From 1f8ab352a18f3e6c85839fcdd2e445f881801439 Mon Sep 17 00:00:00 2001
From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com>
Date: Sun, 10 Dec 2023 15:21:52 +0100
Subject: [PATCH 1/3] Update README.md

add some badges inlcude bioarchive and JCTC DOI
---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index 25c0f73..5183d2d 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,9 @@
 # Shocker
+[![Build Status](https://github.com/marrink-lab/shocker/actions/workflows/python-ci.yml/badge.svg)](https://github.com/marrink-lab/shocker/actions)
+[![BioRxiv:10.1101/2023.08.16.553535](http://img.shields.io/badge/BioRxiv-10.1101/2023.08.16.553535-ad353a.svg)](https://doi.org/10.1101/2023.08.16.553535)
+[![JCTC:10.1021/acs.jctc.3c00961](http://img.shields.io/badge/JCTC-10.1021/acs.jctc.3c00961-007b42.svg)](https://doi.org/10.1021/acs.jctc.3c00961)
+![license](https://img.shields.io/github/license/marrink-lab/shocker)
+
 Shocker is a python package for simulating the effects of water efflux (influx) during a hypertonic (hypotonic) osmotic shock by relocating water particles from the inner to the outer compartment (or vice versa). The algortihm can be applied to any structure containing an enclosed compartment of solvent such as a vesicle, tube or double bilayer system. The tool works with the md code GROMACS and can be applied to both AA systems and CG systems. Shocker is applicable to membranes containing proteins and other molecules such as polymers and DNA. Shocker divides the simulation in pumping cycles, defined as relocation of a number of water particles followed by relaxation time.
 
 # Instructions

From ec03afe9db6508f41b27ac356a7ae9eb196c7c82 Mon Sep 17 00:00:00 2001
From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com>
Date: Sun, 10 Dec 2023 15:25:37 +0100
Subject: [PATCH 2/3] Update python-ci.yml

Update code coverage test run
---
 .github/workflows/python-ci.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
index ad883aa..81a4f7b 100644
--- a/.github/workflows/python-ci.yml
+++ b/.github/workflows/python-ci.yml
@@ -31,10 +31,14 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run: |
-        coverage run --source=shocker $(which pytest) -vv shocker
-        coverage report --omit='*/bin/pytest'
-        codecov
+      run:  pytest --cov polyply --cov-report=xml
+    - name: Upload coverage codecov   
+      uses: codecov/codecov-action@v3 
+      with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            fail_ci_if_error: true
+            verbose: true
         
   lint:
     runs-on: ubuntu-latest

From e16ccc0034b3bce3170a4ffb1cea3e1888c86dc6 Mon Sep 17 00:00:00 2001
From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com>
Date: Sun, 10 Dec 2023 15:34:34 +0100
Subject: [PATCH 3/3] Update README.md

include badge see if it works
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 5183d2d..d137cd8 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
 # Shocker
+[![codecov](https://codecov.io/gh/marrink-lab/shocker/branch/Shocker/graph/badge.svg)](https://codecov.io/gh/marrink-lab/shocker)
 [![Build Status](https://github.com/marrink-lab/shocker/actions/workflows/python-ci.yml/badge.svg)](https://github.com/marrink-lab/shocker/actions)
 [![BioRxiv:10.1101/2023.08.16.553535](http://img.shields.io/badge/BioRxiv-10.1101/2023.08.16.553535-ad353a.svg)](https://doi.org/10.1101/2023.08.16.553535)
 [![JCTC:10.1021/acs.jctc.3c00961](http://img.shields.io/badge/JCTC-10.1021/acs.jctc.3c00961-007b42.svg)](https://doi.org/10.1021/acs.jctc.3c00961)