sequenzo 0.1.17__tar.gz → 0.1.19__tar.gz

{sequenzo-0.1.17/sequenzo.egg-info → sequenzo-0.1.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sequenzo
-Version: 0.1.17
+Version: 0.1.19
 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
@@ -54,10 +54,15 @@ Requires-Dist: cython>=0.29.21
 Requires-Dist: scipy>=1.6.3
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: fastcluster>=1.2.6
+Requires-Dist: rpy2>=3.5.12; python_version >= "3.12"
+Requires-Dist: rpy2>=3.5.6; python_version == "3.11"
+Requires-Dist: rpy2>=3.5.6; python_version == "3.10"
+Requires-Dist: rpy2>=3.5.6; python_version == "3.9"
 Requires-Dist: joblib>=1.0.1
 Requires-Dist: docutils>=0.17
 Requires-Dist: tqdm<5.0.0,>=4.62.3
 Requires-Dist: missingno<0.6.0,>=0.5.2
+Requires-Dist: cffi>=1.15.0
 Provides-Extra: dev
 Requires-Dist: pytest>=6.2.5; extra == "dev"
 Requires-Dist: flake8>=3.9.2; extra == "dev"
@@ -96,6 +101,11 @@ Sequenzo outperforms traditional R-based tools in social sequence analysis, deli
 >  
 > 📖 Available in **English and Chinese**, our docs are written to be approachable, practical, and easy to follow.
 
+## ✨ Be part of the Sequenzo community
+Join our Discord channel to iscuss ideas, get help, and hear about upcoming Sequenzo versions, tutorials, and workshops first.
+
+➡️ https://discord.gg/3bMDKRHW
+
 ## Target Users
 
 Sequenzo is designed for:
@@ -123,12 +133,12 @@ Perfect for research, policy, and business, enabling seamless analysis of catego
 
 Sequenzo provides pre-built Python wheels for maximum compatibility — no need to compile from source.
 
-| Platform         | Architecture                  | Python Versions      | Status            |
+| Platform         | Architecture                  | Python Versions       | Status            |
 |------------------|-------------------------------|-----------------------|-------------------|
-| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.11       | ✅ Pre-built wheel |
-| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
+| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
 
 
 What do these terms mean?
@@ -171,6 +181,22 @@ If you have some issues with the installation, it might because you have both Py
 pip3 install sequenzo
 ```
 
+### Optional R Integration
+
+Sequenzo now checks the system environment variables before running ward.D hierarchical clustering.
+
+If R is missing, a relevant prompt will be displayed along with specific installation instructions. If `fastcluster` is missing, Sequenzo will automatically download `fastcluster`.
+
+Before automatically downloading `fastcluster`, Sequenzo checks whether R is available; if R is not installed, sequenzo will not automatically download fastcluster.
+
+Sequenzo supports advanced Ward clustering methods that require R integration. If you need to use the `ward_d` clustering method, install with R support:
+
+```
+pip install sequenzo[r]
+```
+
+This will install the optional `rpy2` dependency, which provides Python-R interoperability. Note that R must also be installed on your system for `rpy2` to work.
+
 For more information about the latest stable release and required dependencies, please refer to [PyPI](https://pypi.org/project/sequenzo/). 
 
 ## Documentation
@@ -208,7 +234,7 @@ Check out our [contribution guide]() for more details (work in progress).
 If you're contributing or debugging, use:
 
