sequenzo 0.1.0__tar.gz

sequenzo-0.1.0/.gitattributes

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+# 设置默认行为，所有文件都采用LF行结束符和UTF-8编码
+* text=auto eol=lf encoding=utf-8
+
+# 源代码文件
+*.py text diff=python encoding=utf-8
+*.c text diff=c encoding=utf-8
+*.cpp text diff=cpp encoding=utf-8
+*.h text diff=c encoding=utf-8
+*.hpp text diff=cpp encoding=utf-8
+*.pyx text diff=python encoding=utf-8
+*.pxd text diff=python encoding=utf-8
+
+# 配置文件
+*.toml text encoding=utf-8
+*.ini text encoding=utf-8
+*.yaml text encoding=utf-8
+*.yml text encoding=utf-8
+*.json text encoding=utf-8
+*.cfg text encoding=utf-8
+*.conf text encoding=utf-8
+requirements*.txt text encoding=utf-8
+pyproject.toml text encoding=utf-8
+setup.py text encoding=utf-8
+setup.cfg text encoding=utf-8
+
+# 文档文件
+*.txt text encoding=utf-8
+*.md text encoding=utf-8
+*.rst text encoding=utf-8
+LICENSE text encoding=utf-8
+README* text encoding=utf-8
+CHANGELOG* text encoding=utf-8
+
+# 在Windows系统上保留CRLF行尾
+*.bat text eol=crlf encoding=utf-8
+*.cmd text eol=crlf encoding=utf-8
+*.ps1 text eol=crlf encoding=utf-8
+
+# 特殊文件处理
+Makefile text eol=lf encoding=utf-8
+makefile text eol=lf encoding=utf-8
+
+# 数据文件（作为二进制处理，不进行任何转换）
+*.db binary
+*.p binary
+*.pkl binary
+*.pickle binary
+*.pyc binary
+*.pyd binary
+*.pyo binary
+
+# 图像文件（二进制）
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.svg text encoding=utf-8
+
+# Excel和CSV文件（作为文本文件处理，但特别注意编码）
+*.csv text encoding=utf-8
+*.tsv text encoding=utf-8
+*.xls binary
+*.xlsx binary
+
+# 压缩文件（二进制）
+*.gz binary
+*.zip binary
+*.7z binary

