ion-CSP 2.1.5__tar.gz → 2.1.8__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (108) hide show
  1. {ion_csp-2.1.5 → ion_csp-2.1.8}/.github/workflows/conda-env-build.yml +3 -1
  2. ion_csp-2.1.8/CHANGELOG.md +93 -0
  3. {ion_csp-2.1.5 → ion_csp-2.1.8}/CODE_OF_CONDUCT.md +8 -0
  4. {ion_csp-2.1.5 → ion_csp-2.1.8}/LICENSE +1 -1
  5. {ion_csp-2.1.5 → ion_csp-2.1.8}/PKG-INFO +44 -16
  6. {ion_csp-2.1.5 → ion_csp-2.1.8}/README.md +43 -15
  7. {ion_csp-2.1.5 → ion_csp-2.1.8}/environment.yml +1 -0
  8. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_1/config.yaml +2 -2
  9. {ion_csp-2.1.5/src/run → ion_csp-2.1.8/scripts}/update_changelog.py +4 -4
  10. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/__init__.py +2 -2
  11. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/convert_SMILES.py +32 -10
  12. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/empirical_estimate.py +136 -18
  13. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/gen_opt.py +68 -22
  14. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/identify_molecules.py +15 -0
  15. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/log_and_time.py +55 -8
  16. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/mlp_opt.py +52 -6
  17. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/read_mlp_density.py +15 -1
  18. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/task_manager.py +1 -1
  19. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/upload_download.py +0 -1
  20. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/vasp_processing.py +48 -20
  21. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/PKG-INFO +44 -16
  22. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/SOURCES.txt +10 -11
  23. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/top_level.txt +0 -1
  24. ion_csp-2.1.5/.github/workflows/update_changelog.yml +0 -36
  25. ion_csp-2.1.5/CHANGELOG.md +0 -177
  26. {ion_csp-2.1.5 → ion_csp-2.1.8}/.dockerignore +0 -0
  27. {ion_csp-2.1.5 → ion_csp-2.1.8}/.github/workflows/pypi-publish.yml +0 -0
  28. {ion_csp-2.1.5 → ion_csp-2.1.8}/.gitignore +0 -0
  29. {ion_csp-2.1.5 → ion_csp-2.1.8}/.vscode/settings.json +0 -0
  30. {ion_csp-2.1.5 → ion_csp-2.1.8}/CONTRIBUTING.md +0 -0
  31. {ion_csp-2.1.5 → ion_csp-2.1.8}/Dockerfile +0 -0
  32. {ion_csp-2.1.5 → ion_csp-2.1.8}/MANIFEST.in +0 -0
  33. {ion_csp-2.1.5 → ion_csp-2.1.8}/SECURITY.md +0 -0
  34. {ion_csp-2.1.5 → ion_csp-2.1.8}/config/complete_config.yaml +0 -0
  35. {ion_csp-2.1.5 → ion_csp-2.1.8}/config/simple_config.yaml +0 -0
  36. {ion_csp-2.1.5 → ion_csp-2.1.8}/config/usage.md +0 -0
  37. {ion_csp-2.1.5 → ion_csp-2.1.8}/docs/example_usage_CSP.py +0 -0
  38. {ion_csp-2.1.5 → ion_csp-2.1.8}/docs/example_usage_EE.py +0 -0
  39. {ion_csp-2.1.5 → ion_csp-2.1.8}/docs/index.md +0 -0
  40. {ion_csp-2.1.5 → ion_csp-2.1.8}/docs/usage.md +0 -0
  41. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_1/ions.csv +0 -0
  42. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_2/combo_1/ACEGUL.gjf +0 -0
  43. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_2/combo_1/AGIDOM.gjf +0 -0
  44. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_2/combo_1/config.yaml +0 -0
  45. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/example_usage.py +0 -0
  46. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/server/example_local_machine.yaml +0 -0
  47. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/server/example_local_resources.yaml +0 -0
  48. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/server/example_remote_machine.yaml +0 -0
  49. {ion_csp-2.1.5 → ion_csp-2.1.8}/examples/server/example_remote_resources.yaml +0 -0
  50. {ion_csp-2.1.5 → ion_csp-2.1.8}/makefile +0 -0
  51. {ion_csp-2.1.5 → ion_csp-2.1.8}/model/model.pt +0 -0
  52. {ion_csp-2.1.5 → ion_csp-2.1.8}/model/options/README.md +0 -0
  53. {ion_csp-2.1.5 → ion_csp-2.1.8}/model/options/model.ckpt-4000000.pt +0 -0
  54. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/INCAR_0 +0 -0
  55. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/INCAR_1 +0 -0
  56. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/INCAR_2 +0 -0
  57. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/INCAR_3 +0 -0
  58. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/POTCAR_C +0 -0
  59. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/POTCAR_H +0 -0
  60. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/POTCAR_N +0 -0
  61. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/POTCAR_O +0 -0
  62. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/g16_sub.sh +0 -0
  63. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/sub_final.sh +0 -0
  64. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/sub_ori.sh +0 -0
  65. {ion_csp-2.1.5 → ion_csp-2.1.8}/param/sub_supple.sh +0 -0
  66. {ion_csp-2.1.5 → ion_csp-2.1.8}/pyproject.toml +0 -0
  67. {ion_csp-2.1.5 → ion_csp-2.1.8}/requirements.txt +0 -0
  68. {ion_csp-2.1.5 → ion_csp-2.1.8}/scripts/CLI.py +0 -0
  69. {ion_csp-2.1.5 → ion_csp-2.1.8}/scripts/CLI.sh +0 -0
  70. {ion_csp-2.1.5 → ion_csp-2.1.8}/scripts/main_CSP.sh +0 -0
  71. {ion_csp-2.1.5 → ion_csp-2.1.8}/scripts/main_EE.sh +0 -0
  72. {ion_csp-2.1.5 → ion_csp-2.1.8}/setup.cfg +0 -0
