DOCS Add logo

README.md

@@ -1,4 +1,5 @@
-# PyDESeq2
+<img src="docs/source/_static/pydeseq2_logo_green.png" width="600">
+
 
 ## Table of Contents
 - [PyDESeq2](#pydeseq2)

docs/source/conf.py

@@ -157,7 +157,11 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_theme_options = {"analytics_id": "UA-83738774-2"}
+html_theme_options = {
+    "analytics_id": "UA-83738774-2",
+    "logo_only": True,
+    "display_version": True,
+}
 
 # 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,
@@ -246,7 +250,7 @@
     "sidebar.css",
 ]
 
-# html_logo = "static/logo.svg"
+html_logo = "_static/pydeseq2_logo.svg"
 html_show_sourcelink = False
 html_show_sphinx = True
 

pydeseq2/dds.py

@@ -53,8 +53,8 @@ class DeseqDataSet(ad.AnnData):
     ----------
     adata : anndata.AnnData
         AnnData from which to initialize the DeseqDataSet. Must have counts ('X') and
-         clinical metadata ('obs') fields. If ``None``, both ``counts`` and ``clinical``
-         arguments must be provided.
+        clinical metadata ('obs') fields. If ``None``, both ``counts`` and ``clinical``
+        arguments must be provided.
 
     counts : pandas.DataFrame
         Raw counts. One column per gene, rows are indexed by sample barcodes.