make mpie-cmti standalone
#1318
Workflow file for this run
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| name: Docker Testing | |
| on: | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| pip_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build Environment File | |
| run: | | |
| echo -e "channels:\n - conda-forge\n" > .condarc | |
| cp mpie_cmti/environment.yml environment.yml | |
| tail --lines=+5 base/environment.yml >> environment.yml | |
| tail --lines=+5 md/environment.yml >> environment.yml | |
| tail --lines=+5 pyiron/environment.yml >> environment.yml | |
| cat environment.yml | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.11" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: environment.yml | |
| - name: Test | |
| shell: bash -l {0} | |
| timeout-minutes: 30 | |
| run: | | |
| pip install ./.ci_support --no-deps --no-build-isolation | |
| pip check | |
| build: | |
| needs: [pip_check] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build pyiron/base | |
| timeout-minutes: 5 | |
| run: | | |
| docker build -t pyiron/base:latest base/ | |
| docker tag pyiron/base:latest pyiron/base:"$(date +%F)" | |
| - name: Build pyiron/md | |
| timeout-minutes: 5 | |
| run: | | |
| tail --lines=+5 base/environment.yml >> md/environment.yml | |
| docker build -t pyiron/md:latest md/ | |
| docker tag pyiron/md:latest pyiron/md:"$(date +%F)" | |
| #- name: Build pyiron/continuum | |
| # timeout-minutes: 5 | |
| # run: | | |
| # docker build -t pyiron/continuum:latest continuum/ | |
| # docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)" | |
| - name: Build pyiron/pyiron | |
| timeout-minutes: 5 | |
| run: | | |
| tail --lines=+5 md/environment.yml >> pyiron/environment.yml | |
| docker build -t pyiron/pyiron:latest pyiron/ | |
| docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)" | |
| - name: Build pyiron/potentialworkshop | |
| timeout-minutes: 5 | |
| run: | | |
| tail --lines=+5 pyiron/environment.yml >> potentialworkshop/environment.yml | |
| docker build -t pyiron/potentialworkshop:latest potentialworkshop/ | |
| docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)" | |
| - name: Build pyiron/experimental | |
| timeout-minutes: 5 | |
| run: | | |
| tail --lines=+5 base/environment.yml >> experimental/environment.yml | |
| docker build -t pyiron/experimental:latest experimental/ | |
| docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)" | |
| # Testing | |
| - run: docker images | |
| #- name: Test pyiron/continuum | |
| # timeout-minutes: 5 | |
| # run: docker run --rm pyiron/continuum /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;' | |
| - name: Test pyiron/base | |
| timeout-minutes: 5 | |
| run: docker run --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;' | |
| - name: Test pyiron/pyiron | |
| timeout-minutes: 20 | |
| run: docker run --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;' | |
| - name: Test pyiron/experimental | |
| timeout-minutes: 5 | |
| run: docker run --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;' | |
| # Export Environments | |
| - run: mkdir -p environment; chmod 777 environment | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_base_$(date +%F).yml;' | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/md /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_md_$(date +%F).yml;' | |
| #- run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/continuum /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_continuum_$(date +%F).yml;' | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_pyiron_$(date +%F).yml;' | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/potentialworkshop /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_potentialworkshop_$(date +%F).yml;' | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_experimental_$(date +%F).yml;' | |
| - name: cache | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: environment/*.yml | |
| key: all_env_$(date +%F) | |
| build_cmti: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build pyiron/mpie_cmti | |
| timeout-minutes: 15 | |
| run: | | |
| docker build -t pyiron/mpie_cmti:latest mpie_cmti/ | |
| docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)" | |
| - run: docker images | |
| - run: mkdir -p environment; chmod 777 environment | |
| - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/mpie_cmti /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/mpie_cmti_$(date +%F).yml;' | |
| - name: cache | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: environment/*.yml | |
| key: cmti_env_$(date +%F) | |
| check: | |
| needs: [build, build_cmti] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: ls -al environment | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%F)" >> $GITHUB_OUTPUT | |
| - name: cache_cmti | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: environment/*.yml | |
| key: cmti_env_$(date +%F) | |
| - name: cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: environment/*.yml | |
| key: all_env_$(date +%F) | |
| - run: ls -al environment | |
| autobot: | |
| needs: [build, build_cmti] | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| runs-on: ubuntu-latest | |
| if: github.event.pull_request.user.login == 'dependabot[bot]' | |
| steps: | |
| - name: Ignore broken packages | |
| shell: bash -l {0} | |
| run: python .ci_support/checktitle.py "${{ github.event.pull_request.title }}" | |
| - name: Enable auto-merge for bot PRs | |
| run: gh pr merge --auto --squash "$PR_URL" | |
| env: | |
| PR_URL: ${{github.event.pull_request.html_url}} | |
| GH_TOKEN: ${{secrets.GITHUB_TOKEN}} |