setting up github actions

.github/workflows/ci.yml

@@ -0,0 +1,67 @@
+name: Run PyTest
+on:
+  push:
+    branches:
+      - master
+      - 'feature/**'
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: Test on ubuntu Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest #${{ matrix.os }}
+    strategy:
+      max-parallel: 1
+      matrix:
+        #os: [ubuntu-latest, windows-latest] # macOS-latest wouldn't run, so skipping. windows takes 50% longer than ubuntu
+        python-version: [3.8] # [3.6, 3.7, 3.8]
+    steps:
+      - name: Dump GitHub context
+        id: github_context_step
+        run: echo '${{ toJSON(github) }}'
+      #- name: Dump runner context
+      #  run: echo '${{ toJSON(runner) }}'
+      #- name: Dump strategy context
+      #  run: echo '${{ toJSON(strategy) }}'
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: Install Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+            pip install pipenv pytest_cov
+            # pipenv install pytest_cov
+            pipenv install --dev --skip-lock
+            pipenv install -e . --skip-lock
+            # pipenv uses requirements.txt
+
+      - name: Testing and coverage report
+        run: |
+          pipenv run coverage run setup.py test
+          pipenv run coverage xml
+
+      - name: Publish to codecov
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+          #files: ./coverage.xml #./coverage1.xml,./coverage2.xml # optional
+          directory: ./
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
+          verbose: false # optional (default = false)
+
+      - name: Publish to GitHub # cobertura-report format publishes coverage.xml
+        uses: 5monkeys/cobertura-action@v12
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          minimum_coverage: 40
+          fail_below_threshold: 40
+
+# GHA workflow: diffs are limited to 300 files. If there are files changed that aren't matched in the first 300 files returned by the
+# filter, the workflow will not run. You may need to create more specific filters so that the workflow will run automatically.
+# SETUP: use https://github.com/FoxoTech/methylcheck/settings/secrets/actions to setup the CODECOV_TOKEN

conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = '0.8'
 # The full version, including alpha/beta/rc tags
-release = '0.8.3'
+release = '0.8.4'
 
 
 # -- General configuration ---------------------------------------------------

methylcheck/version.py

@@ -2,4 +2,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
-__version__ = '0.8.3'
+__version__ = '0.8.4'

setup.py

@@ -2,6 +2,22 @@
 from setuptools import setup, find_packages
 exec(open('methylcheck/version.py').read())
 
+test_requirements = [
+    'methylprep', # this is not REQUIRED but some functions in unit testing do require it, so in extras.
+    'pytest',
+    'pytest-pep8',
+    'pytest-cov',
+    'flake8',
+    'coverage',
+    'xlrd',
+    'coveralls', # replaces python-coveralls. note that installing both in same environment will break it.
+    'sphinxcontrib-apidoc',
+    'm2r',
+    'nbsphinx',
+    'sphinx',
+    'ipykernel',
+]
+
 # note: ANY param must fit on a single line or twine breaks.
 setup(
     name='methylcheck',
@@ -48,24 +64,10 @@
         'openpyxl', # pandas xlsx support changed to use this
     ],
     extras_require={
-        'dev': [
-            'methylprep', # this is not REQUIRED but some functions in unit testing do require it, so in extras.
-            'pytest',
-            'pytest-pep8',
-            'pytest-cov',
-            'flake8',
-            'coverage',
-            'xlrd',
-            'coveralls', # replaces python-coveralls. note that installing both in same environment will break it.
-            'sphinxcontrib-apidoc',
-            'm2r',
-            'nbsphinx',
-            'sphinx',
-            'ipykernel',
-        ]
+        'dev': test_requirements
     },
     setup_requires=['pytest-runner'],
-    tests_require=['pytest'],
+    tests_require= test_requirements,
     entry_points={
         'console_scripts': [
             'methylcheck-cli = methylcheck.cli:cli_parser',