From dc52bcd98da639119faa11da8bb1770b4636aab1 Mon Sep 17 00:00:00 2001
From: jidicula <johanan.idicula@gmail.com>
Date: Sat, 28 Nov 2020 18:38:45 -0500
Subject: [PATCH] Add GitHub Actions CI builds

Resolves #180

**Why this change was necessary**
Travis doesn't offer great support for macOS and is also beginning to
charge for macOS build minutes.

**What this change does**
 - Factors the Travis CI build config into a shell script
 - Calls that shell script in a GitHub Actions Workflow
 - Adds a matrix build in the GH Actions Workflow for macOS 10.15
 Catalina and 11.0 Big Sur (on Apple Silicon), Windows Server 2019,
 and Ubuntu 18, 20, and 16
 - Adds a matrix build in the GH Actions Workflow for Python 3.7 and
 3.8
 - Adds a build status badge to the README

**Additional context/notes/links**
https://blog.travis-ci.com/2020-11-02-travis-ci-new-billing
---
 .github/tests.yml | 49 +++++++++++++++++++++++++++++++++++++++++++++++
 README.md         |  2 +-
 ci.sh             | 29 ++++++++++++++++++++++++++++
 3 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 .github/tests.yml
 create mode 100644 ci.sh

diff --git a/.github/tests.yml b/.github/tests.yml
new file mode 100644
index 00000000..de493e0e
--- /dev/null
+++ b/.github/tests.yml
@@ -0,0 +1,49 @@
+name: CI-Tests
+
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  branches:
+    - master
+  push:
+  pull_request:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os:
+          - 'macos-10.15'
+          - 'macos-11.0'
+          - 'windows-2019'
+          - 'ubuntu-18.04'
+          - 'ubuntu-20.04'
+          - 'ubuntu-16.04'
+        python-version:
+          - '3.7'
+          - '3.8'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set XCode version
+        if: contains(matrix.os, 'macos-11.0')
+        run: sudo xcode-select -s "/Applications/Xcode_12.2.app"
+
+      - name: Run CI script
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+        run: ./ci.sh
+  # Add test coverage stats to Coveralls.io
+  finish:
+    needs: test
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.github_token }}
+        parallel-finished: true
diff --git a/README.md b/README.md
index 1c5543bc..fd394631 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # shimming-toolbox
 
-[![Build Status](https://travis-ci.com/shimming-toolbox/shimming-toolbox.svg?branch=master)](https://travis-ci.com/shimming-toolbox/shimming-toolbox) [![Documentation Status](https://readthedocs.org/projects/shimming-toolbox/badge/?version=latest)](https://www.shimming-toolbox.org/en/latest/?badge=latest) [![Coverage Status](https://coveralls.io/repos/github/shimming-toolbox/shimming-toolbox/badge.svg?branch=master)](https://coveralls.io/github/shimming-toolbox/shimming-toolbox?branch=master)
+ [![Build Status](https://github.com/shimming-toolbox/shimming-toolbox/actions?query=workflow%3A%22CI-Tests/badge.svg)](https://github.com/shimming-toolbox/shimming-toolbox/actions?query=workflow%3A%22CI-Tests) [![Build Status](https://travis-ci.com/shimming-toolbox/shimming-toolbox.svg?branch=master)](https://travis-ci.com/shimming-toolbox/shimming-toolbox) [![Documentation Status](https://readthedocs.org/projects/shimming-toolbox/badge/?version=latest)](https://www.shimming-toolbox.org/en/latest/?badge=latest) [![Coverage Status](https://coveralls.io/repos/github/shimming-toolbox/shimming-toolbox/badge.svg?branch=master)](https://coveralls.io/github/shimming-toolbox/shimming-toolbox?branch=master)
 
 
 Code for performing real-time shimming using external MRI shim coils
diff --git a/ci.sh b/ci.sh
new file mode 100644
index 00000000..586d4575
--- /dev/null
+++ b/ci.sh
@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+echo "Installation of dependencies"
+
+# Install bleeding-edge dcm2niix
+curl -JLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
+unzip -o dcm2niix_lnx.zip
+sudo install dcm2nii* /usr/bin/
+
+echo "shimming-toolbox installation"
+pip install .
+pip install coveralls
+
+# Tests
+echo "Download prelude"
+st_download_data prelude
+echo "Set up prelude"
+prelude_path="$(pwd)"/prelude
+chmod 500 "${prelude_path}"/prelude
+PATH=${prelude_path}:${PATH}
+export PATH
+FSLOUTPUTTYPE=NIFTI_GZ
+export FSLOUTPUTTYPE
+echo "Launch general integrity test"
+py.test . -v --cov shimmingtoolbox/ --cov-report term-missing
+
+# Fail if any .sh files have warnings
+echo "Check Bash scripts"
+if [[ -n "$(ls examples/*.sh)" ]]; then shellcheck examples/*.sh; fi