Feature/issue 216 GitHub actions

.github/workflows/build.yml

@@ -0,0 +1,75 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install .[test]
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 mavis --count --select=E9,F63,F7,F82 --show-source --statistics
+    - name: Lint with black
+      run: |
+        pip install black
+        # stop the build if black needs to be run
+        black mavis -S -l 100 --check
+    - name: install bwa
+      run: |
+        git clone https://github.com/lh3/bwa.git
+        cd bwa
+        git checkout v0.7.17
+        make
+        cd ..
+    - name: install blat
+      run: |
+        wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
+        chmod a+x blat
+    - name: run short tests with pytest
+      run: |
+        export PATH=$PATH:$(pwd):$(pwd)/bwa
+        pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
+      env:
+        RUN_FULL: 0
+      if: github.event_name != 'pull_request'
+    - name: run full tests with pytest
+      run: |
+        export PATH=$PATH:$(pwd):$(pwd)/bwa
+        pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
+      env:
+        RUN_FULL: 1
+      if: github.event_name == 'pull_request'
+    - name: Upload pytest test results
+      uses: actions/upload-artifact@master
+      with:
+        name: pytest-results-${{ matrix.python-version }}
+        path: junit/test-results-${{ matrix.python-version }}.xml
+        # Use always() to always run this step to publish test results when there are test failures
+      if: always()
+    - name: Update code coverage report to CodeCov
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true

.github/workflows/publish.yml

@@ -0,0 +1,32 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: publish
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel install
+        twine check dist/*
+        twine upload dist/*

README.md

@@ -5,7 +5,7 @@
 </object>
 
 
-![PyPi](https://img.shields.io/pypi/v/mavis.svg) ![Travis](https://travis-ci.org/bcgsc/mavis.svg?branch=master) ![ReadTheDocs](https://readthedocs.org/projects/pip/badge/)
+![PyPi](https://img.shields.io/pypi/v/mavis.svg) ![build](https://github.com/bcgsc/mavis/workflows/build/badge.svg?branch=master) [![codecov](https://codecov.io/gh/bcgsc/mavis/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/mavis) ![ReadTheDocs](https://readthedocs.org/projects/pip/badge/)
 
 
 # About

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 80%
+        threshold: 1%

setup.py

@@ -65,7 +65,6 @@ def check_nonpython_dependencies():
     'pycodestyle>=2.3.1',
     'pytest',
     'pytest-cov',
-    'tox',
 ]
 
 

tests/unit/test_assemble.py

@@ -2,6 +2,7 @@
 import random
 import os
 import unittest
+import pytest
 
 from mavis.assemble import assemble, Contig, DeBruijnGraph, filter_contigs, kmers
 from mavis.constants import DNA_ALPHABET
@@ -91,6 +92,7 @@ def test_drop_similar_different_lengths(self):
 
 
 class TestDeBruijnGraph(unittest.TestCase):
+    @pytest.mark.skipif(os.environ.get('RUN_FULL', '0') != '1', reason='running short tests only')
     def test_trim_tails_by_freq_forks(self):
         g = DeBruijnGraph()
         for s, t in itertools.combinations([1, 2, 3, 4, 5, 6], 2):
@@ -181,6 +183,7 @@ def setUp(self):
         with open(os.path.join(DATA_DIR, 'test_assembly_sequences.txt')) as fh:
             self.seq = [i.strip() for i in fh.readlines()]
 
+    @pytest.mark.skipif(os.environ.get('RUN_FULL', '0') != '1', reason='running short tests only')
     def test_deterministic_assembly(self):
         contig_sequences = set()
         for i in range(20):