Merge pull request #85 from ekg/github_action

Switch from Travis to github workflows for building and testing

.github/workflows/build_and_test_on_push.yml

@@ -0,0 +1,29 @@
+on: [ push ]
+
+name: build and test
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install required packages
+        run: sudo apt-get update && sudo apt-get install -y
+          git
+          bash
+          cmake
+          make
+          g++
+          libatomic-ops-dev
+          autoconf
+          libgsl-dev
+          zlib1g-dev
+          libzstd-dev
+          libjemalloc-dev
+      - name: Init and update submodules
+        run: git submodule update --init --recursive
+      - name: Build seqwish
+        run: sed -i 's/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -mcx16 -g/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -mcx16 -g -fsanitize=address/g' CMakeLists.txt && sed -i 's/CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -mcx16 -g/CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O -mcx16 -g -fsanitize=address/g' CMakeLists.txt && cmake -H. -Bbuild && cmake --build build -- -j 2
+      - name: Execute tests
+        run: cd test && ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 make test
+

README.md

@@ -1,5 +1,8 @@
 # seqwish
 
+[![build and test](https://github.com/ekg/seqwish/actions/workflows/build_and_test_on_push.yml/badge.svg)](https://github.com/ekg/seqwish/actions/workflows/build_and_test_on_push.yml)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/seqwish/README.html)
+
 *These <b>seq</b>uences <b>wish</b> they were squished into a graph.*
 
 ## a variation graph inducer