tardis-carsus-bridge #49
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| name: tardis-carsus-bridge | |
| on: | |
| workflow_call: # to be called by save_atomic_files workflow | |
| outputs: | |
| ref-check-trig: | |
| value: ${{ jobs.tardis-build.outputs.step-ref-check-trig}} | |
| workflow_dispatch: # for running manually | |
| env: | |
| XUVTOP: /tmp/chianti | |
| CHIANTI_DL_URL: https://download.chiantidatabase.org | |
| CHIANTI_DB_VER: CHIANTI_v9.0.1_database.tar.gz | |
| NBCONVERT_FLAGS: --execute --ExecutePreprocessor.timeout=600 --to html | |
| CMFGEN_DL_URL: http://kookaburra.phyast.pitt.edu/hillier/cmfgen_files | |
| CMFGEN_DB_VER: atomic_data_15nov16.tar.gz | |
| # original reference data | |
| REF1_PATH: ${{ github.workspace }}/tardis-refdata/unit_test_data_org.h5 | |
| # generated reference data using the new atomic file | |
| REF2_PATH: ${{ github.workspace }}/tardis-refdata/unit_test_data.h5 | |
| PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata | |
| --generate-reference | |
| CACHE_NUMBER: 1 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| carsus-build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| path: carsus/ | |
| - uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.XUVTOP }} | |
| key: ${{ runner.os }}-${{ env.CHIANTI_DB_VER }} | |
| id: chianti-cache | |
| - name: Download Chianti database | |
| run: | | |
| mkdir -p ${{ env.XUVTOP }} | |
| wget -q ${{ env.CHIANTI_DL_URL }}/${{ env.CHIANTI_DB_VER }} -O ${{ env.XUVTOP }}/chianti.tar.gz | |
| tar -zxf ${{ env.XUVTOP }}/chianti.tar.gz -C ${{ env.XUVTOP }} | |
| if: steps.chianti-cache.outputs.cache-hit != 'true' | |
| - uses: actions/cache@v2 | |
| with: | |
| path: /tmp/atomic | |
| key: ${{ env.CMFGEN_DB_VER }} | |
| id: cmfgen-cache | |
| - name: Download CMFGEN database | |
| run: | | |
| wget -q -U "Mozilla/4.0" ${{ env.CMFGEN_DL_URL }}/${{ env.CMFGEN_DB_VER }} -O /tmp/atomic.tar.gz | |
| tar -zxf /tmp/atomic.tar.gz -C /tmp | |
| if: steps.cmfgen-cache.outputs.cache-hit != 'true' | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: conda-lock.yml | |
| init-shell: bash | |
| cache-environment: true | |
| cache-downloads: true | |
| environment-name: carsus | |
| - name: Install package | |
| run: pip install -e carsus/ | |
| - name: Run notebooks | |
| run: | | |
| jupyter nbconvert ${{ env.NBCONVERT_FLAGS }} carsus/docs/tardis_atomdata_ref.ipynb | |
| env: | |
| CARSUS_REFDATA: ${{ github.workspace }}/carsus-refdata | |
| - name: Upload Atom Data | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: atom-data | |
| path: carsus/docs/kurucz_cd23_chianti_H_He.h5 | |
| tardis-build: | |
| needs: carsus-build | |
| runs-on: ubuntu-latest | |
| outputs: | |
| step-ref-check-trig: ${{ steps.ref-equal-check.outcome }} # success or failure of refdata comparison | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| repository: tardis-sn/tardis | |
| - name: Download refdata_compare notebook | |
| run: wget https://raw.githubusercontent.com/tardis-sn/tardis-refdata/master/notebooks/ref_data_compare_from_paths.ipynb | |
| - name: Clone tardis-sn/tardis-refdata | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: tardis-sn/tardis-refdata | |
| path: tardis-refdata | |
| - name: Create LFS file list | |
| run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
| working-directory: tardis-refdata | |
| - name: Restore LFS cache | |
| uses: actions/cache@v2 | |
| id: lfs-cache | |
| with: | |
| path: tardis-refdata/.git/lfs | |
| key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v${{ env.CACHE_NUMBER }} | |
| - name: Git LFS Pull | |
| run: git lfs pull | |
| working-directory: tardis-refdata | |
| if: steps.lfs-cache.outputs.cache-hit != 'true' | |
| - name: Git LFS Checkout | |
| run: git lfs checkout | |
| working-directory: tardis-refdata | |
| if: steps.lfs-cache.outputs.cache-hit == 'true' | |
| - name: Setup TARDIS environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: tardis | |
| use-mamba: true | |
| - name: Update environment | |
| run: mamba update -n tardis --file conda-linux-64.lock | |
| - name: Install bokeh | |
| run: mamba install bokeh --channel conda-forge --no-update-deps --yes | |
| - name: Install package | |
| run: pip install -e . | |
| - name: Download atom data | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: atom-data | |
| path: carsus/docs/kurucz_cd23_chianti_H_He.h5 | |
| - name: Replace Atomic Data | |
| run: cp carsus/docs/kurucz_cd23_chianti_H_He.h5/kurucz_cd23_chianti_H_He.h5 tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5 | |
| - name: Generate Reference Data Copy | |
| run: cp tardis-refdata/unit_test_data.h5 tardis-refdata/unit_test_data_org.h5 | |
| - name: Generate New Reference Data | |
| run: pytest tardis ${{ env.PYTEST_FLAGS }} | |
| - name: Compare Reference Data | |
| run: | | |
| jupyter nbconvert ${{ env.NBCONVERT_FLAGS }} ref_data_compare_from_paths.ipynb | |
| - name: Upload comparison notebook | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: Comparison Notebook | |
| path: ref_data_compare_from_paths.html | |
| - name: Check if reference data are equal | |
| id: ref-equal-check | |
| continue-on-error: true | |
| run: if [ "$(cat ../refdata_compare_result)" == "REFDATA COMPARISON FAILED" ]; then exit 1; fi | |
| # continue-on-error check would display a green tick even when the step passes | |
| # but is necessary for other steps to run | |
| # if the workflow was called by save-atomic-files workflow(the only other option) | |
| # and refdata comparison failed this workflow would pass but the | |
| # bridge-ref-check job in save-atomic-files about refdata comparison would fail | |
| - name: Fail the workflow if reference data check fails | |
| if: github.event_name == 'workflow_dispatch' && steps.ref-equal-check.outcome == 'failure' | |
| run: exit 1 |