Merge pull request #87 from miRTop/lpantano-ci

Create python-package-conda.yml

.github/workflows/python-package-conda.yml

@@ -0,0 +1,42 @@
+name: Python Package using Conda
+
+on:
+  push:
+    branches:
+    - main
+    - dev
+    - release/*
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # 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: |
+        conda install pytest
+        pytest

environment.yml

@@ -0,0 +1,6 @@
+dependencies:
+  - python=3.11
+  - bioconda::pysam
+  - bioconda::pybedtools
+  - conda-forge::pandas
+  - bioconda::biopython