Use Github Actions to build and test (computational-metabolomics#16)

* Add Github Actions tests

* Remove connectivity database tests

* Add environment variables for codecov

* Test connectivity DB on linux only

* Delete RI for windows and macos

* Test on MacOS and add Python 3.6, 3.8

* Use with: self.assertWarns

Author: jackgisby

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = tests/*,setup.py,metaboblend/__main__.py

.github/workflows/build-test.yml

@@ -0,0 +1,60 @@
+name: metaboblend
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.6, 3.7, 3.8]
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python-version }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup conda - Python ${{ matrix.python-version }}
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge
+
+      - name: Install dependencies
+        run: |
+
+          python --version
+          conda env update --file environment.yml --name base
+
+      - name: Lint with flake8
+        run: |
+
+          conda install flake8
+
+          # stop 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-cov
+        run: |
+
+          python setup.py install
+          metaboblend --help
+
+          conda install pytest codecov pytest-cov -c conda-forge
+          pytest --cov ./ --cov-config=.coveragerc --cov-report=xml
+
+      - name: Upload code coverage to codecov
+        uses: codecov/codecov-action@v1
+        with:
+          flags: unittests
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          verbose: true

.gitignore

@@ -102,6 +102,7 @@ ENV/
 
 *~
 
-# ignore lib files for testing
+# ignore test files
 */libgcc_s_dw2-1.dll
-*/libstdc++-6.dll
+*/libstdc++-6.dll
+tests/test*

.travis.yml

@@ -1,7 +1,5 @@
 include README.rst
 include LICENSE
 include requirements.txt
-include examples/*.*
 include tests/*.py
 include tests/data/*.*
-include tests/results/*.*

MANIFEST.in

@@ -1,6 +1,6 @@
 MetaboBlend
 ===========
-|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
+|Version| |Py versions| |Git| |Bioconda| |Build Status| |License| |RTD doc| |codecov| |binder|
 
 Python package for *de novo* structural elucidation of small molecules in mass spectrometry-based Metabolomics
 
@@ -40,11 +40,8 @@ Licenses
 MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
 
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/metaboblend.svg?style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/metaboblend
-
-.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/metaboblend.svg?style=flat&maxAge=3600&label=AppVeyor
-   :target: https://ci.appveyor.com/project/RJMW/metaboblend/branch/master
+.. |Build Status| image:: https://github.com/computational-metabolomics/metaboblend/workflows/metaboblend/badge.svg
+   :target: https://github.com/computational-metabolomics/metaboblend/actions
 
 .. |Py versions| image:: https://img.shields.io/pypi/pyversions/metaboblend.svg?style=flat&maxAge=3600
    :target: https://pypi.python.org/pypi/metaboblend/
@@ -63,10 +60,9 @@ MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE
 
 .. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
    :target: https://metaboblend.readthedocs.io/en/latest/
-   
+
 .. |codecov| image:: https://codecov.io/gh/computational-metabolomics/metaboblend/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/computational-metabolomics/metaboblend
 
 .. |binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/computational-metabolomics/metaboblend/master?filepath=notebooks%2Fworkflow.ipynb
-

README.rst

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
- - python=3.7
+ - python>=3.6
  - numpy
  - scipy
  - pandas

appveyor.yml

@@ -5,3 +5,4 @@ networkx
 # rdkit
 biopython
 matplotlib
+# nauty

environment.yml

@@ -27,7 +27,8 @@
 
 def main():
 
-    setuptools.setup(name="metaboblend",
+    setuptools.setup(
+        name="metaboblend",
         version=metaboblend.__version__,
         description="",
         long_description=open('README.rst').read(),