Update docs and add logo

docs/conf.py

@@ -21,8 +21,11 @@
 copyright = '2020, John McGuigan'
 author = 'John McGuigan'
 
-# The full version, including alpha/beta/rc tags
-release = 'v0.1.0'
+import pandas_genomics
+# The short X.Y version.
+version = pandas_genomics.__version__
+# The full version, including alpha/beta/rc tags.
+release = pandas_genomics.__version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,8 +34,29 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+    'IPython.sphinxext.ipython_directive',
+    'IPython.sphinxext.ipython_console_highlighting',
+    'numpydoc',
+    'sphinx_copybutton'
 ]
 
+# Configuration options for plot_directive. See:
+# https://github.com/matplotlib/matplotlib/blob/f3ed922d935751e08494e5fb5311d3050a3b637b/lib/matplotlib/sphinxext/plot_directive.py#L81
+plot_html_show_source_link = False
+plot_html_show_formats = False
+
+# Generate the API documentation when building
+autosummary_generate = True
+numpydoc_show_class_members = False
+
+# The master toctree document.
+master_doc = 'index'
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -41,15 +65,41 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
 
-# -- Options for HTML output -------------------------------------------------
+# -- 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 = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+import sphinx_rtd_theme
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # 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']
+html_static_path = ['_static']
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_logo = '_static/logo.png'
+html_theme_options = {
+    'logo_only': True,
+}
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}

pyproject.toml

@@ -8,6 +8,9 @@ authors = ["John McGuigan <jrm5100@psu.edu>"]
 python = "^3.7"
 pandas = "^1.1"
 sphinx = {version = "^3.2.1", optional = true}
+sphinx_rtd_theme = {version = "^0.5.0", extras = ["docs"]}
+numpydoc = {version = "^1.1.0", extras = ["docs"]}
+sphinx-copybutton = {version = "^0.3.0", extras = ["docs"]}
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"