update readme

README.rst

@@ -8,6 +8,9 @@ friendly interface and data visualization routines.
 
 Mutation signature analysis package
 -----------------------------------
+.. image:: docs/images/pypi-logo.png
+   :target: https://pypi.org/project/starsigndna/
+   :alt: PyPI
 
 .. image:: https://img.shields.io/badge/license-MIT-blue.svg
     :target: https://opensource.org/licenses/MIT
@@ -28,16 +31,20 @@ Features
 Stable release
 --------------
 
-To install StarSign, run this command in your terminal::
+To install StarSign,
+
+you can install the package directly from PyPi::
+
+    pip install starsigndna
+
+ Alternatively,  you can install it via terminal by running this command::
 
     1. Download StarSign from https://github.com/uio-bmi/StarSignDNA
     2. Unzip StarSignDNA-master.zip
     3. cd StarSigndna-master/
     4. pip install -e .
 
-Alternatively, you can install the package directly from PyPi::
 
-    pip install starsigndna
 Getting started
 ---------------
 

starsigndna/cli.py

@@ -293,7 +293,7 @@ def refit(matrix_file: Annotated[str, typer.Argument(help='Tab separated matrix
     S = S.to_numpy().astype(float)
     M = M.to_numpy().astype(float)
     O = read_opportunity(M, opportunity_file)
-    lambd = 0.7
+    lambd = 4
 
     if (M.ndim == 2 and M.shape[0] == 1) or M.ndim == 1:
         boostrap_M = _bootstrap(M,n_bootstraps)