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test-spras.yml
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name: Test SPRAS
on: [push, pull_request]
jobs:
# Installs the conda environment but does not run tests because the tests require Linux Docker images
conda-only:
name: Test conda environment
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macos-latest, windows-latest]
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Install conda environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: spras
environment-file: environment.yml
auto-activate-base: false
miniconda-version: 'latest'
# Log conda environment contents
- name: Log conda environment
shell: bash --login {0}
run: conda list
# Runs the test code and Snakemake workflow in the conda environment
test:
name: Run test cases and workflow
# The Docker images will be pulled in both the docker job and this test job
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Install conda environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: spras
environment-file: environment.yml
auto-activate-base: false
miniconda-version: 'latest'
# Log conda environment contents
- name: Log conda environment
shell: bash --login {0}
run: conda list
# Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6)
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
# Choose version from https://github.com/apptainer/apptainer/releases
apptainer-version: 1.2.2
- name: Run tests
shell: bash --login {0}
# Verbose output and disable stdout and stderr capturing
run: pytest -vs
- name: Run Snakemake workflow
shell: bash --login {0}
run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs
# Builds the Docker images
docker:
name: Build Docker images
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [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 images
run: |
docker pull reedcompbio/omics-integrator-1:latest
docker pull reedcompbio/omics-integrator-2:v2
docker pull reedcompbio/pathlinker:v2
docker pull reedcompbio/meo:latest
docker pull reedcompbio/mincostflow:latest
docker pull reedcompbio/allpairs:v2
docker pull reedcompbio/domino:latest
docker pull reedcompbio/py4cytoscape:v3
docker pull reedcompbio/spras:v0.1.0
- name: Build Omics Integrator 1 Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/OmicsIntegrator1/.
dockerfile: docker-wrappers/OmicsIntegrator1/Dockerfile
repository: reedcompbio/omics-integrator-1
tags: latest
cache_froms: reedcompbio/omics-integrator-1:latest
push: false
- name: Build Omics Integrator 2 Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/OmicsIntegrator2/.
dockerfile: docker-wrappers/OmicsIntegrator2/Dockerfile
repository: reedcompbio/omics-integrator-2
tags: v2
cache_froms: reedcompbio/omics-integrator-2:latest
push: false
- name: Build PathLinker Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/PathLinker/.
dockerfile: docker-wrappers/PathLinker/Dockerfile
repository: reedcompbio/pathlinker
tags: v2
cache_froms: reedcompbio/pathlinker:latest
push: false
- name: Build Maximum Edge Orientation Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/MEO/.
dockerfile: docker-wrappers/MEO/Dockerfile
repository: reedcompbio/meo
tags: latest
cache_froms: reedcompbio/meo:latest
push: false
- name: Build MinCostFlow Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/MinCostFlow/.
dockerfile: docker-wrappers/MinCostFlow/Dockerfile
repository: reedcompbio/mincostflow
tags: latest
cache_froms: reedcompbio/mincostflow:latest
push: false
- name: Build All Pairs Shortest Paths Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/AllPairs/.
dockerfile: docker-wrappers/AllPairs/Dockerfile
repository: reedcompbio/allpairs
tags: v2
cache_froms: reedcompbio/allpairs:latest
push: false
- name: Build DOMINO Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/DOMINO/.
dockerfile: docker-wrappers/DOMINO/Dockerfile
repository: reedcompbio/domino
tags: latest
cache_froms: reedcompbio/domino:latest
push: false
- name: Build Cytoscape Docker image
uses: docker/build-push-action@v1
with:
path: docker-wrappers/Cytoscape/.
dockerfile: docker-wrappers/Cytoscape/Dockerfile
repository: reedcompbio/py4cytoscape
tags: v3
cache_froms: reedcompbio/py4cytoscape:v3
push: false
- name: Build SPRAS Docker image
uses: docker/build-push-action@v1
with:
path: .
dockerfile: docker-wrappers/SPRAS/Dockerfile
repository: reedcompbio/spras
tags: v0.1.0
cache_froms: reedcompbio/spras:v0.1.0
push: false
# Run pre-commit checks on source files
pre-commit:
name: Run pre-commit checks
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: '3.11' # Match this to the version specified in environment.yml
- name: Run pre-commit checks
uses: pre-commit/[email protected]