configuration docs

docs/API.rst

@@ -1,10 +1,19 @@
 .. _api:
 
-===
-API
-===
+=================
+API Documentation
+=================
+
+
+.. contents:: Contents
+   :depth: 3
+   :local:
+
 
 .. automodule:: xclone
+   :members:
+
+
 
 Import XClone as::
 
@@ -38,7 +47,60 @@ Read / Load
 Config module-specific parmas
 -----------------------------
 
-.. autofunction:: xclone.XCloneConfig
+Main config manager
+~~~~~~~~~~~~~~~~~~~
+
+.. autoclass:: xclone.PreprocessingConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+.. autoclass:: xclone.XCloneConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Module specific config manager 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autoclass:: xclone.XCloneGeneral_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+.. autoclass:: xclone.RDR_General_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+.. autoclass:: xclone.BAF_General_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: xclone.Combine_General_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+.. autoclass:: xclone.HMM_Configs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: xclone.Smartseq_Config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: xclone.Spatial_Config
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 
 

docs/conf.py

@@ -68,6 +68,20 @@
     'sphinxcontrib.bibtex',
     # "edit_on_github",
 ]
+
+# Add this to include __init__ method docstrings in the class documentation
+autoclass_content = 'both'
+
+autodoc_default_options = {
+    'members': True,
+    'undoc-members': True,
+    'private-members': True,
+    'special-members': True,
+    'inherited-members': True,
+    'show-inheritance': True,
+}
+
+
 bibtex_bibfiles = ['references.bib']
 # Use the APA style
 bibtex_default_style = 'plain' #Or 'unsrt', 'alpha', 'abbrv'

docs/release.rst

@@ -6,12 +6,14 @@ Release History
    :local:
 
 
-
-Version 0.3.7
+Version 0.3.8
 -------------
-- [docs]
+- [docs] Base Configurations class.
 
 
+Version 0.3.7
+-------------
+- [docs] Main functions.
 
 
 Version 0.3.6

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xclone"
-version = "0.3.7"
+version = "0.3.8"
 description = "XClone: Inference of clonal Copy Number Alterations in single cells"
 authors = ["Rongting Huang <[email protected]>"]
 readme = "README.rst"

xclone/__init__.py

@@ -17,4 +17,6 @@
 from .model import mixture as mixture
 
 from ._logging import get_logger
-from ._config import PreprocessingConfig, XCloneConfig, settings
+from ._config import PreprocessingConfig, XCloneConfig, settings
+from ._config import XCloneGeneral_config, RDR_General_config, BAF_General_config, Combine_General_config
+from ._config import HMM_Configs, Smartseq_Config, Spatial_Config