From 3be66e7dd19ce0e3621b72f4e8581c3d1dfeb29d Mon Sep 17 00:00:00 2001
From: Diogo Ribeiro <diogo_dj@hotmail.com>
Date: Fri, 20 Jun 2025 15:30:26 +0100
Subject: [PATCH] docs: document all functions

---
 README.md                    | 22 +++++++++++++---------
 docs/source/_static/.gitkeep |  0
 docs/source/conf.py          |  6 +++++-
 docs/source/index.md         |  8 ++++++++
 docs/source/modules.md       | 24 ++++++++++++++++++++++--
 docs/source/usage.md         | 33 +++++++++++++++++++++++++++++++++
 6 files changed, 81 insertions(+), 12 deletions(-)
 create mode 100644 docs/source/_static/.gitkeep
 create mode 100644 docs/source/usage.md

diff --git a/README.md b/README.md
index b4f34af..41b5254 100644
--- a/README.md
+++ b/README.md
@@ -65,15 +65,19 @@ writing Python code:
 python -m gen_surv dataset aft_ln --n 100 > data.csv
 ```
 
-## 🔧 Available Generators
-
-| Function     | Description                                |
-|--------------|--------------------------------------------|
-| `gen_cphm()` | Cox Proportional Hazards Model             |
-| `gen_cmm()`  | Continuous-Time Multi-State Markov Model   |
-| `gen_tdcm()` | Time-Dependent Covariate Model             |
-| `gen_thmm()` | Time-Homogeneous Markov Model              |
-| `gen_aft_log_normal()` | Accelerated Failure Time Log-Normal  |
+## 🔧 API Overview
+
+| Function | Description |
+|----------|-------------|
+| `generate()` | Unified interface that calls any generator |
+| `gen_cphm()` | Cox Proportional Hazards Model |
+| `gen_cmm()`  | Continuous-Time Multi-State Markov Model |
+| `gen_tdcm()` | Time-Dependent Covariate Model |
+| `gen_thmm()` | Time-Homogeneous Markov Model |
+| `gen_aft_log_normal()` | Accelerated Failure Time Log-Normal |
+| `sample_bivariate_distribution()` | Sample correlated Weibull or exponential times |
+| `runifcens()` | Generate uniform censoring times |
+| `rexpocens()` | Generate exponential censoring times |
 
 
 ```text
diff --git a/docs/source/_static/.gitkeep b/docs/source/_static/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/docs/source/conf.py b/docs/source/conf.py
index cd44dab..9c16f15 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -9,7 +9,7 @@
 import sys
 sys.path.insert(0, os.path.abspath('../../gen_surv'))
 
-project = 'gen_suvr'
+project = 'gen_surv'
 copyright = '2025, Diogo Ribeiro'
 author = 'Diogo Ribeiro'
 release = '0.6.3'
@@ -22,8 +22,11 @@
     "sphinx.ext.napoleon",
     "myst_parser",
     "sphinx.ext.viewcode",
+    "sphinx.ext.autosectionlabel",
 ]
 
+autosectionlabel_prefix_document = True
+
 # Point to index.md or index.rst as the root document
 master_doc = "index"
 
@@ -36,3 +39,4 @@
 html_theme = 'alabaster'
 html_static_path = ['_static']
 
+
diff --git a/docs/source/index.md b/docs/source/index.md
index 83e034d..da7345b 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -10,14 +10,21 @@ It includes generators for:
 - **Time-Homogeneous Hidden Markov Models (THMM)**
 - **Accelerated Failure Time (AFT) Log-Normal Models**
 
+Key functions include `generate()`, `gen_cphm()`, `gen_cmm()`, `gen_tdcm()`,
+`gen_thmm()`, `gen_aft_log_normal()`, `sample_bivariate_distribution()`,
+`runifcens()`, and `rexpocens()`.
+
 ---
 
+See the [Getting Started](usage) guide for installation instructions.
+
 ## 📚 Modules
 
 ```{toctree}
 :maxdepth: 2
 :caption: Contents
 
+usage
 modules
 theory
 ```
@@ -62,3 +69,4 @@ python -m gen_surv dataset aft_ln --n 100 > data.csv
 - [Source Code](https://github.com/DiogoRibeiro7/genSurvPy)
 - [License](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/LICENSE)
 - [Code of Conduct](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/CODE_OF_CONDUCT.md)
+
diff --git a/docs/source/modules.md b/docs/source/modules.md
index 7e9256f..114a344 100644
--- a/docs/source/modules.md
+++ b/docs/source/modules.md
@@ -23,9 +23,29 @@
 ::: gen_surv.interface
     options:
       members: true
-      undoc-members: tru
+      undoc-members: true
 
 ::: gen_surv.aft
     options:
       members: true
-      undoc-members: true
\ No newline at end of file
+      undoc-members: true
+
+::: gen_surv.bivariate
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.censoring
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.cli
+    options:
+      members: true
+      undoc-members: true
+
+::: gen_surv.validate
+    options:
+      members: true
+      undoc-members: true
diff --git a/docs/source/usage.md b/docs/source/usage.md
new file mode 100644
index 0000000..e3f856e
--- /dev/null
+++ b/docs/source/usage.md
@@ -0,0 +1,33 @@
+# Getting Started
+
+This page offers a quick introduction to installing and using **gen_surv**.
+
+## Installation
+
+The project is managed with [Poetry](https://python-poetry.org). Clone the repository and install dependencies:
+
+```bash
+poetry install
+```
+
+This will create a virtual environment and install all required packages.
+
+## Basic Usage
+
+Generate datasets directly in Python:
+
+```python
+from gen_surv import generate
+
+# Cox Proportional Hazards example
+generate(model="cphm", n=100, model_cens="uniform", cens_par=1.0, beta=0.5, covar=2.0)
+```
+
+You can also generate data from the command line:
+
+```bash
+python -m gen_surv dataset aft_ln --n 100 > data.csv
+```
+
+For a full description of available models and parameters, see the API reference.
+