 ```bash
-pip install -r requirements-3.10.txt  # Or matching your Python version
+pip install -r requirements/requirements-3.10.txt  # Or matching your Python version
 ```
     
 For standard installation, use:
@@ -221,23 +247,31 @@ pip install .  # Uses pyproject.toml
 
 **Paper Authors**
 * [Yuqi Liang, University of Oxford](https://www.yuqi-liang.tech/)
-* [Xinyi Li, Heilongjiang University](https://github.com/Fantasy201)
+* [Xinyi Li, Northeastern University](https://github.com/Fantasy201)
 * [Jan Heinrich Ernst Meyerhoff-Liang, Institute for New Economic Thinking Oxford](https://www.inet.ox.ac.uk/people/jan-meyerhoff-liang)
 
 **Package Contributors**
-* [Liangxingyun He, Stockholm School of Economics (Sweden)](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
-* [Yukun Ming, Universidad Carlos III de Madrid (Spain)](www.linkedin.com/in/yukun)
-* [Ziting Yang, Rochester Wniversity (US)](www.linkedin.com/in/ziting-yang-7b33832bb)
+
+Coding contributors:
+* [Sebastian Daza](https://sdaza.com/)
+* [Cheng Deng](https://github.com/de-de-de-de-de)
+* [Liangxingyun He, Stockholm School of Economics, Sweden](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
+
+Documentation contributors:
+* [Liangxingyun He, Stockholm School of Economics, Sweden](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
+* [Yukun Ming, Universidad Carlos III de Madrid (Spain)](https://www.linkedin.com/in/yukun)
 * [Sizhu Qu, Northeastern University (US)](https://www.linkedin.com/in/sizhuq)
+* [Ziting Yang, Rochester Wniversity (US)](https://www.linkedin.com/in/ziting-yang-7b33832bb)
+
+Others
 * With special thanks to our initial testers (alphabetically ordered): [Joji Chia](https://sociology.illinois.edu/directory/profile/jbchia2), [Kass Gonzalez](https://www.linkedin.com/in/kass-gonzalez-72a778276/), [Sinyee Lu](https://sociology.illinois.edu/directory/profile/qianyil4), [Sohee Shin](https://sociology.illinois.edu/directory/profile/sohees2)
 * Website and related technical support: [Mactavish](https://github.com/mactavishz)
-* PAM clustering algorithm implementation: Cheng Deng
 * Sequence data sources compilation - History: Jingrui Chen
 * Visual design consultant: Changyu Yi
 
 **Acknowledgements**
 
-* Methodological advisor in sequence analysis: [Professor Tim Liao, University of Illinois Urbana-Champaign](https://sociology.illinois.edu/directory/profile/tfliao)
-* Yuqi's PhD advisor: [Professor Ridhi Kashyap, University of Oxford](https://www.nuffield.ox.ac.uk/people/profiles/ridhi-kashyap/)
+* Methodological advisor in sequence analysis: [Professor Tim Liao (University of Illinois Urbana-Champaign)](https://sociology.illinois.edu/directory/profile/tfliao)
+* Yuqi's PhD advisor [Professor Ridhi Kashyap (University of Oxford)](https://www.nuffield.ox.ac.uk/people/profiles/ridhi-kashyap/), and mentor [Charles Rahal (University of Oxford)](https://crahal.com/)
 * Yuqi's original programming mentor: [JiangHuShiNian](https://github.com/jianghushinian)
 

{sequenzo-0.1.17 → sequenzo-0.1.19}/README.md

@@ -31,6 +31,11 @@ Sequenzo outperforms traditional R-based tools in social sequence analysis, deli
 >  
 > 📖 Available in **English and Chinese**, our docs are written to be approachable, practical, and easy to follow.
 
+## ✨ Be part of the Sequenzo community
+Join our Discord channel to iscuss ideas, get help, and hear about upcoming Sequenzo versions, tutorials, and workshops first.
+
+➡️ https://discord.gg/3bMDKRHW
+
 ## Target Users
 
 Sequenzo is designed for:
@@ -58,12 +63,12 @@ Perfect for research, policy, and business, enabling seamless analysis of catego
 
 Sequenzo provides pre-built Python wheels for maximum compatibility — no need to compile from source.
 
-| Platform         | Architecture                  | Python Versions      | Status            |
+| Platform         | Architecture                  | Python Versions       | Status            |
 |------------------|-------------------------------|-----------------------|-------------------|
-| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.11       | ✅ Pre-built wheel |
-| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
-| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11       | ✅ Pre-built wheel |
+| **macOS**        | `universal2` (Intel + Apple Silicon) | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Windows**      | `AMD64` (64-bit)              | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (glibc)**| `x86_64` (standard Linux)     | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
+| **Linux (musl)** | `x86_64` (Alpine Linux)       | 3.9, 3.10, 3.11, 3.12 | ✅ Pre-built wheel |
 
 
 What do these terms mean?
@@ -106,6 +111,22 @@ If you have some issues with the installation, it might because you have both Py
 pip3 install sequenzo
 ```
 
+### Optional R Integration
+
+Sequenzo now checks the system environment variables before running ward.D hierarchical clustering.
+
+If R is missing, a relevant prompt will be displayed along with specific installation instructions. If `fastcluster` is missing, Sequenzo will automatically download `fastcluster`.
+
+Before automatically downloading `fastcluster`, Sequenzo checks whether R is available; if R is not installed, sequenzo will not automatically download fastcluster.
+
+Sequenzo supports advanced Ward clustering methods that require R integration. If you need to use the `ward_d` clustering method, install with R support:
+
+```
+pip install sequenzo[r]
+```
+
+This will install the optional `rpy2` dependency, which provides Python-R interoperability. Note that R must also be installed on your system for `rpy2` to work.
+
 For more information about the latest stable release and required dependencies, please refer to [PyPI](https://pypi.org/project/sequenzo/). 
 
