OpenJij 開発環境の近代化 (#489)

# OpenJij開発環境の近代化

## 📋 概要
OpenJijの開発環境を近代化しました。依存関係管理、ビルドシステムのモダン化等が含まれます。

**主要成果**: 
- uvの導入
- scikit-build-coreへの移行
- ruffの導入

## ✨ 期待される改善効果

### 🚀 開発効率の向上
- **環境構築時間**: uvを使用することで依存関係解決の高速化
- **品質チェック**: ruffによる簡単化
- **依存関係管理**: `uv.lock` によるバージョン固定化

### 🛠️ 開発体験の改善
- **統一コマンド**: `uv run` による一貫した実行環境
- **設定の統合**: pyproject.toml への集約

## 🔍 主要な技術変更

### 1. UV移行による依存関係管理の現代化
**変更内容**:
- PEP 735準拠の dependency-groups 構造を採用
- uv.lock による確定的な依存関係管理
- pip-tools廃止（setup.cfg, setup.py, *.inファイルの廃止）

**技術的詳細**:
```toml
[dependency-groups]
build = ["build>=1.2"]
test = ["pytest>=8.0", "pytest-mock", "pytest-cov", "pytest-randomly", "pytest-spec", "coverage", "scipy"]
format = ["ruff>=0.5.0"]
dev = [
    {include-group = "build"},
    {include-group = "test"}, 
    {include-group = "format"}
]
```

### 2. ビルドシステムの現代化
**変更内容**:
- scikit-build-core移行によるPEP 517/518完全対応
- setup.py/setup.cfg廃止、pyproject.toml統合

### 3. 開発ツールの統合
**変更内容**:
- ruffによるlint/format統一
- pre-commit廃止、複数ツールから単一ツールへ
- flake8 + black + isort → ruff統合

## ⚠️ 破壊的変更と対応

### 変更が必要な開発コマンド
| 旧コマンド | 新コマンド |
|-----------|----------|
| `pip install -e .[dev]` | `uv sync --group dev` |
| `black . && isort . && flake8` | `uv run ruff check . && uv run ruff
format .` |
| `pip-compile dev-requirements.in` | `uv lock` |
| `pytest tests/` | `uv run pytest tests/` |

## 📚 技術的背景

### 採用した標準・ツール
- **PEP 735**: Dependency Groups
- **PEP 517/518**: ビルドシステム標準
- **scikit-build-core**: 現代的なC++統合
- **uv**: 高速なPythonパッケージマネージャー
- **ruff**: 高性能なPythonリンター・フォーマッターツール

## 🔗 関連リソース

- [PEP 735: Dependency Groups](https://peps.python.org/pep-0735/)
- [UV公式ドキュメント](https://docs.astral.sh/uv/)
- [scikit-build-core](https://scikit-build-core.readthedocs.io/)
- [ruff](https://docs.astral.sh/ruff/)
- [cimod実装例](Jij-Inc/cimod#195)

---------

Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 3 people

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,40 +1,27 @@
 version: 2
-    
+
 updates:
-- package-ecosystem: docker
-  directory: "/"
-  schedule:
-    interval: "daily"
-  allow:
+  - package-ecosystem: docker
+    directory: "/"
+    schedule:
+      interval: "daily"
+    allow:
       # Allow both direct and indirect updates for all packages
       - dependency-type: "all"
-- package-ecosystem: github-actions
-  directory: "/"
-  schedule:
-    interval: "daily" 
-  allow:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: "daily"
+    allow:
       # Allow both direct and indirect updates for all packages
       - dependency-type: "all"
-      
-- package-ecosystem: pip 
-  directory: "/setup.py" 
-  insecure-external-code-execution: allow
-  versioning-strategy: auto
-  schedule:
-    interval: "daily"
-  allow:
-      # Allow both direct and indirect updates for all packages
-      - dependency-type: "all"
-  labels:
-      - "python"
-      - "dependencies"      
-      
-- package-ecosystem: pip 
-  directory: "/" 
-  insecure-external-code-execution: allow
-  versioning-strategy: auto
-  schedule:
-    interval: "daily"
-  allow:
+
+  - package-ecosystem: pip
+    directory: "/"
+    insecure-external-code-execution: allow
+    versioning-strategy: auto
+    schedule:
+      interval: "daily"
+    allow:
       # Allow both direct and indirect updates for all packages
       - dependency-type: "all"

