From f97cf85c3e098ce9d83633a15d681e2ab622b81d Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Tue, 19 Nov 2024 11:17:16 -0500
Subject: [PATCH 1/4] [MNT] Remove coveralls

---
 .github/workflows/test.yml | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7a1c4c7..40c586a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -15,41 +15,31 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r dev_requirements.txt
         pip install --no-deps .
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
         coverage run -m pytest
         coverage lcov -o ./coverage/lcov.info
+
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-    - name: Coveralls Parallel
-      uses: coverallsapp/github-action@v2.3.4
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        flag-name: run-${{ matrix.python-version }}
-        parallel: true
-  finish:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@v2.3.4
-      with:
-        github-token: ${{ secrets.github_token }}
-        parallel-finished: true
\ No newline at end of file

From f8f55443c0fb71c8f721d6424902f970b88048d2 Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Tue, 19 Nov 2024 12:43:08 -0500
Subject: [PATCH 2/4] update badge to codecov

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ea6ac78..81556f0 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 <div align="center">
 
 # `bagel-cli`
-[![Coverage Status](https://coveralls.io/repos/github/neurobagel/bagel-cli/badge.svg?branch=main)](https://coveralls.io/github/neurobagel/bagel-cli?branch=main)
+[![codecov](https://codecov.io/gh/neurobagel/bagel-cli/graph/badge.svg?token=R1KI9KIP8D)](https://codecov.io/gh/neurobagel/bagel-cli)
 [![Tests](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml/badge.svg)](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml)
 [![Docker Image Version](https://img.shields.io/docker/v/neurobagel/bagelcli?label=docker)](https://hub.docker.com/r/neurobagel/bagelcli/tags)
 [![Python versions](https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?style=flat)](https://www.python.org)

From 524ee7c51a5b12c954c5784ab9a4eb27b7d2cbe2 Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Tue, 19 Nov 2024 12:46:54 -0500
Subject: [PATCH 3/4] add license badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 81556f0..38485a2 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,7 @@
 [![Tests](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml/badge.svg)](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml)
 [![Docker Image Version](https://img.shields.io/docker/v/neurobagel/bagelcli?label=docker)](https://hub.docker.com/r/neurobagel/bagelcli/tags)
 [![Python versions](https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?style=flat)](https://www.python.org)
+[![License](https://img.shields.io/github/license/neurobagel/bagelcli?color=CD5C5C&style=flat)](LICENSE)
 
 </div>
 

From 2e851344f62759f89b285de96a0fe8c98057591f Mon Sep 17 00:00:00 2001
From: Sebastian Urchs <sebastian.urchs@gmail.com>
Date: Tue, 19 Nov 2024 12:50:58 -0500
Subject: [PATCH 4/4] fix repo name in license badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 38485a2..b472d08 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 [![Tests](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml/badge.svg)](https://github.com/neurobagel/bagel-cli/actions/workflows/test.yml)
 [![Docker Image Version](https://img.shields.io/docker/v/neurobagel/bagelcli?label=docker)](https://hub.docker.com/r/neurobagel/bagelcli/tags)
 [![Python versions](https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?style=flat)](https://www.python.org)
-[![License](https://img.shields.io/github/license/neurobagel/bagelcli?color=CD5C5C&style=flat)](LICENSE)
+[![License](https://img.shields.io/github/license/neurobagel/bagel-cli?color=CD5C5C&style=flat)](LICENSE)
 
 </div>