v0.2.0 update

doc/.ipynb_checkpoints/Makefile-checkpoint

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?="-c."
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = "."
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

doc/.ipynb_checkpoints/conf-checkpoint.py

@@ -0,0 +1,55 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Genes2Genes'
+copyright = '2023, Dinithi Sumanaweera, Teichmann Lab'
+author = 'Dinithi Sumanaweera, Teichmann Lab'
+
+# The full version, including alpha/beta/rc tags
+release = 'v0.2.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx_rtd_theme",'sphinx.ext.intersphinx']
+# "myst_parser" removed as myst_nb automatically activates it
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

doc/.ipynb_checkpoints/make-checkpoint.bat

@@ -7,7 +7,7 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
+set SOURCEDIR=.
 set BUILDDIR=build
 
 if "%1" == "" goto help

doc/Makefile

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?="-c."
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = "."
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".