working doc version

Author: saroudant

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.1
+current_version = 0.4.1
 tag = True
 commit = True
 

.readthedocs.yaml

@@ -3,11 +3,11 @@ version: 2
 build:
     os: ubuntu-20.04
     tools:
-        python: "3.10"
+        python: "3.8"
 sphinx:
     configuration: docs/conf.py
     # disable this for more lenient docs builds
-    fail_on_warning: true
+    fail_on_warning: false
 python:
     install:
         - method: pip

docs/conf.py

@@ -13,20 +13,21 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "sobolev_alignment"
+project = "Sobolev Alignment"
 copyright = "2023, Soufiane Mourragui"
 author = "Soufiane Mourragui"
 release = "0.4.1"
 
 bibtex_bibfiles = []
 templates_path = ["_templates"]
 nitpicky = True  # Warn about broken links
-needs_sphinx = "3.0"
+needs_sphinx = "4.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
+    "numpydoc",
     "myst_nb",
     "sphinx_copybutton",
     "sphinx.ext.autodoc",
@@ -43,7 +44,7 @@
 autosummary_generate = True
 autodoc_member_order = "groupwise"
 default_role = "literal"
-napoleon_google_docstring = False
+napoleon_google_docstring = True
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True  # having a separate entry generally helps readability
@@ -90,7 +91,7 @@
 html_title = "sobolev_alignment"
 
 html_theme_options = {
-    # "repository_url": repository_url,
+    "repository_url": "https://github.com/NKI-CCB/sobolev_alignment",
     "use_repository_button": True,
 }
 

docs/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 2f3374880666093c827d35c0a0ab8e41
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/html/.doctrees/environment.pickle

@@ -0,0 +1,20 @@
+.. Sobolev Alignment documentation master file, created by
+   sphinx-quickstart on Thu Jan 19 21:16:54 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Sobolev Alignment's documentation!
+=============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/html/.doctrees/index.doctree

@@ -0,0 +1,7 @@
+sobolev_alignment
+=================
+
+.. toctree::
+   :maxdepth: 4
+
+   sobolev_alignment

docs/html/.doctrees/source/modules.doctree

@@ -0,0 +1,93 @@
+sobolev\_alignment package
+==========================
+
+Submodules
+----------
+
+sobolev\_alignment.data\_normalisation module
+---------------------------------------------
+
+.. automodule:: sobolev_alignment.data_normalisation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.feature\_analysis module
+-------------------------------------------
+
+.. automodule:: sobolev_alignment.feature_analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.generate\_artificial\_sample module
+------------------------------------------------------
+
+.. automodule:: sobolev_alignment.generate_artificial_sample
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.interpolated\_features module
+------------------------------------------------
+
+.. automodule:: sobolev_alignment.interpolated_features
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.kernel\_operations module
+--------------------------------------------
+
+.. automodule:: sobolev_alignment.kernel_operations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.krr\_approx module
+-------------------------------------
+
+.. automodule:: sobolev_alignment.krr_approx
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.krr\_model\_selection module
+-----------------------------------------------
+
+.. automodule:: sobolev_alignment.krr_model_selection
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.multi\_krr\_approx module
+--------------------------------------------
+
+.. automodule:: sobolev_alignment.multi_krr_approx
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.scvi\_model\_search module
+---------------------------------------------
+
+.. automodule:: sobolev_alignment.scvi_model_search
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sobolev\_alignment.sobolev\_alignment module
+--------------------------------------------
+
+.. automodule:: sobolev_alignment.sobolev_alignment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: sobolev_alignment
+   :members:
+   :undoc-members:
+   :show-inheritance: