Merge pull request #18 from lozuponelab/travis2github_actions

Travis2github actions

.github/workflows/main.yaml

@@ -0,0 +1,41 @@
+name: Tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+
+permissions:
+  contents: read
+  pull-requests: read
+
+# This allows a subsequently queued workflow run to interrupt previous runs
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Test with pytest
+        run: |
+          python -m pytest tests/

.github/workflows/python-publish.yaml

@@ -0,0 +1,40 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI }}
+        verbose: true

README.md

@@ -1,5 +1,5 @@
 # AMON
-[![PyPI](https://img.shields.io/pypi/v/AMON-bio.svg)](https://pypi.python.org/pypi/AMON) [![Build Status](https://travis-ci.org/lozuponelab/AMON.svg)](https://travis-ci.org/lozuponelab/AMON) [![Codacy grade](https://img.shields.io/codacy/grade/44d7474307bf4c62a271a9264c0c213a.svg)](https://www.codacy.com/app/lozuponelab/AMON/dashboard) [![Coveralls](https://img.shields.io/coveralls/lozuponelab/AMON.svg)](https://coveralls.io/github/lozuponelab/AMON)
+[![PyPI](https://img.shields.io/pypi/v/KEGG-parser.svg?style=flat)](https://pypi.python.org/pypi/AMON-bio) ![Build Status](https://github.com/lozuponelab/AMON/actions/workflows/main.yml/badge.svg)
 
 A command line tool for predicting the compounds produced by microbes and the host.
 

requirements.txt

@@ -0,0 +1,13 @@
+scipy 
+biom-format 
+pandas 
+matplotlib 
+statsmodels
+numpy
+aiohttp
+seaborn
+matplotlib-venn
+KEGG-parser
+pytest 
+aiohttp 
+asyncio