sequenzo-0.1.0/.github/workflows/python-app.yml

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+# GitHub Actions workflow for Sequenzo package
+name: Sequenzo Package CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # Clear the `pip` cache to prevent conflicts
+    - name: Clear pip cache
+      run: python -m pip cache purge
+
+    # macOS: Handle dependency installation, using different strategies for different Python versions
+    - name: Install dependencies (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        python -m pip install --upgrade pip
+        pip install Cython==0.29.36
+        
+        if [ "${{ matrix.python-version }}" == "3.11" ]; then
+          pip install "setuptools>=60.0.0"
+        else
+          pip install "setuptools==58.1.0"
+        fi
+        
+        if [ "${{ matrix.python-version }}" == "3.11" ]; then
+          pip install "numpy>=1.23.2,<2.0" --only-binary numpy
+        elif [ "${{ matrix.python-version }}" == "3.10" ]; then
+          pip install "numpy>=1.22.4,<2.0" --only-binary numpy
+        else
+          pip install "numpy==1.22.4" --only-binary numpy || pip install "numpy>=1.21.0,<2.0" --only-binary numpy
+        fi
+        
+        pip install pybind11
+        
+        if [ "${{ matrix.python-version }}" == "3.11" ]; then
+          pip install "scipy>=1.8.0"
+        else
+          pip install "scipy==1.7.3" || pip install "scipy>=1.7.0"
+        fi
+        
+        python -m pip install --upgrade wheel
+        pip install fastcluster==1.2.6 || pip install fastcluster
+        
+        if [ -f "requirements-${{ matrix.python-version }}.txt" ]; then
+          pip install -r requirements-${{ matrix.python-version }}.txt --no-build-isolation || echo "⚠️ Some requirements may not be installed"
+        else
+          pip install -r requirements-3.9.txt --no-build-isolation || echo "⚠️ Some requirements may not be installed"
+          echo "⚠️ Using requirements-3.9.txt as fallback"
+        fi
+
+    # macOS: Ensure that Xcode CLI tools are installed – required for all Python versions
+    - name: Install Xcode Command Line Tools
+      if: runner.os == 'macOS'
+      run: |
+        xcode-select --install || echo "Xcode CLI already installed"
+
+    # Windows: Handle numpy & fastcluster version issues, install the complete MSVC toolchain
+    - name: Install dependencies (Windows)
+      if: runner.os == 'Windows'
+      shell: pwsh  # 确保使用 PowerShell，而不是默认 cmd.exe
+      run: |
+        choco install visualstudio2022buildtools --version=17.0.0 -y
+        choco install visualstudio2022-workload-vctools -y
+
+        python -m pip install --upgrade pip
+
+        if ("${{ matrix.python-version }}" -eq "3.11") {
+          pip install "numpy>=1.23.2,<2.0"
+        } else {
+          pip install numpy==1.22.4 --only-binary numpy
+        }
+        
+        pip install wheel setuptools cmake Cython
+        
+        pip uninstall -y pybind11  
+        pip install pybind11==2.10.4  
+        
+        pip install --force-reinstall fastcluster==1.2.6  
+        
+        if (Test-Path "requirements-${{ matrix.python-version }}.txt") {
+          pip install -r requirements-${{ matrix.python-version }}.txt --use-deprecated=legacy-resolver
+        } else {
+          pip install -r requirements-3.9.txt --use-deprecated=legacy-resolver
+          Write-Host "⚠️ Using requirements-3.9.txt as fallback"
+        }
+
+    # Linux: Handle fastcluster version issues, ensure numpy is installed first
+    - name: Install dependencies (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel setuptools
+        
+        sudo apt-get update
+        sudo apt-get install -y build-essential
+        
+        if [ "${{ matrix.python-version }}" == "3.11" ]; then
+          pip install "numpy>=1.23.2,<2.0" --only-binary numpy
+        else
+          pip install numpy==1.22.4 --only-binary numpy
+        fi
+        
+        pip install pybind11 
+        pip install fastcluster==1.2.6  
+        
+        if [ -f "requirements-${{ matrix.python-version }}.txt" ]; then
+          pip install -r requirements-${{ matrix.python-version }}.txt --no-build-isolation
+        else
+          pip install -r requirements-3.9.txt --no-build-isolation
+          echo "⚠️ Using requirements-3.9.txt as fallback"
+        fi
+
+    # Ensure `PYTHONPATH` is set correctly
+    - name: Verify package path
+      shell: bash
+      run: |
+        echo "📂 Current directory:"
+        ls -lah
+        echo "📂 Sequenzo package directory:"
+        ls -lah sequenzo || echo "⚠️ Directory 'sequenzo' not found!"
+
+    # Windows: Fix Unicode encoding issues
+    - name: Set Windows Encoding
+      if: runner.os == 'Windows'
+      run: chcp 65001
+
+    - name: Setup Windows C++ compilation
+      if: runner.os == 'Windows'
+      shell: pwsh
+      run: |
+        choco install visualstudio2019buildtools -y
+        choco install visualstudio2019-workload-vctools -y
+
+        & "C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Auxiliary\Build\vcvars64.bat"
+
+        $Env:CL = "/EHsc /MD /bigobj /Ox"
+        $Env:DISTUTILS_USE_SDK = "1"
+        $Env:MSSdk = "1"
+
+    # Consolidated installation steps for all platforms
+    - name: Install local package
+      if: runner.os != 'Windows'
+      run: |
+        pip install --no-cache-dir -e . --no-build-isolation
+      env:
+        PYTHONUTF8: 1
+        PYTHONPATH: ${{ github.workspace }}
+
+    - name: Install local package (Windows)
+      if: runner.os == 'Windows'
+      shell: pwsh
+      run: |
+        $editable_install = $false
+        try {
+          pip install --no-cache-dir -e . --no-build-isolation --verbose
+          $editable_install = $true
+        } catch {
+          Write-Host "ERROR DETAILS: $_"
+          Write-Host "Editable install failed, trying regular install..."
+          pip install --no-cache-dir . --no-build-isolation --verbose
+        }
+      env:
+        PYTHONUTF8: 1
+        PYTHONPATH: ${{ github.workspace }}
+        DISTUTILS_USE_SDK: 1
+        MSSdk: 1
+
+    # Display installed packages
+    - name: Show installed packages
+      run: pip list
+
+    # Test whether the module is installed correctly
+    - name: Test imports
+      run: |
+        python -c "import sequenzo.dissimilarity_measures; print('Dissimilarity measures module imported successfully')"
+        python -c "import sequenzo.clustering; print('Clustering module imported successfully')"
+      env:
+        PYTHONPATH: ${{ github.workspace }}
+
+    # Build the wheel
+    - name: Build wheel
+      run: python setup.py bdist_wheel
+
+    # Upload build artifacts
+    - name: Upload wheel
+      uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.os }}-${{ matrix.python-version }}
+        path: dist/*.whl

