ci: switch to codecov rather than codacy (#110) (#111)

.github/workflows/ci.yml

@@ -13,6 +13,7 @@ jobs:
           - '3.9'
           - '3.10'
           - '3.11'
+          - '3.12'
 
     steps:
       - name: Install Python via conda.
@@ -34,14 +35,12 @@ jobs:
         run: coverage report
       - name: Create XML report for codacy
         run: coverage xml
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@develop
-      - name: Run codacy-coverage-reporter
-        uses: codacy/codacy-coverage-reporter-action@master
+      - name: Upload Python coverage reports to Codecov
+        uses: codecov/codecov-action@v3
         with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
-        if: ${{ matrix.python-version == '3.7' }}
+          flags: python
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       - name: Check style with black
         run: make black-check
       - name: Check style with flake8

README.md

@@ -1,9 +1,7 @@
 [![PyPI version](https://badge.fury.io/py/altamisa.svg)](https://badge.fury.io/py/altamisa)
+[![codecov](https://codecov.io/gh/bihealth/altamisa/graph/badge.svg?token=R5GXUKCUYJ)](https://codecov.io/gh/bihealth/altamisa)
 [![Install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
 ![Continuous Integration Status](https://github.com/bihealth/altamisa/workflows/CI/badge.svg)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/a853a56253604aa7ab87d2bcdcd9da51)](https://www.codacy.com/app/bihealth/altamisa?utm_source=github.com&utm_medium=referral&utm_content=bihealth/altamisa&utm_campaign=Badge_Grade)
-[![Coverage Badge](https://api.codacy.com/project/badge/Coverage/a853a56253604aa7ab87d2bcdcd9da51)](https://www.codacy.com/app/bihealth/altamisa?utm_source=github.com&utm_medium=referral&utm_content=bihealth/altamisa&utm_campaign=Badge_Coverage)
-[![Coverage Status](https://coveralls.io/repos/github/bihealth/altamisa/badge.svg?branch=master)](https://coveralls.io/github/bihealth/altamisa?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/altamisa/badge/?version=latest)](https://altamisa.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.01610/status.svg)](https://doi.org/10.21105/joss.01610)
 [![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)