  73. {ion_csp-2.1.5 → ion_csp-2.1.8}/setup.py +0 -0
  74. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/__init__.py +0 -0
  75. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/__main__.py +0 -0
  76. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/model/model.pt +0 -0
  77. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/model/options/README.md +0 -0
  78. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/model/options/model.ckpt-4000000.pt +0 -0
  79. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/INCAR_0 +0 -0
  80. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/INCAR_1 +0 -0
  81. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/INCAR_2 +0 -0
  82. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/INCAR_3 +0 -0
  83. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/POTCAR_C +0 -0
  84. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/POTCAR_H +0 -0
  85. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/POTCAR_N +0 -0
  86. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/POTCAR_O +0 -0
  87. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/g16_sub.sh +0 -0
  88. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/sub_final.sh +0 -0
  89. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/sub_ori.sh +0 -0
  90. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/param/sub_supple.sh +0 -0
  91. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/__init__.py +0 -0
  92. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/main_CSP.py +0 -0
  93. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/main_EE.py +0 -0
  94. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_convert_SMILES.py +0 -0
  95. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_empirical_estimate.py +0 -0
  96. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_gen_opt.py +0 -0
  97. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_read_mlp_density.py +0 -0
  98. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_upload_download.py +0 -0
  99. {ion_csp-2.1.5/src → ion_csp-2.1.8/src/ion_CSP}/run/run_vasp_processing.py +0 -0
  100. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP/steps_opt_monitor.sh +0 -0
  101. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/dependency_links.txt +0 -0
  102. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/entry_points.txt +0 -0
  103. {ion_csp-2.1.5 → ion_csp-2.1.8}/src/ion_CSP.egg-info/requires.txt +0 -0
  104. {ion_csp-2.1.5 → ion_csp-2.1.8}/tests/__init__.py +0 -0
  105. {ion_csp-2.1.5 → ion_csp-2.1.8}/tests/test1_task_manager1.py +0 -0
  106. {ion_csp-2.1.5 → ion_csp-2.1.8}/tests/test_log_and_time.py +0 -0
  107. {ion_csp-2.1.5 → ion_csp-2.1.8}/tests/test_task_manager.py +0 -0
  108. {ion_csp-2.1.5 → ion_csp-2.1.8}/uv.lock +0 -0
@@ -1,6 +1,8 @@
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  name: Conda Environment Build
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- on: [push, pull_request]
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+ on:
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+ release:
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+ types: [published]
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  jobs:
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+ ## (2025-06-19)
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+ * Introduce importlib.resourses in multiple modules to improve file path management; ([2ea0ac4](https://github.com/Bagabaga007/ion_CSP/commit/2ea0ac4))
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+ * Update dependencies, improve documentation, and enhance error handling ([b68c9ac](https://github.com/Bagabaga007/ion_CSP/commit/b68c9ac))
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+ * Update GitHub Actions workflow to trigger builds upon release, modify the steps for updating CHANGEL ([bf651e6](https://github.com/Bagabaga007/ion_CSP/commit/bf651e6))
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+ * Update update_changelog.yml ([5c3c950](https://github.com/Bagabaga007/ion_CSP/commit/5c3c950))
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+ * Update update_changelog.yml ([346d034](https://github.com/Bagabaga007/ion_CSP/commit/346d034))
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+ * Use git hooks to automatcally update CHANGELOG.md ([162ddc4](https://github.com/Bagabaga007/ion_CSP/commit/162ddc4))
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+
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+ ## <small>2.1.5 (2025-06-16)</small>
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+ * Add dependency descriptions for the Scipy version; ([934f0fa](https://github.com/Bagabaga007/ion_CSP/commit/934f0fa))
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+ * Added the function of automatically updating CHANGELOG; ([3edd170](https://github.com/Bagabaga007/ion_CSP/commit/3edd170))
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+ * Update version to 2.1.5. ([31087de](https://github.com/Bagabaga007/ion_CSP/commit/31087de))
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+ ## <small>2.1.4 (2025-06-13)</small>
