setup
+
+
+extra_compile_args: list[str] = []
+extra_link_args: list[str] = []
+default_omp_mode = "0" if sys.platform == "darwin" else "auto"
+omp_mode = os.environ.get("NEPKIT_OPENMP", default_omp_mode).strip().lower()
+use_openmp = omp_mode not in {"0", "false", "off", "no"}
+
+if sys.platform == "win32":
+    if use_openmp:
+        extra_compile_args.append("/openmp")
+        extra_link_args.append("/openmp")
+    extra_compile_args.extend(["/O2", "/std:c++11"])
+    extra_link_args.extend(["/O2", "/std:c++11"])
+elif sys.platform == "darwin":
+    extra_compile_args.extend(["-O3", "-std=c++11"])
+    extra_link_args.extend(["-O3", "-std=c++11"])
+    omp_include = os.getenv("OMP_INCLUDE_PATH", "/opt/homebrew/opt/libomp/include")
+    omp_lib = os.getenv("OMP_LIB_PATH", "/opt/homebrew/opt/libomp/lib")
+    if use_openmp and os.path.isdir(omp_include) and os.path.isdir(omp_lib):
+        extra_compile_args.extend(["-Xpreprocessor", "-fopenmp", f"-I{omp_include}"])
+        extra_link_args.extend(["-lomp", f"-L{omp_lib}"])
+else:
+    if use_openmp:
+        extra_compile_args.append("-fopenmp")
+        extra_link_args.append("-fopenmp")
+    extra_compile_args.extend(["-O3", "-std=c++11"])
+    extra_link_args.extend(["-O3", "-std=c++11"])
+
+
+def native_extension(
+    module_name: str,
+    source: str,
+    *,
+    depends: tuple[str, ...] = (),
+) -> Extension:
+    """Create one private application-native extension with shared headers."""
+    return Extension(
+        f"NepTrainKit._native.{module_name}",
+        [source],
+        include_dirs=[pybind11.get_include(), "src/native/include"],
+        extra_compile_args=list(extra_compile_args),
+        extra_link_args=list(extra_link_args),
+        depends=list(depends),
+        language="c++",
+    )
+
+
+neighbor_header = "src/native/include/neptrainkit/native/periodic_neighbors.hpp"
+fast_float_header = "src/native/io/fast_float.h"
+
+setup(
+    ext_modules=[
+        native_extension("_io", "src/native/io/module.cpp", depends=(fast_float_header,)),
+        native_extension("_audit", "src/native/audit/module.cpp", depends=(neighbor_header,)),
+        native_extension("_phase", "src/native/phase/module.cpp", depends=(neighbor_header,)),
+        native_extension("_magnetism", "src/native/magnetism/module.cpp", depends=(neighbor_header,)),
+    ],
+    zip_safe=False,
+)