fixes for doc

aadya940 · aadya940 · commit 2eeb424e00ec · 2024-07-13T16:53:00.000+05:30
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -6,7 +6,8 @@ build:
     python: "3.10"
   jobs:
     pre_build:
-      - sphinx-apidoc -o docs/source chainopy/ *.pyx
+      - python setup.py build_ext --inplace
+      - sphinx-apidoc --private -o docs/source ../chainopy/
 
 python:
   install:
@@ -24,5 +25,4 @@ sphinx:
   fail_on_warning: false
 
 submodules:
-  include: ['chainopy']
   recursive: true
diff --git a/chainopy/__init__.py b/chainopy/__init__.py
@@ -1,6 +1,6 @@
-from .markov_chain import MarkovChain
-from .nn import MarkovChainNeuralNetwork, divergance_analysis
-from .markov_switching import MarkovSwitchingModel
+from ._markov_chain import MarkovChain
+from ._nn import MarkovChainNeuralNetwork, divergance_analysis
+from ._markov_switching import MarkovSwitchingModel
 
 __all__ = [
     "MarkovChain",
diff --git a/chainopy/_caching.py b/chainopy/_caching.py
diff --git a/chainopy/_exceptions.py b/chainopy/_exceptions.py
diff --git a/chainopy/_fileio.py b/chainopy/_fileio.py
diff --git a/chainopy/_markov_chain.py b/chainopy/_markov_chain.py
@@ -4,10 +4,10 @@
 import numpy as np
 import numba
 
-from .exceptions import handle_exceptions
-from .visualizations import _visualize_tpm, _visualize_chain
-from .fileio import _save_model_markovchain, _load_model_markovchain, load_text
-from .caching import cache
+from ._exceptions import handle_exceptions
+from ._visualizations import _visualize_tpm, _visualize_chain
+from ._fileio import _save_model_markovchain, _load_model_markovchain, load_text
+from ._caching import cache
 from ._backend import (
     _simulate,
     _absorbing,
diff --git a/chainopy/_markov_switching.py b/chainopy/_markov_switching.py
@@ -2,7 +2,7 @@
 from typing import List, Tuple
 from statsmodels.tsa.ar_model import AutoReg
 
-from .markov_chain import MarkovChain
+from ._markov_chain import MarkovChain
 
 
 class MarkovSwitchingModel:
@@ -117,8 +117,8 @@ def predict(
 
         Returns:
         --------
-        Tuple[np.ndarray, np.ndarray]: 
-            Tuple containing the array of predicted target values and the predicted regime sequence.
+        Tuple[np.ndarray, np.ndarray]: Tuple containing the array of predicted
+        target values and the predicted regime sequence.
         """
         predictions = np.zeros(steps, dtype=np.float32)
         regime_predictions = self._markov_chain.simulate(start_regime, steps)
diff --git a/chainopy/_nn.py b/chainopy/_nn.py
@@ -6,7 +6,7 @@
 import warnings
 import random
 
-from .markov_chain import MarkovChain
+from ._markov_chain import MarkovChain
 from ._backend import _learn_matrix
 
 
diff --git a/chainopy/_visualizations.py b/chainopy/_visualizations.py
diff --git a/chainopy/tests/test_markovchain.py b/chainopy/tests/test_markovchain.py
@@ -3,7 +3,7 @@
 import numpy as np
 import os
 
-from ..markov_chain import MarkovChain
+from .._markov_chain import MarkovChain
 
 
 def test_init():
diff --git a/chainopy/tests/test_nn.py b/chainopy/tests/test_nn.py
@@ -2,8 +2,8 @@
 import numpy as np
 import torch
 
-from ..nn import MarkovChainNeuralNetwork, divergance_analysis
-from ..markov_chain import MarkovChain
+from .._nn import MarkovChainNeuralNetwork, divergance_analysis
+from .._markov_chain import MarkovChain
 
 
 @pytest.fixture
diff --git a/chainopy/tests/test_switching.py b/chainopy/tests/test_switching.py
@@ -1,7 +1,7 @@
 import numpy as np
 import random
 
-from ..markov_switching import MarkovSwitchingModel
+from .._markov_switching import MarkovSwitchingModel
 
 
 def test_model_fit():
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -38,8 +38,6 @@
     "sphinx_autodoc_typehints",
 ]
 
-bibtex_bibfiles = ["paper.bib"]
-
 source_suffix = {
     ".rst": "restructuredtext",
     ".md": "markdown",
@@ -52,17 +50,21 @@
     "Thumbs.db",
     ".DS_Store",
     "chainopy.tests.rst",
+    "chainopy._backend.rst",
+    "chainopy.rst",
+    "modules.rst",
+    "_templates"
 ]
 
 autodoc_default_options = {
     "members": True,
     "undoc-members": True,
     "private-members": True,
     "special-members": "__init__",
-    "inherited-members": True,
-    "show-inheritance": True,
 }
 
+autosummary_generate=True
+
 napoleon_google_docstring = True
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = True
diff --git a/docs/source/index.md b/docs/source/index.md
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,19 @@
+# Welcome to Chainopy's documentation!
+
+CHAINOPY
+========
+
+.. toctree::
+
+.. autosummary::
+   :toctree: _autosummary
+
+   chainopy._markov_chain
+   chainopy._markov_switching
+   chainopy._nn
+
+
+README File
+===========
+
+.. mdinclude:: ../../README.md
