Merge pull request #175 from ntalluri/decouple-ensemble #685
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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: Remove Omics Integrator 1 Docker image | |
# Remove the image to prevent the cache from being used. Here we use | |
# `|| true` to prevent the job from failing if the image doesn't exist or | |
# can't be removed for some reason | |
run: docker rmi reedcompbio/omics-integrator-1:latest || true | |
- 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: Remove Omics Integrator 2 Docker image | |
run: docker rmi reedcompbio/omics-integrator-2:latest || true | |
- 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: Remove PathLinker Docker image | |
run: docker rmi reedcompbio/pathlinker:latest || true | |
- 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: Remove MEO Docker image | |
run: docker rmi reedcompbio/meo:latest || true | |
- 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: Remove MinCostFlow Docker image | |
run: docker rmi reedcompbio/mincostflow:latest || true | |
- 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: Remove All Pairs Shortest Paths Docker image | |
run: docker rmi reedcompbio/allpairs:latest || true | |
- 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: Remove DOMINO Docker image | |
run: docker rmi reedcompbio/domino:latest || true | |
- 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: Remove Cytoscape Docker image | |
run: docker rmi reedcompbio/py4cytoscape:v3 || true | |
- name: Build SPRAS Docker image | |
uses: docker/build-push-action@v1 | |
with: | |
path: . | |
dockerfile: docker-wrappers/SPRAS/Dockerfile | |
repository: reedcompbio/spras | |
tags: v0.2.0 | |
cache_froms: reedcompbio/spras:v0.2.0 | |
push: false | |
- name: Remove SPRAS Docker image | |
run: docker rmi reedcompbio/spras:v0.2.0 || true | |
# 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] |