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+ * Optimize the packaging behavior when building pypi distribution packages to make them easier to use ([ad5c1d7](https://github.com/Bagabaga007/ion_CSP/commit/ad5c1d7))
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+ ## <small>2.1.3 (2025-06-11)</small>
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+ * Updata version to 2.1.3 ([d503641](https://github.com/Bagabaga007/ion_CSP/commit/d503641))
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+ ## <small>2.1.2 (2025-06-09)</small>
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+
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+ * Implement centralized management of version numbers and automatic synchronization of multiple config ([1befcf7](https://github.com/Bagabaga007/ion_CSP/commit/1befcf7))
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+ ## <small>2.1.1 (2025-06-09)</small>
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+ * 1. Improve the dockerfile to ensure smooth operation inside the container; ([f034fbe](https://github.com/Bagabaga007/ion_CSP/commit/f034fbe))
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+ * Add conda environment configuration ([0675303](https://github.com/Bagabaga007/ion_CSP/commit/0675303))
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+ * Add template configuration files and corresponding usage document in the config folder under the roo ([80a3e3d](https://github.com/Bagabaga007/ion_CSP/commit/80a3e3d))
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+ * Add unit testing module for task_manager. ([070c86f](https://github.com/Bagabaga007/ion_CSP/commit/070c86f))
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+ * Added Python version of interactive main function entry and corresponding app files. ([98f7382](https://github.com/Bagabaga007/ion_CSP/commit/98f7382))
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+ * Added usage and configuration examples in the project root directory. ([bb0d853](https://github.com/Bagabaga007/ion_CSP/commit/bb0d853))
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+ * Adjust the depencies installation order ([3866521](https://github.com/Bagabaga007/ion_CSP/commit/3866521))
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+ * Adjust the installation method of the code, use git clone and pip install - e. commands to install t ([7f383b0](https://github.com/Bagabaga007/ion_CSP/commit/7f383b0))
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+ * After machine learning potential optimization and structure filtering, CSV files were added to summa ([6f29d21](https://github.com/Bagabaga007/ion_CSP/commit/6f29d21))
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+ * After successfully completing the task using the dpdispatcher module, delete the corresponding folde ([d079b70](https://github.com/Bagabaga007/ion_CSP/commit/d079b70))
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+ * Change some certain packages installation way to pip installation. ([ff92e05](https://github.com/Bagabaga007/ion_CSP/commit/ff92e05))
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+ * Change the version number to 2.0.0. ([9ddb0c4](https://github.com/Bagabaga007/ion_CSP/commit/9ddb0c4))
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+ * committed ([2bef3e2](https://github.com/Bagabaga007/ion_CSP/commit/2bef3e2))
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+ * Create python-package-conda.yml ([7b1752b](https://github.com/Bagabaga007/ion_CSP/commit/7b1752b))
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+ * Create python-publish.yml ([1cbba7e](https://github.com/Bagabaga007/ion_CSP/commit/1cbba7e))
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+ * Create SECURITY.md ([30c455b](https://github.com/Bagabaga007/ion_CSP/commit/30c455b))
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+ * Delete 1_preparation directory ([05931e7](https://github.com/Bagabaga007/ion_CSP/commit/05931e7))
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+ * Delete 2_generation directory ([380eedb](https://github.com/Bagabaga007/ion_CSP/commit/380eedb))
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+ * Delete 3_postprocessing directory ([c4400f0](https://github.com/Bagabaga007/ion_CSP/commit/c4400f0))
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+ * Fix the bug in environment.yml file ([049d915](https://github.com/Bagabaga007/ion_CSP/commit/049d915))
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+ * Fully automated EE workflow ([c367bc3](https://github.com/Bagabaga007/ion_CSP/commit/c367bc3))
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+ * Fully automated ion CSP workflow. ([f8e6c73](https://github.com/Bagabaga007/ion_CSP/commit/f8e6c73))
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+ * Ignore the big-size dist files ([cb7dcb0](https://github.com/Bagabaga007/ion_CSP/commit/cb7dcb0))
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+ * Modification of conda package build yml file. ([1d0d5fc](https://github.com/Bagabaga007/ion_CSP/commit/1d0d5fc))
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+ * Modification of conda package build yml file. ([83f25cb](https://github.com/Bagabaga007/ion_CSP/commit/83f25cb))