.github/ISSUE_TEMPLATE/feature_request.md

@@ -13,7 +13,7 @@ concurrency:
       cancel-in-progress: false
 
 env:
-  Python_Version: '3.10'
+  Python_Version: '3.12'
 
 jobs:
   build_docs:
@@ -23,43 +23,18 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        name: Install Python
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{env.Python_Version}}
-      - name: Python Cache Key
-        shell: bash
-        run: |
-          echo $(which python) > /tmp/python_version.txt
-      - name: Get pip cache dir
-        shell: bash
-        id: pip-cache
-        run: |
-          echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      - name: Pip-Tools 
-        shell: bash
-        run: |
-          python -m pip install pip-tools 
-          pip-compile
-          pip-compile dev-requirements.in
-      - name: pip cache
-        uses: actions/cache@v4
-        with:
-           path: ${{ steps.pip-cache.outputs.dir }}
-           key: ${{ runner.os }}-pip-${{ hashFiles('/tmp/python_version.txt') }}
-           restore-keys: |
-              ${{ runner.os }}-pip-
-      - name: Update
-        run: | 
-         pip install --upgrade pip wheel setuptools build cmake ninja 
       - name: Install Dependencies
         shell: bash
         run: |
           set -eux
-          pip-sync requirements.txt dev-requirements.txt
+          uv sync --locked --group build
       - name: Install Dep
         run: | 
-         pip install typing-extensions
+         uv pip install typing-extensions
          sudo apt-get install -y libeigen3-dev lcov graphviz mscgen dia pdf2svg astyle
          sudo apt-get install -y doxygen doxygen-doxyparse fonts-liberation python3-breathe
       - name: Prepare 
@@ -86,11 +61,6 @@ jobs:
         run: |
           set -eux
           cp -r ./build/html/* ./public/
-      - name: du -a 
-        shell: bash
-        if: always()
-        run: |
-          du -a
       - name: Prepare tag
         id: prepare_tag
         if: startsWith(github.ref, 'refs/tags/')
@@ -107,7 +77,7 @@ jobs:
          allow_empty_commit: true
          publish_dir: ./public
          publish_branch: main
-         external_repository: OpenJij/OpenJij-Reference-Page
+         external_repository: Jij-Inc/OpenJij-Reference-Page
          destination_dir: www
          user_name: 'github-actions[bot]'
          user_email: 'github-actions[bot]@users.noreply.github.com'

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,16 +14,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        name: Install Python
+      - name: Install uv and set Python version
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: '3.11'
+          python-version: '3.12'
       - name: Install dependencies 
         run: |
-           pip install --upgrade pip wheel setuptools build 
+           uv sync --locked --group build
       - name: Build sdist
         run: |
-          python -m build --sdist --outdir ./dist
+          uv run python -m build --sdist --outdir ./dist
       - uses: actions/upload-artifact@v4
         with:
           name: wheel-sdist
@@ -39,9 +39,6 @@ jobs:
       fail-fast: false 
       matrix:  
         include:
-         - artifact: wheel-linux_x86_64_python38
-           python: /opt/python/cp38-cp38/bin/python
-           container: ghcr.io/openjij/openjij-builder-minimum-manylinux_2_28_x86_64:latest
          - artifact: wheel-linux_x86_64_python39
            python: /opt/python/cp39-cp39/bin/python
            container: ghcr.io/openjij/openjij-builder-minimum-manylinux_2_28_x86_64:latest
@@ -54,6 +51,9 @@ jobs:
          - artifact: wheel-linux_x86_64_python312
            python: /opt/python/cp312-cp312/bin/python
            container: ghcr.io/openjij/openjij-builder-minimum-manylinux_2_28_x86_64:latest
+         - artifact: wheel-linux_x86_64_python313
+           python: /opt/python/cp313-cp313/bin/python
+           container: ghcr.io/openjij/openjij-builder-minimum-manylinux_2_28_x86_64:latest
 
