Fix docs build and sort imports (#54)

DiogoRibeiro7 · web-flow · commit 908e6d18a8ea · 2025-07-30T14:10:38.000+01:00
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -4,3 +4,4 @@ sphinx-rtd-theme
 sphinx-autodoc-typehints
 sphinx-copybutton
 sphinx-design
+linkify-it-py>=2.0
diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Algorithm Overview
 
 This page provides a short description of each model implemented in **gen_surv**.  For mathematical details see {doc}`theory`.
diff --git a/docs/source/api/index.md b/docs/source/api/index.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # API Reference
 
 Complete documentation for all gen_surv functions and classes.
diff --git a/docs/source/bibliography.md b/docs/source/bibliography.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # References
 
 Below is a selection of references covering the statistical models implemented in **gen_surv**.
diff --git a/docs/source/changelog.md b/docs/source/changelog.md
@@ -1,5 +1,9 @@
+---
+orphan: true
+---
+
 # Changelog
 
 ```{include} ../../CHANGELOG.md
-:relative: true
+:relative-docs: true
 ```
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -64,6 +64,10 @@
     'pandas': ('https://pandas.pydata.org/docs/', None),
 }
 
+# Disable fetching remote inventories when network access is unavailable
+if os.environ.get("SKIP_INTERSPHINX", "1") == "1":
+    intersphinx_mapping = {}
+
 # HTML theme options
 html_theme = 'sphinx_rtd_theme'
 html_theme_options = {
diff --git a/docs/source/contributing.md b/docs/source/contributing.md
@@ -1,5 +1,9 @@
+---
+orphan: true
+---
+
 # Contributing
 
 ```{include} ../../CONTRIBUTING.md
-:relative: true
+:relative-docs: true
 ```
diff --git a/docs/source/examples/index.md b/docs/source/examples/index.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Examples
 
 Real-world examples and use cases for gen_surv.
diff --git a/docs/source/getting_started.md b/docs/source/getting_started.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Getting Started
 
 This guide will help you install gen_surv and generate your first survival dataset.
diff --git a/docs/source/modules.md b/docs/source/modules.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # API Reference
 
 ::: gen_surv.cphm
diff --git a/docs/source/rtd.md b/docs/source/rtd.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Read the Docs
 
 This project uses [Read the Docs](https://readthedocs.org/) to host its documentation. The site is automatically rebuilt whenever changes are pushed to the repository.
diff --git a/docs/source/theory.md b/docs/source/theory.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # 📘 Mathematical Foundations of `gen_surv`
 
 This page presents the mathematical formulation behind the survival models implemented in the `gen_surv` package.
diff --git a/docs/source/tutorials/index.md b/docs/source/tutorials/index.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Tutorials
 
 Step-by-step guides for using gen_surv effectively.
diff --git a/docs/source/usage.md b/docs/source/usage.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Getting Started
 
 This page offers a quick introduction to installing and using **gen_surv**.
diff --git a/gen_surv/interface.py b/gen_surv/interface.py
@@ -58,7 +58,8 @@ def generate(model: str, **kwargs: Any) -> pd.DataFrame:
             ``tdcm``, ``thmm``, ``aft_ln``, ``aft_weibull``, ``aft_log_logistic``,
             ``competing_risks``, ``competing_risks_weibull``, ``mixture_cure``,
             or ``piecewise_exponential``.
-        **kwargs: Arguments forwarded to the chosen generator. These vary by model:
+        **kwargs: Arguments forwarded to the chosen generator. These vary by model.
+
             - cphm: n, model_cens, cens_par, beta, covariate_range
             - cmm: n, model_cens, cens_par, beta, covariate_range, rate
             - tdcm: n, dist, corr, dist_par, model_cens, cens_par, beta, lam
diff --git a/gen_surv/tdcm.py b/gen_surv/tdcm.py
@@ -11,17 +11,18 @@ def generate_censored_observations(n, dist_par, model_cens, cens_par, beta, lam,
     Generate censored TDCM observations.
 
     Parameters:
-    - n (int): Number of individuals
-    - dist_par (list): Not directly used here (kept for API compatibility)
-    - model_cens (str): "uniform" or "exponential"
-    - cens_par (float): Parameter for the censoring model
-    - beta (list): Length-2 list of regression coefficients
-    - lam (float): Rate parameter
-    - b (np.ndarray): Covariate matrix with 2 columns [., z1]
+
+        - n (int): Number of individuals
+        - dist_par (list): Not directly used here (kept for API compatibility)
+        - model_cens (str): "uniform" or "exponential"
+        - cens_par (float): Parameter for the censoring model
+        - beta (list): Length-2 list of regression coefficients
+        - lam (float): Rate parameter
+        - b (np.ndarray): Covariate matrix with 2 columns [., z1]
 
     Returns:
-    - np.ndarray: Shape (n, 6) with columns:
-      [id, start, stop, status, covariate1 (z1), covariate2 (z2)]
+        - np.ndarray: Shape (n, 6) with columns:
+          [id, start, stop, status, covariate1 (z1), covariate2 (z2)]
     """
     rfunc = runifcens if model_cens == "uniform" else rexpocens
     observations = np.zeros((n, 6))
diff --git a/pyproject.toml b/pyproject.toml
@@ -51,6 +51,7 @@ myst-parser = ">=1.0.0,<4.0.0"
 sphinx-autodoc-typehints = "^1.24.0"
 sphinx-copybutton = "^0.5.2"
 sphinx-design = "^0.5.0"
+linkify-it-py = ">=2.0"
 
 [tool.poetry.scripts]
 gen_surv = "gen_surv.cli:app"
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1,9 +1,9 @@
 import os
 import runpy
 import sys
-import pytest
 
 import pandas as pd
+import pytest
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 from gen_surv.cli import dataset, visualize
diff --git a/tests/test_piecewise_functions.py b/tests/test_piecewise_functions.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from gen_surv.piecewise import piecewise_hazard_function, piecewise_survival_function
 
 
diff --git a/tests/test_summary_extra.py b/tests/test_summary_extra.py
@@ -1,11 +1,12 @@
 import pandas as pd
 import pytest
+
+from gen_surv import generate
 from gen_surv.summary import (
+    _print_summary,
     check_survival_data_quality,
     compare_survival_datasets,
-    _print_summary,
 )
-from gen_surv import generate
 
 
 def test_check_survival_data_quality_fix_issues():
diff --git a/tests/test_summary_more.py b/tests/test_summary_more.py
@@ -1,9 +1,10 @@
 import pandas as pd
 import pytest
+
 from gen_surv.summary import (
-    summarize_survival_dataset,
-    check_survival_data_quality,
     _print_summary,
+    check_survival_data_quality,
+    summarize_survival_dataset,
 )
 
 