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+ * Modified the yml file for github actions ([f2a8abc](https://github.com/Bagabaga007/ion_CSP/commit/f2a8abc))
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+ * Modified yml file for github actions ([01f2095](https://github.com/Bagabaga007/ion_CSP/commit/01f2095))
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+ * Modified yml file for Github actions. ([90bfd07](https://github.com/Bagabaga007/ion_CSP/commit/90bfd07))
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+ * ok ([a22b9e8](https://github.com/Bagabaga007/ion_CSP/commit/a22b9e8))
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+ * ok ([7f6d3b1](https://github.com/Bagabaga007/ion_CSP/commit/7f6d3b1))
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+ * ok ([c13cd0c](https://github.com/Bagabaga007/ion_CSP/commit/c13cd0c))
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+ * ok ([1a2b2d5](https://github.com/Bagabaga007/ion_CSP/commit/1a2b2d5))
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+ * ok ([2d8aafd](https://github.com/Bagabaga007/ion_CSP/commit/2d8aafd))
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+ * ok ([7fbfd27](https://github.com/Bagabaga007/ion_CSP/commit/7fbfd27))
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+ * ok ([a0b84fc](https://github.com/Bagabaga007/ion_CSP/commit/a0b84fc))
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+ * ok ([9878e9d](https://github.com/Bagabaga007/ion_CSP/commit/9878e9d))
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+ * ok ([b07065c](https://github.com/Bagabaga007/ion_CSP/commit/b07065c))
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+ * ok ([68b6b0a](https://github.com/Bagabaga007/ion_CSP/commit/68b6b0a))
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+ * ok ([f6a30b0](https://github.com/Bagabaga007/ion_CSP/commit/f6a30b0))
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+ * ok ([0e434f6](https://github.com/Bagabaga007/ion_CSP/commit/0e434f6))
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+ * OK ([fd404eb](https://github.com/Bagabaga007/ion_CSP/commit/fd404eb))
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+ * Refactoring the project structure, configuring packaging parameters, and modifying sub process call ([bde5189](https://github.com/Bagabaga007/ion_CSP/commit/bde5189))
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+ * Remove invalid channel and adapt the mixed installation method. ([24832ea](https://github.com/Bagabaga007/ion_CSP/commit/24832ea))
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+ * Remove the flake8 installation in conda package construction. ([5540449](https://github.com/Bagabaga007/ion_CSP/commit/5540449))
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+ * Remove torchvision package dependencies to allow pip to attempt to solve the dependency conflict. ([72ccfad](https://github.com/Bagabaga007/ion_CSP/commit/72ccfad))
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+ * Significantly optimized the logging system and task management of the interactive program entrance. ([15c4628](https://github.com/Bagabaga007/ion_CSP/commit/15c4628))
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+ * Significantly optimized the program logic of the interactive entrance and fixed a large number of po ([bfec475](https://github.com/Bagabaga007/ion_CSP/commit/bfec475))
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+ * Unified the interactive interface between shell and Python versions, and uploaded distribution files ([ebf54e3](https://github.com/Bagabaga007/ion_CSP/commit/ebf54e3))
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+ * Update information in README.md ([01af54c](https://github.com/Bagabaga007/ion_CSP/commit/01af54c))
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+ * Update README.md and modified the yml file for github action of conda package build ([1ff9020](https://github.com/Bagabaga007/ion_CSP/commit/1ff9020))
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+ * Update the corresponding information yml to resolve the conda environment configuration actions in G ([c2a01ee](https://github.com/Bagabaga007/ion_CSP/commit/c2a01ee))
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  # Code of Conduct
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  ## 1. Purpose
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  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.
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  ## 2. Scope
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  This Code of Conduct applies to all participants, including but not limited to: contributors, maintainers, users, and anyone involved with the project.
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  ## 3. Expected Behavior
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  We encourage all participants to:
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  - **Respect Others**: Honor each person’s viewpoints, experiences, and backgrounds.
@@ -15,6 +18,7 @@ We encourage all participants to:
15
18
  - **Accept Constructive Feedback**: Be open to feedback from others and engage in discussions with an open mind.
16
19
 
