Devel (#147) #113
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# 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. | |
# | |
# See https://github.com/r-lib/actions/tree/master/examples#readme for | |
# additional example workflows available for the R community. | |
name: netZooM | |
env: | |
ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true' | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
on: | |
push: | |
branches: | |
- master | |
- devel | |
pull_request: | |
branches: | |
- master | |
- devel | |
jobs: | |
build: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: [ubuntu-20.04] | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
token: ${{ secrets.GITHUB_TOKEN }} | |
- name: Set up MATLAB | |
uses: matlab-actions/setup-matlab@v1 | |
with: | |
release: R2020a | |
- name: install bedtools ubuntu | |
if: matrix.os == 'ubuntu-20.04' | |
run: | | |
wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz | |
tar -zxvf bedtools-2.29.0.tar.gz | |
cd bedtools2 | |
make | |
ls | |
pwd | |
cd .. | |
- name: install bedtools macos | |
if: matrix.os == 'macos-latest' | |
run: | | |
wget https://github.com/marouenbg/bedtools2/archive/refs/heads/master.zip | |
unzip master.zip | |
mv bedtools2-master bedtools2 | |
cd bedtools2 | |
make | |
ls | |
pwd | |
cd .. | |
- name: Run tests and generate artifacts | |
run: | | |
ls && pwd | |
cd .. | |
git clone https://github.com/MOxUnit/MOxUnit.git # Install MOxUnit, which adds itself to the startup path | |
git clone https://github.com/MOcov/MOcov.git | |
pwd | |
ls | |
shell: bash | |
- name: run actual tests | |
run: | | |
matlab -batch 'cd ../MOcov;addpath(genpath(pwd));cd ../netZooM;addpath(genpath("/home/runner/work/netZooM/"));back=cd("../MOxUnit/MOxUnit/"); moxunit_set_path(); cd(back); pwd; ls; moxunit_runtests tests -recursive -verbose -junit_xml_file testresults.xml -with_coverage -cover netZooM -cover_exclude tests -cover_xml_file coverage.xml -cover_json_file coveralls.json); exit(double(~ans))' | |
- name: report coverage | |
run: | | |
bash <(curl -s https://codecov.io/bash) | |