chore: code coverage

.github/workflows/test.yml

@@ -29,3 +29,9 @@ jobs:
 
       - name: Run tests
         run: poetry run pytest
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}  # optional if public repo

README.md

@@ -1,5 +1,7 @@
 # gen_surv
 
+![Coverage](https://codecov.io/gh/DiogoRibeiro7/genSurvPy/branch/main/graph/badge.svg)
+
 **gen_surv** is a Python package for simulating survival data under a variety of models, inspired by the R package [`genSurv`](https://cran.r-project.org/package=genSurv). It supports data generation for:
 
 - Cox Proportional Hazards Models (CPHM)
@@ -48,19 +50,30 @@ print(df.head())
 
 ```text
 genSurvPy/
-gen_surv/
-├── cphm.py
-├── cmm.py
-├── tdcm.py
-├── thmm.py
-├── censoring.py
-├── validate.py
-examples/
-├── run_cphm.py
-├── run_cmm.py
-├── run_tdcm.py
-├── run_thmm.py
-└── utils.py         # optional for shared config (e.g. seeding)
+├── gen_surv/             # Pacote principal
+│   ├── __main__.py       # Interface CLI via python -m
+│   ├── cphm.py
+│   ├── cmm.py
+│   ├── tdcm.py
+│   ├── thmm.py
+│   ├── censoring.py
+│   ├── bivariate.py
+│   ├── validate.py
+│
+├── tests/                # Testes automatizados
+│   ├── test_cphm.py
+│   ├── test_cmm.py
+│   ├── test_tdcm.py
+│   ├── test_thmm.py
+│
+├── examples/             # Exemplos de uso
+│   ├── run_cphm.py
+│   ├── ...
+│
+├── pyproject.toml        # Configurado com Poetry
+├── README.md
+├── LICENSE
+├── .gitignore
 ```
 
 ## 🧠 License

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,37 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../gen_surv'))
+
+project = 'gen_suvr'
+copyright = '2025, Diogo Ribeiro'
+author = 'Diogo Ribeiro'
+release = '0.2.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "myst_parser",
+]
+
+# Point to index.md or index.rst as the root document
+master_doc = "index"
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+

docs/source/gen_surv.rst

@@ -0,0 +1,69 @@
+gen\_surv package
+=================
+
+Submodules
+----------
+
+gen\_surv.bivariate module
+--------------------------
+
+.. automodule:: gen_surv.bivariate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.censoring module
+--------------------------
+
+.. automodule:: gen_surv.censoring
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.cmm module
+--------------------
+
+.. automodule:: gen_surv.cmm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.cphm module
+---------------------
+
+.. automodule:: gen_surv.cphm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.tdcm module
+---------------------
+
+.. automodule:: gen_surv.tdcm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.thmm module
+---------------------
+
+.. automodule:: gen_surv.thmm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gen\_surv.validate module
+-------------------------
+
+.. automodule:: gen_surv.validate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: gen_surv
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.md

@@ -0,0 +1,36 @@
+# gen_surv
+
+**gen_surv** is a Python package for simulating survival data under various models, inspired by the R package `genSurv`.
+
+It includes generators for:
+
+- **Cox Proportional Hazards Models (CPHM)**
+- **Continuous-Time Markov Models (CMM)**
+- **Time-Dependent Covariate Models (TDCM)**
+- **Time-Homogeneous Hidden Markov Models (THMM)**
+
+---
+
+## 📚 Modules
+
+```{toctree}
+:maxdepth: 2
+:caption: Contents
+
+modules
+```
+
+
+# 🚀 Usage Example
+
+```python
+from gen_surv.cphm import gen_cphm
+
+df = gen_cphm(n=100, model_cens="uniform", cens_par=1.0, beta=0.5, covar=2.0)
+print(df.head())
+```
+
+## 🔗 Project Links
+
+- [Source Code](https://github.com/DiogoRibeiro7/genSurvPy)
+- [License](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/LICENSE)

docs/source/modules.md

@@ -0,0 +1,21 @@
+# API Reference
+
+::: gen_surv.cphm
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.cmm
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.tdcm
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.thmm
+    options:
+      members: true
+      undoc-members: true

pyproject.toml

@@ -16,6 +16,10 @@ pytest-cov = "^6.1.1"
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.5"
 
+
+[tool.poetry.group.docs.dependencies]
+myst-parser = "<4.0.0"
+
 [tool.semantic_release]
 version_source = "tag"
 version_variable = ["pyproject.toml:project.version"]