Switch testing to GitHub Actions

.github/workflows/test.yml

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+name: Test pathway parameter advising
+on:
+- push
+- pull_request
+jobs:
+  Test:
+    name: Test pathway parameter advising
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Install conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: ppa
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniconda-version: 'latest'
+      - name: Install pathway parameter advising
+        shell: bash --login {0}
+        run: |
+          python setup.py install
+          # Install PGD dependency
+          # macOS typically has gcc as an alias for clang, so specifically set gcc
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            # Instructions for installing an older version of a brew package
+            # https://itnext.io/how-to-install-an-older-brew-package-add141e58d32
+            brew install gcc@10
+            export CC=gcc-10
+            export CXX=g++-10
+          fi
+          cd bin
+          bash setupPGD.sh
+      - name: Run and test pathway parameter advising
+        shell: bash --login {0}
+        run: |
+          # Run PPA examples
+          cd bin
+          bash runPPA.sh ../data/Wnt wnt_ranking.txt ../lib/pgd/ 
+          bash runNetBoxIL2.sh
+          # Compare the generated IL2 output with the reference output
+          cmp ../tests/reference/il2_ranking.txt il2_ranking.txt
+          echo "Generated IL2 ranking matches expected ranking"

README.md

@@ -1,17 +1,17 @@
 # Pathway parameter advising
-[![Build Status](https://travis-ci.com/gitter-lab/pathway-parameter-advising.svg?branch=master)](https://travis-ci.com/gitter-lab/pathway-parameter-advising)
+[![Test pathway parameter advising](https://github.com/gitter-lab/pathway-parameter-advising/actions/workflows/test.yml/badge.svg)](https://github.com/gitter-lab/pathway-parameter-advising/actions/workflows/test.yml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3985899.svg)](https://doi.org/10.5281/zenodo.3985899)
 [![PyPI](https://img.shields.io/pypi/v/pathwayParameterAdvising.svg?logo=PyPI)](https://pypi.org/project/pathwayParameterAdvising/)
 
 Parameter advising for biological pathway creation algorithms.
 
 ## Citation
 
-Pathway parameter advising is described in the following preprint:
+Pathway parameter advising is described in the following publication:
 
-[Automating parameter selection to avoid implausible biological pathway models](https://doi.org/10.1101/845834).
+[Automating parameter selection to avoid implausible biological pathway models](https://doi.org/10.1038/s41540-020-00167-1).
 Chris S Magnano, Anthony Gitter.
-*bioRxiv* 2019. doi:10.1101/845834
+*npj Systems Biology and Applications*, 7:12, 2021.
 
 ## Dependencies
 

environment.yml

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+name: ppa
+dependencies:
+- networkx=2.4
+- numpy=1.19
+- python=3.6
+- requests=2.24