17
20
  ## 4. Unacceptable Behavior
21
+
18
22
  The following behaviors are considered unacceptable:
19
23
 
20
24
  - **Harassment**: This includes threats, malicious attacks, sexism, racism, hate speech, etc.
@@ -22,9 +26,11 @@ The following behaviors are considered unacceptable:
22
26
  - **Disruptive Behavior**: Intentionally disrupting others' work or the community environment.
23
27
 
24
28
  ## 5. Reporting Mechanism
29
+
25
30
  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.
26
31
 
27
32
  ## 6. Consequences
33
+
28
34
  For participants who violate the Code of Conduct, we may take the following actions:
29
35
 
30
36
  - Warning
@@ -32,7 +38,9 @@ For participants who violate the Code of Conduct, we may take the following acti
32
38
  - Permanent ban from participation
33
39
 
34
40
  ## 7. Applicability
41
+
35
42
  This Code of Conduct applies to all activities related to the project, including online and offline interactions.
36
43
 
37
44
  ## 8. License
45
+
38
46
  This Code of Conduct follows the [Contributor Covenant](https://opensource.org/osd) and welcomes suggestions and improvements from anyone.
@@ -1,4 +1,4 @@
1
- MIT License
1
+ # MIT License
2
2
 
3
3
  Copyright (c) [2025] [ion_CSP]
4
4
 
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ion_CSP
3
- Version: 2.1.5
3
+ Version: 2.1.8
4
4
  Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
5
5
  Home-page: https://github.com/bagabaga007/ion_CSP
6
6
  Author: Ze Yang
@@ -28,13 +28,16 @@ Dynamic: home-page
28
28
  Dynamic: license-file
29
29
  Dynamic: requires-python
30
30
 
31
- # Crystal Structure Design Software V2.1
31
+ # 基于分子/离子构型的晶体结构设计软件 V2.1
32
32
 
33
33
  ## 项目概述
34
+
34
35
  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。
35
36
 
36
37
  ## 功能特性
38
+
37
39
  ### 核心功能
40
+
38
41
  - **双模块工作流**
39
42
  - **EE模块**:基于经验评估的离子组合生成
40
43
  - **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
48
51
  - 软链接解析显示实际路径
49
52
 
50
53
  ### 技术特性
54
+
51
55
  - 跨平台支持(Linux/Docker)
52
56
  - 基于Python 3.11+的面向对象架构
53
57
  - 集成psutil进程管理
54
58
  - 结构化日志记录系统
55
59
 
56
60
  ## 安装指南
61
+
57
62
  ### 环境要求
63
+
58
64
  | 组件 | 最低版本 |
59
65
  |-------------|----------|
60
66
  | Python | 3.11 |
@@ -71,10 +77,13 @@ Dynamic: requires-python
71
77
  | rdkit | 2024.03.3|
72
78
 
73
79
  ### 安装步骤
80
+
74
81
  ```bash
75
82
  pip install ion-csp
76
83
  ```
84
+
77
85
 
86
+
78
87
  ```bash
79
88
  # 创建虚拟环境
80
89
  python -m venv venv
@@ -87,29 +96,39 @@ pip install -e .
87
96
  ```
88
97
 
89
98
  ## 快速入门
99
+
90
100
  ### 交互模式
101
+
91
102
  ```bash
92
103
  ion-csp
93
104
  ```
105
+
94
106
  启动交互式命令行界面,支持以下操作:
107
+
95
108
  - 模块选择
96
109
  - 日志查看
97
110
  - 进程管理
98
111
 
99
112
  ### 脚本调用
113
+
100
114
  #### EE模块示例
115
+
101
116
  ```bash
102
117
  ./scripts/main_EE.sh examples/example_1
103
118
  ```
119
+
104
120
  从SMILES表格生成离子组合
105
121
 
106
122
  #### CSP模块示例
123
+
107
124
  ```bash
108
125
  ./scripts/main_CSP.sh examples/example_2
109
126
  ```
127
+
110
128
  从离子组合生成并优化晶体结构
111
129
 
112
130
  ## 技术架构
131
+
113
132
  ```mermaid
114
133
  graph TD
115
134
  A[用户界面] --> B[任务管理器]
@@ -118,34 +137,32 @@ graph TD
118
137
  B --> E[日志系统]
119
138
  B --> F[任务调度]
120
139
  C --> G[经验评估引擎]
121
- D --> H[晶体预测引擎]
140
+ D --> H[离子晶体结构预测引擎]
122
141
  E --> I[结构化日志]
123
142
  F --> J[进程终止]
124
143
  ```
125
144
 
126
145
  ## 贡献指南
146
+
127
147
  1. Fork仓库并创建特性分支
128
148
  2. 编写单元测试覆盖新功能
129
149
  3. 提交Pull Request时注明关联Issue
130
150
  4. 遵循PEP8代码规范
131
151
 
132
152
  ## 许可证
133
- 本项目采用MIT许可证,详见LICENSE文件。
134
153
 
135
- ## 技术支持
136
- - **文档更新**:2025年6月
137
- - **最新版本**:v2.1.5
138
- - **问题追踪**:https://github.com/bagabaga007/ion_CSP/issues
154
+ 本项目采用MIT许可证,详见LICENSE文件。
139
155
 
140
156
  ---
141
157
 
142
- # Crystal Structure Design Software V2.1
143
-
144
158
  ## Project Overview
159
+
145
160
  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.
146
161
 
147
162
  ## Key Features
163
+
148
164
  ### Core Functionalities
165
+
149
166
  - **Dual-Module Workflow**
150
167
  - **EE Module**: Empirical evaluation-based ion combination generation
151
168
  - **CSP Module**: Ion crystal structure prediction and optimization
@@ -159,13 +176,16 @@ This software enables efficient crystal structure design from molecular/ion conf
159
176
  - Symlink resolution for actual log paths
160
177
 
161
178
  ### Technical Specifications
179
+
162
180
  - Cross-platform support (Linux/Docker)
163
181
  - Object-oriented architecture with Python 3.11+
164
182
  - Integrated process management via psutil
165
183
  - Structured logging system
166
184
 
167
185
  ## Installation
186
+
168
187
  ### Prerequisites
188
+
169
189
  | Component | Min Version |
170
190
  |-------------|-------------|
171
191
  | Python | 3.11 |
@@ -182,6 +202,7 @@ This software enables efficient crystal structure design from molecular/ion conf
182
202
  | rdkit | 2024.03.3|
183
203
 
184
204
  ### Installation Steps
205
+
185
206
  ```bash
186
207
  # Create virtual environment
187
208
  python -m venv venv
@@ -194,29 +215,39 @@ pip install -e .
194
215
  ```
195
216
 
196
217
  ## Quick Start
218
+
197
219
  ### Interactive Mode
220
+
198
221
  ```bash
199
222
  ion-csp
200
223
  ```
224
+
201
225
  Launches CLI interface with:
226
+
202
227
  - Module selection
203
228
  - Log management
204
229
  - Process control
205
230
 
206
231
  ### Script Execution
232
+
207
233
  #### EE Module Example
234
+
208
235
  ```bash
209
236
  ./scripts/main_EE.sh examples/example_1
210
237
  ```
238
+
211
239
  Generates ion combinations from SMILES tables
212
240
 
213
241
  #### CSP Module Example
242
+
214
243
  ```bash
215
244
  ./scripts/main_CSP.sh examples/example_2
216
245
  ```
246
+
217
247
  Optimizes crystal structures from ion combinations
218
248
 
219
249
  ## Technical Architecture
250
+
220
251
  ```mermaid
221
252
  graph TD
222
253
  A[User Interface] --> B[Task Manager]
@@ -225,21 +256,18 @@ graph TD
225
256
  B --> E[Log System]
226
257
  B --> F[Task Scheduler]
227
258
  C --> G[Empirical Evaluation Engine]
228
- D --> H[Crystal Prediction Engine]
259
+ D --> H[Ionic Crystal Structure Prediction Engine]
229
260
  E --> I[Structured Logs]
230
261
  F --> J[Process Termination]
231
262
  ```
232
263
 
233
264
  ## Contribution Guide
265
+
234
266
  1. Fork repository and create feature branch
235
267
  2. Write unit tests for new features
236
268
  3. Submit PR with issue reference
237
269
  4. Follow PEP8 coding standards
238
270
 
239
271
  ## License
240
- MIT License, see LICENSE file.
241
272
 
242
- ## Support
243
- - Documentation last updated: June 2025
244
- - Latest version: v2.1.5
245
- - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues
273
+ MIT License, see LICENSE file.
@@ -1,10 +1,13 @@
1
- # Crystal Structure Design Software V2.1
1
+ # 基于分子/离子构型的晶体结构设计软件 V2.1
2
2
 
3
3
  ## 项目概述
4
+
4
5
  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。
5
6
 
6
7
  ## 功能特性
8
+
7
9
  ### 核心功能
10
+
8
11
  - **双模块工作流**
9
12
  - **EE模块**:基于经验评估的离子组合生成
10
13
  - **CSP模块**:基于离子晶体结构预测的优化筛选
@@ -18,13 +21,16 @@
18
21
  - 软链接解析显示实际路径
19
22
 
20
23
  ### 技术特性
24
+
21
25
  - 跨平台支持(Linux/Docker)
22
26
  - 基于Python 3.11+的面向对象架构
23
27
  - 集成psutil进程管理
24
28
  - 结构化日志记录系统
25
29
 