 ## Documentation
@@ -143,7 +164,7 @@ Check out our [contribution guide]() for more details (work in progress).
 If you're contributing or debugging, use:
 
 ```bash
-pip install -r requirements-3.10.txt  # Or matching your Python version
+pip install -r requirements/requirements-3.10.txt  # Or matching your Python version
 ```
     
 For standard installation, use:
@@ -156,23 +177,31 @@ pip install .  # Uses pyproject.toml
 
 **Paper Authors**
 * [Yuqi Liang, University of Oxford](https://www.yuqi-liang.tech/)
-* [Xinyi Li, Heilongjiang University](https://github.com/Fantasy201)
+* [Xinyi Li, Northeastern University](https://github.com/Fantasy201)
 * [Jan Heinrich Ernst Meyerhoff-Liang, Institute for New Economic Thinking Oxford](https://www.inet.ox.ac.uk/people/jan-meyerhoff-liang)
 
 **Package Contributors**
-* [Liangxingyun He, Stockholm School of Economics (Sweden)](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
-* [Yukun Ming, Universidad Carlos III de Madrid (Spain)](www.linkedin.com/in/yukun)
-* [Ziting Yang, Rochester Wniversity (US)](www.linkedin.com/in/ziting-yang-7b33832bb)
+
+Coding contributors:
+* [Sebastian Daza](https://sdaza.com/)
+* [Cheng Deng](https://github.com/de-de-de-de-de)
+* [Liangxingyun He, Stockholm School of Economics, Sweden](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
+
+Documentation contributors:
+* [Liangxingyun He, Stockholm School of Economics, Sweden](https://www.linkedin.com/in/liangxingyun-he-6aa128304/)
+* [Yukun Ming, Universidad Carlos III de Madrid (Spain)](https://www.linkedin.com/in/yukun)
 * [Sizhu Qu, Northeastern University (US)](https://www.linkedin.com/in/sizhuq)
+* [Ziting Yang, Rochester Wniversity (US)](https://www.linkedin.com/in/ziting-yang-7b33832bb)
+
+Others
 * With special thanks to our initial testers (alphabetically ordered): [Joji Chia](https://sociology.illinois.edu/directory/profile/jbchia2), [Kass Gonzalez](https://www.linkedin.com/in/kass-gonzalez-72a778276/), [Sinyee Lu](https://sociology.illinois.edu/directory/profile/qianyil4), [Sohee Shin](https://sociology.illinois.edu/directory/profile/sohees2)
 * Website and related technical support: [Mactavish](https://github.com/mactavishz)
-* PAM clustering algorithm implementation: Cheng Deng
 * Sequence data sources compilation - History: Jingrui Chen
 * Visual design consultant: Changyu Yi
 
 **Acknowledgements**
 
-* Methodological advisor in sequence analysis: [Professor Tim Liao, University of Illinois Urbana-Champaign](https://sociology.illinois.edu/directory/profile/tfliao)
-* Yuqi's PhD advisor: [Professor Ridhi Kashyap, University of Oxford](https://www.nuffield.ox.ac.uk/people/profiles/ridhi-kashyap/)
+* Methodological advisor in sequence analysis: [Professor Tim Liao (University of Illinois Urbana-Champaign)](https://sociology.illinois.edu/directory/profile/tfliao)
+* Yuqi's PhD advisor [Professor Ridhi Kashyap (University of Oxford)](https://www.nuffield.ox.ac.uk/people/profiles/ridhi-kashyap/), and mentor [Charles Rahal (University of Oxford)](https://crahal.com/)
 * Yuqi's original programming mentor: [JiangHuShiNian](https://github.com/jianghushinian)
 

{sequenzo-0.1.17 → sequenzo-0.1.19}/pyproject.toml

@@ -29,7 +29,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-version = "0.1.17"
+version = "0.1.19"
 dependencies = [
     "numpy>=1.19.5,<2.5",
     "pandas>=1.2.5",
@@ -41,10 +41,17 @@ dependencies = [
     "scipy>=1.6.3",
     "scikit-learn>=0.24.2",
     "fastcluster>=1.2.6",
+    # rpy2 is required at runtime for Ward D via R fastcluster.
+    # Use PEP 508 markers to select versions per Python runtime.
+    "rpy2>=3.5.12; python_version >= '3.12'",
+    "rpy2>=3.5.6; python_version == '3.11'",
+    "rpy2>=3.5.6; python_version == '3.10'",
+    "rpy2>=3.5.6; python_version == '3.9'",
     "joblib>=1.0.1",
     "docutils>=0.17",
     "tqdm>=4.62.3,<5.0.0",
     "missingno>=0.5.2,<0.6.0",
+    "cffi>=1.15.0",  # Required for C extensions and FFI functionality
 ]
 
 [project.optional-dependencies]

{sequenzo-0.1.17 → sequenzo-0.1.19}/sequenzo/__init__.py

@@ -4,13 +4,6 @@
 @Time    : 11/02/2025 16:41
 @Desc    : 
 """
-# sequenzo/sequenzo/__init__.py (Inside the inner sequenzo package)
-# This file is now needed for making the submodules accessible.
-
-# You *don't* need to handle the Rust extension here.
-# You can have package level docstring here.
-# No need for __all__ here, use relative import in the top-level __init__.py
-
 from .datasets import load_dataset, list_datasets
 
 # Import the core functions that should be directly available from the sequenzo package
@@ -85,6 +78,7 @@ from .sequence_characteristics import (
     get_number_of_transitions,
 
     get_turbulence,
+    get_complexity_index,
     get_within_sequence_entropy,
     get_spell_duration_variance,
     get_state_freq_and_entropy_per_seq,
@@ -95,6 +89,18 @@ from .sequence_characteristics import (
 
 )
 
+# Event History Analysis (SAMM)
+from .with_event_history_analysis import (
+    SAMM,
+    sequence_analysis_multi_state_model,
+    plot_samm,
+    seqsammseq,
+    set_typology,
+    seqsammeha,
+    # Keep old names for backward compatibility
+    seqsamm
+)
+
 # Define `__all__` to specify the public API when using `from sequenzo import *`
 __all__ = [
     # Datasets
@@ -175,10 +181,60 @@ __all__ = [
     "get_subsequences_all_sequences",
     "get_number_of_transitions",
     "get_turbulence",
+    "get_complexity_index",
     "get_within_sequence_entropy",
     "get_spell_duration_variance",
     "get_state_freq_and_entropy_per_seq",
     "get_cross_sectional_entropy",
     "plot_longitudinal_characteristics",
-    "plot_cross_sectional_characteristics"
+    "plot_cross_sectional_characteristics",
+
+    # Event History Analysis (SAMM)
+    "SAMM",
+    "sequence_analysis_multi_state_model",
+    "plot_samm",
+    "seqsammseq",
+    "set_typology",
+    "seqsammeha",
+    # Keep old names for backward compatibility
+    "seqsamm"
 ]
+
+# Auto-setup OpenMP on Apple Silicon (runs on import)
+def _setup_openmp_if_needed():
+    """
+    Automatically setup OpenMP dependencies on Apple Silicon Macs.
+    This function runs on import to ensure OpenMP is available.
+    """
+    import sys
+    import os
+    import platform
+    
+    # Only run on macOS
+    if sys.platform != 'darwin':
+        return
+    
+    # Only run on Apple Silicon
+    if platform.machine() != 'arm64':
+        return
+    
+    # Check if we're in a conda environment (don't interfere)
+    if os.environ.get('CONDA_DEFAULT_ENV'):
+        return
+    
+    # Try to import and run the OpenMP setup
+    try:
+        from .openmp_setup import ensure_openmp_support
+        ensure_openmp_support()
+    except ImportError:
+        # OpenMP setup module not available, skip
+        pass
+    except Exception:
+        # Any other error, skip silently
+        pass
+
+# Run the setup function
+_setup_openmp_if_needed()
+
+# Clean up the setup function from the module namespace
+del _setup_openmp_if_needed

{sequenzo-0.1.17 → sequenzo-0.1.19}/sequenzo/big_data/clara/clara.py

@@ -439,7 +439,7 @@ if __name__ == '__main__':
     # ===============================
     #            detailed
     # ===============================
-    df = pd.read_csv("D:/college/research/QiQi/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
+    df = pd.read_csv("/Users/xinyi/Projects/sequenzo/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
     time = list(df.columns)[4:]
     states = ['data', 'data & intensive math', 'hardware', 'research', 'software', 'software & hardware', 'support & test']
     sequence_data = SequenceData(df[['worker_id', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'C7', 'C8', 'C9', 'C10']],