fix ci #69
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ############################################################################### | |
| # | |
| # AUTHOR: Maciej_Bak | |
| # CONTACT: wsciekly.maciek@gmail.com | |
| # CREATED: 15-02-2022 | |
| # LICENSE: Apache_2.0 | |
| # | |
| ############################################################################### | |
| --- | |
| name: ci-pipeline | |
| on: push | |
| jobs: | |
| pipeline-testruns: | |
| runs-on: ubuntu-20.04 | |
| name: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: "true" | |
| - name: Setup miniconda & conda env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: warlock | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda list | |
| conda clean --all --yes | |
| - name: Print compiler path (Ubuntu) | |
| shell: bash -l {0} | |
| run: which g++ | |
| - name: Compile demon (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| g++ resources/demon_model/src/demon.cpp | |
| -o resources/demon_model/bin/demon | |
| -I/usr/share/miniconda3/envs/warlock/include | |
| -lm | |
| - name: Prepare internal conda envs (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| snakemake | |
| --snakefile="workflow/Snakefile" \ | |
| --configfile="tests/test1/config-Ubuntu.yml" \ | |
| --use-conda \ | |
| --conda-create-envs-only \ | |
| --cores 1 \ | |
| all | |
| # Run the tests sequentially; | |
| # This could be parallelized in the CI but setting up conda | |
| # is expensive; its faster to run the tests one-by-one. | |
| - name: Run the pipeline (test1) (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| bash warlock.sh | |
| --configfile tests/test1/config-Ubuntu.yml | |
| --environment local | |
| - name: Check md5 (test1) (Ubuntu) | |
| shell: bash -l {0} | |
| working-directory: ./tests/test1 | |
| run: md5sum -c output-Ubuntu.md5 | |
| - name: Cleanup (test1) | |
| shell: bash -l {0} | |
| run: rm -rf tests/test1/output | |
| - name: Run the pipeline (test2) (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| bash warlock.sh | |
| --configfile tests/test2/config-Ubuntu.yml | |
| --environment local | |
| --cores 4 | |
| - name: Check md5 (test2) (Ubuntu) | |
| shell: bash -l {0} | |
| working-directory: ./tests/test2 | |
| run: md5sum -c output-Ubuntu.md5 | |
| - name: Cleanup (test2) | |
| shell: bash -l {0} | |
| run: rm -rf tests/test2/output | |
| - name: Run the pipeline (test3) (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| bash warlock.sh | |
| --configfile tests/test3/config-Ubuntu.yml | |
| --environment local | |
| --cores 2 | |
| - name: Check md5 (test3) (Ubuntu) | |
| shell: bash -l {0} | |
| working-directory: ./tests/test3 | |
| run: md5sum -c output-Ubuntu.md5 | |
| - name: Cleanup (test3) | |
| shell: bash -l {0} | |
| run: rm -rf tests/test3/output | |
| ... |