sequenzo-0.1.0/.gitignore

@@ -0,0 +1,37 @@
+.idea
+.vscode
+.DS_Store
+
+# Python build artifacts
+build/
+dist/
+# MacOS built-in
+*.egg-info/
+
+# Ignore compiled Python files
+**/__pycache__/
+# Ignore the topic branch's .pyc files *.pyc
+**/*.pyo
+# Ignore all
+**/*.pyc
+
+# Intermediate files or system-specific binary files generated during compilation
+
+# Shared object (.so) files are Python extension modules on Linux/macOS
+**/*.so
+
+# Python dynamic library (.pyd) files are Python extension modules on Windows,
+# similar to Windows DLL files but specifically for Python
+**/*.pyd
+
+# Windows dynamic link library (.dll)
+**/*.dll
+
+# Intermediate object files, which are later linked to generate the final .so shared library.
+# These files are usually intermediate products of the compilation process and are not directly used by Python.
+**/*.o
+
+# Static library files on Linux/macOS, used for statically linking C/C++ code
+**/*.a
+
+raw_requirements.txt

sequenzo-0.1.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Yuqi Liang
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sequenzo-0.1.0/PKG-INFO

@@ -0,0 +1,141 @@
+Metadata-Version: 2.2
+Name: sequenzo
+Version: 0.1.0
+Summary: A fast, scalable and intuitive Python package for social sequence analysis.
+Author-email: Yuqi Liang <yuqi.liang.1900@gmail.com>, Xinyi Li <1836724126@qq.com>, Jan Heinrich Ernst Meyerhoff-Liang <jan.meyerhoff1@gmail.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2025, Yuqi Liang
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/Liang-Team/Sequenzo
+Project-URL: Documentation, https://sequenzo.yuqi-liang.tech
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: <3.12,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.0,>=1.19.5
+Requires-Dist: pandas>=1.2.5
+Requires-Dist: matplotlib>=3.4.3
+Requires-Dist: seaborn>=0.11.2
+Requires-Dist: Pillow>=8.3.2
+Requires-Dist: pybind11>=2.6.0
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: scikit-learn>=0.24.2
+Requires-Dist: fastcluster>=1.2.6
+Requires-Dist: joblib>=1.0.1
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2.5; extra == "dev"
+Requires-Dist: flake8>=3.9.2; extra == "dev"
+Requires-Dist: memory-profiler>=0.58.0; extra == "dev"
+
+
+# Sequenzo: Fast, scalable, and intuitive social sequence analysis
+
+Sequenzo is a high-performance Python package designed for social sequence analysis. It is built to analyze **any sequence of categorical events**, from individual career paths and migration patterns to corporate growth and urban development. 
+Whether you are working with **people, places, or policies**, Sequenzo helps uncover meaningful patterns efficiently. 
+
+Sequenzo outperforms traditional R-based tools in social sequence analysis, delivering faster processing and superior efficiency, especially for large-scale datasets. **No big data? No problem. You don’t need big data to benefit as Sequenzo is designed to enhance sequence analysis at any scale, making complex methods accessible to everyone.**
+
+## Why Choose Sequenzo?
+
+🚀 **High Performance**
+
+Leverages Python’s computational power to achieve 10× faster processing than traditional R-based tools like TraMineR.
+
+🎯 **Easy-to-Use API**
+
+Designed with simplicity in mind: intuitive functions streamline complex sequence analysis without compromising flexibility.
+
+🌍 **Flexible for Any Scenario**
+
+Perfect for research, policy, and business, enabling seamless analysis of categorical data and its evolution over time.
+
+## Documentation
+
+Explore the full Sequenzo documentation [here](sequenzo.yuqi-liang.tech).
+
+**Where to start on the documentation website?**
+* New to Sequenzo or social sequence analysis? Begin with "About Sequenzo" → "Quickstart Guide" for a smooth introduction.
+* Got your own data? After going through "About Sequenzo" and "Quickstart Guide", you are ready to dive in and start analyzing.
+* Looking for more? Check out our example datasets and tutorials to deepen your understanding.
+
+For Chinese users, additional tutorials are available on [Yuqi's video tutorials on Bilibili](https://space.bilibili.com/263594713/lists/4147974).
+
+## Installation
+
+The latest stable release and required dependencies can be installed from PyPI. You can type the following line in your terminal:
+
+```
+pip install sequenzo
+```
+
+## Join the Community
+
+💬 **Have a question or found a bug?**
+
+Please submit an issue on [GitHub Issues](https://github.com/Liang-Team/Sequenzo/issues). 
+
+For an effective bug report, please include the following:
+* A reproducible code example that clearly demonstrates the issue.
+* The output you’re seeing, such as an error message or an image of the plot.
+* A brief explanation of why you believe this is a bug.
+
+Providing these details will help us diagnose and resolve the issue more efficiently. We are always happy to help and will address it as soon as possible.
+
+🌟 **Enjoying Sequenzo?**
+
+Support the project by starring ⭐ the GitHub repo and spreading the word!
+
+🛠 **Interested in contributing?**
+
+Check out our [contribution guide]() for more details. 
+
+* Write code? Submit a pull request to enhance Sequenzo.
+* Testing? Try Sequenzo and share your feedback. Every suggestion counts!
+
+## Team
+
+**Authors**
+* Yuqi Liang, University of Oxford
+* Xinyi Li, Heilongjiang University
+* Jan Heinrich Ernst Meyerhoff-Liang, Institute for New Economic Thinking Oxford
+
+**Ackowledgements**
+* Technical advisor in sequence analysis: Tim Liao, University of Illinois Urbana-Champaign
+* Website and related technical support: Mactavish
+* Logo and color design: Changyu Yi
+* Sequence data sources compilation
+  * Economics: Jan Meyerhoff-Liang
+  * History: Jingrui Chen
+  * Public health: Yuelu Yin
+* Testing