     steps:
       - uses: actions/checkout@v4       
@@ -64,29 +64,12 @@ jobs:
           ls /opt/python
           ${{matrix.python}} --version > python_version.txt
           cat python_version.txt
-      - name: Pip-Tools 
-        shell: bash
-        run: |
-          set -eux
-          ${{matrix.python}} -m pip install pip-tools 
-          ${{matrix.python}} -m piptools compile setup.cfg
-          ${{matrix.python}} -m piptools compile build-requirements.in
-      - uses: actions/cache@v4
-        with:
-          path: |
-            ~/.cache/pip
-            /var/cache/dnf/
-          key: ${{ runner.os }}-intel-${{ hashFiles('python_version.txt') }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('build-requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-intel-${{ hashFiles('python_version.txt') }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('build-requirements.txt') }}
-            ${{ runner.os }}-intel-${{ hashFiles('python_version.txt') }}-${{ hashFiles('requirements.txt') }}
-            ${{ runner.os }}-intel-${{ hashFiles('python_version.txt') }}
-            ${{ runner.os }}-intel-
       - name: Install Dependencies
         shell: bash
         run: |
           set -eux
-          ${{matrix.python}} -m piptools sync requirements.txt build-requirements.txt 
+          ${{matrix.python}} -m pip install --upgrade pip
+          ${{matrix.python}} -m pip install --upgrade build auditwheel
       - name: Build 
         run: |
           set -x
@@ -117,9 +100,6 @@ jobs:
         run: |
           set -x 
           source /opt/intel/oneapi/setvars.sh --force  --config="/tmp/tmp/config.txt"
-          ${{matrix.python}} -m auditwheel -h
-          ${{matrix.python}} -m auditwheel show -h
-          ${{matrix.python}} -m auditwheel repair -h
           du -ah ./dist
           cd dist
           for f in *.whl; do ${{matrix.python}} -m auditwheel show $f; done 
@@ -140,10 +120,6 @@ jobs:
       fail-fast: false 
       matrix:  
         include:
-          - artifact: wheel-linux_aarch64_python38
-            os: ubuntu-latest
-            arch: aarch64
-            CIBW_BUILD: cp38-manylinux_aarch64
           - artifact: wheel-linux_aarch64_python39
             os: ubuntu-latest
             arch: aarch64
@@ -160,6 +136,10 @@ jobs:
             os: ubuntu-latest
             arch: aarch64
             CIBW_BUILD: cp312-manylinux_aarch64
+          - artifact: wheel-linux_aarch64_python313
+            os: ubuntu-latest
+            arch: aarch64
+            CIBW_BUILD: cp313-manylinux_aarch64
     steps:
       - uses: actions/checkout@v4       
       - name: Set up QEME
@@ -175,7 +155,6 @@ jobs:
         uses: pypa/cibuildwheel@v2.22.0
         env:
           CIBW_BUILD: ${{matrix.CIBW_BUILD}}
-          CIBW_SKIP: "cp313-*"
           CIBW_ENVIRONMENT: ""
           CIBW_PLATFORM:  linux
           CIBW_ARCHS: ${{matrix.arch}}
@@ -189,7 +168,7 @@ jobs:
           CIBW_BEFORE_BUILD_LINUX: >
                source scl_source enable gcc-toolset-11 &&
                pip install 'pybind11<3' cmake ninja
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8,<3.13"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9,<3.14"
       - uses: actions/upload-artifact@v4
         with:
           name: ${{matrix.artifact}}
@@ -216,10 +195,10 @@ jobs:
       - name: Build wheels on macos x86_64
         uses: pypa/cibuildwheel@v2.22.0
         env:
-          CIBW_SKIP: "cp313-* pp*"
+          CIBW_SKIP: "pp*"
           CIBW_PLATFORM: macos
           CIBW_ARCHS: x86_64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8,<3.13"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9,<3.14"
           CIBW_ENVIRONMENT: >
             MACOSX_DEPLOYMENT_TARGET=${{ matrix.MACOSX_DEPLOYMENT_TARGET }}
       - uses: actions/upload-artifact@v4
@@ -248,10 +227,10 @@ jobs:
       - name: Build wheels on macos arm64
         uses: pypa/cibuildwheel@v2.22.0
         env:
-          CIBW_SKIP: "cp313-* pp*"
+          CIBW_SKIP: "pp*"
           CIBW_PLATFORM: macos
           CIBW_ARCHS: arm64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8,<3.13"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9,<3.14"
           CIBW_ENVIRONMENT: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.MACOSX_DEPLOYMENT_TARGET }}"
       - uses: actions/upload-artifact@v4
         with:
@@ -276,24 +255,6 @@ jobs:
       - name: Add msbuild to PATH
         if: ${{ matrix.os == 'windows-latest'}}
         uses: microsoft/setup-msbuild@v2.0.0
-      - name: Prepare Cache 
-        if: ${{ matrix.os == 'windows-latest'}}
-        shell: bash 
-        run: |
-          set -eux
-          ls  C:/vcpkg
-          MSBuild.exe -version > msbuild_version.txt
-          cat msbuild_version.txt
-      - name: Cache vcpkg
-        uses: actions/cache@v4
-        if: ${{ matrix.os == 'windows-latest'}}
-        with:
-           path: |
-             C:/Users/runneradmin/AppData/Local/vcpkg/archives
-           key: ${{ matrix.os }}-vcpkg-${{ hashFiles('msbuild_version.txt') }}
-           restore-keys: |
-             ${{ matrix.os }}-vcpkg-${{ hashFiles('msbuild_version.txt') }}
-             ${{ matrix.os }}-vcpkg
       - name: Install Dependency 
         shell: bash 
         run: |
@@ -307,11 +268,10 @@ jobs:
       - name: Build wheels on ${{ matrix.CIBW_PLATFORM }} ${{matrix.arch}}
         uses: pypa/cibuildwheel@v2.22.0
         env:
-          CIBW_SKIP: "cp313-*"
           CIBW_ENVIRONMENT: ${{ matrix.CIBW_ENVIRONMENT }}
           CIBW_PLATFORM:  ${{ matrix.CIBW_PLATFORM }}
           CIBW_ARCHS: ${{matrix.arch}}
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8,<3.13"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9,<3.14"
 
       - uses: actions/upload-artifact@v4
         with: