initial working version

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: 버그 수정
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+---
+
+**버그에 대해 설명해 주세요 :)**  
+
+[..] 할 때 [..] 에러가 나며 트레이닝이 멈춥니다.  
+(GIF, 동영상 등 드래그해서 첨부할 수도 있습니다.)
+
+**To Reproduce**  
+
+버그 만드는 법:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**  
+
+원래대로라면 [...] 해야 합니다.
+
+**로그 파일을 붙여넣어 주세요 :)**  
+
+<details>
+<code>
+
+여기에 붙여넣어 주세요
+
+</code>
+</details>
+
+**사용하고 계시는 프로그램의 버전을 입력해 주세요 :)**  
+
+```
+여기에 적어주세요
+```
+
+**기타 내용을 적어주세요 :)**  

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: 기능 추가 요청
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**겪고 계신 문제를 설명해 주세요 :)**  
+[...] 할때 항상 [...] 문제가 있습니다.
+
+**원하시는 솔루션을 설명해 주세요 :)**  
+
+**다른 대안을 고려해 보셨다면 설명해 주세요 :)**  
+
+**사용하고 계시는 프로그램의 버전을 적어주세요 :)**  
+
+**기타 내용을 적어주세요 :)**  

.github/workflows/build_and_release.yml

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+name: Build and release to PyPI
+on:
+  workflow_dispatch:
+    inputs:
+      apbs-release-tag:
+        description: APBS version to build
+        required: true
+        default: 3.4.1
+      version-tag:
+        description: Python package version to release to PyPI (without 'v')
+        required: true
+        default: 3.4.1.post1
+      dry-run:
+        description: Dry run
+        type: boolean
+        default: false
+      exclude-types:
+        description: Commit types to exclude from the changelog
+        required: false
+        default: build,docs,style,other
+
+jobs:
+  build-all-platforms:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          pip install uv --break-system-packages
+          uv tool install build
+          uv tool install wheel
+          uv tool install huggingface_hub
+          huggingface-cli download --repo-type dataset --local-dir data Deargen/py-apbs-binary
+      - name: Build python wheels
+        run: |
+          bash build_python.sh ${{ inputs.apbs-release-tag }} ${{ inputs.version-tag }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels
+          path: dist/*.whl
+
+  test-ubuntu:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
+        # python-version: ['3.8']
+        # os: [ubuntu-20.04]
+    needs: [build-all-platforms]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          name: wheels
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Test wheel
+        run: |
+          pip install uv --break-system-packages
+          uv venv
+          source .venv/bin/activate
+          uv pip install -r requirements_test.txt
+          uv pip install dist/*-manylinux*_x86_64.whl
+          pytest
+
+  test-macos:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+        os: [macos-12, macos-13, macos-14, macos-15]
+        # os: [macos-14, macos-15]
+    needs: [build-all-platforms]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          name: wheels
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Test wheel
+        run: |
+          pip install uv --break-system-packages
+          uv venv --python python3
+          source .venv/bin/activate
+          uv pip install -r requirements_test.txt
+          if [[ ${{ matrix.os }} == 'macos-12' ]] || [[ ${{ matrix.os }} == 'macos-13' ]]; then
+            uv pip install dist/*-macosx_*_x86_64.whl
+          else
+            uv pip install dist/*-macosx_*_arm64.whl
+          fi
+          pytest
+
+  # test-windows:
+  #   runs-on: ${{ matrix.os }}
+  #   strategy:
+  #     matrix:
+  #       python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+  #       os: [windows-2019, windows-2022]
+  #   needs: [build-all-platforms]
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/download-artifact@v4
+  #       with:
+  #         path: dist
+  #         name: wheels
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Test wheel
+  #       shell: pwsh
+  #       run: |
+  #         pip install uv --break-system-packages
+  #         uv venv
+  #         .venv\Scripts\activate
+  #         uv pip install -r requirements_test.txt
+  #         uv pip install (get-item dist/*-win_amd64.whl)
+  #         pytest
+
+  commit-changelog-and-release-github:
+    needs: [test-ubuntu, test-macos]
+    uses: deargen/workflows/.github/workflows/commit-changelog-and-release.yml@master
+    with:
+      version-tag: ${{ github.event.inputs.version-tag }}
+      dry-run: ${{ github.event.inputs.dry-run == 'true' }}
+      changelog-path: docs/CHANGELOG.md
+      exclude-types: ${{ github.event.inputs.exclude-types }}
+
+  release:
+    name: Release
+    if: ${{ github.event.inputs.dry-run == 'false' }}
+    runs-on: ubuntu-24.04
+    needs: [commit-changelog-and-release-github]
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          name: wheels
+      - name: Build and upload to PyPI
+        run: |
+          pip install uv --break-system-packages
+          uv tool install twine
+          twine upload dist/* -u __token__ -p ${{ secrets.PYPI_API_TOKEN }} --non-interactive

.gitignore

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+/data/
+
+# some files created when calling apbs?
+io.mc
+.DS_Store
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+