26
30
  ## 安装指南
31
+
27
32
  ### 环境要求
33
+
28
34
  | 组件 | 最低版本 |
29
35
  |-------------|----------|
30
36
  | Python | 3.11 |
@@ -41,10 +47,13 @@
41
47
  | rdkit | 2024.03.3|
42
48
 
43
49
  ### 安装步骤
50
+
44
51
  ```bash
45
52
  pip install ion-csp
46
53
  ```
54
+
47
55
 
56
+
48
57
  ```bash
49
58
  # 创建虚拟环境
50
59
  python -m venv venv
@@ -57,29 +66,39 @@ pip install -e .
57
66
  ```
58
67
 
59
68
  ## 快速入门
69
+
60
70
  ### 交互模式
71
+
61
72
  ```bash
62
73
  ion-csp
63
74
  ```
75
+
64
76
  启动交互式命令行界面,支持以下操作:
77
+
65
78
  - 模块选择
66
79
  - 日志查看
67
80
  - 进程管理
68
81
 
69
82
  ### 脚本调用
83
+
70
84
  #### EE模块示例
85
+
71
86
  ```bash
72
87
  ./scripts/main_EE.sh examples/example_1
73
88
  ```
89
+
74
90
  从SMILES表格生成离子组合
75
91
 
76
92
  #### CSP模块示例
93
+
77
94
  ```bash
78
95
  ./scripts/main_CSP.sh examples/example_2
79
96
  ```
97
+
80
98
  从离子组合生成并优化晶体结构
81
99
 
82
100
  ## 技术架构
101
+
83
102
  ```mermaid
84
103
  graph TD
85
104
  A[用户界面] --> B[任务管理器]
@@ -88,34 +107,32 @@ graph TD
88
107
  B --> E[日志系统]
89
108
  B --> F[任务调度]
90
109
  C --> G[经验评估引擎]
91
- D --> H[晶体预测引擎]
110
+ D --> H[离子晶体结构预测引擎]
92
111
  E --> I[结构化日志]
93
112
  F --> J[进程终止]
94
113
  ```
95
114
 
96
115
  ## 贡献指南
116
+
97
117
  1. Fork仓库并创建特性分支
98
118
  2. 编写单元测试覆盖新功能
99
119
  3. 提交Pull Request时注明关联Issue
100
120
  4. 遵循PEP8代码规范
101
121
 
102
122
  ## 许可证
103
- 本项目采用MIT许可证,详见LICENSE文件。
104
123
 
105
- ## 技术支持
106
- - **文档更新**:2025年6月
107
- - **最新版本**:v2.1.5
108
- - **问题追踪**:https://github.com/bagabaga007/ion_CSP/issues
124
+ 本项目采用MIT许可证,详见LICENSE文件。
109
125
 
110
126
  ---
111
127
 
112
- # Crystal Structure Design Software V2.1
113
-
114
128
  ## Project Overview
129
+
115
130
  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.
116
131
 
117
132
  ## Key Features
133
+
118
134
  ### Core Functionalities
135
+
119
136
  - **Dual-Module Workflow**
120
137
  - **EE Module**: Empirical evaluation-based ion combination generation
121
138
  - **CSP Module**: Ion crystal structure prediction and optimization
@@ -129,13 +146,16 @@ This software enables efficient crystal structure design from molecular/ion conf
129
146
  - Symlink resolution for actual log paths
130
147
 
131
148
  ### Technical Specifications
149
+
132
150
  - Cross-platform support (Linux/Docker)
133
151
  - Object-oriented architecture with Python 3.11+
134
152
  - Integrated process management via psutil
135
153
  - Structured logging system
136
154
 
137
155
  ## Installation
156
+
138
157
  ### Prerequisites
158
+
139
159
  | Component | Min Version |
140
160
  |-------------|-------------|
141
161
  | Python | 3.11 |
@@ -152,6 +172,7 @@ This software enables efficient crystal structure design from molecular/ion conf
152
172
  | rdkit | 2024.03.3|
153
173
 
154
174
  ### Installation Steps
175
+
155
176
  ```bash
156
177
  # Create virtual environment
157
178
  python -m venv venv
@@ -164,29 +185,39 @@ pip install -e .
164
185
  ```
165
186
 
166
187
  ## Quick Start
188
+
167
189
  ### Interactive Mode
190
+
168
191
  ```bash
169
192
  ion-csp
170
193
  ```
194
+
171
195
  Launches CLI interface with:
196
+
172
197
  - Module selection
173
198
  - Log management
174
199
  - Process control
175
200
 
176
201
  ### Script Execution
202
+
177
203
  #### EE Module Example
204
+
178
205
  ```bash
179
206
  ./scripts/main_EE.sh examples/example_1
180
207
  ```
208
+
181
209
  Generates ion combinations from SMILES tables
182
210
 
