CI tests running on pytest

.github/workflows/github-actions.yaml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "master", "v1.1.3" ]
+  pull_request:
+    branches: [ "master", "v1.1.3" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install mash ncbi-blast+ libssl-dev libcurl4-openssl-dev mafft libssl-dev ca-certificates -y
+        sudo apt-get install python3-pip python3-dev python3-pandas python3-requests python3-pycurl python3-biopython -y
+        python3 -m pip install --upgrade pip setuptools
+        pip3 install pytest fastcluster openpyxl
+        if [ -f requirements.txt ]; then 
+          pip3 install -r requirements.txt;
+        else
+          pip3 install -e .
+        fi
+        sistr_init
+    - name: Test  with pytest
+      run: |
+        pytest -o log_cli=true --basetemp=tmp-pytest