sequenzo-0.1.0/README.md

@@ -0,0 +1,81 @@
+
+# Sequenzo: Fast, scalable, and intuitive social sequence analysis
+
+Sequenzo is a high-performance Python package designed for social sequence analysis. It is built to analyze **any sequence of categorical events**, from individual career paths and migration patterns to corporate growth and urban development. 
+Whether you are working with **people, places, or policies**, Sequenzo helps uncover meaningful patterns efficiently. 
+
+Sequenzo outperforms traditional R-based tools in social sequence analysis, delivering faster processing and superior efficiency, especially for large-scale datasets. **No big data? No problem. You don’t need big data to benefit as Sequenzo is designed to enhance sequence analysis at any scale, making complex methods accessible to everyone.**
+
+## Why Choose Sequenzo?
+
+🚀 **High Performance**
+
+Leverages Python’s computational power to achieve 10× faster processing than traditional R-based tools like TraMineR.
+
+🎯 **Easy-to-Use API**
+
+Designed with simplicity in mind: intuitive functions streamline complex sequence analysis without compromising flexibility.
+
+🌍 **Flexible for Any Scenario**
+
+Perfect for research, policy, and business, enabling seamless analysis of categorical data and its evolution over time.
+
+## Documentation
+
+Explore the full Sequenzo documentation [here](sequenzo.yuqi-liang.tech).
+
+**Where to start on the documentation website?**
+* New to Sequenzo or social sequence analysis? Begin with "About Sequenzo" → "Quickstart Guide" for a smooth introduction.
+* Got your own data? After going through "About Sequenzo" and "Quickstart Guide", you are ready to dive in and start analyzing.
+* Looking for more? Check out our example datasets and tutorials to deepen your understanding.
+
+For Chinese users, additional tutorials are available on [Yuqi's video tutorials on Bilibili](https://space.bilibili.com/263594713/lists/4147974).
+
+## Installation
+
+The latest stable release and required dependencies can be installed from PyPI. You can type the following line in your terminal:
+
+```
+pip install sequenzo
+```
+
+## Join the Community
+
+💬 **Have a question or found a bug?**
+
+Please submit an issue on [GitHub Issues](https://github.com/Liang-Team/Sequenzo/issues). 
+
+For an effective bug report, please include the following:
+* A reproducible code example that clearly demonstrates the issue.
+* The output you’re seeing, such as an error message or an image of the plot.
+* A brief explanation of why you believe this is a bug.
+
+Providing these details will help us diagnose and resolve the issue more efficiently. We are always happy to help and will address it as soon as possible.
+
+🌟 **Enjoying Sequenzo?**
+
+Support the project by starring ⭐ the GitHub repo and spreading the word!
+
+🛠 **Interested in contributing?**
+
+Check out our [contribution guide]() for more details. 
+
+* Write code? Submit a pull request to enhance Sequenzo.
+* Testing? Try Sequenzo and share your feedback. Every suggestion counts!
+
+## Team
+
+**Authors**
+* Yuqi Liang, University of Oxford
+* Xinyi Li, Heilongjiang University
+* Jan Heinrich Ernst Meyerhoff-Liang, Institute for New Economic Thinking Oxford
+
+**Ackowledgements**
+* Technical advisor in sequence analysis: Tim Liao, University of Illinois Urbana-Champaign
+* Website and related technical support: Mactavish
+* Logo and color design: Changyu Yi
+* Sequence data sources compilation
+  * Economics: Jan Meyerhoff-Liang
+  * History: Jingrui Chen
+  * Public health: Yuelu Yin
+* Testing