183
211
  #### CSP Module Example
212
+
184
213
  ```bash
185
214
  ./scripts/main_CSP.sh examples/example_2
186
215
  ```
216
+
187
217
  Optimizes crystal structures from ion combinations
188
218
 
189
219
  ## Technical Architecture
220
+
190
221
  ```mermaid
191
222
  graph TD
192
223
  A[User Interface] --> B[Task Manager]
@@ -195,21 +226,18 @@ graph TD
195
226
  B --> E[Log System]
196
227
  B --> F[Task Scheduler]
197
228
  C --> G[Empirical Evaluation Engine]
198
- D --> H[Crystal Prediction Engine]
229
+ D --> H[Ionic Crystal Structure Prediction Engine]
199
230
  E --> I[Structured Logs]
200
231
  F --> J[Process Termination]
201
232
  ```
202
233
 
203
234
  ## Contribution Guide
235
+
204
236
  1. Fork repository and create feature branch
205
237
  2. Write unit tests for new features
206
238
  3. Submit PR with issue reference
207
239
  4. Follow PEP8 coding standards
208
240
 
209
241
  ## License
210
- MIT License, see LICENSE file.
211
242
 
212
- ## Support
213
- - Documentation last updated: June 2025
214
- - Latest version: v2.1.5
215
- - Issue tracker: https://github.com/bagabaga007/ion_CSP/issues
243
+ MIT License, see LICENSE file.
@@ -9,6 +9,7 @@ dependencies:
9
9
  - wheel
10
10
  - setuptools-scm
11
11
  - ase=3.23.0
12
+ - scipy=1.15.2
12
13
  - numpy=1.26.4
13
14
  - paramiko=3.5.1
14
15
  - pyxtal=1.0.4
@@ -5,8 +5,8 @@ convert_SMILES:
5
5
  group_screen: '[N+](=O)[O-]' # 对于官能团SMILES码的筛选
6
6
  group_screen_invert: False # 对官能团的反选与否,默认为否
7
7
  group_name: 'nitro' # 自定义官能团的名字
8
- machine: '/workplace/yz/ion_CSP/server_config/JLU_184/JLU_184_machine.yaml' # 进行Gaussian优化计算的机器参数
9
- resources: '/workplace/yz/ion_CSP/server_config/JLU_184/JLU_184_resources.yaml' # 进行Gaussian优化计算的资源参数
8
+ machine: '/workplace/yz/server_config/JLU_184/JLU_184_machine.yaml' # 进行Gaussian优化计算的机器参数
9
+ resources: '/workplace/yz/server_config/JLU_184/JLU_184_resources.yaml' # 进行Gaussian优化计算的资源参数
10
10
  nodes: 2 # 占用CPU节点数
11
11
 
12
12
  empirical_estimate:
@@ -32,7 +32,7 @@ def generate_changelog(commit_details, tags):
32
32
  new_changelog_content = []
33
33
 
34
34
  # 添加标题
35
- new_changelog_content.append("# Changelog\n\n")
35
+ new_changelog_content.append("# Changelog\n\n## Latest Changes\n\n")
36
36
 
37
37
  # 添加每个提交的详细信息
38
38
  for detail in commit_details:
@@ -43,14 +43,14 @@ def generate_changelog(commit_details, tags):
43
43
  if tags.get(hash_value):
44
44
  # 添加标签信息
45
45
  for tag in tags[hash_value]:
46
- new_changelog_content.append(f"## {tag}\n")
46
+ new_changelog_content.append(f"## {tag}\n\n")
47
47
 
48
48
  # 添加提交信息
49
- new_changelog_content.append(f"### {hash_value} ({date})\n")
49
+ new_changelog_content.append(f"### {hash_value} ({date})\n\n")
50
50
  new_changelog_content.append(f"{message}\n\n")
51
51
  else:
52
52
  # 如果没有标签,直接添加提交信息
53
- new_changelog_content.append(f"### {hash_value} ({date})\n")
53
+ new_changelog_content.append(f"### {hash_value} ({date})\n\n")
54
54
  new_changelog_content.append(f"{message}\n\n")
55
55
 
56
56
  # 写入 CHANGELOG.md
@@ -1,8 +1,8 @@
1
1
  __author__ = "Ze Yang"
2
2
  __contact__ = "yangze1995007@163.com"
3
3
  __license__ = "MIT"
4
- __version__ = "2.1.5"
5
- __date__ = "2025-06-16"
4
+ __version__ = "2.1.8"
5
+ __date__ = "2025-06-23"
6
6
 
7
7
 
8
8
  try: