-
Notifications
You must be signed in to change notification settings - Fork 6
104 lines (102 loc) · 4.89 KB
/
install-test.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
name: Install test SINGE
on: [push, pull_request]
jobs:
# Builds and tests the SINGE Docker image, tests SINGE in a Docker container
docker:
name: Install test Docker
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
# Pull from Docker Hub to use the cache
# https://medium.com/mobileforgood/coding-tips-patterns-for-continuous-integration-with-docker-on-travis-ci-9cedb8348a62
# https://github.com/docker/build-push-action/issues/7
- name: Pull Docker image
run: docker pull agitter/singe:tmp
# Docker image build fails
# The repository 'http://deb.debian.org/debian stretch Release' does no longer have a Release file.
# - name: Build Docker image
# uses: docker/build-push-action@v1
# with:
# username: ${{ secrets.DOCKER_USERNAME }}
# password: ${{ secrets.DOCKER_PASSWORD }}
# path: .
# dockerfile: docker/Dockerfile
# repository: agitter/singe
# tags: tmp
# cache_froms: agitter/singe:tmp
# add_git_labels: true
# # Only push when running on the master branch
# push: ${{ github.ref == 'refs/heads/master' }}
- name: Test SINGE
run: |
# Store the md5sums of the tracked source files before running tests in the Docker image
# The Docker image does not have git installed
md5sum $(git ls-tree -r HEAD --name-only | grep '.*\.m$') > current_code.md5
# Run SINGE tests in the built Docker image
# The conda environment should be activated before running the bash script
# See https://github.com/conda/conda/issues/7980
docker run -v $(pwd):/SINGE -w /SINGE --entrypoint "/bin/bash" agitter/singe:tmp -c "source ~/.bashrc; conda activate singe-test; tests/docker_test.sh"
# Proof-of-concept of running SINGE in a high-throughput style
# Can be moved to run in a parallel job
bash tests/high_throughput_test.sh
# Test standalone SINGE run through Docker
bash tests/standalone_test.sh
# Test standalone SINGE on a branching dataset
bash tests/standalone_branching_test.sh
# Test standalone SINGE on a dataset with regulator indices
bash tests/standalone_regix_test.sh
# Confirm the hyperparameter generation script works
cd scripts
bash generate_hyperparameters.sh
# Installs MATLAB runtime R2020a and tests compiled SINGE for macOS on test data
macos:
name: Install test macOS
# See available macOS software https://github.com/actions/virtual-environments/blob/master/images/macos/macos-10.15-Readme.md
runs-on: macos-latest
env:
SINGE_VERSION: v0.5.1
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Install conda environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: singe-test
environment-file: tests/environment.yml
auto-activate-base: false
miniconda-version: 'latest'
# - name: Cache MATLAB runtime installer
# id: cache-installer
# uses: actions/cache@v1
# with:
# path: installer
# key: ${{ runner.os }}-matlab-R2020a-installer
# - name: Download MATLAB runtime installer
# if: steps.cache-installer.outputs.cache-hit != 'true'
# run: wget --quiet --directory-prefix=installer http://ssd.mathworks.com/supportfiles/downloads/R2020a/Release/2/deployment_files/installer/complete/maci64/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
# - name: Install MATLAB runtime
# run: |
# unzip -d . -q installer/MATLAB_Runtime_R2020a_Update_2_maci64.dmg.zip
# hdiutil mount MATLAB_Runtime_R2020a_Update_2_maci64.dmg
# cp -R /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64 .
# hdiutil unmount /Volumes/MATLAB_Runtime_R2020a_Update_2_maci64
# sudo ./MATLAB_Runtime_R2020a_Update_2_maci64/InstallForMacOSX.app/Contents/MacOS/InstallForMacOSX -mode silent -agreeToLicense yes
# MATLAB_RUNTIME_PATH=/Applications/MATLAB/MATLAB_Runtime/v98
# echo "MATLAB_RUNTIME_PATH=$MATLAB_RUNTIME_PATH" >> $GITHUB_ENV
# echo "DYLD_LIBRARY_PATH=$MATLAB_RUNTIME_PATH/runtime/maci64:$MATLAB_RUNTIME_PATH/sys/os/maci64:$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_ENV
# echo "$MATLAB_RUNTIME_PATH/bin/maci64" >> $GITHUB_PATH
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v2
with:
release: R2020b
- name: Download SINGE
run: |
wget --quiet https://github.com/gitter-lab/SINGE/releases/download/$SINGE_VERSION/SINGE_mac.tgz
tar -xf SINGE_mac.tgz
- name: Run and test SINGE
shell: bash -l {0}
run: |
bash SINGE.sh ${{ steps.setup-matlab.outputs.matlabroot }} standalone data1/X_SCODE_data.mat data1/gene_list.mat Output tests/example_hyperparameters.txt
ls -l Output
bash tests/compare_example_output.sh Output tests/reference/latest 1e-02 1e-02