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docs: add Sphinx configuration with Markdown support and index.md setup
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‎README.md‎

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```text
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genSurvPy/
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gen_surv/
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├── cphm.py
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├── cmm.py
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├── tdcm.py
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├── thmm.py
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├── censoring.py
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├── validate.py
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examples/
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├── run_cphm.py
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├── run_cmm.py
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├── run_tdcm.py
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├── run_thmm.py
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└── utils.py # optional for shared config (e.g. seeding)
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├── gen_surv/ # Pacote principal
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│ ├── __main__.py # Interface CLI via python -m
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│ ├── cphm.py
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│ ├── cmm.py
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│ ├── tdcm.py
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│ ├── thmm.py
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│ ├── censoring.py
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│ ├── bivariate.py
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│ ├── validate.py
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│
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├── tests/ # Testes automatizados
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│ ├── test_cphm.py
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│ ├── test_cmm.py
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│ ├── test_tdcm.py
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│ ├── test_thmm.py
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│
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├── examples/ # Exemplos de uso
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│ ├── run_cphm.py
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│ ├── ...
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│
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├── pyproject.toml # Configurado com Poetry
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├── README.md
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├── LICENSE
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├── .gitignore
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```
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## 🧠 License

‎docs/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../../gen_surv'))
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project = 'gen_suv'
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copyright = '2025, Diogo Ribeiro'
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author = 'Diogo Ribeiro'
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release = '0.2.0'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon",
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"myst_parser",
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]
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# Point to index.md or index.rst as the root document
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master_doc = "index"
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templates_path = ['_templates']
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = 'alabaster'
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html_static_path = ['_static']
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‎docs/source/gen_surv.rst‎

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gen\_surv package
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=================
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Submodules
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----------
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gen\_surv.bivariate module
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--------------------------
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.. automodule:: gen_surv.bivariate
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.censoring module
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--------------------------
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.. automodule:: gen_surv.censoring
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.cmm module
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--------------------
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.. automodule:: gen_surv.cmm
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.cphm module
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---------------------
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.. automodule:: gen_surv.cphm
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.tdcm module
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---------------------
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.. automodule:: gen_surv.tdcm
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.thmm module
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---------------------
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.. automodule:: gen_surv.thmm
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:members:
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:undoc-members:
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:show-inheritance:
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gen\_surv.validate module
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-------------------------
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.. automodule:: gen_surv.validate
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: gen_surv
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/index.md‎

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# gen_surv
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**gen_surv** is a Python package for simulating survival data under various models, inspired by the R package `genSurv`.
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It includes generators for:
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- **Cox Proportional Hazards Models (CPHM)**
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- **Continuous-Time Markov Models (CMM)**
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- **Time-Dependent Covariate Models (TDCM)**
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- **Time-Homogeneous Hidden Markov Models (THMM)**
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---
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## 📚 Modules
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```{toctree}
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:maxdepth: 2
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:caption: Contents
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modules
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```
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# 🚀 Usage Example
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```python
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from gen_surv.cphm import gen_cphm
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df = gen_cphm(n=100, model_cens="uniform", cens_par=1.0, beta=0.5, covar=2.0)
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print(df.head())
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```
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## 🔗 Project Links
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- [Source Code](https://github.com/DiogoRibeiro7/genSurvPy)
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- [License](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/LICENSE)

‎docs/source/modules.rst‎

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gen_surv
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========
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.. toctree::
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:maxdepth: 4
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gen_surv

‎pyproject.toml‎

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[tool.poetry.group.dev.dependencies]
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pytest = "^8.3.5"
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[tool.poetry.group.docs.dependencies]
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myst-parser = "<4.0.0"
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[tool.semantic_release]
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version_source = "tag"
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version_variable = ["pyproject.toml:project.version"]

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