name change

.github/workflows/tracs_test.yml

@@ -0,0 +1,79 @@
+name: tracs-CI
+
+on:
+  push:
+    branches:
+    - main
+    - dev
+  pull_request:
+    branches:
+    - main
+    - dev
+  schedule:
+    - cron:  '1 1 1 * *'
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9, '3.10']
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: | 
+          sudo apt-get update && sudo apt-get install -y build-essential wget zlib1g-dev libncurses5-dev libbz2-dev liblzma-dev
+          sudo apt-get install -y libboost-all-dev
+          sudo apt-get install -y python3-pybind11
+          python --version
+          python -m pip install --upgrade pip setuptools
+          python -m pip install pybind11 pytest
+          # Check if pybind11 was installed correctly
+          python -m pip list | grep pybind11
+          
+    - name: Install python dependencies
+      run: |
+          pip install scipy --prefer-binary
+          pip install sourmash
+  
+    - name: Install Minimap2
+      run: |
+        wget https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2
+        tar -xvf minimap2-2.26_x64-linux.tar.bz2
+        sudo cp minimap2-2.26_x64-linux/minimap2 /usr/local/bin/
+
+    - name: Install Samtools
+      run: |
+        wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2
+        tar -xjf samtools-1.18.tar.bz2
+        cd samtools-1.18
+        ./configure --prefix=/usr/local/
+        make
+        sudo make install
+
+    - name: Install Htsbox
+      run: |
+        git clone https://github.com/lh3/htsbox
+        cd htsbox
+        make
+        sudo cp htsbox /usr/local/bin/
+
+    - name: Download test data
+      run: |
+        wget https://github.com/gtonkinhill/tracs-test-data/archive/refs/tags/v0.0.2.zip
+        unzip v0.0.2.zip
+        
+    - name: Install
+      run: python setup.py install
+
+    - name: Validation Tests
+      run: pytest -W ignore -q --datafolder="${{ github.workspace }}/tracs-test-data-0.0.2/"
+
+